Search results for: molecular pathology

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: Atefeh Abedini, Fatemeh Razavi, Mihan Pourabdollah Toutkaboni, Hossein Mehravaran, Arda Kiani

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In countries with the highest prevalence of tuberculosis, such as Iran, the differentiation of malignant tumors from non-malignant is very important. In this study, which was conducted for the first time among the Iranian population, the utility of the ultrasonographic morphological characteristics in patients undergoing EBUS was used to distinguish the non-malignant versus malignant lymph nodes. The morphological characteristics of lymph nodes, which consist of size, shape, vascular pattern, echogenicity, margin, coagulation necrosis sign, calcification, and central hilar structure, were obtained during Endobronchial Ultrasound-Guided Trans-Bronchial Needle Aspiration and were compared with the final pathology results. During this study period, a total of 253 lymph nodes were evaluated in 93 cases. Round shape, non-hilar vascular pattern, heterogeneous echogenicity, hyperechogenicity, distinct margin, and the presence of necrosis sign were significantly higher in malignant nodes. On the other hand, the presence of calcification and also central hilar structure were significantly higher in the benign nodes (p-value ˂ 0.05). Multivariate logistic regression showed that size>1 cm, heterogeneous echogenicity, hyperechogenicity, the presence of necrosis signs and, the absence of central hilar structure are independent predictive factors for malignancy. The accuracy of each of the aforementioned factors is 42.29 %, 71.54 %, 71.90 %, 73.51 %, and 65.61 %, respectively. Of 74 malignant lymph nodes, 100% had at least one of these independent factors. According to our results, the morphological characteristics of lymph nodes based on Endobronchial Ultrasound-Guided Trans-Bronchial Needle Aspiration can play a role in the prediction of malignancy.

Keywords: EBUS-TBNA, malignancy, nodal characteristics, pathology

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Authors: Wenjun Zhang, Yunqing Du, Steven W. Cranford, Ming L. Wang

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The beginning of 21st century has witnessed new advancements in the design and use of new materials for biosensing applications, from nano to macro, protein to tissue. Traditional analytical methods lack a complete toolset to describe the complexities introduced by living systems, pathological relations, discrete hierarchical materials, cross-phase interactions, and structure-property dependencies. Materiomics – via systematic molecular dynamics (MD) simulation – can provide structure-process-property relations by using a materials science approach linking mechanisms across scales and enables oriented biosensor design. With this approach, DNA biosensors can be utilized to detect disease biomarkers present in individuals’ breath such as acetone for diabetes. Our wireless sensor array based on single-stranded DNA (ssDNA)-decorated single-walled carbon nanotubes (SWNT) has successfully detected trace amount of various chemicals in vapor differentiated by pattern recognition. Here, we present how MD simulation can revolutionize the way of design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. It demonstrates great potential to be utilized to build a library of DNDA sequences for reliable detection of several biomarkers of one specific disease, and as well provides a new methodology of creating, designing, and applying of biosensors.

Keywords: biosensor, DNA, biomarker, molecular dynamics simulation

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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: Atena Sadat Hosseini, Mohammadhossein Habibi

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Acute myeloid leukemia (AML) is the most typically diagnosed leukemia. In older adults, AML imposes a dismal outcome. AML originates with a dominant mutation, then adds collaborative, transformative mutations leading to myeloid transformation and clinical/biological heterogeneity. Several chemotherapeutic drugs are used for this cancer. These drugs are naturally associated with several side effects, and finding a more accurate molecular mechanism of these drugs can have a significant impact on the selection and better candidate of drugs for treatment. In this study, we evaluated bortezomibin myeloma cells using bioinformatics analysis and evaluation of RNA-Seq data. Then investigated the molecular pathways proteins- proteins interactions associated with this chemotherapy drug. A total of 658upregulated genes and 548 downregulated genes were sorted.AUF1 (hnRNP D0) binds and destabilizes mRNA, degradation of GLI2 by the proteasome, the role of GTSE1 in G2/M progression after G2 checkpoint, TCF dependent signaling in response to WNT demonstrated in upregulated genes. Besides insulin resistance, AKT phosphorylates targets in the nucleus, cytosine methylation, Longevity regulating pathway, and Signal Transduction of S1P Receptor were related to low expression genes. With respect to this results, HIST2H2AA3, RP11-96O20.4, ZED9, PRDX1, and DOK2, according to node degrees and betweenness elements candidates from upregulated genes. in the opposite side, PYURF, NRSN1, FGF23, UPK3BL, and STAG3 were a prominent role in downregulated genes. Sum up, Using in silico analysis in the present study, we conducted a precise study ofbortezomib molecular mechanisms in myeloma cells. so that we could take further evaluation to discovermolecular cancer therapy. Naturally, more additional experimental and clinical procedures are needed in this survey.

Keywords: myeloma cells, acute myeloid leukemia, bioinformatics analysis, bortezomib

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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: 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: Yahia Massinissa, Yahia Mouloud

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Cystic fibrosis (CF), the most common lethal genetic disease in the Europe population, is caused by mutations in the transmembrane conductance regulator gene (CFTR). It affects most organs including an epithelial tissue, base of hydroelectrolytic transepithelial transport, notably that aerial ways, the pancreas, the biliary ways, the intestine, sweat glands and the genital tractus. The gene whose anomalies are responsible of the cystic fibrosis codes for a protein Cl channel named CFTR (cystic fibrosis transmembrane conductance regulator) that exercises multiple functions in the cell, one of the most important in control of sodium and chlorine through epithelia. The deficient function translates itself notably by an abnormal production of viscous secretion that obstructs the execrator channels of this target organ: one observes then a dilatation, an inflammation and an atrophy of these organs. It also translates itself by an increase of the concentration in sodium and in chloride in sweat, to the basis of the sweat test. In order to do a phenotypical and genotypical diagnosis at a part of the Algerian population, our survey has been carried on 16 patients with evocative symptoms of the cystic fibrosis at that the clinical context has been confirmed by a sweat test. However, anomalies of the CFTR gene have been determined by electrophoresis in gel of polyacrylamide of the PCR products (polymerase chain reaction), after enzymatic digestion, then visualized to the ultraviolet (UV) after action of the ethidium bromide. All mutations detected at the time of our survey have already been identified at patients attained by this pathology in other populations of the world. However, the important number of found mutation with regard to the one of the studied patients testifies that the origin of this big clinical variability that characterizes the illness in the consequences of an enormous diversity of molecular defects of the CFTR gene.

Keywords: cystic fibrosis, CFTR gene, polymorphism, algerian population, sweat test, genotypical diagnosis

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Authors: Abu Salim Mustafa

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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: 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: Mary Deyo, Zmara Harrison

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This study reports the outcomes of an 8-week experiential learning program for 6 adults with Intellectual and Developmental Disabilities (IDD) at a day habilitation program. The intervention foci for this program include executive function, language learning in the domains of expressive, receptive, and pragmatic language, and quality of life. The interprofessional collaboration aimed at supporting adults with IDD to reach person-centered, functional goals across skill domains is critical. This study is a significant addition to the speech-language pathology literature in that it examines a therapy method that potentially meets this need while targeting domains within the speech-language pathology scope of practice. Communication therapy was provided during highly valued and meaningful hands-on learning experiences, referred to as the Garden Club, which incorporated all aspects of planting and caring for a garden as well as related journaling, sensory, cooking, art, and technology-based activities. Direct care staff and an undergraduate research assistant were trained by SLP to be impactful language guides during their interactions with participants in the Garden Club. SLP also provided direct therapy and modeling during Garden Club. Research methods used in this study included a mixed methods analysis of a literature review, a quasi-experimental implementation of communication therapy in the context of experiential learning activities, Quality of Life participant surveys, quantitative pre- post- data collection and linear mixed model analysis, qualitative data collection with qualitative content analysis and coding for themes. Outcomes indicated overall positive changes in expressive vocabulary, following multi-step directions, sequencing, problem-solving, planning, skills for building and maintaining meaningful social relationships, and participant perception of the Garden Project’s impact on their own quality of life. Implementation of this project also highlighted supports and barriers that must be taken into consideration when planning similar projects. Overall findings support the use of experiential learning projects in day habilitation programs for adults with IDD, as well as additional research to deepen understanding of best practices, supports, and barriers for implementation of experiential learning with this population. This research provides an important contribution to research in the fields of speech-language pathology and other professions serving adults with IDD by describing an interprofessional experiential learning program with positive outcomes for executive function, language learning, and quality of life.

Keywords: experiential learning, adults, intellectual and developmental disabilities, expressive language, receptive language, pragmatic language, executive function, communication therapy, day habilitation, interprofessionalism, quality of life

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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: Aarti M. Shetty, Estela Davoodi, Subrata Gangooly, Anita Rao-Coppisetty

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Background: Testing Patency of Fallopian Tubes is among one of the several protocols for investigating Subfertile Couples. Both, Hysterosalpingogram (HSG) and Laparoscopy and dye test have been used as Tubal patency test for several years, with well-known limitation. Hysterosalpingo Contrast Sonography (HyCoSy) can be used as an alternative tool to HSG, to screen patency of Fallopian tubes, with an advantage of being non-ionising, and also, use of transvaginal scan to diagnose pelvic pathology. Aim: To determine the indication and analyse the performance of transvaginal scan and HyCoSy in Broomfield Hospital. Methods: We retrospectively analysed fertility workup of 282 women, who attended HyCoSy clinic at our institution from January 2015 to June 2016. An Audit proforma was designed, to aid data collection. Data was collected from patient notes and electronic records, which included patient demographics; age, parity, type of subfertility (primary or secondary), duration of subfertility, past medical history and base line investigation (hormone profile and semen analysis). Findings of the transvaginal scan, HyCoSy and Laparoscopy were also noted. Results: The most common indication for referral were as a part of primary fertility workup on couples who had failure to conceive despite intercourse for a year, other indication for referral were recurrent miscarriage, history of ectopic pregnancy, post reversal of sterilization(vasectomy and tuboplasty), Post Gynaecology surgery(Loop excision, cone biopsy) and amenorrhea. Basic Fertility workup showed 34% men had abnormal semen analysis. HyCoSy was successfully completed in 270 (95%) women using ExEm foam and Transvaginal Scan. Of the 270 patients, 535 tubes were examined in total. 495/535 (93%) tubes were reported as patent, 40/535 (7.5%) tubes were reported as blocked. A total of 17 (6.3%) patients required laparoscopy and dye test after HyCoSy. In these 17 patients, 32 tubes were examined under laparoscopy, and 21 tubes had findings similar to HyCoSy, with a concordance rate of 65%. In addition to this, 41 patients had some form of pelvic pathology (endometrial polyp, fibroid, cervical polyp, fibroid, bicornuate uterus) detected during transvaginal scan, who referred to corrective surgeries after attending HyCoSy Clinic. Conclusion: Our audit shows that HyCoSy and Transvaginal scan can be a reliable screening test for low risk women. Furthermore, it has competitive diagnostic accuracy to HSG in identifying tubal patency, with an additional advantage of screening for pelvic pathology. With addition of 3D Scan, pulse Doppler and other non-invasive imaging modality, HyCoSy may potentially replace Laparoscopy and chromopertubation in near future.

Keywords: hysterosalpingo contrast sonography (HyCoSy), transvaginal scan, tubal infertility, tubal patency test

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Authors: Akarsh Verma, Avinash Parashar

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The aim of this article is to study the effects of hydroxyl functional group on the mechanical strength and fracture toughness of graphene. This functional group forms the backbone of intrinsic atomic structure of graphene oxide (GO). Molecular dynamics-based simulations were performed in conjunction with reactive force field (ReaxFF) parameters to capture the mode-I fracture toughness of hydroxyl functionalised graphene. Moreover, these simulations helped in concluding that spatial distribution and concentration of hydroxyl functional group significantly affects the fracture morphology of graphene nanosheet. In contrast to literature investigations, atomistic simulations predicted a transition in the failure morphology of hydroxyl functionalised graphene from brittle to ductile as a function of its spatial distribution on graphene sheet.

Keywords: graphene, graphene oxide, ReaxFF, molecular dynamics

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Authors: Titus A. Beu

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Many modern gene-delivery protocols rely on condensed complexes of DNA with polycations to introduce the genetic payload into cells by endocytosis. In particular, polyethyleneimine (PEI) stands out by a high buffering capacity (enabling the efficient condensation of DNA) and relatively simple fabrication. Realistic computational studies can offer essential insights into the formation process of DNA-PEI polyplexes, providing hints on efficient designs and engineering routes. We present comprehensive computational investigations of solvated PEI and DNA-PEI polyplexes involving calculations at three levels: ab initio, all-atom (AA), and coarse-grained (CG) molecular mechanics. In the first stage, we developed a rigorous AA CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field (FF) for PEI on the basis of accurate ab initio calculations on protonated model pentamers. We validated this atomistic FF by matching the results of extensive molecular dynamics (MD) simulations of structural and dynamical properties of PEI with experimental data. In a second stage, we developed a CG MARTINI FF for PEI by Boltzmann inversion techniques from bead-based probability distributions obtained from AA simulations and ensuring an optimal match between the AA and CG structural and dynamical properties. In a third stage, we combined the developed CG FF for PEI with the standard MARTINI FF for DNA and performed comprehensive CG simulations of DNA-PEI complex formation and condensation. Various technical aspects which are crucial for the realistic modeling of DNA-PEI polyplexes, such as options of treating electrostatics and the relevance of polarizable water models, are discussed in detail. Massive CG simulations (with up to 500 000 beads) shed light on the mechanism and provide time scales for DNA polyplex formation independence of PEI chain size and protonation pattern. The DNA-PEI condensation mechanism is shown to primarily rely on the formation of DNA bundles, rather than by changes of the DNA-strand curvature. The gained insights are expected to be of significant help for designing effective gene-delivery applications.

Keywords: DNA condensation, gene-delivery, polyethylene-imine, molecular dynamics.

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Authors: Ebraheem Al-Jouri, Youssef Abu-Ahmad, Ramasamy Srinivasan

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The parasitoid, Diadegma semiclausum (Hymenoptera: Ichneumonidae) is one of the most effective exotic parasitoids of diamondback moth (DBM), Plutella xylostella in the lowland areas of Homs, Syria. Molecular evolution studies are useful tools to shed light on the molecular bases of insect geographical spread and adaptation to new hosts and environment and for designing better control strategies. In this study, molecular evolution analysis was performed based on the 42 nuclear internal transcribed spacer-2 (ITS2) sequences representing the D. semiclausum and eight other Diadegma spp. from Syria and worldwide. Possible recombination events were identified by RDP4 program. Four potential recombinants of the American D. insulare and D. fenestrale (Jeju) were detected. After detecting and removing recombinant sequences, the ratio of non-synonymous (dN) to synonymous (dS) substitutions per site (dN/dS=ɷ) has been used to identify codon positions involved in adaptive processes. Bayesian techniques were applied to detect selective pressures at a codon level by using five different approaches including: fixed effects likelihood (FEL), internal fixed effects likelihood (IFEL), random effects method (REL), mixed effects model of evolution (MEME) and Program analysis of maximum liklehood (PAML). Among the 40 positively selected amino acids (aa) that differed significantly between clades of Diadegma species, three aa under positive selection were only identified in D. semiclausum. Additionally, all D. semiclausum branches tree were highly found under episodic diversifying selection (EDS) at p≤0.05. Our study provide evidence that both recombination and positive selection have contributed to the molecular diversity of Diadegma spp. and highlights the significant contribution of D. semiclausum in adaptive evolution and influence the fitness in the DBM parasitoid.

Keywords: diadegma sp, DBM, ITS2, phylogeny, recombination, dN/dS, evolution, positive selection

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Authors: Zain Ul Abdin, Mirza Aizaz Asim, Rao Sohail Ahmad Khan, Luqman Amrao, Fiaz Hussain, Hasooba Hira, Saqi Kosar Abbas

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The success of Integrated vector management programmes mainly depends on the correct identification of insect vector species involved in vector borne diseases. Based on molecular data the most important insect species involved as vectors for Zoonotic diseases in Pakistan were identified. The precise and accurate identification of such type of organism is only possible through molecular based techniques like “DNA barcoding”. Morphological species identification in insects at any life stage, is very challenging, therefore, DNA barcoding was used as a tool for rapid and accurate species identification in a wide variety of taxa across the globe and parallel studies revealed that DNA barcoding data can be effectively used in resolving taxonomic ambiguities, detection of cryptic diversity, invasion biology, description of new species etc. A comprehensive survey was carried out for the collection of insects (both adult and immature stages) in district Faisalabad, Pakistan and their DNA was extracted and mitochondrial cytochrome oxidase subunit I (COI-59) barcode sequences was used for molecular identification of immature and adult life stage.This preliminary research work opens new frontiers for developing sustainable insect vectors management programmes for saving lives of mankind from fatal diseases.

Keywords: zoonotic diseases, cytochrome oxidase, and insect vectors, CO1

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Authors: Hanaa M. Abu El Einin, Ahmed T. Sharaf El- Din

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Biomphalaria snails play an integral role in the transmission of Schistosoma mansoni, the causative agent for human schistosomiasis. Two species of Biomphalaria were reported from Egypt, Biomphalaria alexandrina and Biomphalaria glabrata, and later on a hybrid of B. alexandrina and B. glabrata was reported in streams at Nile Delta. All were known to be excellent hosts of S. mansoni. Host-parasite relationship can be viewed in terms of snail susceptibility and parasite infectivity. The objective of this study will highlight the progress that has been made in using molecular approaches to describe the correct identification of snail species that participating in transmission of schistosomiasis, rapid diagnose of infection in addition to susceptibility and resistance type. Snails were identified using of molecular methods involving Randomly Amplified Polymorphic DNA (RAPD), Polymerase Chain Reaction, Restriction Fragment Length Polymorphisms (PCR-RFLP) and Species - specific- PCR. Molecular approaches to diagnose parasite in snails from Egypt: Nested PCR assay and small subunit (SSU) rRNA gene. Also RAPD PCR for study susceptible and resistance phenotype. The results showed that RAPD- PCR, PCR-RFLP and species-specific-PCR techniques were confirmed that: no evidence for the presence of B. glabrata in Egypt, All Biomphalaria snails collected identified as B. alexandrina snail i-e B alexandrinia is a common and no evidence for hybridization with B. glabrata. The adopted specific nested PCR assay revealed much higher sensitivity which enables the detection of S. mansoni infected snails down to 3 days post infection. Nested PCR method for detection of infected snails using S. mansoni fructose -1,6- bisphosphate aldolase (SMALDO) primer, these primers are specific only for S. mansoni and not cross reactive with other schistosomes or molluscan aldolases Nested PCR for such gene is sensitive enough to detect one cercariae. Genetic variations between B. alexandrina strains that are susceptible and resistant to Schistosoma infec¬tion using a RAPD-PCR showed that 39.8% of the examined snails collected from the field were resistant, while 60.2% of these snails showed high infection rates. In conclusion the genetics of the intermediate host plays a more important role in the epidemiological control of schistosomiasis.

Keywords: biomphalaria, molecular differentiation, parasite detection, schistosomiasis

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Authors: Somayeh Akrami, Habib Onsori, Elham Tahmassebian

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Species of Anemone narcissiflora is belonged to Anemone genus of Ranunculaceae family. This species has two subspecies named narcissiflora and willdenowii which the latest is recorded in Iran in 2010. Some samples of A. narcissiflora is gathered from kuhkamar-zonouz region of East -Azerbaijan province, Iran to study the genetic diversity of the species by using RAPD molecular markers, and estimation of genetic diversity were evaluated with the using 10mer RAPD primers by PCR-RAPD method. 39 polymorphic bands were produced from the six primers used in this technique that the maximum band is related to the RP1 primer, the lowest band is related to the RP7 and the average band for all primers were 6.5 polymorphic bands. Cluster analysis of samples in done by UPGMA method in NTSYSpc 2.02 software. Dendrogram resulting from migrating bands showed that the studied samples can be divided into two groups. The first group includes samples with 1-2 flowers and the second group consists of two sub-groups which the first subgroup consists of samples with 3-5 flowers, and the second subgroup consists of samples with 6-7 flowers. The results of the comparison and analysis of the data obtained from RAPD technique and similarity matrix represents the genetic variation between collected samples. This study shows that RAPD markers can determine the polymorphisms between different genotypes of A. narcissiflora and their hybrids. So RAPD technique can serve as a suitable molecular method to determine the genetic diversity of samples.

Keywords: Anemone narcissiflora, genetic diversity, RAPD-PCR

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Authors: Richa Mardianingrum, Srie R. N. Endah

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In this research, we have designed four isoniazid derivatives i.e., isonicotinohydrazide (1-isonicotinoyl semicarbazide, 1-thiosemi isonicotinoyl carbazide, N '-(1,3-dimethyl-1 h-pyrazole-5-carbonyl) isonicotino hydrazide, and N '-(1,2,3- 4-thiadiazole-carbonyl) isonicotinohydrazide. The docking and molecular dynamic have performed to them in order to study its interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (InhA). Based on this research, all of the compounds were predicted to have a stable interaction with Mycobacterium tuberculosis Enoyl-Acyl Carrier Protein Reductase (INHA) receptor, so they could be used as an anti-tuberculosis drug candidate.

Keywords: anti-tuberculosis, docking, Inhibin alpha subunit, InhA, inhibition, synthesis, isonicotinohydrazide

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Authors: Khabat Barkhordari

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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.

Keywords: HDV, genotype, epidemiology, distribution

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Authors: Tahani H. Alluhaybi, Leila Mejrissi

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In the present theoretical study, we investigated adiabatically the electronic structure of the (BaNa)+ by the use of the ab initio calculation. We optimized a large atomic GTO basis set for Na and Ba atoms. The (BaNa)+ molecular ion is considered a two-electron thank to a non-empirical pseudo-potentials approach applied to Ba and Na cores with the Core Polarization Potentials operator (CPP). Then, we performed the Full Configuration Interaction (FCI) method. Accordingly, we calculated the adiabatic Potential Energy Curves (PECs) and their spectroscopic constants (well depth De, transition energies Te, the equilibrium distances Re, vibrational constant ⍵e, and anharmonic constant ⍵exe) for 10 electronic states in Σ+ symmetry. Then we determined the vibrational level energies and their spacing, and the electric Permanent Dipole Moments (PDM).

Keywords: Ab initio, dipole moment, non-empirical pseudo-potential, potential energy curves, spectroscopic constants, vibrational energy

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Authors: M. Nazim, S. Ameen, H. K. Seo, H. S. Shin

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Energy is the basis of life and strong attention has been growing for the cost-effective energy production. Recently, solution-processed small molecule organic solar cells (SMOSCs) have grown much attention due to the wages such as well-defined molecular structures, definite molecular weight, easy synthesis and easy purification techniques. In particular, the size of donor (D) and acceptor (A) unit is a crucial factor for the exciton-diffusion towards D-A interface and then charge-separation for the effective charge-transport to the electrodes. Furan-bridged materials are more electron-rich, high fluorescence, with better molecular-packing, and greater rigidity and greater solubility than their thiophene-counterparts In this work, a furan-bridged thiazolo[5,4-d]thiazole based organic small molecule (RFTzR) was formulated and applied for BHJ organic solar cells (OSCs). The introduction of furan spacer with two terminal alkyl units improved its absorption and solubility in the common organic solvents, significantly. RFTzR exhibited a HOMO and LUMO energy levels of -5.36 eV and -3.14 eV, respectively. The fabricated solar cell devices of RFTzR (donor) with PC60BM (acceptor) as photoactive materials showed high performance of 2.72% (RFTzR:PC60BM, 2:1, w/w) ratio with open-circuit voltage of 0.756 V and high photocurrent density of 10.13 mA/cm².

Keywords: chromophore, organic solar cells, photoactive materials, small molecule

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Authors: Walid Ibrahim, Abdul Kasem, Sudeendra Doddi, Ilaria Giono, Tareq Sabagh, Muhammad Ammar, Nermin Osman

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Background: wire-guided localization (WL) is the most widely used method for the localization of non-palpable breast lesions. SAVI SCOUT occult lesion localization (SSL) is a new technique in breast-conservative surgery. SSL has the potential benefit of improving radiology workflow as well as accurate localization. Purpose: The purpose of this study is to compare the breast tissue specimen volume and weight and margin excision between WL and SSL. Materials and methods: A single institution retrospective analysis of 377 female patients who underwent wide local breast excision with SAVI SCOUT and or wire-guided technique between 2018 and 2021 in a UK University teaching hospital. Breast department. Breast tissue specimen volume and weight, and margin excision have been evaluated in the three groups of different localization. Results: Three hundred and seventy-seven patients were studied. Of these, 261 had wire localization, 88 had SCOUT and 28 had dual localization techniques. Tumor size ranged from 1 to 75mm (Median 20mm). The pathology specimen weight ranged from 1 to 466gm (Median 46.8) and the volume ranged from 1.305 to 1560cm³ (Median 106.32 cm³). SCOUT localization was associated with a significantly low specimen weight than wire or the dual technique localization (Median 41gm vs 47.3gm and 47gm, p = 0.029). SCOUT was not associated with better specimen volume with a borderline significance in comparison to wire and combined techniques (Median 108cm³ vs 105cm³ and 105cm³, p = 0.047). There was a significant correlation between tumor size and pathology specimen weight in the three groups. SCOUT showed a better >2mm safety margin in comparison to the other 2 techniques (p = 0.031). Conclusion: Preoperative SCOUT localization is associated with better specimen weight and better specimen margin. SCOUT did not show any benefits in terms of specimen volume which may be due to difficulty in getting the accurate specimen volume due to the irregularity of the soft tissue specimen.

Keywords: scout, wire, localization, breast

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Authors: Christina Eleftheria Tzeliou, Demeter Tzeli

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Introduction: Molecular Logic Gates (MLGs) are molecular machines that can perform complex work, such as solving logic operations. Molecular switches, which are molecules that can experience chemical changes are examples of successful types of MLGs. Recently, Quintana-Romero and Ariza-Castolo studied experimentally six stable pseudo-hemi-indigo-derived MLGs capable of solving complex logic operations. The MLG design relies on a molecular switch that experiences Z and E isomerism, thus the molecular switch's axis has to be a double bond. The hemi-indigo structure was preferred for the assembly of molecular switches due to its interaction with visible light. Z and E pseudo-hemi-indigo isomers can also be utilized for selective isomerization as they have distinct absorption spectra. Methodology: Here, the photophysical properties of pseudo-hemi-indigo derivatives are examined, i.e., derivatives of molecule 1 with anthracene, naphthalene, phenanthrene, pyrene, and pyrrole. In conjunction with some trials that were conducted, the level of theory mentioned subsequently was determined. The structures under study were optimized in both cis and trans conformations at the PBE0/6-31G(d,p) level of theory. The absorption spectra of the structures were calculated at PBE0/DEF2TZVP. In all cases, the absorption spectra of the studied systems were calculated including up to 50 singlet- and triplet-spin excited electronic states. Transition states (cis → cis, cis → trans, and trans → trans) were obtained in cases where it was possible, with PBE0/6-31G(d,p) for the optimization of the transition states and PBE0/DEF2TZVP for the respective absorption spectra. Emission spectra were obtained for the first singlet state of each molecule in cis both and trans conformations in PBE0/DEF2TZVP as well. All studies were performed in chloroform solvent that was added as a dielectric constant and the polarizable continuum model was also employed. Findings: Shifts of up to 25 nm are observed in the absorption spectra due to cis-trans isomerization, while the transition state is shifted up to about 150 nm. The electron density distribution is also examined, where charge transfer and electron transfer phenomena are observed regarding the three excitations of interest, i.e., H-1 → L, H → L and H → L+1. Emission spectra calculations were also carried out at PBE0/DEF2TZVP for the complete investigation of these molecules. Using protonation as input, selected molecules act as MLGs. Conclusion: Theoretical data so far indicate that both cis-trans isomerization, and cis-cis and trans-trans conformer isomerization affect the UV-visible absorption and emission spectra. Specifically, shifts of up to 30 nm are observed, while the transition state is shifted up to about 150 nm in cis-cis isomerization. The computational data obtained are in agreement with available experimental data, which have predicted that the pyrrole derivative is a MLG at 445 nm and 400 nm using protonation as input, while the anthracene derivative is a MLG that operates at 445 nm using protonation as input. Finally, it was found that selected molecules are candidates as MLG using protonation and light as inputs. These MLGs could be used as chemical sensors or as particular intracellular indicators, among several other applications. Acknowledgements: The author acknowledges the Hellenic Foundation for Research and Innovation for the financial support of this project (Fellowship Number: 21006).

Keywords: absorption spectra, DFT calculations, isomerization, molecular logic gates

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Authors: Ambrish Singh

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The corrosion inhibition performance of pyran (AP) and benzimidazole (BI) derivatives on J55 steel in 3.5% NaCl solution saturated with CO₂ was investigated by electrochemical, weight loss, surface characterization, and theoretical studies. The electrochemical studies included electrochemical impedance spectroscopy (EIS), potentiodynamic polarization (PDP), electrochemical frequency modulation (EFM), and electrochemical frequency modulation trend (EFMT). Surface characterization was done using contact angle, scanning electron microscopy (SEM), and atomic force microscopy (AFM) techniques. DFT and molecular dynamics (MD) studies were done using Gaussian and Materials Studio softwares. All the studies suggested the good inhibition by the synthesized inhibitors on J55 steel in 3.5% NaCl solution saturated with CO₂ due to the formation of a protective film on the surface. Molecular dynamic simulation was applied to search for the most stable configuration and adsorption energies for the interaction of the inhibitors with Fe (110) surface.

Keywords: corrosion, inhibitor, EFM, AFM, DFT, MD

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Authors: Majid Farsadrooh, Mehran Feizi-Dehnayebi

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Serum albumin is the most abundant protein that is present in the circulatory system of a wide variety of organisms. Although it is a significant macromolecule, it can contribute to osmotic blood pressure and also, plays a superior role in drug disposition and efficiency. Molecular docking simulation can improve in silico drug design and discovery procedures to propound a lead compound and develop it from the discovery step to the clinic. In this study, the molecular docking simulation was applied to select a lead molecule through an investigation of the interaction of the two anticancer drugs (Alitretinoin and Abemaciclib) with Human Serum Albumin (HSA). Then, a series of new compounds (a-e) were suggested using lead molecule modification. Density functional theory (DFT) including MEP map and HOMO-LUMO analysis were used for the newly proposed compounds to predict the reactivity zones on the molecules, stability, and chemical reactivity. DFT calculation illustrated that these new compounds were stable. The estimated binding free energy (ΔG) values for a-e compounds were obtained as -5.78, -5.81, -5.95, -5,98, and -6.11 kcal/mol, respectively. Finally, the pharmaceutical properties and toxicity of these new compounds were estimated through OSIRIS DataWarrior software. The results indicated no risk of tumorigenic, irritant, or reproductive effects and mutagenicity for compounds d and e. As a result, compounds d and e, could be selected for further study as potential therapeutic candidates. Moreover, employing molecular docking simulation with the prediction of pharmaceutical properties helps to discover new potential drug compounds.

Keywords: drug design, anticancer, computational studies, DFT analysis

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Authors: Eric Chabrol, Sidonia B.G. Eckle, Renate de Boer, James McCluskey, Jamie Rossjohn, Mirjam H.M. Heemskerk, Stephanie Gras

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αβ and γδ T-cells are disparate T-cell lineages that, via their use of either αβ or γδ T-cell antigen receptors (TCRs) respectively, can respond to distinct antigens. Here we characterise a new population of human T-cells, term δβ T-cells, that express TCRs comprising a TCR-δ variable gene fused to a Joining-α/Constant-α domain, paired with an array of TCR-β chains. We characterised the cellular, functional, biophysical and structural characteristic feature of this new T-cells population that reveal some new insight into TCR diversity. We provide molecular bases of how δβ T-cells can recognise viral peptide presented by Human Leukocyte Antigen (HLA) molecule. Our findings highlight how components from αβ and γδTCR gene loci can recombine to confer antigen specificity thus expanding our understanding of T-cell biology and TCR diversity.

Keywords: new delta-beta TCR, HLA, viral peptide, structural immunology

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