Search results for: human%20immunodeficiency%20virus.

Authors: Mohammed Sghir Taleb

Abstract:

Morocco is characterized by a great richness and diversity in aromatic and medicinal plants and it has an ancestral knowledge in the use of plants for medicinal and cosmetic purposes. In effect, the poverty of riparian, specially, mountain populations have greatly contributed to the development of traditional pharmacopoeia in Morocco. The analysis of the bibliographic data showed that a large number of plants in Morocco are exploited for aromatic and medicinal purposes and several of them are commercialized internationally. However, these potentialities of aromatic and medicinal plants are currently subjected to climate change and strong human pressures: Collecting fruits, agriculture development, harvesting plants, urbanization, overgrazing...

Keywords: Aromatic, medicinal, plants, socioeconomy, Morocco.

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Authors: Antonios Maniatis

Abstract:

The present paper focuses on human rights to the water and to the energy and has a scope to promote the legal status on sustainable construction. The right to water constitutes a typical example of 3G fundamental rights, like the right to enjoyment of energy, particularly of electricity, whilst the right to energy efficiency is a right of fourth generation. Both rights to water and energy are examined through their consecration in the framework of the above-mentioned generations. It results that not only decision-makers but also citizens should fight for the further consecration and adequate use of these crucial rights, having to do with the urgent problem of climate change and the sustainable development. The time for the principle of water and energy “rule of law” has come.

Keywords: Climate change law, energy (en + ergon) efficiency, fundamental rights, prosumer, water.

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Authors: Mikel Alonso López

Abstract:

This paper explores, in depth, the idea that emotions are present in all consumer decision making processes, meaning that purchase decisions have never been purely cognitive or as they traditionally have been defined, rational. Human beings, in all kinds of decisions, has "always" used neural systems related to emotions along with neural systems related to cognition, regardless of the type of purchase or the product or service in question. Therefore, all purchase decisions are, at the same time, cognitive and emotional. This paper presents an analysis of the main contributions of researchers in this regard.

Keywords: Emotions, decision making, consumer behavior.

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Authors: Zuzana Crhova, Karel Kolman, Drahomíra Pavelkova

Abstract:

Knowledge is considered as an important asset which can help organizations to create competitive advantage. The necessity of taking care of these assets is more important in these days – in days of turbulent changes in business environment. Knowledge could facilitate adaption to constant changes. The aim of this paper is to describe how the knowledge sharing can be supported in the manufacturing companies. The methods of case studies and grounded theory were used to present information gained by carrying out semistructured interviews. Results show that knowledge sharing is supported in very similar ways in respondent companies.

Keywords: Case Study, Human Resource Management, Knowledge, Knowledge Sharing.

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Authors: TamásMatuszka, Attila Kiss

Abstract:

Due the proliferation of smartphones in everyday use, several different outdoor navigation systems have become available. Since these smartphones are able to connect to the Internet, the users can obtain location-based information during the navigation as well. The users could interactively get to know the specifics of a particular area (for instance, ancient cultural area, Statue Park, cemetery) with the help of thus obtained information. In this paper, we present an Augmented Reality system which uses Semantic Web technologies and is based on the interaction between the user and the smartphone. The system allows navigating through a specific area and provides information and details about the sight an interactive manner.

Keywords: Augmented Reality, Semantic Web, Human Computer Interaction, Mobile Application.

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Authors: Juyi Park, Sang-Bum Lee, Jin-Wook Kim, Ji-Yoon Kim, Jung-Min Kim, Hee-Hwan Park, Jae-Won Seo, Gye-Hyung Kang, Soo-Ho Kim

Abstract:

This paper presents a portable robot that is to use for welding process in shipbuilding yard. It has six degree of freedom and 3kg payload capability. Its weight is 21.5kg so that human workers can carry it to the work place. Its body mainly made of magnesium alloy and aluminum alloy for few parts that require high strength. Since the distance between robot and controller should be 50m at most, the robot controller controls the robot through EtherCAT. RTX and KPA are used for real time EtherCAT control on Windows XP. The performance of the developed robot was satisfactory, in welding of U type cell in shipbuilding yard.

Keywords: Portable welding robot, Shipbuilding, EtherCAT

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Authors: Karel Frydrýšek, Pavel Koštial, Karla Barabaszová, Jana Kukutschová

Abstract:

This paper deals with a new way for designing external fixators applied in traumatology and orthopaedics. These fixators can be applied in the treatment of open and unstable fractures or for lengthening human or animal bones etc. The new design is based on the development of Ilizarov and other techniques (i.e. shape and weight optimalization based on composite materials, application of smart materials, nanotechnology, low x-ray absorption, antibacterial protection, patient's comfort, reduction in the duration of the surgical treatment, and cost).

Keywords: biomechanics, design, external fixators, newmaterials, traumatology

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Authors: Alberto Hananel

Abstract:

The aim of this work is to modelize the occlusion of a person with temporomandibular disorders as an evolutionary equation and approach its solution by the construction and characterizing of discrete variational splines. To formulate the problem, certain boundary conditions have been considered. After showing the existence and the uniqueness of the solution of such a problem, a convergence result of a discrete variational evolutionary spline is shown. A stress analysis of the occlusion of a human jaw with temporomandibular disorders by finite elements is carried out in FreeFem++ in order to prove the validity of the presented method.

Keywords: Approximation, evolutionary PDE, finite element method, temporomandibular disorders, variational spline.

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Authors: F. Yaghobian, R. Stosch, B. Güttler

Abstract:

This study aims to demonstrate the quantification of peptides based on isotope dilution surface enhanced Raman scattering (IDSERS). SERS spectra of phenylalanine (Phe), leucine (Leu) and two peptide sequences TGQIFK (T13) and YSFLQNPQTSLCFSESIPTPSNR (T6) as part of the 22-kDa human growth hormone (hGH) were obtained on Ag-nanoparticle covered substrates. On the basis of the dominant Phe and Leu vibrational modes, precise partial least squares (PLS) prediction models were built enabling the determination of unknown T13 and T6 concentrations. Detection of hGH in its physiological concentration in order to investigate the possibility of protein quantification has been achieved.

Keywords: Surface Enhanced Raman Scattering, Quantification, Peptides.

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Authors: M. Liebherr, P. Schubert, S. Kersten, C. Dietz, L. Franz, C. T. Haas

Abstract:

With a long history, dual-task has become one of the most intriguing research fields regarding human brain functioning and cognition. However, findings considering effects of taskinterrelations are limited (especially, in combined motor and cognitive tasks). Therefore, we aimed at developing a measurement system in order to analyse interrelation effects of cognitive and motor tasks. On the one hand, the present study demonstrates the applicability of the measurement system and on the other hand first results regarding a systematisation of different task combinations are shown. Future investigations should combine imagine technologies and this developed measurement system.

Keywords: Dual-task, interference, cognition, measurement.

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Authors: Hemant Kumar, Nilendu Das

Abstract:

A study based on ANN structure gives us the information to predict the size of the future in realizing a past event. ANN, IMD (Indian meteorological department) data and remote sensing were used to enable a number of parameters for calculating the size that may occur in the future. A threshold selected specifically above the high-frequency harvest reached the area during the selected seismic activity. In the field of human and local biodiversity it remains to obtain the right parameter compared to the frequency of impact. But during the study the assumption is that predicting seismic activity is a difficult process, not because of the parameters involved here, which can be analyzed and funded in research activity.

Keywords: ANN, Bayesian class, earthquakes, IMD.

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Authors: Yuhei Kunihiro, Sorin V. Sabau, Kazuhiro Shibuya

Abstract:

We study the molecular evolution of insulin from metric geometry point of view. In mathematics, and in particular in geometry, distances and metrics between objects are of fundamental importance. Using a weaker notion than the classical distance, namely the weighted quasi-metrics, one can study the geometry of biological sequences (DNA, mRNA, or proteins) space. We analyze from geometrical point of view a family of 60 insulin homologous sequences ranging on a large variety of living organisms from human to the nematode C. elegans. We show that the distances between sequences provide important information about the evolution and function of insulin.

Keywords: Metric geometry, evolution, insulin.

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Authors: O. L. Kukla, S. V. Marchenko, O. A. Zinchenko, O. S. Pavluchenko, O. M. KKuukla, S. V. Dzyadevych, O. P. Soldatkin

Abstract:

An application of the highly biosensor based on pH-sensitive field immobilized urease for urea analysis was demo The main analytical characteristics of the bios determined; the conditions of urea measureme blood were optimized. A conceptual possibility biosensor for detection of urea concentratio patients suffering from renal insufficiency was sensitive and selective effect transistor and monstrated in this work. iosensor developed were ment in real samples of ility of application of the tion in blood serum of as shown.

Keywords: Biosensor, blood serum, pH transistor, urea, urease, field-effect

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Authors: P. C. Kutschera, Elena C. Tesoro, Mary Grace Talamera-Sandico, Jose Maria G. Pelayo III

Abstract:

Second generation military Filipino Amerasians comprise a formidable contemporary segment of the estimated 250,000-plus biracial Amerasians in the Philippines today. Overall, they are a stigmatized and socioeconomically marginalized diaspora; historically, they were abandoned or estranged by U.S. military personnel fathers assigned during the century-long Colonial, Post- World War II and Cold War Era of permanent military basing (1898- 1992). Indeed, U.S. military personnel are assigned in smaller numbers in the Philippines today. This inquiry is an outgrowth of two recent small sample studies. The first surfaced the impact of the U.S. military prostitution system on formation of the ‘Derivative Amerasian Family Construct’ on first generation Amerasians; a second, qualitative case study suggested the continued effect of the prostitution systems' destructive impetuous on second generation Amerasians. The intent of this current qualitative, multiple-case study was to actively seek out second generation sex industry toilers. The purpose was to focus further on this human phenomenon in the postbasing and post-military prostitution system eras. As background, the former military prostitution apparatus has transformed into a modern dynamic of rampant sex tourism and prostitution nationwide. This is characterized by hotel and resorts offering unrestricted carnal access, urban and provincial brothels (casas), discos, bars and pickup clubs, massage parlors, local barrio karaoke bars and street prostitution. A small case study sample (N = 4) of female and male second generation Amerasians were selected. Sample formation employed a non-probability ‘snowball’ technique drawing respondents from the notorious Angeles, Metro Manila, Olongapo City ‘AMO Amerasian Triangle’ where most former U.S. military installations were sited and modern sex tourism thrives. A six-month study and analysis of in-depth interviews of female and male sex laborers, their families and peers revealed a litany of disturbing, and troublesome experiences. Results showed profiles of debilitating human poverty, history of family disorganization, stigmatization, social marginalization and the ghost of the military prostitution system and its harmful legacy on Amerasian family units. Emerging were testimonials of wayward young people ensnared in a maelstrom of deep economic deprivation, familial dysfunction, psychological desperation and societal indifference. The paper recommends that more study is needed and implications of unstudied psychosocial and socioeconomic experiences of distressed younger generations of military Amerasians require specific research. Heretofore apathetic or disengaged U.S. institutions need to confront the issue and formulate activist and solution-oriented social welfare, human services and immigration easement policies and alternatives. These institutions specifically include academic and social science research agencies, corporate foundations, the U.S. Congress, and Departments of State, Defense and Health and Human Services, and Homeland Security (i.e. Citizen and Immigration Services) It is them who continue to endorse a laissez-faire policy of non-involvement over the entire Filipino Amerasian question. Such apathy, the paper concludes, relegates this consequential but neglected blood progeny to the status of humiliating destitution and exploitation. Amerasians; thus, remain entrapped in their former colonial, and neo-colonial habitat. Ironically, they are unwitting victims of a U.S. American homeland that fancies itself geo-politically as a strong and strategic military treaty ally of the Philippines in the Western Pacific.

Keywords: Asian Americans, Filipino Amerasians, diaspora, military prostitution, stigmatization.

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Authors: Thomas Adi Purnomo Sidhi

Abstract:

Nowadays, network is an essential need in almost every part of human daily activities. People now can seamlessly connect to others through the Internet. With advanced technology, our personal data now can be more easily accessed. One of many components we are concerned for delivering the best network is a security issue. This paper is proposing a method that provides more options for security. This research aims to improve network security by focusing on the physical layer which is the first layer of the OSI model. The layer consists of the basic networking hardware transmission technologies of a network. With the use of observation method, the research produces a schematic design for enhancing the network security through the gray code converter.

Keywords: Network, network security, gray code, physical layer.

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Authors: Jiraporn Rojtinnakorn

Abstract:

ICAM-2 (intercellular adhesion molecule 2) or CD102 (Cluster of Differentiation 102) is type I transmembrane glycoproteins, composing 2-9 immunoglobulin-like C2-type domains. ICAM-2 plays the particular role in immune response and cell surveillance. It is concerned in innate and specific immunity, cell survival signal, apoptosis, and anticancer. EST clone of ICAM-2, from P. gigas blood cell EST libraries, showed high identity to human ICAM-2 (92%) with conserve region of ICAM N-terminal domain and part of Ig superfamily. Gene and protein of ICAM-2 has been founded in mammals. This is the first report of ICAM-2 in fish

Keywords: ICAM-2, CD102, Pangasianodon gigas, antitumor.

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Authors: Naira Sahakyan, Margarit Petrosyan, Armen Trchounian

Abstract:

One of the tasks in contemporary biotechnology, pharmacology and other fields of human activities is to obtain biologically active substances from plants. They are very essential in the treatment of many diseases due to their actually high therapeutic value without visible side effects. However, sometimes the possibility of obtaining the metabolites is limited due to the reduction of wild-growing plants. That is why the plant cell cultures are of great interest as alternative sources of biologically active substances. Besides, during the monitored cultivation, it is possible to obtain substances that are not synthesized by plants in nature. Isolated culture of Ajuga genevensis with high growth activity and ability of regeneration was obtained using MS nutrient medium. The agar-diffusion method showed that aqueous extracts of callus culture revealed high antimicrobial activity towards various gram-positive (Bacillus subtilis A1WT; B. mesentericus WDCM 1873; Staphylococcus aureus WDCM 5233; Staph. citreus WT) and gram-negative (Escherichia coli WKPM M-17; Salmonella typhimurium TA 100) microorganisms. The broth dilution method revealed that the minimal and half maximal inhibitory concentration values against E. coli corresponded to the 70 μg/mL and 140 μg/mL concentration of the extract respectively. According to the photochemiluminescent analysis, callus tissue extracts of leaf and root origin showed higher antioxidant activity than the same quantity of A. genevensis intact plant extract. A. genevensis intact plant and callus culture extracts showed no cytotoxic effect on K-562 suspension cell line of human chronic myeloid leukemia. The GC-MS analysis showed deep differences between the qualitative and quantitative composition of callus culture and intact plant extracts. Hexacosane (11.17%); n-hexadecanoic acid (9.33%); and 2-methoxy-4-vinylphenol (4.28%) were the main components of intact plant extracts. 10-Methylnonadecane (57.0%); methoxyacetic acid, 2-tetradecyl ester (17.75%) and 1-Bromopentadecane (14.55%) were the main components of A. genevensis callus culture extracts. Obtained data indicate that callus culture of A. genevensis can be used as an alternative source of biologically active substances.

Keywords: Ajuga genevensis, antibacterial activity, antioxidant activity, callus cultures.

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Authors: Jadwiga R. Ziolkowska

Abstract:

In this paper, a fuzzy algorithm and a fuzzy multicriteria decision framework are developed and used for a practical question of optimizing biofuels policy making. The methodological framework shows how to incorporate fuzzy set theory in a decision process of finding a sustainable biofuels policy among several policy options. Fuzzy set theory is used here as a tool to deal with uncertainties of decision environment, vagueness and ambiguities of policy objectives, subjectivities of human assessments and imprecise and incomplete information about the evaluated policy instruments.

Keywords: Fuzzy set theory, multi-criteria decision-makingsupport, uncertainties, policy making, biofuels

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Authors: Ahmad M. Shafiee, Mehrdad Montazeri, Mahdi Nikdast

Abstract:

Every day human life experiences new equipments more automatic and with more abilities. So the need for faster processors doesn-t seem to finish. Despite new architectures and higher frequencies, a single processor is not adequate for many applications. Parallel processing and networks are previous solutions for this problem. The new solution to put a network of resources on a chip is called NOC (network on a chip). The more usual topology for NOC is mesh topology. There are several routing algorithms suitable for this topology such as XY, fully adaptive, etc. In this paper we have suggested a new algorithm named Intermittent X, Y (IX/Y). We have developed the new algorithm in simulation environment to compare delay and power consumption with elders' algorithms.

Keywords: Computer architecture, parallel computing, NOC, routing algorithm.

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Authors: Prof. Chokri SLIM

Abstract:

A Novel fuzzy neural network combining with support vector learning mechanism called support-vector-based fuzzy neural networks (SVBFNN) is proposed. The SVBFNN combine the capability of minimizing the empirical risk (training error) and expected risk (testing error) of support vector learning in high dimensional data spaces and the efficient human-like reasoning of FNN.

Keywords: Neural network, fuzzy inference, machine learning, fuzzy modeling and rule extraction, support vector regression.

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Authors: Koushlendra Kumar Singh, Manish Kumar Bajpai, Rajesh K. Pandey

Abstract:

The edges of low contrast images are not clearly distinguishable to human eye. It is difficult to find the edges and boundaries in it. The present work encompasses a new approach for low contrast images. The Chebyshev polynomial based fractional order filter has been used for filtering operation on an image. The preprocessing has been performed by this filter on the input image. Laplacian of Gaussian method has been applied on preprocessed image for edge detection. The algorithm has been tested on two test images.

Keywords: Chebyshev polynomials, Fractional order differentiator, Laplacian of Gaussian (LoG) method, Low contrast image.

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Authors: Tadatsugu Kitamoto

Abstract:

Recently, a quality of motors is inspected by human ears. In this paper, I propose two systems using a method of speech recognition for automation of the inspection. The first system is based on a method of linear processing which uses K-means and Nearest Neighbor method, and the second is based on a method of non-linear processing which uses neural networks. I used motor sounds in these systems, and I successfully recognize 86.67% of motor sounds in the linear processing system and 97.78% in the non-linear processing system.

Keywords: Acoustical diagnosis, Neural networks, K-means, Short-time Fourier transformation

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Authors: Martin Kendra, Tomas Skrucany, Jaroslav Masek

Abstract:

The noise is one of the negative elements which affects the human health. This article presents the measurement of emitted noise by road vehicle and its parts during the operation. Measurement was done in the interior of common passenger cars with a digital sound meter. The results compare the noise value in different cars with different body shape, which influences the driver’s health. Transport has considerable ecological effects; many of them are detrimental to environmental sustainability. Roads and traffic exert a variety of direct and mostly detrimental effects on nature.

Keywords: Driver, noise measurement, passenger road vehicle, road transport.

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Authors: Surbhi Gupta, Alka Handa, Parvinder S.Sandhu

Abstract:

Stegnography is a new way of secret communication the most widely used mechanism on account of its simplicity is the use of the least significant bit. We have used the least significant bit (2 LSB and 4 LSB) substitution method. Depending upon the characteristics of the individual portions of cover image we decide whether to use 2 LSB or 4 LSB thus it is an adaptive stegnography technique. We used one of the three channels to behave as indicator to indicate the presence of hidden data in other two channels. The module showed impressive results in terms of capacity to hide the data. In proposed method, instead of using RGB color space directly, YCbCr color space is used to make use of human visual system characteristic.

Keywords: Stegoimage, steganography, Pixel indicator, segmentation, YCbCr..

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Authors: Petra Horváthová, Irena Durdová

Abstract:

The article is aimed at bringing information on the scope and the level of use of talent management by organizations in one of the Czech Republic regions, in the Moravian-Silesian Region. On the basis of data acquired by a questionnaire survey it has been found out that organizations in the above-mentioned region are implementing the system of talent management on a small scale: this approach is used by 3.8 % of organizations only that is 9 from 237 (100 %) of the approached respondents. The main reasons why this approach is not used is either that organizations have no knowledge of it or there is lack of financial and personnel resources. In the article recommendations suggested by the author can be found for a wider application of talent management in the Czech practice.

Keywords: Talent, talent management, use, mind map of talent management.

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Authors: Muhammad Raza Ali, Tim Morris

Abstract:

Skin color is an important visual cue for computer vision systems involving human users. In this paper we combine skin color and optical flow for detection and tracking of skin regions. We apply these techniques to gesture recognition with encouraging results. We propose a novel skin similarity measure. For grouping detected skin regions we propose a novel skin region grouping mechanism. The proposed techniques work with any number of skin regions making them suitable for a multiuser scenario.

Keywords: Bayesian tracking, chromaticity space, optical flowgesture recognition

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Authors: Alan Luo, Hunter N. B. Moseley

Abstract:

Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for X-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across X-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: Biomacromolecular structure, coenzyme, electron density discrepancy analysis, X-ray crystallography.

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Authors: Halim Djerroud, Arab Ali Cherif

Abstract:

We assume that conscious functions are implemented automatically. In other words that consciousness as well as the non-consciousness aspect of human thought, planning and perception, are produced by biologically adaptive algorithms. We propose that the mechanisms of consciousness can be produced using similar adaptive algorithms to those executed by the mechanism. In this paper, we present a computational model of consciousness, the ”Global Abstraction Workspace” which is an internal environmental modelling perceived as a multi-agent system. This system is able to evolve and generate new data and processes as well as actions in the environment.

Keywords: Artificial consciousness, cognitive architecture, global abstraction workspace, mutli-agents system.

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Authors: Maciej Zasuwa, Grzegorz Ptasinski, Antoni Kopyt

Abstract:

Nowadays flight simulators offer tremendous possibilities for safe and cost-effective pilot training, by utilization of powerful, computational tools. Due to technology outpacing methodology, vast majority of training related work is done by human instructors. It makes assessment not efficient, and vulnerable to instructors’ subjectivity. The research presents an Objective Assessment Tool (gOAT) developed at the Warsaw University of Technology, and tested on SW-4 helicopter flight simulator. The tool uses database of the predefined manoeuvres, defined and integrated to the virtual environment. These were implemented, basing on Aeronautical Design Standard Performance Specification Handling Qualities Requirements for Military Rotorcraft (ADS-33), with predefined Mission-Task-Elements (MTEs). The core element of the gOAT enhanced algorithm that provides instructor a new set of information. In details, a set of objective flight parameters fused with report about psychophysical state of the pilot. While the pilot performs the task, the gOAT system automatically calculates performance using the embedded algorithms, data registered by the simulator software (position, orientation, velocity, etc.), as well as measurements of physiological changes of pilot’s psychophysiological state (temperature, sweating, heart rate). Complete set of measurements is presented on-line to instructor’s station and shown in dedicated graphical interface. The presented tool is based on open source solutions, and flexible for editing. Additional manoeuvres can be easily added using guide developed by authors, and MTEs can be changed by instructor even during an exercise. Algorithm and measurements used allow not only to implement basic stress level measurements, but also to reduce instructor’s workload significantly. Tool developed can be used for training purpose, as well as periodical checks of the aircrew. Flexibility and ease of modifications allow the further development to be wide ranged, and the tool to be customized. Depending on simulation purpose, gOAT can be adjusted to support simulator of aircraft, helicopter, or unmanned aerial vehicle (UAV).

Keywords: Automated assessment, flight simulator, human factors, pilot training.

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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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