Search results for: abundance estimation.

Authors: Carolina B. Baguio

Abstract:

One of the purposes of the robust method of estimation is to reduce the influence of outliers in the data, on the estimates. The outliers arise from gross errors or contamination from distributions with long tails. The trimmed mean is a robust estimate. This means that it is not sensitive to violation of distributional assumptions of the data. It is called an adaptive estimate when the trimming proportion is determined from the data rather than being fixed a “priori-. The main objective of this study is to find out the robustness properties of the adaptive trimmed means in terms of efficiency, high breakdown point and influence function. Specifically, it seeks to find out the magnitude of the trimming proportion of the adaptive trimmed mean which will yield efficient and robust estimates of the parameter for data which follow a modified Weibull distribution with parameter λ = 1/2 , where the trimming proportion is determined by a ratio of two trimmed means defined as the tail length. Secondly, the asymptotic properties of the tail length and the trimmed means are also investigated. Finally, a comparison is made on the efficiency of the adaptive trimmed means in terms of the standard deviation for the trimming proportions and when these were fixed a “priori". The asymptotic tail lengths defined as the ratio of two trimmed means and the asymptotic variances were computed by using the formulas derived. While the values of the standard deviations for the derived tail lengths for data of size 40 simulated from a Weibull distribution were computed for 100 iterations using a computer program written in Pascal language. The findings of the study revealed that the tail lengths of the Weibull distribution increase in magnitudes as the trimming proportions increase, the measure of the tail length and the adaptive trimmed mean are asymptotically independent as the number of observations n becomes very large or approaching infinity, the tail length is asymptotically distributed as the ratio of two independent normal random variables, and the asymptotic variances decrease as the trimming proportions increase. The simulation study revealed empirically that the standard error of the adaptive trimmed mean using the ratio of tail lengths is relatively smaller for different values of trimming proportions than its counterpart when the trimming proportions were fixed a 'priori'.

Keywords: Adaptive robust estimate, asymptotic efficiency, breakdown point, influence function, L-estimates, location parameter, tail length, Weibull distribution.

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Authors: Maxence Queyrel, Edi Prifti, Alexandre Templier, Jean-Daniel Zucker

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Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and stored as fastq files. Conventional processing pipelines consist in multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimensionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life data-sets as well a simulated one, we demonstrated that this original approach reaches high performance, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks.

Keywords: Metagenomics, phenotype prediction, deep learning, embeddings, multiple instance learning.

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Authors: Wan-Yu Liu

Abstract:

To respond to the Kyoto Protocol, the policy of Payment for Environmental Service (PES), which was entitled “Plain Landscape Afforestation Program (PLAP)", was certified by Executive Yuan in Taiwan on 31 August 2001 and has been implementing for six years since 1 January 2002. Although the PLAP has received a lot of positive comments, there are still many difficulties during the process of implementation, such as insufficient technology for afforestation, private landowners- low interests in participating in PLAP, insufficient subsidies, and so on, which are potential threats that hinder the PLAP from moving forward in future. In this paper, selecting Ping-Tung County in Taiwan as a sample region and targeting those private landowners with and without intention to participate in the PLAP, respectively, we conduct an empirical analysis based on the Logit model to investigate the factors that determine whether those private landowners join the PLAP, so as to realize the incentive effects of the PLAP upon the personal decision on afforestation. The possible factors that might determine private landowner-s participation in the PLAP include landowner-s characteristics, cropland characteristics, as well as policy factors. Among them, the policy factors include afforestation subsidy amount (+), duration of afforestation subsidy (+), the rules on adjoining and adjacent areas (+), and so on, which do not reach the remarkable level in statistics though, but the directions of variable signs are consistent with the intuition behind the policy. As for the landowners- characteristics, each of age (+), education level (–), and annual household income (+) variables reaches 10% of the remarkable level in statistics; as for the cropland characteristics, each of cropland area (+), cropland price (–), and the number of cropland parcels (–) reaches 1% of the remarkable level in statistics. In light of the above, the cropland characteristics are the dominate factor that determines the probability of landowner-s participation in the PLAP. In the Logit model established by this paper, the probability of correctly estimating nonparticipants is 98%, the probability of correctly estimating the participants is 71.8%, and the probability for the overall estimation is 95%. In addition, Hosmer-Lemeshow test and omnibus test also revealed that the Logit model in this paper may provide fine goodness of fit and good predictive power in forecasting private landowners- participation in this program. The empirical result of this paper expects to help the implementation of the afforestation programs in Taiwan.

Keywords: Forestry policy, logit, afforestation subsidy, afforestation policy.

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Authors: Alia Alghosoun, Nabil El Moçayd, Mohammed Seaid

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Modeling dam-break flows over non-flat beds requires an accurate representation of the topography which is the main source of uncertainty in the model. Therefore, developing robust and accurate techniques for reconstructing topography in this class of problems would reduce the uncertainty in the flow system. In many hydraulic applications, experimental techniques have been widely used to measure the bed topography. In practice, experimental work in hydraulics may be very demanding in both time and cost. Meanwhile, computational hydraulics have served as an alternative for laboratory and field experiments. Unlike the forward problem, the inverse problem is used to identify the bed parameters from the given experimental data. In this case, the shallow water equations used for modeling the hydraulics need to be rearranged in a way that the model parameters can be evaluated from measured data. However, this approach is not always possible and it suffers from stability restrictions. In the present work, we propose an adaptive optimal control technique to numerically identify the underlying bed topography from a given set of free-surface observation data. In this approach, a minimization function is defined to iteratively determine the model parameters. The proposed technique can be interpreted as a fractional-stage scheme. In the first stage, the forward problem is solved to determine the measurable parameters from known data. In the second stage, the adaptive control Ensemble Kalman Filter is implemented to combine the optimality of observation data in order to obtain the accurate estimation of the topography. The main features of this method are on one hand, the ability to solve for different complex geometries with no need for any rearrangements in the original model to rewrite it in an explicit form. On the other hand, its achievement of strong stability for simulations of flows in different regimes containing shocks or discontinuities over any geometry. Numerical results are presented for a dam-break flow problem over non-flat bed using different solvers for the shallow water equations. The robustness of the proposed method is investigated using different numbers of loops, sensitivity parameters, initial samples and location of observations. The obtained results demonstrate high reliability and accuracy of the proposed techniques.

Keywords: Optimal control, ensemble Kalman Filter, topography reconstruction, data assimilation, shallow water equations.

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Authors: Hayder H. Kareem, Shunqi Pan

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The geological environment where the groundwater is collected represents the most important element that affects the behaviour of groundwater aquifer. As groundwater is a worldwide vital resource, it requires knowing the parameters that affect this source accurately so that the conceptualized mathematical models would be acceptable to the broadest ranges. Therefore, groundwater models have recently become an effective and efficient tool to investigate groundwater aquifer behaviours. Groundwater aquifer may contain aquitards, aquicludes, or interfaces within its geological formations. Aquitards and aquicludes have geological formations that forced the modellers to include those formations within the conceptualized groundwater models, while interfaces are commonly neglected from the conceptualization process because the modellers believe that the interface has no effect on aquifer behaviour. The current research highlights the impact of an interface existing in a real unconfined groundwater aquifer called Dibdibba, located in Al-Najaf City, Iraq where it has a river called the Euphrates River that passes through the eastern part of this city. Dibdibba groundwater aquifer consists of two types of soil layers separated by an interface soil layer. A groundwater model is built for Al-Najaf City to explore the impact of this interface. Calibration process is done using PEST 'Parameter ESTimation' approach and the best Dibdibba groundwater model is obtained. When the soil interface is conceptualized, results show that the groundwater tables are significantly affected by that interface through appearing dry areas of 56.24 km² and 6.16 km² in the upper and lower layers of the aquifer, respectively. The Euphrates River will also leak water into the groundwater aquifer of 7359 m³/day. While these results are changed when the soil interface is neglected where the dry area became 0.16 km², the Euphrates River leakage became 6334 m³/day. In addition, the conceptualized models (with and without interface) reveal different responses for the change in the recharge rates applied on the aquifer through the uncertainty analysis test. The aquifer of Dibdibba in Al-Najaf City shows a slight deficit in the amount of water supplied by the current pumping scheme and also notices that the Euphrates River suffers from stresses applied to the aquifer. Ultimately, this study shows a crucial need to represent the interface soil layer in model conceptualization to be the intended and future predicted behaviours more reliable for consideration purposes.

Keywords: Al-Najaf City, groundwater aquifer behaviour, groundwater modelling, interface soil layer, Visual MODFLOW.

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Authors: Yanping Liao, Zenan Wu, Ruigang Zhao

Abstract:

Frequency diverse array (FDA) beamforming is a technology developed in recent years, and its antenna pattern has a unique angle-distance-dependent characteristic. However, the beam is always required to have strong concentration, high resolution and low sidelobe level to form the point-to-point interference in the concentrated set. In order to eliminate the angle-distance coupling of the traditional FDA and to make the beam energy more concentrated, this paper adopts a multi-carrier FDA structure based on proposed power exponential frequency offset to improve the array structure and frequency offset of the traditional FDA. The simulation results show that the beam pattern of the array can form a dot-shape beam with more concentrated energy, and its resolution and sidelobe level performance are improved. However, the covariance matrix of the signal in the traditional adaptive beamforming algorithm is estimated by the finite-time snapshot data. When the number of snapshots is limited, the algorithm has an underestimation problem, which leads to the estimation error of the covariance matrix to cause beam distortion, so that the output pattern cannot form a dot-shape beam. And it also has main lobe deviation and high sidelobe level problems in the case of limited snapshot. Aiming at these problems, an adaptive beamforming technique based on exponential correction for multi-carrier FDA is proposed to improve beamforming robustness. The steps are as follows: first, the beamforming of the multi-carrier FDA is formed under linear constrained minimum variance (LCMV) criteria. Then the eigenvalue decomposition of the covariance matrix is ​​performed to obtain the diagonal matrix composed of the interference subspace, the noise subspace and the corresponding eigenvalues. Finally, the correction index is introduced to exponentially correct the small eigenvalues ​​of the noise subspace, improve the divergence of small eigenvalues ​​in the noise subspace, and improve the performance of beamforming. The theoretical analysis and simulation results show that the proposed algorithm can make the multi-carrier FDA form a dot-shape beam at limited snapshots, reduce the sidelobe level, improve the robustness of beamforming, and have better performance.

Keywords: Multi-carrier frequency diverse array, adaptive beamforming, correction index, limited snapshot, robust.

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Authors: E. Menga, S. Hernandez

Abstract:

Finite Element Models (FEMs) are widely used in order to study and predict the dynamic properties of structures and usually, the prediction can be obtained with much more accuracy in the case of a single component than in the case of assemblies. Especially for structural dynamics studies, in the low and middle frequency range, most complex FEMs can be seen as assemblies made by linear components joined together at interfaces. From a modelling and computational point of view, these types of joints can be seen as localized sources of stiffness and damping and can be modelled as lumped spring/damper elements, most of time, characterized by nonlinear constitutive laws. On the other side, most of FE programs are able to run nonlinear analysis in time-domain. They treat the whole structure as nonlinear, even if there is one nonlinear degree of freedom (DOF) out of thousands of linear ones, making the analysis unnecessarily expensive from a computational point of view. In this work, a methodology in order to obtain the nonlinear frequency response of structures, whose nonlinearities can be considered as localized sources, is presented. The work extends the well-known Structural Dynamic Modification Method (SDMM) to a nonlinear set of modifications, and allows getting the Nonlinear Frequency Response Functions (NLFRFs), through an ‘updating’ process of the Linear Frequency Response Functions (LFRFs). A brief summary of the analytical concepts is given, starting from the linear formulation and understanding what the implications of the nonlinear one, are. The response of the system is formulated in both: time and frequency domain. First the Modal Database is extracted and the linear response is calculated. Secondly the nonlinear response is obtained thru the NL SDMM, by updating the underlying linear behavior of the system. The methodology, implemented in MATLAB, has been successfully applied to estimate the nonlinear frequency response of two systems. The first one is a two DOFs spring-mass-damper system, and the second example takes into account a full aircraft FE Model. In spite of the different levels of complexity, both examples show the reliability and effectiveness of the method. The results highlight a feasible and robust procedure, which allows a quick estimation of the effect of localized nonlinearities on the dynamic behavior. The method is particularly powerful when most of the FE Model can be considered as acting linearly and the nonlinear behavior is restricted to few degrees of freedom. The procedure is very attractive from a computational point of view because the FEM needs to be run just once, which allows faster nonlinear sensitivity analysis and easier implementation of optimization procedures for the calibration of nonlinear models.

Keywords: Frequency response, nonlinear dynamics, structural dynamic modification, softening effect, rubber.

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Authors: Moustafa Osman Mohammed

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Construction industry, as one of the main contributor in depletion of natural resources, influences climate change. This paper discusses incremental and evolutionary development of the proposed models for optimization of a life-cycle analysis to explicit strategy for evaluation systems. The main categories are virtually irresistible for introducing uncertainties, uptake composite structure model (CSM) as environmental management systems (EMSs) in a practice science of evaluation small and medium-sized enterprises (SMEs). The model simplified complex systems to reflect nature systems’ input, output and outcomes mode influence “framework measures” and give a maximum likelihood estimation of how elements are simulated over the composite structure. The traditional knowledge of modeling is based on physical dynamic and static patterns regarding parameters influence environment. It unified methods to demonstrate how construction systems ecology interrelated from management prospective in procedure reflects the effect of the effects of engineering systems to ecology as ultimately unified technologies in extensive range beyond constructions impact so as, - energy systems. Sustainability broadens socioeconomic parameters to practice science that meets recovery performance, engineering reflects the generic control of protective systems. When the environmental model employed properly, management decision process in governments or corporations could address policy for accomplishment strategic plans precisely. The management and engineering limitation focuses on autocatalytic control as a close cellular system to naturally balance anthropogenic insertions or aggregation structure systems to pound equilibrium as steady stable conditions. Thereby, construction systems ecology incorporates engineering and management scheme, as a midpoint stage between biotic and abiotic components to predict constructions impact. The later outcomes’ theory of environmental obligation suggests either a procedures of method or technique that is achieved in sustainability impact of construction system ecology (SICSE), as a relative mitigation measure of deviation control, ultimately.

Keywords: Sustainability, constructions ecology, composite structure model, design structure matrix, environmental impact assessment, life cycle analysis, climate change.

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Authors: A. Basu, A. A. Purohit, M. M. Vaidya, M. D. Kudale

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Mumbai, being traditionally the epicenter of India's trade and commerce, the existing major ports such as Mumbai and Jawaharlal Nehru Ports (JN) situated in Thane estuary are also developing its waterfront facilities. Various developments over the passage of decades in this region have changed the tidal flux entering/leaving the estuary. The intake at Pir-Pau is facing the problem of shortage of water in view of advancement of shoreline, while jetty near Ulwe faces the problem of ship scheduling due to existence of shallower depths between JN Port and Ulwe Bunder. In order to solve these problems, it is inevitable to have information about tide levels over a long duration by field measurements. However, field measurement is a tedious and costly affair; application of artificial intelligence was used to predict water levels by training the network for the measured tide data for one lunar tidal cycle. The application of two layered feed forward Artificial Neural Network (ANN) with back-propagation training algorithms such as Gradient Descent (GD) and Levenberg-Marquardt (LM) was used to predict the yearly tide levels at waterfront structures namely at Ulwe Bunder and Pir-Pau. The tide data collected at Apollo Bunder, Ulwe, and Vashi for a period of lunar tidal cycle (2013) was used to train, validate and test the neural networks. These trained networks having high co-relation coefficients (R= 0.998) were used to predict the tide at Ulwe, and Vashi for its verification with the measured tide for the year 2000 & 2013. The results indicate that the predicted tide levels by ANN give reasonably accurate estimation of tide. Hence, the trained network is used to predict the yearly tide data (2015) for Ulwe. Subsequently, the yearly tide data (2015) at Pir-Pau was predicted by using the neural network which was trained with the help of measured tide data (2000) of Apollo and Pir-Pau. The analysis of measured data and study reveals that: The measured tidal data at Pir-Pau, Vashi and Ulwe indicate that there is maximum amplification of tide by about 10-20 cm with a phase lag of 10-20 minutes with reference to the tide at Apollo Bunder (Mumbai). LM training algorithm is faster than GD and with increase in number of neurons in hidden layer and the performance of the network increases. The predicted tide levels by ANN at Pir-Pau and Ulwe provides valuable information about the occurrence of high and low water levels to plan the operation of pumping at Pir-Pau and improve ship schedule at Ulwe.

Keywords: Artificial neural network, back-propagation, tide data, training algorithm.

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Authors: A.H. Sajedipoor, N. Hedayat, A.Rohani, Z.Yazdi

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Sediment formation and its transport along the river course is considered as important hydraulic consideration in river engineering. Their impact on the morphology of rivers on one hand and important considerations of which in the design and construction of the hydraulic structures on the other has attracted the attention of experts in arid and semi-arid regions. Under certain conditions where the momentum energy of the flow stream reaches a specific rate, the sediment materials start to be transported with the flow. This can usually be analyzed in two different categories of suspended and bed load materials. Sedimentation phenomenon along the waterways and the conveyance of vast volume of materials into the canal networks can potentially influence water abstraction in the intake structures. This can pose a serious threat to operational sustainability and water delivery performance in the canal networks. The situation is serious where ineffective watershed management (poor vegetation cover in the water basin) is the underlying cause of soil erosion which feeds the materials into the waterways that intern would necessitate comprehensive study. The present paper aims to present an analytical investigation of the sediment process in the waterways on one hand and estimation of the sediment load transport into the lined canals using the SHARC software on the other. For this reason, the paper focuses on the comparative analysis of the hydraulic behaviors of the Sabilli main canal that feeds the pumping station with that of the Western canal in the Greater Dezful region to identify effective factors in sedimentation and ways of mitigating their impact on water abstraction in the canal systems. The method involved use of observational data available in the Dezful Dastmashoon hydrometric station along a 6 km waterway of the Sabilli main canal using the SHARC software to estimate the suspended load concentration and bed load materials. Results showed the transport of a significant volume of sediment loads from the waterways into the canal system which is assumed to have arisen from the absence of stilling basin on one hand and the gravity flow on the other has caused serious challenges. This is contrary to what occurs in the Sabilli canal, where the design feature which incorporates a settling basin just before the pumping station is the major cause of reduced sediment load transport into the canal system.Results showed that modification of the present design features by constructing a settling basin just upstream of the western intake structure can considerably reduce the entry of sediment materials into the canal system. Not only this can result in the sustainability of the hydraulic structures but can also improve operational performance of water conveyance and distribution system, all of which are the pre-requisite to secure reliable and equitable water delivery regime for the command area.

Keywords: Sedimentation, main canal, Sabilli, western canal, dez diversion weir.

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Authors: Oksana G. Cherednichenko, Anastasia L. Pilyugina, Sergey N.Lukashenko, Elena G. Gubitskaya

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The estimation of accumulated radiation doses in people professionally exposed to ionizing radiation was performed using methods of biological (chromosomal aberrations frequency in lymphocytes) and physical (radionuclides analysis in urine, whole-body radiation meter, individual thermoluminescent dosimeters) dosimetry. A group of 84 "A" category employees after their work in the territory of former Semipalatinsk test site (Kazakhstan) was investigated. The dose rate in some funnels exceeds 40 μSv/h. After radionuclides determination in urine using radiochemical and WBC methods, it was shown that the total effective dose of personnel internal exposure did not exceed 0.2 mSv/year, while an acceptable dose limit for staff is 20 mSv/year. The range of external radiation doses measured with individual thermo-luminescent dosimeters was 0.3-1.406 µSv. The cytogenetic examination showed that chromosomal aberrations frequency in staff was 4.27±0.22%, which is significantly higher than at the people from non-polluting settlement Tausugur (0.87±0.1%) (р ≤ 0.01) and citizens of Almaty (1.6±0.12%) (р≤ 0.01). Chromosomal type aberrations accounted for 2.32±0.16%, 0.27±0.06% of which were dicentrics and centric rings. The cytogenetic analysis of different types group radiosensitivity among «professionals» (age, sex, ethnic group, epidemiological data) revealed no significant differences between the compared values. Using various techniques by frequency of dicentrics and centric rings, the average cumulative radiation dose for group was calculated, and that was 0.084-0.143 Gy. To perform comparative individual dosimetry using physical and biological methods of dose assessment, calibration curves (including own ones) and regression equations based on general frequency of chromosomal aberrations obtained after irradiation of blood samples by gamma-radiation with the dose rate of 0,1 Gy/min were used. Herewith, on the assumption of individual variation of chromosomal aberrations frequency (1–10%), the accumulated dose of radiation varied 0-0.3 Gy. The main problem in the interpretation of individual dosimetry results is reduced to different reaction of the objects to irradiation - radiosensitivity, which dictates the need of quantitative definition of this individual reaction and its consideration in the calculation of the received radiation dose. The entire examined contingent was assigned to a group based on the received dose and detected cytogenetic aberrations. Radiosensitive individuals, at the lowest received dose in a year, showed the highest frequency of chromosomal aberrations (5.72%). In opposite, radioresistant individuals showed the lowest frequency of chromosomal aberrations (2.8%). The cohort correlation according to the criterion of radio-sensitivity in our research was distributed as follows: radio-sensitive (26.2%) — medium radio-sensitivity (57.1%), radioresistant (16.7%). Herewith, the dispersion for radioresistant individuals is 2.3; for the group with medium radio-sensitivity — 3.3; and for radio-sensitive group — 9. These data indicate the highest variation of characteristic (reactions to radiation effect) in the group of radio-sensitive individuals. People with medium radio-sensitivity show significant long-term correlation (0.66; n=48, β ≥ 0.999) between the values of doses defined according to the results of cytogenetic analysis and dose of external radiation obtained with the help of thermoluminescent dosimeters. Mathematical models based on the type of violation of the radiation dose according to the professionals radiosensitivity level were offered.

Keywords: Biodosimetry, chromosomal aberrations, ionizing radiation, radiosensitivity.

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