Search results for: bacterial gene clusters

Authors: Abiodun Olayinka, Daniel Dzidzienyo, Pangirayi Tongoona, Samuel Offei, Edwige Gaby Nkouaya Mbanjo, Chiedozie Egesi, Ismail Yusuf Rabbi

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Cassava (Manihot esculenta Crantz) is a major source of starch for various industrial applications. However, the traditional cultivation and harvesting methods of cassava are labour-intensive and inefficient, limiting the supply of fresh cassava roots for industrial starch production. To achieve improved productivity and quality of fresh cassava roots through mechanized cultivation, cassava cultivars with compact plant architecture and moderate plant height are needed. Plant architecture-related traits, such as plant height, harvest index, stem diameter, branching angle, and lodging tolerance, are critical for crop productivity and suitability for mechanized cultivation. However, the genetics of cassava plant architecture remain poorly understood. This study aimed to identify the genetic bases of the relationships between plant architecture traits and productivity-related traits, particularly starch content. A panel of 453 clones developed at the International Institute of Tropical Agriculture, Nigeria, was genotyped and phenotyped for 18 plant architecture and productivity-related traits at four locations in Nigeria. A genome-wide association study (GWAS) was conducted using the phenotypic data from a panel of 453 clones and 61,238 high-quality Diversity Arrays Technology sequencing (DArTseq) derived Single Nucleotide Polymorphism (SNP) markers that are evenly distributed across the cassava genome. Five significant associations between ten SNPs and three plant architecture component traits were identified through GWAS. We found five SNPs on chromosomes 6 and 16 that were significantly associated with shoot weight, harvest index, and total yield through genome-wide association mapping. We also discovered an essential candidate gene that is co-located with peak SNPs linked to these traits in M. esculenta. A review of the cassava reference genome v7.1 revealed that the SNP on chromosome 6 is in proximity to Manes.06G101600.1, a gene that regulates endodermal differentiation and root development in plants. The findings of this study provide insights into the genetic basis of plant architecture and yield in cassava. Cassava breeders could leverage this knowledge to optimize plant architecture and yield in cassava through marker-assisted selection and targeted manipulation of the candidate gene.

Keywords: Manihot esculenta Crantz, plant architecture, DArtseq, SNP markers, genome-wide association study

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Authors: Sujata Sharma, Avinash Singh, Lovely Gautam, Pradeep Sharma, Mau Sinha, Asha Bhushan, Punit Kaur, Tej P. Singh

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Peptidyl-tRNA hydrolase (Pth) Pth is an essential bacterial enzyme that catalyzes the release of free tRNA and peptide moeities from peptidyl tRNAs during stalling of protein synthesis. In order to design inhibitors of Pth from Pseudomonas aeruginosa (PaPth), we have determined the structures of PaPth in its native state and in the bound states with two compounds, amino acylate-tRNA analogue (AAtA) and 5-azacytidine (AZAC). The peptidyl-tRNA hydrolase gene from Pseudomonas aeruginosa was amplified by Phusion High-Fidelity DNA Polymerase using forward and reverse primers, respectively. The E. coliBL21 (λDE3) strain was used for expression of the recombinant peptidyl-tRNA hydrolase from Pseudomonas aeruginosa. The protein was purified using a Ni-NTA superflow column. The crystallization experiments were carried out using hanging drop vapour diffusion method. The crystals diffracted to 1.50 Å resolution. The data were processed using HKL-2000. The polypeptide chain of PaPth consists of 194 amino acid residues from Met1 to Ala194. The centrally located β-structure is surrounded by α-helices from all sides except the side that has entrance to the substrate binding site. The structures of the complexes of PaPth with AAtA and AZAC showed the ligands bound to PaPth in the substrate binding cleft and interacted with protein atoms extensively. The residues that formed intermolecular hydrogen bonds with the atoms of AAtA included Asn12, His22, Asn70, Gly113, Asn116, Ser148, and Glu161 of the symmetry related molecule. The amino acids that were involved in hydrogen bonded interactions in case of AZAC included, His22, Gly113, Asn116, and Ser148. As indicated by fittings of two ligands and the number of interactions made by them with protein atoms, AAtA appears to be a more compatible with the structure of the substrate binding cleft. However, there is a further scope to achieve a better stacking than that of O-tyrosyl moiety because it is not still ideally stacked. These observations about the interactions between the protein and ligands have provided the information about the mode of binding of ligands, nature and number of interactions. This information may be useful for the design of tight inhibitors of Pth enzymes.

Keywords: peptidyl tRNA hydrolase, Acinetobacter baumannii, Pth enzymes, O-tyrosyl

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Authors: Kathy Stein, Mariola Lysson, Anja Schmidt, Beatrix Schumak, Sabine Specht, Hicham Bouabe, Jürgen Heesemann, Axel Roers, Joerg C. Kalff, Sven Wehner

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Objective: Postoperative ileus (POI) is a common complication of abdominal surgery. Monocyte infiltration is a hallmark of POI. The polarization of macrophages/monocytes in this process is not well understood. We aimed to investigate if and how M2 macrophage/monocyte differentiation is involved in POI pathogenesis. Design: POI was induced by intestinal manipulation (IM). C57Bl/6, CCR2-/-, IL-10 reporter (ITIB), IL-10-/- and LysMcre/IL-10fl/fl mice underwent IM. At various points in time leukocyte influx, gene and protein expression of cytokines, chemokines and M2 differentiation markers and intestinal motility were analyzed. Results: IM induced the postoperative expression of the M2 markers Arginase-1 and YM-1, predominantly in F4/80+Ly6C+ monocytes. Gene expression analyses indicated an IL-10-dependent, IL-4-independent M2 polarization of these monocytes. IL-10 dependency of M2 differentiation was confirmed in IL-10 deficient mice. Leukocytes, in the order of infiltrating monocytes, neutrophils, and resident macrophages were the main IL-10 producers during POI. IL-10 producing monocytes as well as M2 marker expression were almost absent in CCR2-deficient mice. However, postoperative IL-10 expression was not altered in CCR2-/- mice. The loss of M2 polarized monocytes neither protected CCR2-/- mice from nor affected resolution of POI. In contrast, IL-10 deficiency reduced postoperative neutrophil numbers and ameliorated POI. IL-10Ra expression was strongly induced in neutrophils but not in monocytes. Conclusion: We conclude that IL-10 counteracts POI resolution by activating IL-10Ra-expressing neutrophils in the late phase of disease while IL-10-dependent M2 differentiation is not pivotal to POI manifestation and resolution.

Keywords: interleukin-10, macrophages, neutrophils, postoperative ileus

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Authors: K. Alafogiannis, E. E. Houssos, E. Anagnostou, G. Kouvarakis, N. Mihalopoulos, A. Fotiadi

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The Mediterranean basin is an area where different aerosol types coexist, including urban/industrial, desert dust, biomass burning and marine particles. Particularly, mineral dust aerosols, mostly originated from North African deserts, significantly contribute to high aerosol loads above the Mediterranean. Dust transport, controlled by the variation of the atmospheric circulation throughout the year, results in a strong spatial and temporal variability of aerosol properties. In this study, the synoptic conditions which favor dust transport over the Eastern Mediterranean are thoroughly investigated. For this reason, three datasets are employed. Firstly, ground-based daily data of aerosol properties, namely Aerosol Optical Thickness (AOT), Ångström exponent (α440-870) and fine fraction from the FORTH-AERONET (Aerosol Robotic Network) station along with measurements of PM10 concentrations from Finokalia station, for the period 2003-2011, are used to identify days with high coarse aerosol load (episodes) over Crete. Then, geopotential height at 1000, 850 and 700 hPa levels obtained from the NCEP/NCAR Reanalysis Project, are utilized to depict the atmospheric circulation during the identified episodes. Additionally, air-mass back trajectories, calculated by HYSPLIT, are used to verify the origin of aerosols from neighbouring deserts. For the 227 identified dust episodes, the statistical methods of Factor and Cluster Analysis are applied on the corresponding atmospheric circulation data to reveal the main types of the synoptic conditions favouring dust transport towards Crete (Eastern Mediterranean). The 227 cases are classified into 11 distinct types (clusters). Dust episodes in Eastern Mediterranean, are found to be more frequent (52%) in spring with a secondary maximum in autumn. The main characteristic of the atmospheric circulation associated with dust episodes, is the presence of a low-pressure system at surface, either in southwestern Europe or western/central Mediterranean, which induces a southerly air flow favouring dust transport from African deserts. The exact position and the intensity of the low-pressure system vary notably among clusters. More rarely dust may originate from deserts of Arabian Peninsula.

Keywords: aerosols, atmospheric circulation, dust particles, Eastern Mediterranean

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Authors: Maria Manzoor, Iram Gul, Muhammad Arshad

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Bacterial strains were isolated from contaminated soil collected from Rawalpindi and Islamabad. The strains were investigated for lead resistance and their effect on Pb solubility and PGPR activity. Incubation experiments were carried for inoculated and unoculated soil containing different levels of Pb. Results revealed that few stains (BTM-4, BTM-11, BTM-14) were able to tolerate Pb up to 600 mg L-1, whereas five strains (BTM-3, BTM-6, BTM-10, BTM-21 and BTM-24) showed significant increase in solubility of Pb when compared to all other strains and control. The CaCl2 extractable Pb was increased by 13.6, 6.8, 4.4 and 2.4 folds compared to un-inoculated control soil at increased soil Pb concentration (500, 1000, 1500 and 200 mg kg-1, respectively). The selected bacterial strains (11) were further investigated for plant growth promotion activity through PGPR assays including. Germination and root elongation assays were also conducted under elevated metal concentration in controlled conditions to elucidate the effects of microbial strains upon plant growth and development. The results showed that all the strains tested in this study, produced significantly varying concentrations of IAA, siderophores and gibberellic acid along with ability to phosphorus solubilization index (PSI). The results of germination and root elongation assay further confirmed the beneficial role of the microbial strains in elevating metal stress through PGPR activity. Among all tested strains, BTM-10 significantly improved plant growth. 1.3 and 2.7 folds increase in root and shoot length was observed when compared to control. Which may be attributed to presence of important plant growth promoting enzymes (IAA 74.6 μg/ml; GA 19.23 μg/ml; Sidrophore units 49% and PSI 1.3 cm). The outcome of this study indicates that these Pb tolerant and solubilizing strains may have the potential for plant growth promotion under metal stress and can be used as mediator when coupled with heavy metal hyperaccumulator plants for phytoremediation of Pb contaminated soil.

Keywords: Pb resistant bacteria, Pb mobilizing bacteria, Phytoextraction of Pb, PGPR activity of bacteria

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Authors: Ramin Mehdiabadi, Neda Menbari, Mohammad Nazir Menbari

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As a pressing public health concern, breast cancer stands as the predominant oncological diagnosis and principal cause of cancer-related mortality among women globally, accounting for 11.7% of new cancer incidences and 6.9% of cancer-related deaths. The annual figures indicate that approximately 230,480 women are diagnosed with breast cancer in the United States alone, with 39,520 succumbing to the disease. While developed economies have reported a deceleration in both incidence and mortality rates across various forms of cancer, including breast cancer, emerging and low-income economies manifest a contrary escalation, largely attributable to lifestyle-mediated risk factors such as tobacco usage, physical inactivity, and high caloric intake. Breast cancer is distinctly characterized by molecular heterogeneity, manifesting in specific subtypes delineated by biomarkers—Estrogen Receptors (ER), Progesterone Receptors (PR), and Human Epidermal Growth Factor Receptor 2 (HER2). These subtypes, comprising Luminal A, Luminal B, HER2-enriched, triple-negative/basal-like, and normal-like, necessitate nuanced, subtype-specific therapeutic regimens, thereby challenging the applicability of generalized treatment protocols. Within this molecular complexity, the transcription factor Forkhead Box M1 (FoxM1) has garnered attention as a significant driver of cellular proliferation, tumorigenesis, metastatic progression, and treatment resistance in a spectrum of human malignancies, including breast cancer. Concurrently, microRNAs (miRs), specifically miR-216b-5p, have been identified as post-transcriptional gene expression regulators and potential tumor suppressors. The overarching objective of this academic investigation is to explicate the multifaceted interrelationship between FoxM1 and miR-216b-5p across the disparate molecular subtypes of breast cancer. Employing a methodologically rigorous, interdisciplinary research design that incorporates cutting-edge molecular biology techniques, sophisticated bioinformatics analytics, and exhaustive meta-analyses of extant clinical data, this scholarly endeavor aims to unveil novel biomarker-specific therapeutic pathways. By doing so, this research is positioned to make a seminal contribution to the advancement of personalized, efficacious, and minimally toxic treatment paradigms, thus profoundly impacting the global efforts to ameliorate the burden of breast cancer.

Keywords: breast cancer, fox m1, microRNAs, mir-216b-5p, gene expression

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Authors: Yi H. Wong, Li L. Chan, Chee O. Leong, Stephen Ambu, Joon W. Mak, Priyadashi S. Sahu

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Background: Acanthamoeba is a free-living opportunistic protist which is ubiquitously distributed in the environment. Virulent Acanthamoeba can cause fatal encephalitis in immunocompromised patients and potential blinding keratitis in immunocompetent contact lens wearers. Approximately 24 species have been identified but only the A. castellanii, A. polyphaga and A. culbertsoni are commonly associated with human infections. Until to date, the precise molecular basis for Acanthamoeba pathogenesis remains unclear. Previous studies reported that Acanthamoeba virulence can be diminished through prolonged axenic culture but revived through serial mouse passages. As no clear explanation on this reversible pathogenesis is established, hereby, we postulate that the epigenetic regulators, DNA-methyltransferases (DNMT) and histone-deacetylases (HDAC), could possibly be involved in granting the virulence plasticity of Acanthamoeba spp. Methods: Four rounds of mouse passages were conducted to revive the virulence potential of the virulence-attenuated Acanthamoeba castellanii strain (ATCC 50492). Briefly, each mouse (n=6/group) was inoculated intraperitoneally with Acanthamoebae cells (2x 105 trophozoites/mouse) and incubated for 2 months. Acanthamoebae cells were isolated from infected mouse organs by culture method and subjected to subsequent mouse passage. In vitro cytopathic, encystment and gelatinolytic assays were conducted to evaluate the virulence characteristics of Acanthamoebae isolates for each passage. PCR primers which targeted on the 2 members (DNMT1 and DNMT2) and 5 members (HDAC1 to 5) of the DNMT and HDAC gene families respectively were custom designed. Quantitative real-time PCR (qPCR) was performed to detect and quantify the relative expression of the two gene families in each Acanthamoeba isolates. Beta-tubulin of A. castellanii (Genbank accession no: XP_004353728) was included as housekeeping gene for data normalisation. PCR mixtures were also analyzed by electrophoresis for amplicons detection. All statistical analyses were performed using the paired one-tailed Student’s t test. Results: Our pathogenicity tests showed that the virulence-reactivated Acanthamoeba had a higher degree of cytopathic effect on vero cells, a better resistance to encystment challenge and a higher gelatinolytic activity which was catalysed by serine protease. qPCR assay showed that DNMT1 expression was significantly higher in the virulence-reactivated compared to the virulence-attenuated Acanthamoeba strain (p ≤ 0.01). The specificity of primers which targeted on DNMT1 was confirmed by sequence analysis of PCR amplicons, which showed a 97% similarity to the published DNA-methyltransferase gene of A. castellanii (GenBank accession no: XM_004332804.1). Out of the five primer pairs which targeted on the HDAC family genes, only HDAC4 expression was significantly difference between the two variant strains. In contrast to DNMT1, HDAC4 expression was much higher in the virulence-attenuated Acanthamoeba strain. Conclusion: Our mouse passages had successfully restored the virulence of the attenuated strain. Our findings suggested that DNA-methyltransferase (DNMT1) and histone deacetylase (HDAC4) expressions are associated with virulence potential of Acanthamoeba spp.

Keywords: acanthamoeba, DNA-methyltransferase, histone deacetylase, virulence-associated proteins

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Authors: K. D. Mroczek

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In the study presented institutional context is discussed in terms of companies’ entry mode choice. In contrary to many previous analyses, instead of using one or two aggregated variables, a set of eleven determinants is used to establish equity and non-equity internationalization friendly conditions. Based on secondary data, 140 countries are analysed and grouped into clusters revealing similar framework. The range of the economies explored is wide as it covers all regions distinguished by The World Bank. The results can prove a useful alternative for operationalization of institutional variables in further research concerning entry modes or strategic management in international markets.

Keywords: clustering, entry mode choice, institutional environment, transaction costs

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Authors: Eun-Ji Lee, Hye-Sung Park, Chan-Jung Lee, Won-Sik Kong

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We analyzed the DNA sequence of the ITS (Internal Transcribed Spacer) region of the 18S ribosomal gene and compared it with the gene sequence of T. fuciformis and Hypoxylon sp. in the BLAST database. The sequences of collected T. fuciformis and Hypoxylon sp. have over 99% homology in the T. fuciformis and Hypoxylon sp. sequence BLAST database. In order to select the optimal medium for T. fuciformis, five kinds of a medium such as Potato Dextrose Agar (PDA), Mushroom Complete Medium (MCM), Malt Extract Agar (MEA), Yeast extract (YM), and Compost Extract Dextrose Agar (CDA) were used. T. fuciformis showed the best growth on PDA medium, and Hypoxylon sp. showed the best growth on MCM. So as to investigate the optimum pH and temperature, the pH range was set to pH4 to pH8 and the temperature range was set to 15℃ to 35℃ (5℃ degree intervals). Optimum culture conditions for the T. fuciformis growth were pH5 at 25℃. Hypoxylon sp. were pH6 at 25°C. In order to confirm the most suitable carbon source, we used fructose, galactose, saccharose, soluble starch, inositol, glycerol, xylose, dextrose, lactose, dextrin, Na-CMC, adonitol. Mannitol, mannose, maltose, raffinose, cellobiose, ethanol, salicine, glucose, arabinose. In the optimum carbon source, T. fuciformis is xylose and Hypoxylon sp. is arabinose. Using the column test, we confirmed sawdust a suitable for T. fuciformis, since the composition of sawdust affects the growth of fruiting bodies of T. fuciformis. The sawdust we used is oak tree, pine tree, poplar, birch, cottonseed meal, cottonseed hull. In artificial cultivation of T. fuciformis with sawdust medium, T. fuciformis and Hypoxylon sp. showed fast mycelial growth on mixture of oak tree sawdust, cottonseed hull, and wheat bran.

Keywords: cultivation, optimal condition, tremella fuciformis, nutritional source

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Authors: Hanouf A. S. Al Nuwaysir, Nadine Moubayed, Abir Ben Bacha, Islem Abid

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Consumption of waste water continues to cause significant problems for human health in both developed and developing countries. Many regulations have been implied by different world authorities controlling water quality for the presence of coliforms used as standard indicators of water quality deterioration and historically leading health protection concept. In this study, the European directive for the detection of Escherichia coli, ISO 9308-1, was applied to examine and monitor coliforms in water samples collected from Wadi Hanifa and neighboring wells, Riyadh governorate, kingdom of Saudi Arabia, which is used for irrigation and industrial purposes. Samples were taken from different locations for 8 months consecutively, chlorine concentration ranging from 0.1- 0.4 mg/l, was determined using the DPD FREE CHLORINE HACH kit. Water samples were then analyzed following the ISO protocol which relies on the membrane filtration technique (0.45µm, pore size membrane filter) and a chromogenic medium TTC, a lactose based medium used for the detection and enumeration of total coliforms and E.coli. Data showed that the number of bacterial isolates ranged from 60 to 300 colonies/100ml for well and surface water samples respectively; where higher numbers were attributed to the surface samples. Organisms which apparently ferment lactose on TTC agar plates, appearing as orange colonies, were selected and additionally cultured on EMB and MacConkey agar for a further differentiation among E.coli and coliform bacteria. Two additional biochemical tests (Cytochrome oxidase and indole from tryptophan) were also investigated to detect and differentiate the presence of E.coli from other coliforms, E. coli was identified in an average of 5 to 7colonies among 25 selected colonies.On the other hand, a more rapid, specific and sensitive analytical molecular detection namely single colony PCR was also performed targeting hha gene to sensitively detect E.coli, giving more accurate and time consuming identification of colonies considered presumptively as E.coli. Comparative methodologies, such as ultrafiltration and direct DNA extraction from membrane filters (MoBio, Grermany) were also applied; however, results were not as accurate as the membrane filtration, making it a technique of choice for the detection and enumeration of water coliforms, followed by sufficiently specific enzymatic confirmatory stage.

Keywords: coliform, cytochrome oxidase, hha primer, membrane filtration, single colony PCR

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Authors: Himanshu Lal, Bipasha Ghosh, Arun Srivastava

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A pilot study of indoor air quality in terms of bioaerosol (fungus and bacteria) and few selective microbial volatile organic compounds (MVOCs) was carried out in different indoor sections of a library for two seasons, namely monsoon and post monsoon. Bioaerosol sampling was carried out using Anderson six stage viable sampler at a flow rate of 28.3 L/min while MVOCs were collected on activated charcoal tubes ORBOTM 90 Carboxen 564.Collected MVOCs were desorbed using carbon disulphide (CS2) and analysed by GC-FID. Microscopic identification for fungus was only carried out. Surface dust was collected by sterilised buds and cultured to identify fungal contaminants. Unlike bacterial size distribution, fungal bioaerosol concentration was found to be highest in the fourth stage in different sections of the library. In post monsoon season both fungal bioaerosol (710 to 3292cfu/m3) and bacterial bioaerosol (298 to 1475cfu/m3) were fund at much greater concentration than in monsoon. In monsoon season unlike post monsoon, I/O ratio for both the bioaerosol fractions was more than one. Rain washout could be the reason of lower outdoor concentration in monsoon season. On the contrary most of the MVOCs namely 1-hexene, 1-pentanol and 1-octen-3-ol were found in the monsoon season instead of post monsoon season with the highest being 1-hexene with 7.09µg/m3 concentration. Among the six identified fungal bioaerosol Aspergillus, Cladosporium and Penicillium were found in maximum concentration while Aspergillus niger, Curvuleria lunata, Cladosporium cladosporioides and Penicillium sp., was indentified in surface dust samples. According to regression analysis apart from environmental factors other factors also played an important role. Thus apart from outdoor infiltration and human sources, accumulated surface dust mostly on organic materials like books, wooden furniture and racks can be attributed to being one of the major sources of both fungal bioaerosols as well as MVOCs found in the library.

Keywords: bacteria, Fungi, indoor air, MVOCs

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Authors: Rong Li, Brian D. Wirth, Bing Liu

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Graphite is the matrix, and structural material in the high temperature gas-cooled reactor exhibits an irradiation response. It is of significant importance to analyze the defect production and evaluate the role of graphite under irradiation. A vast experimental literature exists for graphite on the dimensional change, mechanical properties, and thermal behavior. However, simulations have not been applied to the atomistic perspective. Remarkably few molecular dynamics simulations have been performed to study the irradiation response in graphite. In this paper, irradiation-induced damage cascades in graphite were investigated with molecular dynamics simulation. Statistical results of the graphite defects were obtained by sampling a wide energy range (1–30 KeV) and 10 different runs for every cascade simulation with different random number generator seeds to the velocity scaling thermostat function. The chemical bonding in carbon was described using the adaptive intermolecular reactive empirical bond-order potential (AIREBO) potential coupled with the standard Ziegler–Biersack–Littmack (ZBL) potential to describe close-range pair interactions. This study focused on analyzing the number of defects, the final cascade morphology and the distribution of defect clusters in space, the length-scale cascade properties such as the cascade length and the range of primary knock-on atom (PKA), and graphite mechanical properties’ variation. It can be concluded that the number of surviving Frenkel pairs increased remarkably with the increasing initial PKA energy but did not exhibit a thermal spike at slightly lower energies in this paper. The PKA range and cascade length approximately linearly with energy which indicated that increasing the PKA initial energy will come at expensive computation cost such as 30KeV in this study. The cascade morphology and the distribution of defect clusters in space mainly related to the PKA energy meanwhile the temperature effect was relatively negligible. The simulations are in agreement with known experimental results and the Kinchin-Pease model, which can help to understand the graphite damage cascades and lifetime span under irradiation and provide a direction to the designs of these kinds of structural materials in the future reactors.

Keywords: graphite damage cascade, molecular dynamics, cascade morphology, cascade distribution

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Authors: Elif Coskun Daggecen, Seyma Dokucu, Yekta Gezginc, Ismail Akyol

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Fermented dairy food quality is mainly determined by the sensory perception and influenced by many factors. Today, starter cultures for fermented foods are being developed to have a constant quality in these foods. Streptococcus thermophilus is one of the main species of most a starter cultures of yogurt fermentation. This species produces lactate by lactose fermentation from pyruvate. On the other hand, a small amount of pyruvate can alternatively be converted to various typical yoghurt flavor compounds such as diacetyl, acetoin, acetaldehyde, or acetic acid, for which the activity of three genes are shown to be especially important; ldh, nox and als. Up to date, commercially produced yoghurts have not yet met the desired aromatic properties that Turkish consumers find in traditional homemade yoghurts. Therefore, it is important to select starters carrying favorable metabolic characteristics from natural isolates. In this study, 30 strains of Str. Thermophilus were isolated from traditional Turkish yoghurts obtained from different regions of the country. In these strains, transcriptional levels of ldh, nox and als genes were determined via a newly developed qPCR protocol, which is a more reliable and precision method for analyzing the quantitative and qualitative expression of specific genes in different experimental conditions or in different organisms compared to conventional analytical methods. Additionally, the metabolite production potentials of the isolates were measured. Of all the strains examined, 60% were found to carry the metabolite production potential and the gene activity which appeared to be suitable to be used as a starter culture. Probable starter cultures were determined according to real-time PCR results.

Keywords: gene expression, RT-PCR, starter culture, Streptococcus thermophilus

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Authors: J. J. Mathew

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Pulmonary tuberculosis is highly prevalent in the Indian subcontinent. Most cases of pulmonary tuberculosis are diagnosed with sputum examinations and the vast majority of these are undertaken by the government run establishments. However, mycobacterial cultures are not routinely done, unless drug resistance is detected based on clinical response. Modern diagnostic tests like bronchoscopy and Genexpert are not routinely employed in the government institutions for the diagnosis of pulmonary tuberculosis, but have been accepted widely by good private institutions. The utility of these investigations in the private sector is not yet well recognized. This retrospective study aims to assess the usefulness of bronchoscopy and Genexpert in the diagnosis of pulmonary tuberculosis in quaternary care private hospital in India. 30 patients with respiratory symptoms raising the possibility of tuberculosis based on clinical and radiological features, but without any significant sputum production, were subject to bronchoscopy and BAL samples taken for microbiological studies, including Genexpert. 6 out of the 30 patients were found to be Genexpert positive and none of them showed Rifampicin resistance. All the 6 cases had upper zone predominant disease. One of the 6 cases of tuberculosis had another co-existent bacterial infection according to the routine culture studies. 6 other cases were proven to be due to other bacterial infections alone, 2 had a malignant diagnosis and the remaining cases were thought to be non-infective pathologies. The Genexpert results were made available within 48 hours in the 6 positive cases. All of them were commenced on standard anti-tuberculous regimen with excellent clinical response. The other infective cases were also managed successfully based on the drug susceptibilities. The study has shown the usefulness of these investigations as early intervention enabled diagnosis facilitating treatment and prevention of any clinical deterioration. The study lends support to early bronchoscopy and Genexpert testing in suspected cases of pulmonary tuberculosis without significant sputum production, in a high prevalence country which normally relies on sputum examination for the diagnosis of pulmonary tuberculosis.

Keywords: pulmonary, tuberculosis, bronchoscopy, genexpert

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Authors: Irfan Turetgen

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Closed-circuit cooling towers are cooling units that operate according to the indirect cooling principle. Unlike the open-loop cooling tower, the filler material includes a closed-loop water-operated heat exchanger. The main purpose of this heat exchanger is to prevent the cooled process water from contacting with the external environment. In order to ensure that the hot water is cooled, the water is cooled by the air flow and the circulation water of the tower as it passes through the pipe. They are now more commonly used than open loop cooling towers that provide cooling with plastic filling material. As with all surfaces in contact with water, there is a biofilm formation on the outer surface of the pipe. Although biofilm has been studied very well on plastic surfaces in open loop cooling towers, studies on biofilm layer formed on the heat exchangers of the closed circuit tower have not been found. In the recent study, natural biofilm formation was observed on the heat exchangers of the closed loop tower for 6 months. At the same time, nano-silica coating, which is known to reduce the formation of the biofilm layer, a comparison was made between the two different surfaces in terms of biofilm formation potential. Test surfaces were placed into biofilm reactor along with the untreated control coupons up to 6-months period for biofilm maturation. Natural bacterial communities were monitored to analyze the impact to mimic the real-life conditions. Surfaces were monthly analyzed in situ for their microbial load using epifluorescence microscopy. Wettability is known to play a key role in biofilm formation on surfaces, because characteristics of surface properties affect the bacterial adhesion. Results showed that surface-conditioning with nano-silica significantly reduce (up to 90%) biofilm formation. Easy coating process is a facile and low-cost method to prepare hydrophobic surface without any kinds of expensive compounds or methods.

Keywords: biofilms, cooling towers, fill material, nano silica

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Authors: S. M. M. Syairah, M. H. Rajikin, A. R. Sharaniza

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Several embryonic cellular mechanism including cell cycle, growth and apoptosis are regulated by phosphatidylinositol-3-kinase (PI3K)/Akt signaling pathway. The goal of present study is to determine the effects of annatto (Bixa orellana)-derived δ-tocotrienol (δ-TCT) on the regulations of PI3K/Akt genes in murine morula. Twenty four 6-8 week old (23-25g) female balb/c mice were randomly divided into four groups (G1-G4; n=6). Those groups were subjected to the following treatments for 7 consecutive days: G1 (control) received tocopherol stripped corn oil, G2 was given 60 mg/kg/day of δ-TCT mixture (contains 90% delta & 10% gamma isomers), G3 was given 60 mg/kg/day of pure δ-TCT (>98% purity) and G4 received 60 mg/kg/day α-TOC. On Day 8, females were superovulated with 5 IU Pregnant Mare’s Serum Gonadotropin (PMSG) for 48 hours followed with 5 IU human Chorionic Gonadotropin (hCG) before mated with males at the ratio of 1:1. Females were sacrificed by cervical dislocation for embryo collection 48 hours post-coitum. About fifty morula from each group were used in the gene expression analyses using Affymetrix QuantiGene Plex 2.0 Assay. Present data showed a significant increase (p<0.05) in the average number (mean + SEM) of morula produced in G2 (26.0 + 0.45), G3 (23.0 + 0.63) and G4 (25.0 + 0.73) compared to control group (G1 – 16.0 + 0.63). This is parallel with the high expression of PDK1 gene with increase of 2.75-fold (G2), 3.07-fold (G3) and 3.59-fold (G4) compared to G1 (1.78-fold). From the present data, it can be concluded that supplementation with δ-TCT(s) and α-TOC induced high expression of PDK1 in G2-G4 which enhanced the PI3K/Akt signaling activity, resulting in the increased number of morula.

Keywords: delta-tocotrienol, embryonic development, nicotine, vitamin E

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Authors: Hamidreza Fallah Lajimi , Elham Karami, Fatemeh Ali nasab, Mostafa Mahdavikia

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Being responsive is an increasingly important skill for firms in today’s global economy; thus firms must be agile. Naturally, it follows that an organization’s agility depends on its supply chain being agile. However, achieving supply chain agility is a function of other abilities within the organization. This paper analyses results from a survey of 71 Iran manufacturing companies in order to identify some of the factors for agile organizations in managing their supply chains. Then we classification this company in four cluster with fuzzy c-mean technique and with four validations functional determine automatically the optimal number of clusters.

Keywords: agile supply chain, clustering, fuzzy clustering

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Authors: Ankita Singh, Chandan Gorain, Amirul I. Mallick

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Successful adherence of the mucosal epithelial cells is the key early step for Campylobacter jejuni pathogenesis (C. jejuni). A set of Surface Exposed Colonization Proteins (SECPs) are among the major factors involved in host cell adherence and invasion of C. jejuni. Among them, constitutively expressed surface-exposed lipoprotein adhesin of C. jejuni, JlpA, interacts with intestinal heat shock protein 90 (hsp90α) and contributes in disease progression by triggering pro-inflammatory response via activation of NF-κB and p38 MAP kinase pathway. Together with its ability to express in the bacterial surface, higher sequence conservation and predicted predominance of several B cells epitopes, JlpA protein reserves its potential to become an effective vaccine candidate against wide range of Campylobacter sps including C. jejuni. Given that chickens are the primary sources for C. jejuni and persistent gut colonization remain as major cause for foodborne pathogenesis to humans, present study explicitly used chickens as model to test the immune-protective efficacy of JlpA protein. Taking into account that gastrointestinal tract is the focal site for C. jejuni colonization, to extrapolate the benefit of mucosal (intragastric) delivery of JlpA protein, a food grade Nisin inducible Lactic acid producing bacteria, Lactococcus lactis (L. lactis) was engineered to express recombinant JlpA protein (rJlpA) in the surface of the bacteria. Following evaluation of optimal surface expression and functionality of recombinant JlpA protein expressed by recombinant L. lactis (rL. lactis), the immune-protective role of intragastric administration of live rL. lactis was assessed in commercial broiler chickens. In addition to the significant elevation of antigen specific mucosal immune responses in the intestine of chickens that received three doses of rL. lactis, marked upregulation of Toll-like receptor 2 (TLR2) gene expression in association with mixed pro-inflammatory responses (both Th1 and Th17 type) was observed. Furthermore, intragastric delivery of rJlpA expressed by rL. lactis, but not the injectable form, resulted in a significant reduction in C. jejuni colonization in chickens suggesting that mucosal delivery of live rL. lactis expressing JlpA serves as a promising vaccine platform to induce strong immune-protective responses against C. jejuni in chickens.

Keywords: chickens, lipoprotein adhesion of Campylobacter jejuni, immuno-protection, Lactococcus lactis, mucosal delivery

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Authors: Uraib Sharaha, Ahmad Salman, Eladio Rodriguez-Diaz, Elad Shufan, Klaris Riesenberg, Irving J. Bigio, Mahmoud Huleihel

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Antimicrobial drugs have played an indispensable role in controlling illness and death associated with infectious diseases in animals and humans. However, the increasing resistance of bacteria to a broad spectrum of commonly used antibiotics has become a global healthcare problem. Many antibiotics had lost their effectiveness since the beginning of the antibiotic era because many bacteria have adapted defenses against these antibiotics. Rapid determination of antimicrobial susceptibility of a clinical isolate is often crucial for the optimal antimicrobial therapy of infected patients and in many cases can save lives. The conventional methods for susceptibility testing require the isolation of the pathogen from a clinical specimen by culturing on the appropriate media (this culturing stage lasts 24 h-first culturing). Then, chosen colonies are grown on media containing antibiotic(s), using micro-diffusion discs (second culturing time is also 24 h) in order to determine its bacterial susceptibility. Other methods, genotyping methods, E-test and automated methods were also developed for testing antimicrobial susceptibility. Most of these methods are expensive and time-consuming. Fourier transform infrared (FTIR) microscopy is rapid, safe, effective and low cost method that was widely and successfully used in different studies for the identification of various biological samples including bacteria; nonetheless, its true potential in routine clinical diagnosis has not yet been established. The new modern infrared (IR) spectrometers with high spectral resolution enable measuring unprecedented biochemical information from cells at the molecular level. Moreover, the development of new bioinformatics analyses combined with IR spectroscopy becomes a powerful technique, which enables the detection of structural changes associated with resistivity. The main goal of this study is to evaluate the potential of the FTIR microscopy in tandem with machine learning algorithms for rapid and reliable identification of bacterial susceptibility to antibiotics in time span of few minutes. The UTI E.coli bacterial samples, which were identified at the species level by MALDI-TOF and examined for their susceptibility by the routine assay (micro-diffusion discs), are obtained from the bacteriology laboratories in Soroka University Medical Center (SUMC). These samples were examined by FTIR microscopy and analyzed by advanced statistical methods. Our results, based on 700 E.coli samples, were promising and showed that by using infrared spectroscopic technique together with multivariate analysis, it is possible to classify the tested bacteria into sensitive and resistant with success rate higher than 90% for eight different antibiotics. Based on these preliminary results, it is worthwhile to continue developing the FTIR microscopy technique as a rapid and reliable method for identification antibiotic susceptibility.

Keywords: antibiotics, E.coli, FTIR, multivariate analysis, susceptibility, UTI

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Authors: Saeideh Salimpour, Sophie-Charlotte Viaux, Ahmed Azab, Mohammed Fazle Baki

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The Facility Layout Problem (FLP) is key to the efficient and cost-effective operation of a system. This paper presents a hybrid heuristic- and mathematical-programming-based approach that divides the problem conceptually into those of clustering and sequencing. First, clusters of vertically aligned facilities are formed, which are later on sequenced horizontally. The developed methodology provides promising results in comparison to its counterparts in the literature by minimizing the inter-distances for facilities which have more interactions amongst each other and aims at placing the facilities with more interactions at the centroid of the shop.

Keywords: clustering-sequencing approach, mathematical modeling, optimization, unequal facility layout problem

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Authors: M. H. Pazandeh, M. Doudi, S. Barahimi, L. Rahimzadeh Torabi

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The use of antibiotics is essential in reducing the occurrence of adverse effects and inhibiting the emergence of antibiotic resistance in microbial populations. The necessity for a novel methodology concerning local administration of antibiotics has arisen, with particular focus on dealing with localized infections prompted by bacterial colonization of medical devices or implant materials. Bioactive glasses (BG) are extensively employed in the field of regenerative medicine, encompassing a diverse range of materials utilized for drug delivery systems. In the present investigation, various drug carriers for imipenem and tetracycline, namely single systems BG/SnO2, BG/NiO with varying proportions of metal oxide, and nanocomposite BG/SnO2/NiO, were synthesized through the sol-gel technique. The antibacterial efficacy of the synthesized samples was assessed through the utilization of the disk diffusion method with the aim of neutralizing Staphylococcus aureus as the bacterial model. The current study involved the examination of the bioactivity of two samples, namely BG10SnO2/10NiO and BG20SnO2, which were chosen based on their heightened bacterial inactivation properties. This evaluation entailed the employment of two techniques: the measurement of the pH of simulated body fluid (SBF) solution and the analysis of the sample tablets through X-ray diffraction (XRD), scanning electron microscopy (SEM), and Fourier transform infrared (FTIR) spectroscopy. The sample tablets were submerged in SBF for varying durations of 7, 14, and 28 days. The bioactivity of the composite bioactive glass sample was assessed through characterization of alterations in its surface morphology, structure, and chemical composition. This evaluation was performed using scanning electron microscopy (SEM), Fourier-transform infrared (FTIR) spectroscopy, and X-ray diffraction spectroscopy. Subsequently, the sample was immersed in simulated liquids to simulate its behavior in biological environments. The specific body fat percentage (SBF) was assessed over a 28-day period. The confirmation of the formation of a hydroxyapatite surface layer serves as a distinct indicator of bioactivity. The infusion of antibiotics into the composite bioactive glass specimen was done separately, and then the release kinetics of tetracycline and imipenem were tested in simulated body fluid (SBF). Antimicrobial effectiveness against various bacterial strains have been proven in numerous instances using both melt and sol-gel techniques to create multiple bioactive glass compositions. An elevated concentration of calcium ions within a solution has been observed to cause an increase in the pH level. In aqueous suspensions, bioactive glass particles manifest a significant antimicrobial impact. The composite bioactive glass specimen exhibits a gradual and uninterrupted release, which is highly desirable for a drug delivery system over a span of 72 hours. The reduction in absorption, which signals the loss of a portion of the antibiotic during the loading process from the initial phosphate-buffered saline solution, indicates the successful bonding of the two antibiotics to the surfaces of the bioactive glass samples. The sample denoted as BG/10SnO2/10NiO exhibits a higher loading of particles compared to the sample designated as BG/20SnO2 in the context of bioactive glass. The enriched sample demonstrates a heightened bactericidal impact on the bacteria under investigation while concurrently preserving its antibacterial characteristics. Tailored bioactive glass that incorporates hydroxyapatite, with a regulated and efficient release of drugs targeting bacterial infections, holds promise as a potential framework for bone implant scaffolds following rigorous clinical evaluation, thereby establishing potential future biomedical uses. During the modification process, the introduction of metal oxides into bioactive glass resulted in improved antibacterial characteristics, particularly in the composite bioactive glass sample that displayed the highest level of efficiency.

Keywords: antibacterial, bioactive glasses, implant infections, multi drug resistant

Procedia PDF Downloads 83

Authors: Sandeep Singh Waraich

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Wireless sensor network (WSN ) consists of a large number of sensor nodes. The disparity in their energy consumption usually lead to the loss of equilibrium in wireless sensor network which may further results in an energy hole problem in wireless network. In this paper, we have considered the inclusion of orphan nodes which usually remain unutilized as intermediate nodes in multi-hop routing. The Orphan Node Inclusion (ONI) Protocol lets the cluster member to bring the orphan nodes into their clusters, thereby saving important resources and increasing network lifetime in critical applications of WSN.

Keywords: wireless sensor network, orphan node, clustering, ONI protocol

Procedia PDF Downloads 404

Authors: Sammy Kibor, Filip Huyghe, Marc Kochzius, James Kairo

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Goldstripe Sardinella, Sardinella gibbosa, (Bleeker, 1849) is a commercially and ecologically important small pelagic fish common in the Western Indian Ocean region. The present study aimed to assess genetic diversity and population structure of the species in the Kenya-Tanzania transboundary area using mtDNA and msDNA markers. Some 630 bp sequence in the mitochondrial DNA (mtDNA) Cytochrome C Oxidase I (COI) and five polymorphic microsatellite DNA loci were analyzed. Fin clips of 309 individuals from eight locations within the transboundary area were collected between July and December 2018. The S. gibbosa individuals from the different locations were distinguishable from one another based on the mtDNA variation, as demonstrated with a neighbor-joining tree and minimum spanning network analysis. None of the identified 22 haplotypes were shared between Kenya and Tanzania. Gene diversity per locus was relatively high (0.271-0.751), highest Fis was 0.391. The structure analysis, discriminant analysis of Principal component (DAPC) and the pair-wise (FST = 0.136 P < 0.001) values after Bonferroni correction using five microsatellite loci provided clear inference on genetic differentiation and thus evidence of population structure of S. gibbosa along the Kenya-Tanzania coast. This study shows a high level of genetic diversity and the presence of population structure (Φst =0.078 P < 0.001) resulting to the existence of four populations giving a clear indication of minimum gene flow among the population. This information has application in the designing of marine protected areas, an important tool for marine conservation.

Keywords: marine connectivity, microsatellites, population genetics, transboundary

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Authors: Heide Imai

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The paper will introduce and discuss specific examples of urban practices which take place within the dynamic urban landscape of contemporary Tokyo. The rising interest and importance of derelict places as resilient and creative clusters will be analysed, before relating this to the rediscovery of small urban niches and the emergence of different forms of social entrepreneurs. Secondly, two different case study areas will be introduced before discussing different forms of hybrid lifestyles, social micro scale enterprises and social innovations, understanding the concept of ‘small places of resilience’ as zones of human interaction, desire and care in which spontaneous practices take place.

Keywords: entrepreneurship, social innovation, Tokyo, urban regeneration

Procedia PDF Downloads 464

Authors: Moustafa Osman Mohammed

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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

Procedia PDF Downloads 107

Authors: Hamzeh Alipour, Masoumeh Bagheri, Tahereh Karamzadeh, Abbasali Raz, Kourosh Azizi

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Netrin-A, a protein identified for conducting commissural axons, has a similar role in angiogenesis. In addition, studies have shown that one of the netrin-A receptors is expressed in the growing cells of small capillaries. It will be interesting to study this new group of molecules because their role in wound healing will become clearer in the future due to angiogenesis. The greenbottle blowfly Luciliasericata (L. sericata) larvae are increasingly used in maggot therapy of chronic wounds. This aim of this was the identification of moleculareatures of Netrin-A in L. sericata larvae. Larvae were reared under standard maggotarium conditions. The nucleic acid sequence of L. sericataNetrin-A (LSN-A) was then identified using Rapid Amplification of cDNA Ends (RACE) and Rapid Amplification of Genomic Ends (RAGE). Parts of the Netrin-A gene, including the middle, 3′-, and 5′-ends were identified, TA cloned in pTG19 plasmid, and transferred into DH5ɑ Escherichia coli. Each part was sequenced and assembled using SeqMan software. This gene structure was further subjected to in silico analysis. The DNA of LSN-A was identified to be 2407 bp, while its mRNA sequence was recognized as 2115 bp by Oligo0.7 software. It translated the Netrin-A protein with 704 amino acid residues. Its molecular weight is estimated to be 78.6 kDa. The 3-D structure ofNetrin-A drawn by SWISS-MODEL revealed its similarity to the Netrin-1 of humans with 66.8% identity. The LSN-A protein conduces to repair the myelin membrane in neuronal cells. Ultimately, it can be an effective candidate in neural regeneration and wound healing. Furthermore, our next attempt is to deplore recombinant proteins for use in medical sciences.

Keywords: maggot therapy, netrin-A, RACE, RAGE, lucilia sericata

Procedia PDF Downloads 94

Authors: Henry Ataburo, Dominic Essuman, Emmanuel Kwabena Anin

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Recent trends of catastrophic events, such as the Covid-19 pandemic, the Suez Canal blockage, the Russia-Ukraine conflict, the Israel-Hamas conflict, and the climate change crisis, continue to devastate supply chains and the broader society. Prior authors have advocated for a simultaneous pursuit of resilience and sustainability as crucial for navigating these challenges. Nevertheless, the relationship between resilience and sustainability is a rather complex one: resilience and sustainability are considered unrelated, substitutes, or complements. Scholars also suggest that different firms prioritize resilience and sustainability differently for varied strategic reasons. However, we know little about whether, how, and when these choices produce different typologies of firms to explain differences in financial and market performance outcomes. This research draws inferences from the systems configuration approach to organizational fit to contend that a taxonomy of firms may emerge based on how firms configure resilience and environmental sustainability. The study further examines the effects of these taxonomies on financial and market performance in differing transportation disruption conditions. Resilience is operationalized as a firm’s ability to adjust current operations, structure, knowledge, and resources in response to disruptions, whereas environmental sustainability is operationalized as the extent to which a firm deploys resources judiciously and keeps the ecological impact of its operations to the barest minimum. Using primary data from 199 firms in Ghana and cluster analysis as an analytical tool, the study identifies four clusters of firms based on how they prioritize resilience and sustainability: Cluster 1 - "strong, moderate resilience, high sustainability firms," Cluster 2 - "sigh resilience, high sustainability firms," Cluster 3 - "high resilience, strong, moderate sustainability firms," and Cluster 4 - "weak, moderate resilience, strong, moderate sustainability firms". In addition, ANOVA and regression analysis revealed the following findings: Only clusters 1 and 2 were significantly associated with both market and financial performance. Under high transportation disruption conditions, cluster 1 firms excel better in market performance, whereas cluster 2 firms excel better in financial performance. Conversely, under low transportation disruption conditions, cluster 1 firms excel better in financial performance, whereas cluster 2 firms excel better in market performance. The study provides theoretical and empirical evidence of how resilience and environmental sustainability can be configured to achieve specific performance objectives under different disruption conditions.

Keywords: resilience, environmental sustainability, developing economy, transportation disruption

Procedia PDF Downloads 56

Authors: Ahmed M. Debela, Mayreli Ortiz , Ciara K. O´Sullivan

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The completion of the human genome Project (HGP) has paved the way for mapping the diversity in the overall genome sequence which helps to understand the genetic causes of inherited diseases and susceptibility to drugs or environmental toxins. Arrayed primer extension (APEX) is a microarray based minisequencing strategy for screening disease causing mutations. It is derived from Sanger DNA sequencing and uses fluorescently dideoxynucleotides (ddNTPs) for termination of a growing DNA strand from a primer with its 3´- end designed immediately upstream of a site where single nucleotide polymorphism (SNP) occurs. The use of DNA polymerase offers a very high accuracy and specificity to APEX which in turn happens to be a method of choice for multiplex SNP detection. Coupling the high specificity of this method with the high sensitivity, low cost and compatibility for miniaturization of electrochemical techniques would offer an excellent platform for detection of mutation as well as sequencing of DNA templates. We are developing an electrochemical APEX for the analysis of SNPs found in the MYH7 gene for group of cardiomyopathy patients. ddNTPs were labeled with four different redox active compounds with four distinct potentials. Thiolated oligonucleotide probes were immobilised on gold and glassy carbon substrates which are followed by hybridisation with complementary target DNA just adjacent to the base to be extended by polymerase. Electrochemical interrogation was performed after the incorporation of the redox labelled dedioxynucleotide. The work involved the synthesis and characterisation of the redox labelled ddNTPs, optimisation and characterisation of surface functionalisation strategies and the nucleotide incorporation assays.

Keywords: array based primer extension, labelled ddNTPs, electrochemical, mutations

Procedia PDF Downloads 233

Authors: Umar Rehman, Holly Roy, K. T. Tsang, D. S. Jeyaretna, W Singleton, B. Fisher, P. A. Glew, J. Greig, Peter C. Whitfield

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Introduction: A brain abscess is a life-threatening condition, carrying significant mortality. It requires rapid identification and treatment. Management involves a combination of antibiotics and surgery. The aim of the current study was to identify common bacteria responsible for cerebral abscesses as well as the long term functional and neurological outcomes of patients following treatment in a retrospective series at a single UK neurosurgical centre. Methodology: We analysed patients that had received a diagnosis of 'cerebral abscess' or 'subdural empyema' between June 2002 and June 2018. This was done in the form of a retrospective review. The search resulted in a total of 180 patients; with 37 patients being excluded (spinal abscess, below 18 or non-abscess related admissions). Data were collected from medical case notes including information about demographics, comorbidities, immunosuppression, presentation, size/location of lesions, pathogens, treatment, and outcomes. Results: In total, we analysed 143 patients between the ages of 18-90. Focal neurological deficit and headaches were seen in 84% and 68% of patients respectively. 108 positive brain cultures were seen; with the largest proportion, 59.2% being gram-positive cocci, with strep intermedius being the most common pathogen identified in 13.9% of patients. Of the patients with positive blood cultures (n=11), 72.7% showed the same organism both in the blood and on the brain cultures. Long term outcomes (n=72) revealed that 48% of patients seizure-free without requiring anti-epileptics, 51.3% of patients had full recovery of their neurological symptoms. There was a mortality rate of 13.9% in the series. Conclusion: In conclusion, the largest bacterial cause of abscess within our population was due to gram-positive cocci. The majority of the patient demonstrated full neurological recovery with close to half of patients not requiring anti-epileptics following discharge.

Keywords: bacteria, cerebral abscess, long term outcome, neurological deficit

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Authors: Guenther Schuh, Michael Riesener, Frederic Diels

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Nowadays, manufacturing companies are faced with the challenge of meeting heterogeneous customer requirements in short product life cycles with a variety of product functions. So far, some of the functional requirements remain unknown until late stages of the product development. A way to handle these uncertainties is the highly iterative product development (HIP) approach. By structuring the development project as a highly iterative process, this method provides customer oriented and marketable products. There are first approaches for combined, hybrid models comprising deterministic-normative methods like the Stage-Gate process and empirical-adaptive development methods like SCRUM on a project management level. However, almost unconsidered is the question, which development scopes can preferably be realized with either empirical-adaptive or deterministic-normative approaches. In this context, a development scope constitutes a self-contained section of the overall development objective. Therefore, this paper focuses on a methodology that deals with the uncertainty of requirements within the early development stages and the corresponding selection of the most appropriate development approach. For this purpose, internal influencing factors like a company’s technology ability, the prototype manufacturability and the potential solution space as well as external factors like the market accuracy, relevance and volatility will be analyzed and combined into an Agile-Indicator. The Agile-Indicator is derived in three steps. First of all, it is necessary to rate each internal and external factor in terms of the importance for the overall development task. Secondly, each requirement has to be evaluated for every single internal and external factor appropriate to their suitability for empirical-adaptive development. Finally, the total sums of internal and external side are composed in the Agile-Indicator. Thus, the Agile-Indicator constitutes a company-specific and application-related criterion, on which the allocation of empirical-adaptive and deterministic-normative development scopes can be made. In a last step, this indicator will be used for a specific clustering of development scopes by application of the fuzzy c-means (FCM) clustering algorithm. The FCM-method determines sub-clusters within functional clusters based on the empirical-adaptive environmental impact of the Agile-Indicator. By means of the methodology presented in this paper, it is possible to classify requirements, which are uncertainly carried out by the market, into empirical-adaptive or deterministic-normative development scopes.

Keywords: agile, highly iterative development, agile-indicator, product development

Procedia PDF Downloads 230