Search results for: DNA sequence analysis

Authors: Aouiche Abdelaziz, Soudani Mouhamed Salah, Aouiche El Moundhe

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The present paper addresses the utilization of Artificial Neural Networks (ANNs) and Fuzzy Inference Systems (FISs) for the identification and control of dynamical systems with some degree of uncertainty. Because ANNs and FISs have an inherent ability to approximate functions and to adapt to changes in input and parameters, they can be used to control systems too complex for linear controllers. In this work, we show how ANNs and FISs can be put in order to form nets that can learn from external data. In sequence, it is presented structures of inputs that can be used along with ANNs and FISs to model non-linear systems. Four systems were used to test the identification and control of the structures proposed. The results show the ANNs and FISs (Back Propagation Algorithm) used were efficient in modeling and controlling the non-linear plants.

Keywords: non-linear systems, fuzzy set Models, neural network, control law

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Authors: Martina I. Reinhold, Theresa Bacon-Baguley

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A core challenge of physician assistant education is preparing professionals for lifelong learning. While this conventionally has encompassed scientific advances, students must also embrace new care delivery models and technologies. Telemedicine, the provision of care via two-way audio and video, is an example of a technological advance reforming health care. During a three-semester sequence of Hospital Community Experiences, physician assistant students were assigned experiences with Answer Health on Demand, a telemedicine collaborative. Preceding the experiences, the agency lectured on the application of telemedicine. Students were then introduced to the technology and partnered with a provider. Prior to observing the patient-provider interaction, patient consent was obtained. Afterwards, students completed a reflection paper on lessons learned and the potential impact of telemedicine on their careers. Thematic analysis was completed on the students’ reflection papers (n=13). Preceding the lecture and experience, over 75% of students (10/13) were unaware of telemedicine. Several stated they were 'skeptical' about the effectiveness of 'impersonal' health care appointments. After the experience, all students remarked that telemedicine will play a large role in the future of healthcare and will provide benefits by improving access in rural areas, decreasing wait time, and saving cost. More importantly, 30% of students (4/13) commented that telemedicine is a technology they can see themselves using in their future practice. Initial results indicate that collaborative interaction between students and telemedicine providers enhanced student learning and exposed students to technological advances in the delivery of care. Further, results indicate that students perceived telemedicine more favorably as a viable delivery method after the experience.

Keywords: collaboration, physician assistant education, teaching innovative health care delivery method, telemedicine

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Authors: M. Kazou, A. Gavriil, O. Kalagkatsi, T. Paschos, E. Tsakalidou

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Kopanisti cheese is a Greek soft Protected Designation of Origin (PDO) cheese made of raw cow, sheep or goat milk, or mixtures of them, with similar organoleptic characteristics to that of Roquefort cheese. Traditional manufacturing of Kopanisti cheese is limited in small-scale dairies, without the addition of starter cultures. Instead, an amount of over-mature Kopanisti cheese, called Mana Kopanisti, is used to initiate ripening. Therefore, the selection of proper starter cultures and the understanding of the contribution of various microbial groups to its overall quality is crucial for the production of a high-quality final product with standardized organoleptic and physicochemical characteristics. Taking the above into account, the aim of the present study was the investigation of Kopanisti cheese microbiota and its role in cheese quality. For this purpose, four different types of Kopanisti were produced in triplicates, all with pasteurized cow milk, with the addition of (A) the typical mesophilic species Lactococcus lactis and Lactobacillus paracasei used as starters in the production of soft spread cheeses, (B) strains of Lactobacillus acidipiscis and Lactobacillus rennini previously isolated from Kopanisti and Mana Kopanisti, (C) all the species from (A) and (B) as inoculum, and finally (D) the species from (A) and Mana Kopanisti. Physicochemical and microbiological analysis was performed for milk and cheese samples during ripening. Enumeration was performed for major groups of lactic acid bacteria (LAB), total mesophilic bacteria, yeasts as well as hygiene indicator microorganisms. Bacterial isolates from all the different LAB groups, apart from enterococci, alongside yeasts isolates, were initially grouped using repetitive sequence-based polymerase chain reaction (rep-PCR) and then identified at the species level using 16S rRNA gene and internal transcribed spacer (ITS) DNA region sequencing, respectively. Sensory evaluation was also performed for final cheese samples at the end of the ripening period (35 days). Based on the results of the classical microbiological analysis, the average counts of the total mesophilic bacteria and LAB, apart from enterococci, ranged between 7 and 10 log colony forming unit (CFU) g⁻¹, phychrotrophic bacteria, and yeast extract glucose chloramphenicol (YGC) isolates between 4 and 8 log CFU g⁻¹, while coliforms and enterococci up to 2 log CFU g⁻¹ throughout ripening in cheese samples A, C and D. In contrast, in cheese sample B, the average counts of the total mesophilic bacteria and LAB, apart from enterococci, phychrotrophic bacteria, and YGC isolates ranged between 0 and 10 log CFU g⁻¹ and coliforms and enterococci up to 2 log CFU g⁻¹. Although the microbial counts were not that different among samples, identification of the bacterial and yeasts isolates revealed the complex microbial community structure present in each cheese sample. Differences in the physicochemical characteristics among the cheese samples were also observed, with pH ranging from 4.3 to 5.3 and moisture from 49.6 to 58.0 % in the final cheese products. Interestingly, the sensory evaluation also revealed differences among samples, with cheese sample B ranking first based on the total score. Overall, the combination of these analyses highlighted the impact of different starter cultures on the Kopanisti microbiota as well as on the physicochemical and sensory characteristics of the final product.

Keywords: Kopanisti cheese, microbiota, classical microbiological analysis, physicochemical analysis

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Authors: Jorge Maestre Vidal, Ana Lucila Sandoval Orozco, Luis Javier García Villalba

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With the increase in popularity of mobile devices, new and varied forms of malware have emerged. Consequently, the organizations for cyberdefense have echoed the need to deploy more effective defensive schemes adapted to the challenges posed by these recent monitoring environments. In order to contribute to their development, this paper presents a malware detection strategy for mobile devices based on sequence alignment algorithms. Unlike the previous proposals, only the system calls performed during the startup of applications are studied. In this way, it is possible to efficiently study in depth, the sequences of system calls executed by the applications just downloaded from app stores, and initialize them in a secure and isolated environment. As demonstrated in the performed experimentation, most of the analyzed malicious activities were successfully identified in their boot processes.

Keywords: android, information security, intrusion detection systems, malware, mobile devices

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Authors: Tze Jin Wong, Lee Feng Koo, Pang Hung Yiu

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Lenstra’s attack uses Chinese remainder theorem as a tool and requires a faulty signature to be successful. This paper reports on the security responses of fourth and sixth order Lucas based (LUC_4,6) cryptosystem under the Lenstra’s attack as compared to the other two Lucas based cryptosystems such as LUC and LUC₃ cryptosystems. All the Lucas based cryptosystems were exposed mathematically to the Lenstra’s attack using Chinese Remainder Theorem and Dickson polynomial. Result shows that the possibility for successful Lenstra’s attack is less against LUC_4,6 cryptosystem than LUC₃ and LUC cryptosystems. Current study concludes that LUC_4,6 cryptosystem is more secure than LUC and LUC₃ cryptosystems in sustaining against Lenstra’s attack.

Keywords: Lucas sequence, Dickson polynomial, faulty signature, corresponding signature, congruence

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Authors: A. Hocine, A. Ghouaoula, S. M. Medjdoub, M. Cherifi

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The present paper proposed a meso–macro model describing the mechanical behaviour composite laminates of staking sequence [+θ/-θ]s under tensil loading. The behaviour of a layer is ex-pressed through elasticity coupled to damage. The elastic strain is due to the elasticity of the layer and can be modeled by using the classical laminate theory, and the laminate is considered as an orthotropic material. This means that no coupling effect between strain and curvature is considered. In the present work, the damage is associated to cracking of the matrix and parallel to the fibers and it being taken into account by the changes in the stiffness of the layers. The anisotropic damage is completely described by a single scalar variable and its evolution law is specified from the principle of maximum dissipation. The stress/strain relationship is investigated in plane stress loading.

Keywords: damage, behavior modeling, meso-macro model, composite laminate, membrane loading

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Authors: Anuj Tyagi, Balwinder Singh, Naveen Kumar B. T., Niraj K. Singh

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Characterization of diverse microbial communities in specific environment plays a crucial role in the better understanding of their functional relationship with the ecosystem. It is now well established that gut microbiome of fish is not the simple replication of microbiota of surrounding local habitat, and extensive species, dietary, physiological and metabolic variations in fishes may have a significant impact on its composition. Moreover, overuse of antibiotics in human, veterinary and aquaculture medicine has led to rapid emergence and propagation of antibiotic resistance genes (ARGs) in the aquatic environment. Microbial communities harboring specific ARGs not only get a preferential edge during selective antibiotic exposure but also possess the significant risk of ARGs transfer to other non-resistance bacteria within the confined environments. This phenomenon may lead to the emergence of habitat-specific microbial resistomes and subsequent emergence of virulent antibiotic-resistant pathogens with severe fish and consumer health consequences. In this study, gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. Metagenomic DNA, extracted from the fish gut, was subjected to sequencing on Illumina NextSeq to generate paired-end (PE) 2 x 150 bp sequencing reads. After the QC of raw sequencing data by Trimmomatic, taxonomic analysis by Kraken2 taxonomic sequence classification system revealed the presence of 36 phyla, 326 families and 985 genera in the fish gut microbiome. At phylum level, Proteobacteria accounted for more than three-fourths of total bacterial populations followed by Actinobacteria (14%) and Cyanobacteria (3%). Commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) were found to be very less prevalent in fish gut. After sequencing data assembly by MEGAHIT v1.1.2 assembler and PROKKA automated analysis pipeline, pathway analysis revealed the presence of 1,608 Metacyc pathways in the fish gut microbiome. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy-metabolism (4%) and fermentation (2%). Almost one-third (33%) of biosynthesis pathways were involved in the synthesis of secondary metabolites. Metabolic pathways for the biosynthesis of 35 antibiotic types were also present, and these accounted for 5% of overall metabolic pathways in the fish gut microbiome. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. More than 90% ARGs in fish gut microbiome were against beta-lactams (penicillins, cephalosporins, penems, and monobactams). Resistance against tetracycline, macrolides, fluoroquinolones, and phenicols ranged from 0.7% to 1.3%. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment.

Keywords: antibiotic resistance, fish gut, metabolic pathways, microbial diversity

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Authors: Irtaza M. Syed, Kaamran Raahemifar

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This paper presents a model predictive control (MPC) of a utility interactive (UI) single phase inverter (SPI) for a photovoltaic (PV) system at residential/distribution level. The proposed model uses single-phase phase locked loop (PLL) to synchronize SPI with the grid and performs MPC control in a dq reference frame. SPI model consists of boost converter (BC), maximum power point tracking (MPPT) control, and a full bridge (FB) voltage source inverter (VSI). No PI regulators to tune and carrier and modulating waves are required to produce switching sequence. Instead, the operational model of VSI is used to synthesize sinusoidal current and track the reference. Model is validated using a three kW PV system at the input of UI-SPI in Matlab/Simulink. Implementation and results demonstrate simplicity and accuracy, as well as reliability of the model.

Keywords: phase locked loop, voltage source inverter, single phase inverter, model predictive control, Matlab/Simulink

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Authors: Majid Forghani, Michael Khachay

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In genetics, the impact of neighboring amino acids on a target site is referred as the nearest-neighbor effect or simply neighbor effect. In this paper, a new method called wavelet particle decomposition representing the one-dimensional neighbor effect using wavelet packet decomposition is proposed. The main idea lies in known dependence of wavelet packet sub-bands on location and order of neighboring samples. The method decomposes the value of a signal sample into small values called particles that represent a part of the neighbor effect information. The results have shown that the information obtained from the particle decomposition can be used to create better model variables or features. As an example, the approach has been applied to improve the correlation of test and reference sequence distance with titer in the hemagglutination inhibition assay.

Keywords: antigenic variants, neighbor effect, wavelet packet, wavelet particle decomposition

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Authors: Azam Fazelpour, Saeed R. Dehghani, Vlastimil Masek, Yuri S. Muzychka

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The study uses an image analysis technique employing thermal imaging to measure the percentage of areas with various temperatures on a freezing surface. An image segmentation method using threshold values is applied to a sequence of image recording the freezing process. The phenomenon is transient and temperatures vary fast to reach the freezing point and complete the freezing process. Freezing salt water is subjected to the salt rejection that makes the freezing point dynamic and dependent on the salinity at the phase interface. For a specific area of freezing, nucleation starts from one side and end to another side, which causes a dynamic and transient temperature in that area. Thermal cameras are able to reveal a difference in temperature due to their sensitivity to infrared radiance. Using Experimental setup, a video is recorded by a thermal camera to monitor radiance and temperatures during the freezing process. Image processing techniques are applied to all frames to detect and classify temperatures on the surface. Image processing segmentation method is used to find contours with same temperatures on the icing surface. Each segment is obtained using the temperature range appeared in the image and correspond pixel values in the image. Using the contours extracted from image and camera parameters, stratified areas with different temperatures are calculated. To observe temperature contours on the icing surface using the thermal camera, the salt water sample is dropped on a cold surface with the temperature of -20°C. A thermal video is recorded for 2 minutes to observe the temperature field. Examining the results obtained by the method and the experimental observations verifies the accuracy and applicability of the method.

Keywords: ice contour boundary, image processing, image segmentation, salt ice, thermal image

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Authors: Catherine K. Derow

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Possibly a slime mold somehow mutated or already was mutated at progeniture and so stayed as a metazoan when it developed into the fruiting stage and so the slime mold(s) we are evolved and similar to are genetically differ from the slime molds in existence now. This may be why there are genetic links between humans and other metazoa now alive and slime molds now alive but we are now divergent branches of the evolutionary tree compared to the original slime mold, or perhaps slime mold-like organisms, that gave rise to metazoan animalia and perhaps algae and plantae as slime molds were undifferentiated enough in many ways that could allow their descendants to evolve into these three separate phylogenetic categories. Or it may be a slime mold was born or somehow progenated as multicellular, as the particular organism was mutated enough to have say divided in a a 'pseudo-embryonic' stage, and this could have happened for algae, plantae as well as animalia or all the branches may be from the same line but the missing link might be covered in 'phylogenetic sequence comparison noise'.

Keywords: metazoan evolution, unicellular bridge to metazoans, evolution, slime mold

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Authors: Saul Estrin, Ute Stephan, Suncica Vujic

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Background and research question: Gender differences in pay are present at all organisational levels, including at the very top. One possible way for women to circumvent organizational norms and discrimination is to engage in entrepreneurship because, as CEOs of their own organizations, entrepreneurs largely determine their own pay. While commercial entrepreneurship plays an important role in job creation and economic growth, social entrepreneurship has come to prominence because of its promise of addressing societal challenges such as poverty, social exclusion, or environmental degradation through market-based rather than state-sponsored activities. This opens the research question whether social entrepreneurship might be a form of entrepreneurship in which the pay of men and women is the same, or at least more similar; that is to say there is little or no gender pay gap. If the gender gap in pay persists also at the top of social enterprises, what are the factors, which might explain these differences? Methodology: The Oaxaca-Blinder Decomposition (OBD) is the standard approach of decomposing the gender pay gap based on the linear regression model. The OBD divides the gender pay gap into the ‘explained’ part due to differences in labour market characteristics (education, work experience, tenure, etc.), and the ‘unexplained’ part due to differences in the returns to those characteristics. The latter part is often interpreted as ‘discrimination’. There are two issues with this approach. (i) In many countries there is a notable convergence in labour market characteristics across genders; hence the OBD method is no longer revealing, since the largest portion of the gap remains ‘unexplained’. (ii) Adding covariates to a base model sequentially either to test a particular coefficient’s ‘robustness’ or to account for the ‘effects’ on this coefficient of adding covariates might be problematic, due to sequence-sensitivity when added covariates are correlated. Gelbach’s decomposition (GD) addresses latter by using the omitted variables bias formula, which constructs a conditional decomposition thus accounting for sequence-sensitivity when added covariates are correlated. We use GD to decompose the differences in gaps of pay (annual and hourly salary), size of the organisation (revenues), effort (weekly hours of work), and sources of finances (fees and sales, grants and donations, microfinance and loans, and investors’ capital) between men and women leading social enterprises. Database: Our empirical work is made possible by our collection of a unique dataset using respondent driven sampling (RDS) methods to address the problem that there is as yet no information on the underlying population of social entrepreneurs. The countries that we focus on are the United Kingdom, Spain, Romania and Hungary. Findings and recommendations: We confirm the existence of a gender pay gap between men and women leading social enterprises. This gap can be explained by differences in the accumulation of human capital, psychological and social factors, as well as cross-country differences. The results of this study contribute to a more rounded perspective, highlighting that although social entrepreneurship may be a highly satisfying occupation, it also perpetuates gender pay inequalities.

Keywords: Gelbach’s decomposition, gender gap, returns to social entrepreneurship, values and preferences

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Authors: Kouassi Louis Kra

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The nearshore deep-water gravity flow deposits in the Northern steep slope of Dongying depression, Bohai Bay basin, have been acknowledged as important reservoirs in the rift lacustrine basin. These deep strata term as coarse clastic sediment, deposit at the root of the slope have complex depositional processes and involve wide diagenetic events which made high-quality reservoir prediction to be complex. Based on the integrated study of seismic interpretation, sedimentary analysis, petrography, cores samples, wireline logging data, 3D seismic and lithological data, the reservoir formation mechanism deciphered. The Geoframe software was used to analyze 3-D seismic data to interpret the stratigraphy and build a sequence stratigraphic framework. Thin section identification, point counts were performed to assess the reservoir characteristics. The software PetroMod 1D of Schlumberger was utilized for the simulation of burial history. CL and SEM analysis were performed to reveal diagenesis sequences. Backscattered electron (BSE) images were recorded for definition of the textural relationships between diagenetic phases. The result showed that the nearshore steep slope deposits mainly consist of conglomerate, gravel sandstone, pebbly sandstone and fine sandstone interbedded with mudstone. The reservoir is characterized by low-porosity and ultra-low permeability. The diagenesis reactions include compaction, precipitation of calcite, dolomite, kaolinite, quartz cement and dissolution of feldspars and rock fragment. The main types of reservoir space are primary intergranular pores, residual intergranular pores, intergranular dissolved pores, intergranular dissolved pores, and fractures. There are three obvious anomalous high-porosity zones in the reservoir. Overpressure and early hydrocarbon filling are the main reason for abnormal secondary pores development. Sedimentary facies control the formation of high-quality reservoir, oil and gas filling preserves secondary pores from late carbonate cementation.

Keywords: Bohai Bay, Dongying Sag, deep strata, formation mechanism, high-quality reservoir

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Authors: M. F. F. Ab Rashid, A. N. Mohd Rose, N. M. Z. Nik Mohamed, W. S. Wan Harun, S. A. Che Ghani

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Traveling salesman problem with precedence constraint (TSPPC) is one of the most complex problems in combinatorial optimization. The existing algorithms to solve TSPPC cost large computational time to find the optimal solution. The purpose of this paper is to present an efficient genetic algorithm that guarantees optimal solution with less number of generations and iterations time. Unlike the existing algorithm that generates priority factor as chromosome, the proposed algorithm directly generates sequence of solution as chromosome. As a result, the proposed algorithm is capable of generating optimal solution with smaller number of generations and iteration time compare to existing algorithm.

Keywords: traveling salesman problem, sequencing, genetic algorithm, precedence constraint

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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

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Authors: Tahereh Habibi

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The Oligocene carbonates are widespread along Fars Province, Zagros Basin, SW Iran. Distribution of planktonic and larger benthic foraminfera, stratal patterns and facies architecture are used as a tool to define microfacies and foraminiferal associations of these strata at Kavar Section. The presence of Nummulites spp. indicated the age of the sequence as Rupelian-Chattian (Nummulites vascus-Nummulites fichteli and Archaias asmaricus/hensoni-Miogypsinoides complanatus assemblage zones). The paleoenvironmental setting is interpreted as a homoclinal ramp environment according to the recognition of eight microfacies types. Four foraminiferal associations are recognized in the investigated ramp setting. They represent a salinity of 34-40 to 50 psu and higher than 50 psu in more restricted conditions. The depth ranges from 200 m as evidenced by the presence of planktonic foraminifera and to less than 30m in the more restricted inner ramp environment. Warm tropical and subtropical water with temperature of 18-25° C is proposed.

Keywords: foraminiferal associations, microfacies, oligocene, paleoecology

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Authors: Shweta Dhindhwal

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Dopamine is an essential neurotransmitter in the central nervous system of all vertebrates and plays an important role in many processes such as motor function, learning and behavior, and sensory activity. One of the important functions of dopamine is release of pituitary hormones. It is synthesized from the amino acid tyrosine. Two types of dopamine receptors, D1-like and D2-like, have been reported in fish. The dopamine containing neurons are located in the olfactory bulbs, the ventral regions of the pre-optic area and tuberal hypothalamus. Distribution of the dopaminergic system has not been studied in the murrel, Channa punctatus. The present study deals with identification of D2 receptors in the brain of murrel. A phylogenetic tree has been constructed using partial sequence of D2 receptor. Distribution of putative dopaminergic neurons in the brain has been investigated. Also, formalin induced hypertrophy of neurosecretory cells in murrel has been studied.

Keywords: dopamine, fish, pre-optic area, murrel

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Authors: Ali Akbar Attari, Ali Asghar Beheshti Shirazi

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In this paper, we propose a blind and robust audio watermarking scheme based on spread spectrum in Discrete Wavelet Transform (DWT) domain. Watermarks are embedded in the low-frequency coefficients, which is less audible. The key idea is dividing the audio signal into small frames, and magnitude of the 6^th level of DWT approximation coefficients is modifying based upon the Direct Sequence Spread Spectrum (DSSS) technique. Also, the psychoacoustic model for enhancing in imperceptibility, as well as Savitsky-Golay filter for increasing accuracy in extraction, is used. The experimental results illustrate high robustness against most common attacks, i.e. Gaussian noise addition, Low pass filter, Resampling, Requantizing, MP3 compression, without significant perceptual distortion (ODG is higher than -1). The proposed scheme has about 83 bps data payload.

Keywords: audio watermarking, spread spectrum, discrete wavelet transform, psychoacoustic, Savitsky-Golay filter

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Authors: Yuzhi Cai

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This talk presents a Bayesian approach to quantile autoregressive (QAR) time series model estimation and forecasting. We establish that the joint posterior distribution of the model parameters and future values is well defined. The associated MCMC algorithm for parameter estimation and forecasting converges to the posterior distribution quickly. We also present a combining forecasts technique to produce more accurate out-of-sample forecasts by using a weighted sequence of fitted QAR models. A moving window method to check the quality of the estimated conditional quantiles is developed. We verify our methodology using simulation studies and then apply it to currency exchange rate data. An application of the method to the USD to GBP daily currency exchange rates will also be discussed. The results obtained show that an unequally weighted combining method performs better than other forecasting methodology.

Keywords: combining forecasts, MCMC, quantile modelling, quantile forecasting, predictive density functions

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Authors: Irene Capecchi, Tommaso Borghini, Iacopo Bernetti

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One of the most common pieces of equipment still used today for pruning, felling, and processing trees is the chainsaw in forestry. However, chainsaw use highlights dangers and one of the highest rates of accidents in both professional and non-professional work. Felling is proportionally the most dangerous phase, both in severity and frequency, because of the risk of being hit by the plant the operator wants to cut down. To avoid this, a correct sequence of chainsaw cuts must be taught concerning the different conditions of the tree. Virtual reality (VR) makes it possible to virtually simulate chainsaw use without danger of injury. The limitations of the existing applications are as follow. The existing platforms are not symmetrical collaborative because the trainee is only in virtual reality, and the trainer can only see the virtual environment on a laptop or PC, and this results in an inefficient teacher-learner relationship. Therefore, most applications only involve the use of a virtual chainsaw, and the trainee thus cannot feel the real weight and inertia of a real chainsaw. Finally, existing applications simulate only a few cases of tree felling. The objectives of this research were to implement and test a symmetrical collaborative training application based on VR and mixed reality (MR) with the overlap between real and virtual chainsaws in MR. The research and training platform was developed for the Meta quest 2 head-mounted display. The research and training platform application is based on the Unity 3D engine, and Present Platform Interaction SDK (PPI-SDK) developed by Meta. PPI-SDK avoids the use of controllers and enables hand tracking and MR. With the combination of these two technologies, it was possible to overlay a virtual chainsaw with a real chainsaw in MR and synchronize their movements in VR. This ensures that the user feels the weight of the actual chainsaw, tightens the muscles, and performs the appropriate movements during the test allowing the user to learn the correct body posture. The chainsaw works only if the right sequence of cuts is made to felling the tree. Contact detection is done by Unity's physics system, which allows the interaction of objects that simulate real-world behavior. Each cut of the chainsaw is defined by a so-called collider, and the felling of the tree can only occur if the colliders are activated in the right order simulating a safe technique felling. In this way, the user can learn how to use the chainsaw safely. The system is also multiplayer, so the student and the instructor can experience VR together in a symmetrical and collaborative way. The platform simulates the following tree-felling situations with safe techniques: cutting the tree tilted forward, cutting the medium-sized tree tilted backward, cutting the large tree tilted backward, sectioning the trunk on the ground, and cutting branches. The application is being evaluated on a sample of university students through a special questionnaire. The results are expected to test both the increase in learning compared to a theoretical lecture and the immersive and telepresence of the platform.

Keywords: chainsaw, collaborative symmetric virtual reality, mixed reality, operator training

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Authors: Nader Mohamed

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The Late Cretaceous deposits are well developed through-out Egypt. This is due to a ‎transgression phase associated with the subsidence caused by the neo-Tethyan rift event that ‎took place across the northern margin of Africa, resulting in a period of dominantly marine ‎deposits in the Gulf of Suez. The Late Cretaceous Nezzazat Group represents the Cenomanian, ‎Turonian and clastic sediments of the Lower Senonian. The Nezzazat Group has been divided ‎into four formations namely, from base to top, the Raha Formation, the Abu Qada Formation, ‎the Wata Formation and the Matulla Formation. The Cenomanian Raha and the Lower Senonian ‎Matulla formations are the most important clastic sequence in the Nezzazat Group because they ‎provide the highest net reservoir thickness and the highest net/gross ratio. This study emphasis ‎on Matulla formation located in the eastern part of the Gulf of Suez. The three stratigraphic ‎surface sections (Wadi Sudr, Wadi Matulla and Gabal Nezzazat) which represent the exposed ‎Coniacian-Santonian sediments in Sinai are used for correlating Matulla sediments of Ras ‎Budran field. Cutting description, petrographic examination, log behaviors, biostratigraphy with ‎outcrops are used to identify the reservoir characteristics, lithology, facies environment logs and ‎subdivide the Matulla formation into three units. The lower unit is believed to be the main ‎reservoir where it consists mainly of sands with shale and sandy carbonates, while the other ‎units are mainly carbonate with some streaks of shale and sand. Reservoir modeling is an ‎effective technique that assists in reservoir management as decisions concerning development ‎and depletion of hydrocarbon reserves, So It was essential to model the Matulla reservoir as ‎accurately as possible in order to better evaluate, calculate the reserves and to determine the ‎most effective way of recovering as much of the petroleum economically as possible. All ‎available data on Matulla formation are used to build the reservoir structure model, lithofacies, ‎porosity, permeability and water saturation models which are the main parameters that describe ‎the reservoirs and provide information on effective evaluation of the need to develop the oil ‎potentiality of the reservoir. This study has shown the effectiveness of; 1) the integration of ‎geological data to evaluate and subdivide Matulla formation into three units. 2) Lithology and ‎facies environment interpretation which helped in defining the nature of deposition of Matulla ‎formation. 3) The 3D reservoir modeling technology as a tool for adequate understanding of the ‎spatial distribution of property and in addition evaluating the unlocked new reservoir areas of ‎Matulla formation which have to be drilled to investigate and exploit the un-drained oil. 4) This ‎study led to adding a new room of production and additional reserves to Ras Budran field. ‎

Keywords: geology, oil and gas, geoscience, sequence stratigraphy

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Authors: Aouina Nabila Yasmina, Zine El Abidine Chaoui

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Recently, understanding the interactions of electrons with the DNA molecule and its components has attracted considerable interest because DNA is the main site damaged by ionizing radiation. The interactions of radiation with DNA induce a variety of molecular damage such as single-strand breaks, double-strand breaks, basic damage, cross-links between proteins and DNA, and others, or the formation of free radicals, which, by chemical reactions with DNA, can also lead to breakage of the strand. One factor that can contribute significantly to these processes is the effect of water hydration on the formation and reaction of radiation induced by these radicals in and / or around DNA. B-DNA requires about 30% by weight of water to maintain its native conformation in the crystalline state. The transformation depends on various factors such as sequence, ion composition, concentration and water activity. Partial dehydration converts it to DNA-A. The present study shows the results of theoretical calculations for positrons and electrons elastic scattering with DNA medium and water over a broad energy range from 10 eV to 100 keV. Indeed, electron elastic cross sections and elastic mean free paths are calculated using a corrected form of the independent atom method, taking into account the geometry of the biomolecule (SCAR macro). Moreover, the elastic scattering of electrons and positrons by atoms of the biomolecule was evaluated by means of relativistic (Dirac) partial wave analysis. Our calculated results are compared with theoretical data available in the literature in the absence of experimental data, in particular for positron. As a central result, our electron elastic cross sections are in good agreement with existing theoretical data in the range of 10 eV to 1 keV.

Keywords: elastic cross scrion, elastic mean free path, scar macro method, electron collision

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Authors: Irakli Gamkrelidze, David Shengelia, Tamara Tsutsunava, Giorgi Chichinadze, Giorgi Beridze, Ketevan Tedliashvili, Tamara Tsamalashvili

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The Loki crystalline massif crops out in the Caucasian region and the geological retrospective represent the northern marginal part of the Baiburt-Sevanian terrain (island arc), bordering with the Paleotethys oceanic basin in the north. The pre-Alpine basement of the massif is built up of Lower-Middle Paleozoic metamorphic complex (metasedimentary and metabasite rocks), Upper Devonian quartz-diorites and Late Variscan granites. Earlier metamorphic complex was considered as an indivisible set including suites with different degree of metamorphism. Systematic geologic, petrologic and geochemical investigations of the massif’s rocks suggest the different conception on composition, structure and formation conditions of the massif. In particular, there are two main rock types in the Loki massif: the oldest autochthonous series of gneissic quartz-diorites and cutting them granites. The massif is flanked on its western side by a volcano-sedimentary sequence, metamorphosed to low-T facies. Petrologic, metamorphic and structural differences in this sequence prove the existence of a number of discrete units (overthrust sheets). One of them, the metabasic sheet represents the fragment of ophiolite complex. It comprises transition types of the second and third layers of the Paleooceanic crust: the upper noncumulated part of the third layer gabbro component and the following lowest part of the parallel diabase dykes of the second layer. The ophiolites are represented by metagabbros, metagabbro-diabases, metadiabases and amphibolite schists. According to the content of petrogenic components and additive elements in metabasites is stated that the protolith of metabasites belongs to petrochemical type of tholeiitic series of basalts. The parental magma of metaophiolites is of E-MORB composition, and by petrochemical parameters, it is very close to the composition of intraplate basalts. The dykes of hypabissal leucocratic siliceous and medium magmatic rocks associated with the metaophiolite sheet form the separate complex. They are granitoids with the extremely low content of CaO and quartz-diorite porphyries. According to various petrochemical parameters, these rocks have mixed characteristics. Their formation took place in spreading conditions or in the areas of manifestation of plumes most likely of island arc type. The metamorphism degree of the metaophiolites corresponds to a very low stage of green schist facies. The rocks of the metaophiolite complex are obducted from the Paleotethys Ocean. Geological and paleomagnetic data show that the primary location of the ocean is supposed to be to the north of the Loki crystalline massif.

Keywords: the Caucasus, crystalline massif, ophiolites, tectonic sheet

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Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu

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Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.

Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment

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Authors: Fahad Suleiman

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Queuing, in medical system is the process of moving patients in a specific sequence to a specific service according to the patients’ nature of illness. The term scheduling stands for the process of computing a schedule. This may be done by a queuing based scheduler. This paper focuses on the medical consultancy system, the different queuing algorithms that are used in healthcare system to serve the patients, and the average waiting time. The aim of this paper is to build automatic queuing system for organizing the medical queuing system that can analyses the queue status and take decision which patient to serve. The new queuing architecture model can switch between different scheduling algorithms according to the testing results and the factor of the average waiting time. The main innovation of this work concerns the modeling of the average waiting time is taken into processing, in addition with the process of switching to the scheduling algorithm that gives the best average waiting time.

Keywords: queuing systems, queuing system models, scheduling algorithms, patients

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Authors: Natascha C. D'Amico, Enzo Grossi, Giovanni Valbusa, Ala Malasevschi, Gianpiero Cardone, Sergio Papa

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Purpose: To characterize, through a radiomic approach, the nature of areas classified PI-RADS (Prostate Imaging Reporting and Data System) 3/5, recognized in multiparametric prostate magnetic resonance with T2-weighted (T2w), diffusion and perfusion sequences with paramagnetic contrast. Methods and Materials: 24 cases undergoing multiparametric prostate MR and biopsy were admitted to this pilot study. Clinical outcome of the PI-RADS 3/5 was found through biopsy, finding 8 malignant tumours. The analysed images were acquired with a Philips achieva 1.5T machine with a CE- T2-weighted sequence in the axial plane. Semi-automatic tumour segmentation was carried out on MR images using 3DSlicer image analysis software. 45 shape-based, intensity-based and texture-based features were extracted and represented the input for preprocessing. An evolutionary algorithm (a TWIST system based on KNN algorithm) was used to subdivide the dataset into training and testing set and select features yielding the maximal amount of information. After this pre-processing 20 input variables were selected and different machine learning systems were used to develop a predictive model based on a training testing crossover procedure. Results: The best machine learning system (three-layers feed-forward neural network) obtained a global accuracy of 90% ( 80 % sensitivity and 100% specificity ) with a ROC of 0.82. Conclusion: Machine learning systems coupled with radiomics show a promising potential in distinguishing benign from malign tumours in PI-RADS 3/5 areas.

Keywords: machine learning, MR prostate, PI-Rads 3, radiomics

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Authors: Mona Vijayaran, Gurleen Oberoi, Sanjay Mishra

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Introduction: p190 BCR‐ABL1 in CML is often associated with monocytosis. In the case described here, monocytosis is associated with coexisting p210 BCR‐ABL and CMML clones. Mutation analysis using next‐generation sequence (NGS) in our case showed TET2 and SRSF2 mutations. Aims & Objectives: A 75-year male was evaluated for monocytosis and thrombocytopenia. CBC showed Hb-11.8g/dl, TLC-12,060/cmm, Monocytes-35%, Platelets-39,000/cmm. Materials & Methods: Bone marrow examination showed a hypercellular marrow with myeloid series showing sequential maturation up to neutrophils with 30% monocytes. Immunophenotyping by flow cytometry from bone marrow had 3% blasts. Making chronic myelomonocytic leukemia as the likely diagnosis. NGS for myeloid mutation panel had TET2 (48.9%) and SRSF2 (32.5%) mutations. This report further supported the diagnosis of CMML. To fulfil the WHO diagnostic criteria for CMML, a BCR ABL1 by RQ-PCR was sent. The report came positive for p210 (B3A2, B2A2) Major Transcript (M-BCR) % IS of 38.418. Result: The patient was counselled regarding the unique presentation of the presence of 2 clones- P210 CML and CMML. After discussion with an international faculty with vast experience in CMML. It was decided to start this elderly gentleman on Imatinib 200mg and not on azacytidine, as ASXL1 was not present; hence, his chances of progressing to AML would be less and on the other end, if CML is left untreated then chances of progression to blast phase would always be a possibility. After 3 months on Imatinib his platelet count improved to 80,000 to 90,000/cmm, but his monocytosis persists. His 3rd month BCR-ABL1 IS% is 0.004%. Conclusion: After searching the literature, there were no case reports of a coexisting CML p210 with CMML. This case might be the first case report. p190 BCR ABL1 is often associated with monocytosis. There are few case reports of p210 BCR ABL1 positivity in patients with monocytosis but none with coexisting CMML. This case highlights the need for extensively evaluating patients with monocytosis with next-generation sequencing for myeloid mutation panel and BCR-ABL1 by RT-PCR to correctly diagnose and treat them.

Keywords: CMML, NGS, p190 CML, Imatinib

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Authors: Paula I. Buonfiglio, Carlos David Bruque, Lucia Salatino, Vanesa Lotersztein, Sebastián Menazzi, Paola Plazas, Ana Belén Elgoyhen, Viviana Dalamón

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Hearing loss (HL) is the most prevalent sensorineural disorder affecting about 10% of the global population, with more than half due to genetic causes. About 1 in 500-1000 newborns present congenital HL. Most of the patients are non-syndromic with an autosomal recessive mode of inheritance. To date, more than 100 genes are related to HL. Therefore, the Whole-exome sequencing (WES) technique has become a cost-effective alternative approach for molecular diagnosis. Nevertheless, new challenges arise from the detection of novel variants, in particular missense changes, which can lead to a spectrum of genotype-to-phenotype correlations, which is not always straightforward. In this work, we aimed to identify the genetic causes of HL in isolated and familial cases by designing a multistep approach to analyze target genes related to hearing impairment. Moreover, we performed in silico and in vivo analyses in order to further study the effect of some of the novel variants identified in the hair cell function using the zebrafish model. A total of 650 patients were studied by Sanger Sequencing and Gap-PCR in GJB2 and GJB6 genes, respectively, diagnosing 15.5% of sporadic cases and 36% of familial ones. Overall, 50 different sequence variants were detected. Fifty of the undiagnosed patients with moderate HL were tested for deletions in STRC gene by Multiplex ligation-dependent probe amplification technique (MLPA), leading to 6% of diagnosis. After this initial screening, 50 families were selected to be analyzed by WES, achieving diagnosis in 44% of them. Half of the identified variants were novel. A missense variant in MYO6 gene detected in a family with postlingual HL was selected to be further analyzed. A protein modeling with AlphaFold2 software was performed, proving its pathogenic effect. In order to functionally validate this novel variant, a knockdown phenotype rescue assay in zebrafish was carried out. Injection of wild-type MYO6 mRNA in embryos rescued the phenotype, whereas using the mutant MYO6 mRNA (carrying c.2782C>A variant) had no effect. These results strongly suggest the deleterious effect of this variant on the mobility of stereocilia in zebrafish neuromasts, and hence on the auditory system. In the present work, we demonstrated that our algorithm is suitable for the sequential multigenic approach to HL in our cohort. These results highlight the importance of a combined strategy in order to identify candidate variants as well as the in silico and in vivo studies to analyze and prove their pathogenicity and accomplish a better understanding of the mechanisms underlying the physiopathology of the hearing impairment.

Keywords: diagnosis, genetics, hearing loss, in silico analysis, in vivo analysis, WES, zebrafish

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Authors: Vishnu Pratap Singh Kirar, Madhuri Saxena

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Advancement in sequence data generation technologies is churning out voluminous omics data and posing a massive challenge to annotate the biological functional features. With so much data available, the use of machine learning methods and tools to make novel inferences has become obvious. Machine learning methods have been successfully applied to a lot of disciplines, including computational biology and bioinformatics. Researchers in computational biology are interested to develop novel machine learning frameworks to classify the huge amounts of biological data. In this proposal, it plan to employ novel machine learning approaches to aid the understanding of how apparently innocuous mutations (in intergenic DNA and at synonymous sites) cause diseases. We are also interested in discovering novel functional sites in the genome and mutations in which can affect a phenotype of interest.

Keywords: genome wide association studies (GWAS), next generation sequencing (NGS), deep learning, omics

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Authors: Helen K. Buteme, Rebecca Axelsson-Robertson, Moses L. Joloba, Henry W. Boom, Gunilla Kallenius, Markus Maeurer

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Background: The Ugandan population is heavily affected by infectious diseases and Human leukocyte antigen (HLA) diversity plays a crucial role in the host-pathogen interaction and affects the rates of disease acquisition and outcome. The identification of HLA class 1 alleles and determining which alleles are associated with tuberculosis (TB) outcomes would help in screening individuals in TB endemic areas for susceptibility to TB and to predict resistance or progression to TB which would inevitably lead to better clinical management of TB. Aims: To be able to determine the HLA class 1 phenotype distribution in a Ugandan TB cohort and to establish the relationship between these phenotypes and active and latent TB. Methods: Blood samples were drawn from 32 HIV negative individuals with active TB and 45 HIV negative individuals with latent MTB infection. DNA was extracted from the blood samples and the DNA samples HLA typed by the polymerase chain reaction-sequence specific primer method. The allelic frequencies were determined by direct count. Results: HLA-A*02, A*01, A*74, A*30, B*15, B*58, C*07, C*03 and C*04 were the dominant phenotypes in this Ugandan cohort. There were differences in the distribution of HLA types between the individuals with active TB and the individuals with LTBI with only HLA-A*03 allele showing a statistically significant difference (p=0.0136). However, after FDR computation the corresponding q-value is above the expected proportion of false discoveries (q-value 0.2176). Key findings: We identified a number of HLA class I alleles in a population from Central Uganda which will enable us to carry out a functional characterization of CD8+ T-cell mediated immune responses to MTB. Our results also suggest that there may be a positive association between the HLA-A*03 allele and TB implying that individuals with the HLA-A*03 allele are at a higher risk of developing active TB.

Keywords: HLA, phenotype, tuberculosis, Uganda

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