Search results for: genetic differentiation

Authors: Julia V. F. Cortes, Maria E. V. Amarante, Carolina L. Cerdeira, Roberta B. V. Silva

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Nonmelanoma skin cancer is more commonly diagnosed than all other malignancies combined. In that group, cutaneous squamous cell carcinoma stands out for having the highest probability of metastasis and recurrence after treatment, in addition to being the second most prevalent form of skin cancer. Its main risk factors include exposure to carcinogens, such as ultraviolet radiation related to sunlight exposure, smoking, alcohol consumption, and human papillomavirus (HPV) infection. Considering the increased risk of skin cancer in the Brazilian population, caused by the high incidence of solar radiation, and the importance of identifying risk phenotypes for the accomplishment of public health actions, an epidemiological study was conducted in a city with a tropical climate located in southeastern Brazil, aiming to identify the target population and assist in primary and secondary prevention. This study describes the profile of patients with cutaneous squamous cell cancer, correlating the variables, sex, age, and differentiation. The study used as primary data source the results of anatomopathological exams delivered from January 2015 to December 2019 for patients registered at one pathology service, which analyzes the results of biopsies, Thus, 66 patients with cutaneous squamous cell carcinoma were analyzed. The most affected age group was 60 years or older (78.79%), emphasizing that moderately differentiated (79.49%) and well-differentiated forms (66.67%) are prevalent in this age group, resulting in a difference of 12.82 percentage points between them. In addition, the predominant sex was male (58%), and it was found that half of the women and 65.79% of men had a moderately differentiated type, whereas the well-differentiated type was slightly more frequent in women. It is worth noting that the moderately differentiated subtype has a 59.20% prevalence among all cases. Thus, it was concluded that the most affected age group was 60 years or older and that men were more affected. As for the subtype, the moderately differentiated one, which is recognized for presenting the second-highest risk for metastasis, was prevalent in this study, affecting 6.6% more men and predominating in the elderly.

Keywords: cutaneous squamous cell carcinoma, epidemiology, skin cancer, spinal cell cancer

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Authors: Yahia I. Mohamed, Ahmed I. Marzouk, Mohamed A. Yacout

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Aim of this work was to study the genetic basis for oil accumulation in olive fruit via tracking DGAT2 (Diacylglycerol acyltransferase type-2) gene in three Egyptian Origen Olive cultivars namely Toffahi, Hamed and Maraki using molecular marker techniques and bioinformatics tools. Results illustrate that, firstly: specific genomic band of Maraki cultivars was identified as DGAT2 (Diacylglycerol acyltransferase type-2) and identical for this gene in Olea europaea with 100 % of similarity. Secondly, differential genomic band of Maraki cultivars which produced from RAPD fingerprinting technique reflected predicted distinguished sequence which identified as DGAT2 (Diacylglycerol acyltransferase type-2) in Fragaria vesca subsp. Vesca with 76% of sequential similarity. Third and finally, specific genomic specific band of Hamed cultivars was indentified as two fragments, 1-Olea europaea cultivar Koroneiki diacylglycerol acyltransferase type 2 mRNA, complete cds with two matches regions with 99% or 2-PREDICTED: Fragaria vesca subsp. vesca diacylglycerol O-acyltransferase 2-like (LOC101313050), mRNA with 86% of similarity.

Keywords: Olea europaea, fingerprinting, diacylglycerol acyltransferase type-2 (DGAT2), Egypt

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Authors: Gopi Kerekere Rangaraju, Madhu Puttegowda

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Natural fibres composites include coir, jute, bagasse, cotton, bamboo, and hemp. Natural fibers come from plants. These fibers contain lingo cellulose in nature. Natural fibers are eco-friendly; lightweight, strong, renewable, cheap, and biodegradable. The natural fibers can be used to reinforce both thermosetting and thermoplastic matrices. Thermosetting resins such as epoxy, polyester, polyurethane, and phenolic are commonly used composites requiring higher performance applications. They provide sufficient mechanical properties, in particular, stiffness and strength at acceptably low-price levels. Recent advances in natural fibers development are genetic engineering. The composites science offers significant opportunities for improved materials from renewable resources with enhanced support for global sustainability. Natural fibers composites are attractive to industry because of their low density and ecological advantages over conventional composites. These composites are gaining importance due to their non-carcinogenic and bio-degradable nature. Natural fibers composites are a very costeffective material, especially in building and construction, packaging, automobile and railway coach interiors, and storage devices. These composites are potential candidates for the replacement of high- cost glass fibers for low load bearing applications. Natural fibers have the advantages of low density, low cost, and biodegradability

Keywords: PMC, basalt, coir, carbon fibers

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Authors: Jinkoo Kim, Minsung Kim

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This study develops a hybrid seismic energy dissipation device composed of a viscoelastic damper and a steel slit damper connected in parallel. A cyclic loading test is conducted on a test specimen to validate the seismic performance of the hybrid damper. Then a moment-framed model structure is designed without seismic load so that it is retrofitted with the hybrid dampers. The model structure is transformed into an equivalent simplified system to find out optimum story-wise damper distribution pattern using genetic algorithm. The effectiveness of the hybrid damper is investigated by fragility analysis and the life cycle cost evaluation of the structure with and without the dampers. The analysis results show that the model structure has reduced probability of reaching damage states, especially the complete damage state, after seismic retrofit. The expected damage cost and consequently the life cycle cost of the retrofitted structure turn out to be significantly small compared with those of the original structure. Acknowledgement: This research was supported by the Ministry of Trade, Industry and Energy (MOTIE) and Korea Institute for Advancement of Technology (KIAT) through the International Cooperative R & D program (N043100016).

Keywords: seismic retrofit, slit dampers, friction dampers, hybrid dampers

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Authors: Elham Jelodari Mamaghani, Christian Prins, Haoxun Chen

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In this paper, there is concentration on collaborative transportation planning (CTP) among multiple carriers with pickup and delivery requests and time windows. This problem is a vehicle routing problem with constraints from standard vehicle routing problems and new constraints from a real-world application. In the problem, each carrier has a finite number of vehicles, and each request is a pickup and delivery request with time window. Moreover, each carrier has reserved requests, which must be served by itself, whereas its exchangeable requests can be outsourced to and served by other carriers. This collaboration among carriers can help them to reduce total transportation costs. A mixed integer programming model is proposed to the problem. To solve the model, a hybrid algorithm that combines Genetic Algorithm and Simulated Annealing (GASA) is proposed. This algorithm takes advantages of GASA at the same time. After tuning the parameters of the algorithm with the Taguchi method, the experiments are conducted and experimental results are provided for the hybrid algorithm. The results are compared with those obtained by a commercial solver. The comparison indicates that the GASA significantly outperforms the commercial solver.

Keywords: centralized collaborative transportation, collaborative transportation with pickup and delivery, collaborative transportation with time windows, hybrid algorithm of GA and SA

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Authors: Shih-Ping Liu, Cheng-Hsuan Chang, Yu-Chuen Huang, Shih-Yin Chen, Woei-Cherng Shyu

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Embryonic stem cells (ES) and induced pluripotnet stem cells (iPS) are both pluripotent stem cells. For mouse stem cells culture technology, leukemia inhibitory factor (LIF) was used to maintain the pluripotency of stem cells in vitro. However, LIF is an expensive reagent. The goal of this study was to find out a pure compound extracted from Chinese herbal medicine that could maintain stem cells pluripotency to replace LIF and improve the iPS generation efficiency. From 20 candidates traditional Chinese medicine we found that Cordycepsmilitaris triggered the up-regulation of stem cells activating genes (Oct4 and Sox2) expression levels in MEF cells. Cordycepin, a major active component of Cordycepsmilitaris, also could up-regulate Oct4 and Sox2 gene expression. Furthermore, we used ES and iPS cells and treated them with different concentrations of Cordycepin (replaced LIF in the culture medium) to test whether it was useful to maintain the pluripotency. The results showed higher expression levels of several stem cells markers in 10 μM Cordycepin-treated ES and iPS cells compared to controls that did not contain LIF, including alkaline phosphatase, SSEA1, and Nanog. Embryonic body formation and differentiation confirmed that 10 μM Cordycepin-containing medium was capable to maintain stem cells pluripotency after four times passages. For mechanism analysis, microarray analysis indicated extracellular matrix and Jak/Stat signaling pathway as the top two deregulated pathways. In ECM pathway, we determined that the integrin αVβ5 expression levels and phosphorylated Src levels increased after Cordycepin treatment. In addition, the phosphorylated Jak2 and phosphorylated Sat3 protein levels were increased after Cordycepin treatment and suppressed with the Jak2 inhibitor, AG490. The expression of cytokines associated with Jak2/Stat3 signaling pathway were also up-regulated by Q-PCR and ELISA assay. Lastly, we used Oct4-GFP MEF cells to test iPS generation efficiency following Cordycepin treatment. We observed that 10 Μm Cordycepin significantly increased the iPS generation efficiency in day 21. In conclusion, we demonstrated Cordycepin could maintain the pluripotency of stem cells through both of ECM and Jak2/Stat3 signaling pathway and improved iPS generation efficiency.

Keywords: cordycepin, iPS cells, Jak2/Stat3 signaling pathway, molecular biology

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Authors: Adel Gurel, Ozge Ceylin Yildirim

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Nowadays, design and architecture are being affected and underwent change with the rapid advancements in technology, economics, politics, society and culture. Architecture has been transforming with the latest developments after the inclusion of computers into design. Integration of design into the computational environment has revolutionized the architecture and new perspectives in architecture have been gained. The history of architecture shows the various technological developments and changes in which the architecture has transformed with time. Therefore, the analysis of integration between technology and the history of the architectural process makes it possible to build a consensus on the idea of how architecture is to proceed. In this study, each period that occurs with the integration of technology into architecture is addressed within historical process. At the same time, changes in architecture via technology are identified as important milestones and predictions with regards to the future of architecture have been determined. Developments and changes in technology and the use of technology in architecture within years are analyzed in charts and graphs comparatively. The historical process of architecture and its transformation via technology are supported with detailed literature review and they are consolidated with the examination of focal points of 20th-century architecture under the titles; parametric design, genetic architecture, simulation, and biomimicry. It is concluded that with the historical research between past and present; the developments in architecture cannot keep up with the advancements in technology and recent developments in technology overshadow the architecture, even the technology decides the direction of architecture. As a result, a scenario is presented with regards to the reach of technology in the future of architecture and the role of the architect.

Keywords: computer technologies, future architecture, scientific developments, transformation

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Authors: Jingyuan Hu, Zhandong Liu

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CRISPR genome editing technology has transformed molecular biology by accurately targeting and altering an organism’s DNA. Despite the state-of-art precision of CRISPR genome editing, the imprecise mutation outcome and off-target effects present considerable risk, potentially leading to unintended genetic changes. Targeted deep sequencing, combined with bioinformatics sequence alignment, can detect such unwanted mutations. Nevertheless, the classical method, Needleman-Wunsch (NW) algorithm may produce false alignment outcomes, resulting in inaccurate mutation identification. The key to precisely identifying CRISPR-induced mutations lies in determining optimal parameters for the sequence alignment algorithm. Hidden Markov models (HMM) are ideally suited for this task, offering flexibility across CRISPR systems by leveraging forward-backward algorithms for parameter estimation. In this study, we introduce CRISPR-HMM, a statistical software to precisely call CRISPR-induced mutations. We demonstrate that the software significantly improves precision in identifying CRISPR-induced mutations compared to NW-based alignment, thereby enhancing the overall understanding of the CRISPR gene-editing process.

Keywords: CRISPR, HMM, sequence alignment, gene editing

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Authors: Qasim Idrees, Gao Liangtian, Liu Bo, Miao Yiran

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In order to improve the efficiency and accuracy of the pressure hull structure, optimization of underwater vehicle based on response surface methodology, a method for optimizing the design of pressure hull structure was studied. To determine the pressure shell of five dimensions as a design variable, the application of thin shell theory and the Chinese Classification Society (CCS) specification was carried on the preliminary design. In order to optimize variables of the feasible region, different methods were studied and implemented such as Opt LHD method (to determine the design test sample points in the feasible domain space), parametric ABAQUS solution for each sample point response, and the two-order polynomial response for the surface model of the limit load of structures. Based on the ultimate load of the structure and the quality of the shell, the two-generation genetic algorithm was used to solve the response surface, and the Pareto optimal solution set was obtained. The final optimization result was 41.68% higher than that of the initial design, and the shell quality was reduced by about 27.26%. The parametric method can ensure the accuracy of the test and improve the efficiency of optimization.

Keywords: parameterization, response surface, structure optimization, pressure hull

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Authors: Ana Marie T. Acevedo

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This study was conducted to describe variations in the shapes of the elytra, head and pronotum of populations of adult Brontispa longissima (Gestro) infesting coconut farms from selected areas in the Philippines using Cluster Analysis, Relative Warp Analysis coupled with box plot and histograms and Procustean analysis. The data used in this study included shape residuals captured using the method of landmark based geometric morphometrics. Results: The results of the cluster analyses based on the average shapes of the elytra, head and pronotum shows no consistent pattern of similarity between and among five populations of B. longissima. When localized variations using Relative Warp Analysis coupled with box plot and histograms was done, the findings revealed that RWA was only successful in summarizing variations using two relative warps in the shape of the elytra where the first two warps contained 86.29% of the variations of the female and 85.48% for the males. For the head and pronotum, the first two relative warps captured less than 50% of the overall variation. Looking at the shapes of the frequency histograms, all were found to follow a unimodal distribution. The box plots reveal no consistent results. Among the three characters studied only the elytra were more robust and reliable compared to head and pronotum and then Tandag differ from the rest of the other over-lapping populations. On the other hand, Procustean Analyses revealed that elytra were more spread in the posterior region both in male and female. The coordinates in head and pronotum were evenly distributed. In the overlapping consensus configurations show that variability was exaggerated in the right side of the elytra and the posterior parts of the head and pronotum. Results also showed expansion among females while compression among males in elytra. For males, expansion are localized in the posterior part of the elytra, For the head, results showed asymmetry in the distribution of expansion areas where expansion are observed in the right postero-lateral aspect of the female head. Conclusion: The overall results may imply that they might belong to one operational taxonomic unit or ecotype or biotype. Geography might not be the factor responsible for the differentiation of the populations of B. longissima.

Keywords: cluster analysis, relative warp analysis, procrustean analysis, environmental parameters

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Authors: Xue Li, Hui Xu

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Mild cognitive impairment (MCI) is a clinical stage that occurs between normal aging and dementia. Although MCI increases the risk of developing dementia, individuals with MCI may maintain stable cognitive function and even recover to a typical cognitive state. An intervention to prevent or delay the progression to dementia in individuals with MCI may involve promoting social engagement. Social participation is the engagement in socially relevant social exchanges and meaningful activities. Older adults with MCI may encounter restricted cognitive abilities, mood changes, and behavioral difficulties during social participation, influencing their willingness to engage. Therefore, this study aims to employ qualitative research methods to gain an in-depth comprehension of the authentic social participation experiences of older adults with mild cognitive impairment, which will establish a foundation for designing appropriate intervention programs. A phenomenological research was conducted. The study participants were selected using the purposive sampling method in combination with the maximum differentiation sampling strategy. Face-to-face semistructured interviews were conducted among 12 elderly individuals suffering from mild cognitive impairment in a community in Zhengzhou City from May to July 2023. Colaizzi 7-step method was used to analyze the data and extract the theme. The real experience of social participation in older adults with mild cognitive impairment can be summarized into 3 themes: (1) a single social relationship but a strong desire to participate, (2) a dual experience of social participation with both positive and negative aspects, (3) multiple barriers to social participation, including impaired memory capacity, heavy family responsibilities and lack of infrastructure. The study found that elderly individuals with mild cognitive impairment and one social interaction display an increased desire to engage in society. To improve social participation levels and reduce cognitive function decline, healthcare providers should work with relevant government agencies and the community to create a comprehensive social participation system. It is important for healthcare providers to note the social participation status of the elderly with mild cognitive impairment.

Keywords: mild cognitive impairment, the elderly, social participation, qualitative research

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Authors: Santhita Tungkajiwangkoon, Yoshikazu Hoshi

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Three Japaneses Drosera species are the good model to study genome organization with highly specialized morphological group for insect trapping, and has revealed anti-inflammatory, and antibacterial effects, so there must be a reason for botanists are so appealing in these plants. Cytology and Flow cytometry were used to investigate the genetic stability and ploidy estimation in three related species. The cytological and Flow cytometry analysis were done in Drosera rotundifolia L., Drosera spatulata Labill and Drosera tokaiensis. The cytological studies by fluorescence staining (DAPI) showed that D. tokaiensis was an alloploid (2n=6x=60, hexaploid) which is a natural hybrid polyploids of D. rotundifolia and D. spatulata. D. rotundifolia was a diploid with the middle size of metaphase chromosomes (2n=2x=20) as a paternal origin and D. spatulata was a tetraploid with small size of metaphase chromosome (2n=4x=40) as a maternal origin. We confirmed by Flow cytometry analysis to determine the ploidy level and DNA content of the plants. The 2C-DNA values of D. rotundiflolia were 2.8 pg, D. spatulata was 1.6 pg and D. tokaiensis was 3.9 pg. However, 2C- DNA values of D. tokaiensis should be related from their parents but in the present study the 2C-DNA values of D. tokaiensis was no relation from the theoretical of hybrids representing additive parental. Possibility of D. tokaiensis is a natural hybrid, which is also hybridization in natural evolution can cause the genome reduction in plant.

Keywords: drosera, hybrid, cytology, flow cytometry

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Authors: Ireneusz Majsterek, Karolina Przybylowska, Lukasz Dziki, Adam Dziki, Jacek Kabzinski

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Colorectal cancer (CRC) is one of the deadliest cancers. Every year we see an increase in the number of cases, and in spite of intensive research etiology of the disease remains unknown. For many years, researchers are seeking to associate genetic factors with an increased risk of CRC, so far it has proved to be a compelling link between the MMR system of DNA repair and hereditary nonpolyposis colorectal cancers (HNPCC). Currently, research is focused on finding the relationship between the remaining DNA repair systems and an increased risk of developing colorectal cancer. The aim of the study was to determine the relationship between gene polymorphisms Ser835Ser of XPF gene and Gly23Ala of XPA gene–elements of NER DNA repair system, and modulation of the risk of colorectal cancer in the Polish population. Determination of the molecular basis of carcinogenesis process and predicting increased risk will allow qualifying patients to increased risk group and including them in preventive program. We used blood collected from 110 patients diagnosed with colorectal cancer. The control group consisted of equal number of healthy people. Genotyping was performed by TaqMan method. The obtained results indicate that the genotype 23Gly/Ala of XPA gene is associated with an increased risk of colorectal cancer, while 23Ala/Ala as well as TCT allele of Ser835Ser of XPF gene may reduce the risk of CRC.

Keywords: NER, colorectal cancer, XPA, XPF, polymorphisms

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Authors: Abdul Qayyum, Hafiz Muhammad Saeed, Mamoona Hanif, Etrat Noor, Waqas Malik, Shoaib Liaqat

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Salinity is extremely serious problem that has a drastic effect on maize crop, environment and causes economic losses of country. An advance technique to overcome salinity is to develop salt tolerant geno types which require screening of huge germplasm to start a breeding program. Therefore, present study was undertaken to screen out 25 maize hybrids of different origin for salinity tolerance at seedling stage under three levels of salt stress 250 and 300 mM NaCl including one control. The existence of variation for tolerance to enhanced NaCl salinity levels at seedling stage in maize proved that hybrids had differing ability to grow under saline environment and potential variability within specie. Almost all the twenty five maize hybrids behaved varyingly in response to different salinity levels. However, the maize hybrids H6, H13, H21, H23 and H24 expressed better performance under salt stress in terms of all six characters and proved to be as highly tolerant while H22, H17 H20, H18, H4, H9, and H8 were identified as moderately tolerant. Hybrids H14, H5, H11 and H3 H12, H2, were expressed as most sensitive to salinity suggesting that screening is an effective tool to exploit genetic variation among maize hybrids and salt tolerance in maize can be enhanced through selection and breeding procedure.

Keywords: salinity, hybrids, maize, variation

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Authors: Marek Dlapa

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The algebraic approach is applied to the control of the HiMAT (Highly Maneuverable Aircraft Technology). The objective is to find a robust controller which guarantees robust stability and decoupled control of longitudinal model of a scaled remotely controlled vehicle version of the advanced fighter HiMAT. Control design is performed by decoupling the nominal MIMO (multi-input multi-output) system into two identical SISO (single-input single-output) plants which are approximated by a 4th order transfer function. The algebraic approach is then used for pole placement design, and the nominal closed-loop poles are tuned so that the peak of the µ-function is minimal. As an optimization tool, evolutionary algorithm Differential Migration is used in order to overcome the multimodality of the cost function yielding simple controller with decoupling for nominal plant which is compared with the D-K iteration through simulations of standard longitudinal manoeuvres documenting decoupled control obtained from algebraic approach for nominal plant as well as worst case perturbation.

Keywords: algebraic approach, evolutionary computation, genetic algorithms, HiMAT, robust control, structured singular value

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Authors: Hai Chi, Ibrahim Mehmeti, Kirill Ovchinnikov, Hegle Holo, Ingolf F. Nes, Dzung B. Diep

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By using a panel of multiple indicator strains of different bacterial species and genera, we screened a large collection of bacterial isolates (over 1800 isolates) derived from raw milk, for bacteriocin producers with broad inhibition spectra (BIS). Fourteen isolates with BIS were identified, and by 16S rDNA sequencing they were found to belong to Lactococcus garvieae (10 isolates) and Enterococcus feacalis (4 isolates). Further analysis of the ten L. garvieae isolates revealed that they were very similar, if not identical, to each other in metabolic and genetic terms: they had the same fermentation profile on different types of sugars, repetitive sequence-based PCR (rep-PCR) DNA pattern as well as they all had the same inhibition profile towards over 50 isolates of different species. The bacteriocin activity from one of the L. garvieae isolates was assessed further. The bacteriocin which was termed garvicin KS, was found to be heatstable and proteinase-labile and its inhibition spectrum contained many distantly related genera of Firmicutes, comprising most lactic acid bacteria (LAB) as well as problematic species of Bacillus, Listeria, Streptococcus and Staphylococcus and their antibiotic resistant derivatives (e.g. VRE, MRSA). Taken together, the results indicate that this is a potent bacteriocin from L. garvieae and that its very broad inhibition spectrum can be a very useful property for use in food preservation as well as in infection treatments caused by gram-positive pathogens and their antibiotic-derivatives.

Keywords: bacteriocin, lactic acid bacteria, Lactococcus garvieae, antibiotics resistance

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Authors: Fitria D. Ayuningtyas, Anggraini Barlian

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Green turtle (Chelonia mydas) is one of TSD (Temperature-dependent Sex Determination, TSD) animals which sex is determined by the egg’s incubation temperature. GSD (Genotypic Sex Determination) homologous genes such as Wilms’ Tumor (Wt1) and Forkhead Box L2 (FoxL2) play a role in TSD animal sex determination process. Wt1 plays a role in both male pathway, as a transcription factor for Sf1 gene and in female pathway, as a transcription factor for Dax1. FoxL2 plays a role specifically in female sex determination, and known as transcriptional factor for Aromatase gene. Until now, research on the pattern of Wt1 and FoxL2 genes expression in C.mydas has not been conducted yet. The aim of this research is to know the pattern of Wt1 and FoxL2 genes expression in Mesonephros-Gonad (MG) complexes of Chelonia mydas embryos incubated in masculinizing temperature (MT) and feminizing temperature (FT). Eggs of C.mydas incubated in 3 different stage of TSP (Thermosensitive Period) at masculinizing temperature (26±10C, MT) and feminizing temperature (31±10C FT). Mesonefros-gonad complexes were isolated at Pre-TSP stage (FT at days 14th, MT at days 24th), TSP stage (FT at days 24th, MT at days 36th) and differentiated stage (FT at days 40th, MT at days 58th). RNA from mesonephros-gonad (MG) complexes were converted into cDNA by RT-PCR process, and the pattern of Wt1 and FoxL2 genes expression is analyzed by quantitative Real Time PCR (qPCR) method, β-actin gene is used as an internal control. The pattern of Wt1 gene expression in Pre-TSP stage was almost the same between MG complexes incubated at MT or FT, while TSP and differentiation stage, the pattern of Wt1 gene expression in MG complexes incubated at MT or FT was increased. Wt1 gene expression of MG complexes that incubated at FT was higher than at MT. There was a difference pattern between Wt1 gene expression in this research compared to the previous research in protein level. It could be assumed that the difference caused by post-transcriptional regulation mechanisms before mRNA of Wt1 gene translated into protein structure. The pattern of FoxL2 gene expression in Pre-TSP stage was almost the same between MG complexes that incubated at MT and FT, and increased in both TSP and differentiated stage. The FoxL2 gene expression in MG complexes that incubated in FT is higher than MT on TSP and differentiated stage. Based on the results of this research, it can be assumed that Wt1 and FoxL2 gene were expressed in MG complexes that incubated both at MT and FT since Pre-TSP stage. The pattern of Wt1 gene expression was increased in every stage of gonadal development, and so do the pattern of FoxL2 gene expression. Wt1 and FoxL2 gene expressions were higher in MG complexes incubated at FT than MT.

Keywords: chelonia mydas, FoxL2, gene expression, TSD, Wt1

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Authors: Saima Suleman, Kalsoom Sughra, Naeem Mahmood Ashraf

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Mycobacterium tuberculosis is a communicable chronic illness. This disease is being highly focused by researchers as it is present approximately in one third of world population either in active or latent form. The genetic makeup of a person plays an important part in producing immunity against disease. And one important factor association is single nucleotide polymorphism of relevant gene. In this study, we have studied association between single nucleotide polymorphism of CD-209 gene (encode DC-SIGN receptor) and patients of tuberculosis. Dry lab (in silico) and wet lab (RFLP) analysis have been carried out. GWAS catalogue and GEO database have been searched to find out previous association data. No association study has been found related to CD-209 nsSNPs but role of CD-209 in pulmonary tuberculosis have been addressed in GEO database.Therefore, CD-209 has been selected for this study. Different databases like ENSEMBLE and 1000 Genome Project has been used to retrieve SNP data in form of VCF file which is further submitted to different software to sort SNPs into benign and deleterious. Selected SNPs are further annotated by using 3-D modeling techniques using I-TASSER online software. Furthermore, selected nsSNPs were checked in Gujrat and Faisalabad population through RFLP analysis. In this study population two SNPs are found to be associated with tuberculosis while one nsSNP is not found to be associated with the disease.

Keywords: association, CD209, DC-SIGN, tuberculosis

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Authors: Ammara Mehmood, Aneela Zameer, Muhammad Asif Zahoor Raja, Muhammad Faisal Fateh

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In this work, the strength of bio-inspired computational intelligence based technique is exploited for parameter estimation for the periodic signals using Continuous Differential Evolution (CDE) by defining an error function in the mean square sense. Multidimensional and nonlinear nature of the problem emerging in sinusoidal signal models along with noise makes it a challenging optimization task, which is dealt with robustness and effectiveness of CDE to ensure convergence and avoid trapping in local minima. In the proposed scheme of Continuous Differential Evolution based Signal Parameter Estimation (CDESPE), unknown adjustable weights of the signal system identification model are optimized utilizing CDE algorithm. The performance of CDESPE model is validated through statistics based various performance indices on a sufficiently large number of runs in terms of estimation error, mean squared error and Thiel’s inequality coefficient. Efficacy of CDESPE is examined by comparison with the actual parameters of the system, Genetic Algorithm based outcomes and from various deterministic approaches at different signal-to-noise ratio (SNR) levels.

Keywords: parameter estimation, bio-inspired computing, continuous differential evolution (CDE), periodic signals

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Authors: L. K. Davis

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The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time-based DNA codes, writing DNA code from scratch

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Authors: Qingjin Liu, Jinpeng Niu, Kangjia Chen, Jiao Li, Huafu Chen, Wei Liao

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Functional connectomics is essential in cognitive science and neuropsychiatry, offering insights into the brain's complex network structures and dynamic interactions. Although neuroimaging has uncovered functional connectivity issues in Major Depressive Disorder (MDD) patients, the dynamic shifts in connectome topology and their link to gene expression are yet to be fully understood. To explore the differences in dynamic connectome topology between MDD patients and healthy individuals, we conducted an extensive analysis of resting-state functional magnetic resonance imaging (fMRI) data from 434 participants (226 MDD patients and 208 controls). We used multilayer network models to evaluate brain module dynamics and examined the association between whole-brain gene expression and dynamic module variability in MDD using publicly available transcriptomic data. Our findings revealed that compared to healthy individuals, MDD patients showed lower global mean values and higher standard deviations, indicating unstable patterns and increased regional differentiation. Notably, MDD patients exhibited more frequent module switching, primarily within the executive control network (ECN), particularly in the left dorsolateral prefrontal cortex and right fronto-insular regions, whereas the default mode network (DMN), including the superior frontal gyrus, temporal lobe, and right medial prefrontal cortex, displayed lower variability. These brain dynamics predicted the severity of depressive symptoms. Analyzing human brain gene expression data, we found that the spatial distribution of MDD-related gene expression correlated with dynamic module differences. Cell type-specific gene analyses identified oligodendrocytes (OPCs) as major contributors to the transcriptional relationships underlying module variability in MDD. To the best of our knowledge, this is the first comprehensive description of altered brain module dynamics in MDD patients linked to depressive symptom severity and changes in whole-brain gene expression profiles.

Keywords: major depressive disorder, module dynamics, magnetic resonance imaging, transcriptomic

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Authors: Purva Mishra, Rajesh Potlia, Kuljeet Singh Sandhu

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The role of glycyl residues in the protein structure has lingered within the research community for the last several decades. Glycyl residue is the only amino acid that is achiral due to the lack of a side chain and can, therefore, exhibit Ramachandran conformations that are disallowed for L-amino acids. The structural and functional significance of glycyl residues with L-disallowed conformation, however, remains obscure. Through statistical analysis of various datasets, we found that the glycyls with L-disallowed conformations are over-represented at disease-associated sites and tend to be evolutionarily conserved. The mutations of L-disallowed glycyls tend to destabilize the native conformation, reduce protein solubility, and promote inter-molecular aggregations. We uncovered a structural motif referred to as “β-crescent” formed around the L-disallowed glycyl, which prevents β-sheet aggregation by disrupting the alternating pattern of β-pleats. The L-disallowed conformation of glycyls also holds predictive power to infer the pathogenic missense variants. Altogether, our observations highlight that the L-disallowed conformation of glycyls is selected to facilitate native folding and prevent inter-molecular aggregations. The findings may also have implications for designing more stable proteins and prioritizing the genetic lesions implicated in diseases.

Keywords: Ramachandran plot, β-sheet, protein stability, protein aggregation

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Authors: Mohammad Najmuddin Khan, Mohamad Khaleel Albalwi

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The prevalence of obesity has risen dramatically in past several decades. Hormonal and genetic factors are rarely the cause of childhood obesity. Because obese adult may suffer life-long physical and emotional consequences, it is imperative to discuss prevention with parents during well-child examinations. Purpose of the study was to compare the serum lipid profile of obese and non-obese males. Twenty two male students were selected from Al-Jouf University. Their age ranged from 19 to 29. They were divided into groups. One group (N=15) having more than 20% fat was considered as obese group, another group (N=7) was considered as non-obese group. Fasting blood samples were analysed for blood cholesterol, triglycerides, low density lipoprotein cholesterol (LDL-C) and high density lipoprotein cholesterol (HDL-C). Independent test was applied to compare mean difference. In obese group, significantly higher cholesterol and triglycerides were observed. On the contrary, obese group had significantly lower HDL-C concentration than the non-obese group. The adult obese has relatively larger changes in serum lipids at any given level of obesity. On the average, higher amount of fat makes it more likely for an individual to be dyslipidemic and to express elements of the metabolic syndrome. Increased triglycerides level in obese impaired lipolysis which reduced the HDL-C concentrations.

Keywords: obesity, serum lipid profile, Al-Jouf, HDL, LDL

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Authors: Mohammad Ahangari

Abstract:

Schizophrenia is a psychiatric disorder with symptoms that include cognitive deficits and nicotine has been suggested to have an effect on cognition. In recent years, the advents of Genome-Wide Association Studies(GWAS) has evolved our understanding about the genetic causes of complex disorders such as schizophrenia and studying the role of genome-wide significant genes could potentially lead to the development of new therapeutic agents for treatment of cognitive deficits in schizophrenia. The current study identified six Single Nucleotide Polymorphisms (SNP) from schizophrenia and smoking GWAS that are located on or in close proximity to the nicotinic receptor gene cluster (CHRN) and studied their association with cognition in an Irish sample of 1297 cases and controls using linear regression analysis. Further on, the interaction between CHRN gene cluster and Dopamine receptor D2 gene (DRD2) during working memory was investigated. The effect of these polymorphisms on nicotinic and dopaminergic neurotransmission, which is disrupted in schizophrenia, have been characterized in terms of their effects on memory, attention, social cognition and IQ as measured by a neuropsychological test battery and significant effects in two polymorphisms were found across global IQ domain of the test battery.

Keywords: cognition, dopamine, GWAS, nicotine, schizophrenia, SNPs

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Authors: M. Ben Jrad, A. Belhaj Mohamed, S. Riahi, I. Bouazizi, M. Saidi, M. Soussi

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The generative potential, depositional environment, thermal maturity and oil seeps of the organic-rich Bou Dabbous Formation (Ypresian) from the thrust belt northwestern Tunisia, were determined by Rock Eval and molecular analyses. The paleo-tectonic units in the area show some similarities with equivalent facies in Mediterranean Sea and Sicilian. The Bou Dabbous Formation displays variable source rock characteristics through the various units Tellian and Numidian nappes Units. Organic matter contents and petroleum potentials are fair to high (reaching 1.95% and 6 kg of HC/t of rock respectively) marine type II kerogen. An increasing SE-NW maturity gradient is well documented in the study area. The Bou Dabbous organic-rich facies are marginally mature stage in the Tellian Unit (Kasseb domain), whilst they are mature-late mature stage within Nefza-Ain Allega tectonic windows. A long and north of Cap Serrat-Ghardimaou Master Fault these facies are overmature. Oil/Oil and Oil/source rock correlation, based on biomarker and carbon isotopic composition, shows a positive genetic correlation between the oil seeps and Bou Dabbous source rock.

Keywords: biomarkers, Bou Dabbous Formation, Northern Tunisia, source rock

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Authors: Boumesbah Asma, Chergui Mohamed El-amine

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Since it has been shown that the multi-objective minimum spanning tree problem (MOST) is NP-hard even with two criteria, we propose in this study a hybrid NSGA-II algorithm with an exact mutation operator, which is only used with low probability, to find an approximation to the Pareto front of the problem. In a connected graph G, a spanning tree T of G being a connected and cycle-free graph, if k edges of G\T are added to T, we obtain a partial graph H of G inducing a reduced size multi-objective spanning tree problem compared to the initial one. With a weak probability for the mutation operator, an exact method for solving the reduced MOST problem considering the graph H is then used to give birth to several mutated solutions from a spanning tree T. Then, the selection operator of NSGA-II is activated to obtain the Pareto front approximation. Finally, an adaptation of the VNS metaheuristic is called for further improvements on this front. It allows finding good individuals to counterbalance the diversification and the intensification during the optimization search process. Experimental comparison studies with an exact method show promising results and indicate that the proposed algorithm is efficient.

Keywords: minimum spanning tree, multiple objective linear optimization, combinatorial optimization, non-sorting genetic algorithm, variable neighborhood search

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Authors: Luz Hurtado, Rodrigo Rojas, Jaime Romero, Christopher Concha

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The culture of the marine fish red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture which is a Chilean native species of high gastronomic demand and market value. The microbiota was analyzed in terms of diversity and structure using massive Illumina sequencing. The analysis of alpha diversity was performed in samples of G. chilensis larvae of 6, 18 and 32 dph (days post-hatching) and it was observed that there were significant differences (P = 0.05) between the days of culture for the Chao1 index, being the larvae of 18 dph the one with the highest index followed by the larvae of 6 dph, The lowest value for this index was presented in larvae of 32 dph. There were no significant differences in larvae between the days of culture for the Shannon (P=0.0857) and Simpson (P=0.0714) indices. In general, the larvae of G. chilensis have high rates of diversity. When analyzing the beta diversity, a differentiation between the bacterial communities is observed depending on the day of the culture of the larvae. Considering the PCoA elaborated from the unweighted UniFrac statistic, the explained variance was 46.2% (PC1 29.2% and PC2 17.0%) and in the case of the PCoA elaborated with the weighted UniFrac statistic; the explained variance was 65.5% (PC1 41.8% and PC2 23.7%) these differences were significant based on the Permanova statistical analysis (P= 0.002 and 0.037 respectively). When analyzing the taxonomic composition of the microbiota of the larvae in the different days of culture it was observed that at the phyla level the most abundant in the larvae of 6 dph were Proteobacteria (57%) Verrucomicrobia (24%) and Firmicutes (14%), for the larvae of 18 dph the predominant phyla were Proteobacteria (90%), Dependientiae (5%), Actinobacteria (2%) and Plactomyces (2%), for the larvae of 32 dph the phyla that presented the highest relative abundance were Proteobacteria (57%), Firmicutes (29%), Verrucomicrobia (5%) and Actinobacteria (5%), when comparing the larvae between the days it was observed that the phylum Proteobacteria was the most abundant in the samples of larvae of 6, 18 and 32 dph being the larvae of 18 dph those that present the highest relative abundance, the larvae of 6 dph were those that presented the highest relative abundance for the phylum Verrucomicrobia and in the larvae of 32 dph was observed greater abundance of the phylum Firmicutes compared to the other days of larval culture. At the level of genera, those with the highest relative abundance in larvae of 6 dph were Rubritalea (30%), Psychrobacter (28%), staphylococcus (17%) and Ralstonia (10%), for the larvae of 18 dph the genera with the highest abundance were Psychrobacter (47%), Litoreibacter (13%), Nautella (9%) and Cohesibacter (8%), for the larvae of 32 dph the most abundant genera were Alloiococcus (25%), Dialister (14%), Neptunomonas (13%) and Piscirickettsia (11%). When observing the taxonomic composition of the larvae between the days of larval culture, it is observed that there are differences between them.

Keywords: microbiota, diversity, G. Chilensis, larvae

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Authors: Ghazanfar Ali, Fahad N Almajhdi

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This study provides data on the viral diagnosis and molecular epidemiology of influenza A(H3N2) virus isolated in Riyadh, Saudi Arabia. Nasopharyngeal aspirates from 80 clinically infected patients in the peak of the 2010-2011 winter seasons were processed for viral diagnosis by RT-PCR. Sequencing of entire HA and NA genes of representative isolates and molecular epidemiological analysis were performed. A total of 06 patients were positive for influenza A, B and respiratory syncytial viruses by RT-PCR assays; out of these only one sample was positive for influenza A(H3N2) by RT-PCR. Phylogenetic analysis of the HA and NA gene sequences showed identities higher than 99-98.8 % in both genes. They were also similar to reference isolates in HA sequences (99 % identity) and in NA sequences (99 % identity). Amino acid sequences predicted for the HA gene were highly identical to reference strains. The NA amino acid substitutions identified did not include the oseltamivir-resistant H275Y substitution. Conclusion: Viral isolation and RT-PCR together were useful for diagnosis of the influenza A (H3N2) virus. Variations in HA and NA sequences are similar to those identified in worldwide reference isolates and no drug resistance was found.

Keywords: influenza A (H3N2), genetic characterization, viral isolation, RT-PCR, Saudi Arabia

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Authors: Adel Omar Ashour, Paul S. Dyer

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Aspergillus nidulans can reproduce by asexual or sexual means, producing green conidiospores or red-purple ascospores respectively. The latter one is produced in dark-purple globose ‘cleistothecia’ which are surrounded by Hülle cells. The species has a homothallic (self fertile) sexual breeding system. Given the extra metabolic costs associated with sexual compared to asexual reproduction it would be predicted that ascospore production would confer evolutionary benefits. However, due to the homothallic breeding system there is very rarely any increased genetic variation in ascospore offspring and traditionally conidia and ascospores are considered to be equally environmental resistant. We therefore examined in detail whether conidia and ascospores might exhibit as yet undetected differences in spore viability when subjected to certain environmental stressors. Spores from two strains of A. nidulans (comprising wild-type and KU mutants) were exposed to various levels of temperature (50-70°C for 30 min) and UV (350 nm for 10-60 min) stress. Results of experiments will be presented, including comparison of ‘D’ (decimal point reduction) values of conidia versus ascospores of A. nidulans. We detected that under certain exposure levels ascospores have significantly increased resistance compared to conidia. The increased environmental resistance of ascospores might be a key factor explaining the persistence of sexuality in this homothallic species, and reasons for differential survival are suggested.

Keywords: Aspergillus nidulans, asexual reproduction, conidia, ascospores, cleistothecia, d-value

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Authors: Feby Zaki Raouf Fawzy

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Nowadays, design and architecture are being affected and undergoing change with the rapid advancements in technology, economics, politics, society, and culture. Architecture has been transforming with the latest developments after the inclusion of computers in design. Integration of design into the computational environment has revolutionized architecture and unique perspectives in architecture have been gained. The history of architecture shows the various technological developments and changes in which architecture has transformed with time. Therefore, the analysis of integration between technology and the history of the architectural process makes it possible to build a consensus on the idea of how architecture is to proceed. In this study, each period that occurs with the integration of technology into architecture is addressed within the historical process. At the same time, changes in architecture via technology are identified as important milestones and predictions with regards to the future of architecture have been determined. Developments and changes in technology and the use of technology in architecture within years are analyzed in charts and graphs comparatively. The historical process of architecture and its transformation via technology is supported by a detailed literature review, and they are consolidated with the examination of focal points of 20th-century architecture under the titles parametric design, genetic architecture, simulation, and biomimicry. It is concluded that with the historical research between past and present, the developments in architecture cannot keep up with the advancements in technology, and recent developments in technology overshadow architecture; even technology decides the direction of architecture. As a result, a scenario is presented with regard to the reach of technology in the future of architecture and the role of the architect.

Keywords: design and development the information technology architecture, enterprise architecture, enterprise architecture design result, TOGAF architecture development method (ADM)

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