Search results for: Biological sequence

Authors: A. Sayadi, A. Khodadadi D., S. Partani

Abstract:

Today Environmental Impact Assessment (EIA) is known as one of the most important tools for decision makers in the construction of civil and industrial projects towards sustainable development. In the past, projects were evaluated based on cost and benefit analysis regardless of the physical and biological environmental effects and its socio-economical impacts. According to the Department of Environment (DOE) of Iran's regulations, the construction of hydroelectric dams is an activity that requires an EIA report. In this paper the environmental impact assessment of the Gotvand hydro-electrical dam has been evaluated in the three environment elements, biological, Physical-chemical and cultural units. This dam is one of the largest dams in Iran with a volume of 4500 MCM and is going to be the last dam on the Karoon River in the south of Iran. In this paper the ICOLD (International Commission on Large Dams) technique was employed for the environmental impact assessment of the dam. The research includes all socio economical and environmental effects of the dam during the construction and operation of the hydro electric dam and Environmental management, monitoring and mitigation of negative impacts were analyzed. In this project the results led to using some techniques to protect the destructive impacts on biological aspects beside the effective long time period impacts on the biological aspects. The impacts on physical aspects are temporary and negative commonly that could be restored and rehabilitated in natural process in the long time in operation period.

Keywords: "Gotvand Hydro Electric Dam", "EIA", "ICOLD and Leopold matrices"

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Authors: Werner Sandmann, Verena Wolf

Abstract:

Stochastic models of biological networks are well established in systems biology, where the computational treatment of such models is often focused on the solution of the so-called chemical master equation via stochastic simulation algorithms. In contrast to this, the development of storage-efficient model representations that are directly suitable for computer implementation has received significantly less attention. Instead, a model is usually described in terms of a stochastic process or a "higher-level paradigm" with graphical representation such as e.g. a stochastic Petri net. A serious problem then arises due to the exponential growth of the model-s state space which is in fact a main reason for the popularity of stochastic simulation since simulation suffers less from the state space explosion than non-simulative numerical solution techniques. In this paper we present transition class models for the representation of biological network models, a compact mathematical formalism that circumvents state space explosion. Transition class models can also serve as an interface between different higher level modeling paradigms, stochastic processes and the implementation coded in a programming language. Besides, the compact model representation provides the opportunity to apply non-simulative solution techniques thereby preserving the possible use of stochastic simulation. Illustrative examples of transition class representations are given for an enzyme-catalyzed substrate conversion and a part of the bacteriophage λ lysis/lysogeny pathway.

Keywords: Computational Modeling, Biological Networks, Stochastic Models, Markov Chains, Transition Class Models.

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Authors: M. Antonelli, G. Frosini, B. Lazzerini, F. Marcelloni

Abstract:

In this paper we describe a computer-aided diagnosis (CAD) system for automated detection of pulmonary nodules in computed-tomography (CT) images. After extracting the pulmonary parenchyma using a combination of image processing techniques, a region growing method is applied to detect nodules based on 3D geometric features. We applied the CAD system to CT scans collected in a screening program for lung cancer detection. Each scan consists of a sequence of about 300 slices stored in DICOM (Digital Imaging and Communications in Medicine) format. All malignant nodules were detected and a low false-positive detection rate was achieved.

Keywords: computer assisted diagnosis, medical imagesegmentation, shape recognition.

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Authors: Younis R. Elhaddad

Abstract:

Combinatorial optimization problems arise in many scientific and practical applications. Therefore many researchers try to find or improve different methods to solve these problems with high quality results and in less time. Genetic Algorithm (GA) and Simulated Annealing (SA) have been used to solve optimization problems. Both GA and SA search a solution space throughout a sequence of iterative states. However, there are also significant differences between them. The GA mechanism is parallel on a set of solutions and exchanges information using the crossover operation. SA works on a single solution at a time. In this work SA and GA are combined using new technique in order to overcome the disadvantages' of both algorithms.

Keywords: Genetic Algorithm, Optimization problems, Simulated Annealing, Traveling Salesman Problem

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Authors: M.Asif, M.R.Arshad, P.A.Wilson

Abstract:

In this paper, a simple active contour based visual tracking algorithm is presented for outdoor AGV application which is currently under development at the USM robotic research group (URRG) lab. The presented algorithm is computationally low cost and able to track road boundaries in an image sequence and can easily be implemented on available low cost hardware. The proposed algorithm used an active shape modeling using the B-spline deformable template and recursive curve fitting method to track the current orientation of the road.

Keywords: Active contour, B-spline, recursive curve fitting.

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

Abstract:

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: J. Trarbach, S. Schosser, B. Vogt

Abstract:

Decision-makers tend to prefer the first alternative over subsequent alternatives which is called the primacy effect. To reliably measure this effect, we conducted an experiment with real consequences for preference statements. Therefore, we elicit preferences of subjects using a rating scale, i.e. hypothetical preferences, and willingness to pay, i.e. real preferences, for two sequences of pain. Within these sequences, both overall intensity and duration of pain are identical. Hence, a rational decision-maker should be indifferent, whereas the primacy effect predicts a stronger preference for the first sequence. What we see is a primacy effect only for hypothetical preferences. This effect vanishes for real preferences.

Keywords: Decision making, primacy effect, real incentives, willingness to pay.

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Authors: Fendri Emna, Ben-Abdallah Hanêne, Ben-Hamadou Abdelmajid

Abstract:

In this paper, we present an approach for soccer video edition using a multimodal annotation. We propose to associate with each video sequence of a soccer match a textual document to be used for further exploitation like search, browsing and abstract edition. The textual document contains video meta data, match meta data, and match data. This document, generated automatically while the video is analyzed, segmented and classified, can be enriched semi automatically according to the user type and/or a specialized recommendation system.

Keywords: XML, Multimodal Annotation, recommendation system.

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Authors: Kavita Khairnar, Shikha Nema

Abstract:

DS-CDMA system is well known wireless technology. This system suffers from MAI (Multiple Access Interference) caused by Direct Sequence users. Multi-User Detection schemes were introduced to detect the users- data in presence of MAI. This paper focuses on linear multi-user detection schemes used for data demodulation. Simulation results depict the performance of three detectors viz-conventional detector, Decorrelating detector and Subspace MMSE (Minimum Mean Square Error) detector. It is seen that the performance of these detectors depends on the number of paths and the length of Gold code used.

Keywords: Cross Correlation Matrix, MAI, Multi-UserDetection, Multipath Effect.

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Authors: S. Park, J. Hwang, K. Rou, E. Kim

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In this paper, we consider a new particle filter inspired by biological evolution. In the standard particle filter, a resampling scheme is used to decrease the degeneracy phenomenon and improve estimation performance. Unfortunately, however, it could cause the undesired the particle deprivation problem, as well. In order to overcome this problem of the particle filter, we propose a novel filtering method called the genetic filter. In the proposed filter, we embed the genetic algorithm into the particle filter and overcome the problems of the standard particle filter. The validity of the proposed method is demonstrated by computer simulation.

Keywords: Particle filter, genetic algorithm, evolutionary algorithm.

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Authors: Ismat Beg, Asma Rashid Butt

Abstract:

Let (X,) be a partially ordered set and d be a metric on X such that (X, d) is a complete metric space. Assume that X satisfies; if a non-decreasing sequence xn → x in X, then xn  x, for all n. Let F be a set valued mapping from X into X with nonempty closed bounded values satisfying; (i) there exists κ ∈ (0, 1) with D(F(x), F(y)) ≤ κd(x, y), for all x  y, (ii) if d(x, y) < ε < 1 for some y ∈ F(x) then x  y, (iii) there exists x0 ∈ X, and some x1 ∈ F(x0) with x0  x1 such that d(x0, x1) < 1. It is shown that F has a fixed point. Several consequences are also obtained.

Keywords: Fixed point, partially ordered set, metric space, set valued mapping.

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Authors: MA. Ansari

Abstract:

In cancer progress, the optical properties of tissues like absorption and scattering coefficient change, so by these changes, we can trace the progress of cancer, even it can be applied for pre-detection of cancer. In this paper, we investigate the effects of changes of optical properties on light penetrated into tissues. The diffusion equation is widely used to simulate light propagation into biological tissues. In this study, the boundary integral method (BIM) is used to solve the diffusion equation. We illustrate that the changes of optical properties can modified the reflectance or penetrating light.

Keywords: Diffusion equation, boundary element method, refractive index

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Authors: J. T. Manhire

Abstract:

A tax authority wants to take actions it knows will foster the greatest degree of voluntary taxpayer compliance to reduce the “tax gap.” This paper suggests that even if a tax authority could attain a state of complete knowledge, there are constraints on whether and to what extent such actions would result in reducing the macro-level tax gap. These limits are not merely a consequence of finite agency resources. They are inherent in the system itself. To show that this is one possible interpretation of the tax gap data, the paper formulates known results in a different way by analyzing tax compliance as a population with a single covariate. This leads to a standard use of the logistic map to analyze the dynamics of non-compliance growth or decay over a sequence of periods. This formulation gives the same results as the tax gap studies performed over the past fifty years in the U.S. given the published margins of error. Limitations and recommendations for future work are discussed, along with some implications for tax policy.

Keywords: Tax law, tax compliance, tax gap, income tax.

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Authors: Abdel Rodríguez, Isis Bonet, Ricardo Grau, María M. García

Abstract:

In this paper we designed and implemented a new ensemble of classifiers based on a sequence of classifiers which were specialized in regions of the training dataset where errors of its trained homologous are concentrated. In order to separate this regions, and to determine the aptitude of each classifier to properly respond to a new case, it was used another set of classifiers built hierarchically. We explored a selection based variant to combine the base classifiers. We validated this model with different base classifiers using 37 training datasets. It was carried out a statistical comparison of these models with the well known Bagging and Boosting, obtaining significantly superior results with the hierarchical ensemble using Multilayer Perceptron as base classifier. Therefore, we demonstrated the efficacy of the proposed ensemble, as well as its applicability to general problems.

Keywords: classifiers, delegation, ensemble

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Authors: Adam Rabcewicz

Abstract:

Variational methods for optical flow estimation are known for their excellent performance. The method proposed by Brox et al. [5] exemplifies the strength of that framework. It combines several concepts into single energy functional that is then minimized according to clear numerical procedure. In this paper we propose a modification of that algorithm starting from the spatiotemporal gradient constancy assumption. The numerical scheme allows to establish the connection between our model and the CLG(H) method introduced in [18]. Experimental evaluation carried out on synthetic sequences shows the significant superiority of the spatial variant of the proposed method. The comparison between methods for the realworld sequence is also enclosed.

Keywords: optical flow, variational methods, gradient constancy assumption.

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Authors: Urszula Wachowska, Anna Daria Stasiulewicz-Paluch, Iwona Konopka, Katarzyna Kucharska, Justyna Borowska

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The biological activity of A. pullulans isolates against species of the genus Fusarium, bacteria of the genus Azotobacter and pseudomonads colonizing wheat kernels was evaluated. A field experiment was carried out in 2009-2011, in north-eastern Poland. Winter wheat (cv. Bogatka) plants were sprayed with a cell suspension of A. pullulans at a density of 106 - 108 per cm3 water at the stem elongation stage and the heading stage. Untreated plants served as control. The abundance of epiphytic yeasts, bacteria of the genus Azotobacter, pseudomonads and Fusarium pathogens on wheat grain was estimated at harvest and after six months’ storage. The average size of yeast communities was significantly greater on wheat kernels treated with a cell suspension of A. pullulans, compared with control samples. In 2010-2011, biological control reduced the abundance of some species of the genus Fusarium.

Keywords: Aureobasidium pullulans, winter wheat grain, Fusarium, bacteria.

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Authors: M. S. Muhammad, S. M. W. Masra, K. Kipli, N. Zamhari

Abstract:

The capturing of gel electrophoresis image represents the output of a DNA computing algorithm. Before this image is being captured, DNA computing involves parallel overlap assembly (POA) and polymerase chain reaction (PCR) that is the main of this computing algorithm. However, the design of the DNA oligonucleotides to represent a problem is quite complicated and is prone to errors. In order to reduce these errors during the design stage before the actual in-vitro experiment is carried out; a simulation software capable of simulating the POA and PCR processes is developed. This simulation software capability is unlimited where problem of any size and complexity can be simulated, thus saving cost due to possible errors during the design process. Information regarding the DNA sequence during the computing process as well as the computing output can be extracted at the same time using the simulation software.

Keywords: DNA computing, PCR, POA, simulation software

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Authors: Maha Sharkas, Dahlia R. ElShafie, Nadder Hamdy

Abstract:

Image watermarking has proven to be quite an efficient tool for the purpose of copyright protection and authentication over the last few years. In this paper, a novel image watermarking technique in the wavelet domain is suggested and tested. To achieve more security and robustness, the proposed techniques relies on using two nested watermarks that are embedded into the image to be watermarked. A primary watermark in form of a PN sequence is first embedded into an image (the secondary watermark) before being embedded into the host image. The technique is implemented using Daubechies mother wavelets where an arbitrary embedding factor α is introduced to improve the invisibility and robustness. The proposed technique has been applied on several gray scale images where a PSNR of about 60 dB was achieved.

Keywords: Image watermarking, Multimedia Security, Wavelets, Image Processing.

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Authors: Tao Zhao, Zhao Liu, Changxin Zhao, Cui Mao

Abstract:

At present, the severe oil crisis and greenhouse effect are booming, which is a growing worry for China. Over a long period of study, choosing the development of biological diesel is a feasible way in the desertification region in China. With considering the adaptability of Micro-algae in desertification region and analyzing energy consumption and carbon calculations of Micro-algae biodiesel produced by JJ company , this paper, make the microalgae our optimal choice to develop biological diesel in china's desertification region.

Keywords: Biodiesel, Microalgae, Energy Consumption, CarbonCalculations

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Authors: Mohamed Boulouird, Moha M'Rabet Hassani

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In this paper, many techniques for blind identification of moving average (MA) process are presented. These methods utilize third- and fourth-order cumulants of the noisy observations of the system output. The system is driven by an independent and identically distributed (i.i.d) non-Gaussian sequence that is not observed. Two nonlinear optimization algorithms, namely the Gradient Descent and the Gauss-Newton algorithms are exposed. An algorithm based on the joint-diagonalization of the fourth-order cumulant matrices (FOSI) is also considered, as well as an improved version of the classical C(q, 0, k) algorithm based on the choice of the Best 1-D Slice of fourth-order cumulants. To illustrate the effectiveness of our methods, various simulation examples are presented.

Keywords: Cumulants, Identification, MA models, Parameter estimation

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Authors: Yali Zheng, Peipei Luo, Shinan Chen, Jiasheng Hao, Hong Cheng

Abstract:

Most of traditional visual indoor navigation algorithms and methods only consider the localization in ordinary daytime, while we focus on the indoor re-localization in low light in the paper. As RGB images are degraded in low light, less discriminative infrared and depth image pairs are taken, as the input, by RGB-D cameras, the most similar candidates, as the output, are searched from databases which is built in the bag-of-word framework. Epipolar constraints can be used to relocalize the query infrared and depth image sequence. We evaluate our method in two datasets captured by Kinect2. The results demonstrate very promising re-localization results for indoor navigation system in low light environments.

Keywords: Indoor navigation, low light, RGB-D camera, vision based.

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Authors: Y.Ben Jemaa, M.Jaidane

Abstract:

In wireless communication system, a Decision Feedback Equalizer (DFE) to cancel the intersymbol interference (ISI) is required. In this paper, an exact convergence analysis of the (DFE) adapted by the Least Mean Square (LMS) algorithm during the training phase is derived by taking into account the finite alphabet context of data transmission. This allows us to determine the shortest training sequence that allows to reach a given Mean Square Error (MSE). With the intention of avoiding the problem of ill-convergence, the paper proposes an initialization strategy for the blind decision directed (DD) algorithm. This then yields a semi-blind DFE with high speed and good convergence.

Keywords: Adaptive Decision Feedback Equalizer, PerformanceAnalysis, Finite Alphabet Case, Ill-Convergence, Convergence speed.

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Authors: Abdulrahim Shamayleh

Abstract:

In this work, the surgical theater of a local hospital in KSA was analyzed using simulation. The focus was on attempting to answer questions related to how many Operating Rooms (ORs) to open and to analyze the performance of the surgical theater in general and mainly the Post Anesthesia Care Unit (PACU) to assist making decisions regarding PACU staffing. The surgical theater consists of ten operating rooms and the PACU unit which has a maximum capacity of fifteen beds. Different sequencing rules to sequence the surgical cases were tested and the Longest Case First (LCF) were superior to others. The results of the different alternatives developed and tested can be used by the manager as a tool to plan and manage the OR and PACU

Keywords: Operating room, post anesthesia care unit, PACUstaffing, sequencing, healthcare

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Authors: Zhan Haiyang, Zhang Lei, Ning Juan

Abstract:

This paper presents a configuration software solution in Linux, which is used for the control of space environment simulator. After introducing the structure and basic principle, it is said that the developing of QT software frame and the dynamic data exchanging between PLC and computer. The OPC driver in Linux is also developed. This driver realizes many-to-many communication between hardware devices and SCADA software. Moreover, an algorithm named “Scan PRI” is put forward. This algorithm is much more optimizable and efficient compared with "Scan in sequence" in Windows. This software has been used in practical project. It has a good control effect and can achieve the expected goal.

Keywords: Linux OS, configuration software, OPC server driver, MYSQL database.

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Authors: Truong Quang Dang Khoa, Masahiro Nakagawa

Abstract:

Chaos and fractals are novel fields of physics and mathematics showing up a new way of universe viewpoint and creating many ideas to solve several present problems. In this paper, a novel algorithm based on the chaotic sequence generator with the highest ability to adapt and reach the global optima is proposed. The adaptive ability of proposal algorithm is flexible in 2 steps. The first one is a breadth-first search and the second one is a depth-first search. The proposal algorithm is examined by 2 functions, the Camel function and the Schaffer function. Furthermore, the proposal algorithm is applied to optimize training Multilayer Neural Networks.

Keywords: learning and evolutionary computing, Chaos Optimization Algorithm, Artificial Neural Networks, nonlinear optimization, intelligent computational technologies.

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Authors: Maged Ahmed, Ahmed El-Mahdy

Abstract:

In this paper, Selective Adaptive Parallel Interference Cancellation (SA-PIC) technique is presented for Multicarrier Direct Sequence Code Division Multiple Access (MC DS-CDMA) scheme. The motivation of using SA-PIC is that it gives high performance and at the same time, reduces the computational complexity required to perform interference cancellation. An upper bound expression of the bit error rate (BER) for the SA-PIC under Rayleigh fading channel condition is derived. Moreover, the implementation complexities for SA-PIC and Adaptive Parallel Interference Cancellation (APIC) are discussed and compared. The performance of SA-PIC is investigated analytically and validated via computer simulations.

Keywords: Adaptive interference cancellation, communicationsystems, multicarrier signal processing, spread spectrum

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Authors: Abida Harbi

Abstract:

We provide a maximum norm analysis of a finite element Schwarz alternating method for a nonlinear elliptic boundary value problem of the form -Δu = f(u), on two overlapping sub domains with non matching grids. We consider a domain which is the union of two overlapping sub domains where each sub domain has its own independently generated grid. The two meshes being mutually independent on the overlap region, a triangle belonging to one triangulation does not necessarily belong to the other one. Under a Lipschitz assumption on the nonlinearity, we establish, on each sub domain, an optimal L∞ error estimate between the discrete Schwarz sequence and the exact solution of the boundary value problem.

Keywords: Error estimates, Finite elements, Nonlinear PDEs, Schwarz method.

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Authors: Aylin Alin

Abstract:

In this paper, penalized power-divergence test statistics have been defined and their exact size properties to test a nested sequence of log-linear models have been compared with ordinary power-divergence test statistics for various penalization, λ and main effect values. Since the ordinary and penalized power-divergence test statistics have the same asymptotic distribution, comparisons have been only made for small and moderate samples. Three-way contingency tables distributed according to a multinomial distribution have been considered. Simulation results reveal that penalized power-divergence test statistics perform much better than their ordinary counterparts.

Keywords: Contingency table, Log-linear models, Penalization, Power-divergence measure, Penalized power-divergence measure.

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Authors: Herbert Ugrinowitsch, Suziane Peixoto dos Santos-Naves, Michele Viviene Carbinatto, Rodolfo NovellinoBenda, Go Tani

Abstract:

An experiment was conducted to examine the effect of the level of performance stabilization on the human adaptability to perceptual-motor perturbation in a complex coincident timing task. Three levels of performance stabilization were established operationally: pre-stabilization, stabilization, and super-stabilization groups. Each group practiced the task until reached its level of stabilization in a constant sequence of movements and under a constant time constraint before exposure to perturbation. The results clearly showed that performance stabilization is a pre-condition for adaptation. Moreover, variability before reaching stabilization is harmful to adaptation and persistent variability after stabilization is beneficial. Moreover, the behavior of variability is specific to each measure.

Keywords: Adaptation, motor skill, perturbation, stabilization.

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Authors: Liliana Feleagă, Niculae Feleagă, Vasile Răileanu

Abstract:

Although agriculture is an important part of the world economy, accounting in agriculture still has many shortcomings. The adoption of IAS 41 “Agriculture” has tried to improve this situation and increase the comparability of financial statements of entities in the agricultural sector. Although controversial, IAS 41 is the first step of a consistent transition to fair value assessment in the agricultural sector. The objective of our work is the analysis of IAS 41 and current accounting agricultural situation in Romania. Accounting regulations in Romania are in accordance with European directives and, in many respects, converged with IFRS referential. Provisions of IAS 41, however, are not reflected directly in Romanian regulations. With the increase of forest land transactions, it is expected that recognition and measurement of biological assets under IAS 41 to become a necessity.

Keywords: Accounting Agricultural, Biological Assets, Fair value, IAS 41

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