Search results for: Ivan Dario Romero Fonseca

Authors: Iván Castelló, Georgiana Stoica, Emilio Palomares, Fernando Bravo

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We present herein two colour encoded silica nanospheres (2nanoSi) for the fluorescence quantitative ratiometric determination of trypsin in humans. The system proved to be a faster (minutes) method, with two times higher sensitivity than the state-of-the-art biomarkers based sensors for cystic fibrosis (CF), allowing the quantification of trypsin concentrations in a wide range (0-350 mg/L). Furthermore, as trypsin is directly related to the development of cystic fibrosis, different human genotypes, i.e. healthy homozygotic (> 80 mg/L), CF homozygotic (< 50 mg/L), and heterozygotic (> 50 mg/L), respectively, can be determined using our 2nanoSi nanospheres.

Keywords: cystic fibrosis, trypsin, quantum dots, biomarker, homozygote, heterozygote

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Authors: Claudia Marcela Munoz Gonzalez, Diego Fernando Hernandez Losada, Hugo Alberto Herrera Fonseca

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The project owner's role in the public-private investment consists of controlling and verifying the correct execution of the project's objectives and resources. Likewise, it is a discipline little explored in the academic field, whereby this work wishes to contribute with a model of good practices based on the project management methodology proposed by the Project Management Body of Knowledge® Guide. In the same way, highlight what are the controls that an integral project owner should take into account in its exercise and application, through the stages in which its contract runs. This proposal aims to structure its practice and integrate its functions according to a project management methodology. In addition, these practices will be applied in a case study of projects in the agricultural sector, particularly in the construction of irrigation district in Cundinamarca, Colombia.

Keywords: controls, construction of irrigation district, PMBOK®, project owner

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Authors: Asier Romero Andonegi, Irati De Pablo Delgado

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The objective of this study is to explore the different methodological procedures that are used to obtain information on the early linguistic development of children. To this end, two different methodological procedures were carried out on the same sample: on the one hand, the MacArthur-Bates Communicative Development Inventories, in its adaptations in Spanish and Basque; and on the other hand, longitudinal observation through professional software: ELAN and CHAT. The sample consists of 8 Basque children/ages 16 to 30 months with different mother tongue (L1). The results show the usefulness of inventories in obtaining information on the development of early communication and language skills, but also their limitations mostly focused on the interpretive overvaluation of their children’s lexical development.

Keywords: early language development, language evaluation, lexicon, MacArthur-Bates communicative development inventories

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Authors: Ivan Baravy

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Interpolation problem, as it was initially posed in terms of polynomials, is well researched. However, further mathematical developments extended it significantly. Trigonometric interpolation is widely used in Fourier analysis, while its generalized representation as exponential interpolation is applicable to such problem of mathematical physics as modelling of Ziegler-Biersack-Littmark repulsive interatomic potentials. Formulated for finite fields, this problem arises in decoding Reed--Solomon codes. This paper shows the relation between different interpretations of the problem through the class of matrices of special structure - Hankel matrices.

Keywords: Berlekamp-Massey algorithm, exponential interpolation, finite fields, Hankel matrices, Hankel polynomials

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Authors: Darko Babic, Maja Modric, Dario Babic, Mario Fiolic

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For road markings as a part of traffic control plan, it is considered to have a positive impact on road safety. Their importance is particularly evident in low visibility conditions when the field of vision and the driver's visual acuity are significantly reduced. The aim of this article is to analyze how road marking retroreflectivity affects the frequency of traffic accidents in low visibility conditions. For this purpose, 10,417.4 km single carriageway roads were analysed across Croatia in the period from 2012 to 2016. The research included accidents that may be significantly affected by marking retroreflectivity: head-on collisions, running off the road, hitting a stationary object on the road and hitting a stationary roadside object. The results have shown that the retroreflectivity level is negatively correlated to the total number of accidents and the number of casualties and injuries, which ultimately means that the risk of traffic accidents and deaths and/or injuries of participants will be lower with the increase of road markings retroreflectivity. These results may assist in defining minimum values of retroreflectivity that the markings must meet at any time as well as the suitable technologies and materials for their implementation.

Keywords: retroreflectivity, road markings, traffic accidents, traffic safety

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Authors: J. J. M. Trienekens, H. L. Romero, L. Cuenca

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While process harmonization is increasingly mentioned and unanimously associated with several benefits, there is a need for more understanding of how it contributes to business process redesign and improvement. This paper presents the application, in an industrial case study, of a conceptual harmonization model on the relationship between drivers and effects of process harmonization. The drivers are called contextual factors which influence harmonization. Assessment of these contextual factors in a particular business domain, clarifies the extent of harmonization that can be achieved, or that should be strived at. The case study shows how the conceptual harmonization model can be made operational and can act as a valuable assessment tool. From both qualitative, as well as some quantitative, assessment results, insights are being discussed on the extent of harmonization that can be achieved, and action plans are being defined for business (process) harmonization.

Keywords: case study, contextual factors, process harmonization, industrial company

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Authors: Mladen Djuric, Ivan Janicijevic, Sasa Lazarevic

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One of the organizational issues is how to develop and shape decision making and knowledge management systems which will continually avoid traps of both paralyses by analyses“ and extinction by instinct“, the concepts that are a kind of tolerant limits anti-patterns which define what we can call decision making and knowledge management patterns control zone. This paper discusses potentials for development of a core base for recognizing, capturing, and analyzing anti-patterns in the educational organization, thus creating a space for improving decision making and knowledge management processes in education.

Keywords: anti-patterns, decision making, education, knowledge management

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Authors: Joselito Medina-Marin, Alexandr Karelin, Ana Tarasenko, Juan Carlos Seck-Tuoh-Mora, Norberto Hernandez-Romero, Eva Selene Hernandez-Gress

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A production line designer faces with several challenges in manufacturing system design. One of them is the assignment of buffer slots in between every machine of the production line in order to maximize the throughput of the whole line, which is known as the Buffer Allocation Problem (BAP). The BAP is a combinatorial problem that depends on the number of machines and the total number of slots to be distributed on the production line. In this paper, we are proposing a Petri Net (PN) Model to obtain the throughput in unreliable production lines, based on PN mathematical tools and the decomposition method. The results obtained by this methodology are similar to those presented in previous works, and the number of machines is not a hard restriction.

Keywords: buffer allocation problem, Petri Nets, throughput, production lines

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Authors: M. E. Velásquez Torres, F. Tzompantzi, J. C. Castillo-Rodríguez, A. G. Romero Villegas, S. Mendéz-Salazar, C. E. Santolalla-Vargas, J. Cardoso-Martínez

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Photocatalytic degradation, as an advanced oxidation technology, is a promising method in organic pollutant degradation. In this sense, chlorophenols should be removed from the water because they are highly toxic. The TiO₂ - X% ZnS photocatalysts, where X represents the molar percentage of ZnS (3%, 5%, 10%, and 15%), were synthesized using the one-step sol-gel method to use them as photocatalysts to degrade 4-chlorophenol. The photocatalysts were synthesized by a one-step sol-gel method. They were refluxed for 36 hours, dried at 80°C, and calcined at 400°C. They were labeled TiO₂ - X%ZnS, where X represents the molar percentage of ZnS (3%, 5%, 10%, and 15%). The band gap was calculated using a Cary 100 UV-Visible Spectrometer with an integrating sphere accessory. Ban gap value of each photocatalyst was: 2.7 eV of TiO₂, 2.8 eV of TiO₂ - 3%ZnS and TiO₂ - 5%ZnS, 2.9 eV of TiO₂ - 10%ZnS and 2.6 eV of TiO2 - 15%ZnS. In a batch type reactor, under the irradiation of a mercury lamp (λ = 254 nm, Pen-Ray), degradations of 55 ppm 4-chlorophenol were obtained at 360 minutes with the synthesized photocatalysts: 60% (3% ZnS), 66% (5% ZnS), 74% (10% ZnS) and 58% (15% ZnS). In this sense, the best material as a photocatalyst was TiO₂ -10%ZnS with a degradation percentage of 74%.

Keywords: 4-chlorophenol, photocatalysis, water pollutant, sol-gel

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Authors: Ivan Belik

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In terms of social networks split graphs correspond to the variety of interpersonal and intergroup relations. In this paper we analyse the interaction between the cliques (socially strong and trusty groups) and the independent sets (fragmented and non-connected groups of people) as the basic components of any split graph. Based on the Semi-Lagrangean relaxation for the k-cardinality assignment problem we show the way of how to minimize the socially risky interactions between the cliques and the independent sets within the social network.

Keywords: cliques, independent sets, k-cardinality assignment, social networks, split graphs

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Authors: Cassandra Pratt Romero, Andres Gomez de Silva Garza

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This paper describes a computational system designed to imitate human inspiration during musical composition. The system is called MIS (Musical Inspiration Simulator). The MIS system is inspired by media to which human beings are exposed daily (visual, textual, or auditory) to create new musical compositions based on the emotions detected in said media. After building the system we carried out a series of evaluations with volunteer users who used MIS to compose music based on images, texts, and audio files. The volunteers were asked to judge the harmoniousness and innovation in the system's compositions. An analysis of the results points to the difficulty of computational analysis of the characteristics of the media to which we are exposed daily, as human emotions have a subjective character. This observation will direct future improvements in the system.

Keywords: human inspiration, musical composition, musical composition by computer, theory of sensation and human perception

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Authors: Valentina Narvaez Gaitan, Laura Valentina Rodriguez Leguizamon, Ruben Dario Hernandez B.

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This work describes a physiological signal emulation system that uses electromyography (EMG) signals obtained from muscle sensors in the first instance. These signals are used to extract their characteristics to model and emulate specific arm movements. The main objective of this effort is to develop a new biomedical software system capable of generating physiological signals through the use of embedded systems by establishing the characteristics of the acquired signals. The acquisition system used was Biosignals, which contains two EMG electrodes used to acquire signals from the forearm muscles placed on the extensor and flexor muscles. Processing algorithms were implemented to classify the signals generated by the arm muscles when performing specific movements such as wrist flexion extension, palmar grip, and wrist pronation-supination. Matlab software was used to condition and preprocess the signals for subsequent classification. Subsequently, the mathematical modeling of each signal is performed to be generated by the embedded system, with a validation of the accuracy of the obtained signal using the percentage of cross-correlation, obtaining a precision of 96%. The equations are then discretized to be emulated in the embedded system, obtaining a system capable of generating physiological signals according to the characteristics of medical analysis.

Keywords: classification, electromyography, embedded system, emulation, physiological signals

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Authors: Alexander P. Eremeev, Ivan E. Kurilenko, Pavel R. Varshavskiy

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In this paper, the problem of the application of temporal reasoning and case-based reasoning in intelligent decision support systems is considered. The method of case-based reasoning with temporal dependences for the solution of problems of real-time diagnostics and forecasting in intelligent decision support systems is described. This paper demonstrates how the temporal case-based reasoning system can be used in intelligent decision support systems of the car access control. This work was supported by RFBR.

Keywords: analogous reasoning, case-based reasoning, intelligent decision support systems, temporal reasoning

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Authors: Joselito Medina Marin, Norberto Hernández Romero, Juan Carlos Seck Tuoh Mora, Erick S. Martinez Gomez

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The Flow Shop Scheduling Problem (FSSP) is a typical problem that is faced by production planning managers in Flexible Manufacturing Systems (FMS). This problem consists in finding the optimal scheduling to carry out a set of jobs, which are processed in a set of machines or shared resources. Moreover, all the jobs are processed in the same machine sequence. As in all the scheduling problems, the makespan can be obtained by drawing the Gantt chart according to the operations order, among other alternatives. On this way, an FMS presenting the FSSP can be modeled by Petri nets (PNs), which are a powerful tool that has been used to model and analyze discrete event systems. Then, the makespan can be obtained by simulating the PN through the token game animation and incidence matrix. In this work, we present an adaptive PN to obtain the makespan of FSSP by applying PN analytical tools.

Keywords: flow-shop scheduling problem, makespan, Petri nets, state equation

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Authors: Ivan Stanev, Maria Koleva

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Automated software development issues are addressed in this paper. Layers and packages of a Common Platform for Automated Programming (CPAP) are defined based on Service Oriented Architecture, Cloud computing, Knowledge based automated software engineering (KBASE) and Method of automated programming. Tools of seven leading companies (AWS of Amazon, Azure of Microsoft, App Engine of Google, vCloud of VMWare, Bluemix of IBM, Helion of HP, OCPaaS of Oracle) are analyzed in the context of CPAP. Based on the results of the analysis CPAP requirements are formulated

Keywords: automated programming, cloud computing, knowledge based software engineering, service oriented architecture

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Authors: Henrique Veras De Paiva Fonseca

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This paper investigates the long-term relationship between early life exposure to malaria and adult socioeconomic outcomes in Brazil. The identification strategy relies on exogenous variation in the risk of malaria outbreaks in different states and seasons of the year to identify early life exposure according to the timing and location of birth. Furthermore, Brazil has undergone a successful campaign of malaria eradication during the late 1950s, which allows for comparing outcomes of birth cohorts born just prior to and just after eradication to identify the extent of in utero exposure. Instrumental variables estimates find consistent negative treatment effects of in utero exposure to malaria on socioeconomic outcomes, such as educational attainment and health status. The effects are stronger for exposure during the first trimester of pregnancy than during other periods of gestation. Additionally, consistent with previous findings, men are more likely to exhibit larger long-term effects.

Keywords: malaria, exposure, eradication, instrumental variables, education, health

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Authors: Marco Morini, Nicolandrea Calabrese, Dario Chello

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Despite the international commitment of Algeria towards the development of energy efficiency and renewable energy in the country, the internal energy demand has been continuously growing during the last decade due to the substantial increase of population and of living conditions, which in turn has led to an unprecedented expansion of the residential building sector. The thermal building regulation is the technical document that establishes the calculation framework for the thermal performance of buildings in Algeria, setting up minimum obligatory targets for the thermal performance of new buildings. An update of this regulation is due in the coming years, and this paper discusses some proposals in this regard, with the aim to improve the energy efficiency of the building sector, particularly with regard to social housing. In particular, it proposes a methodology for drafting an energy performance label of new Algerian residential buildings, moving from the results of the thermal compliance verification and sizing of technical systems as defined in the RTB. Such an energy performance label – whose calculation method is briefly described in the paper – aims to raise citizens' awareness of the benefits of energy efficiency. It can represent the first step in a process of integrating technical installations into the calculation of the energy performance of buildings in Algeria.

Keywords: building, energy certification, energy efficiency, social housing, international cooperation, Mediterranean region

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Authors: Todor Penchev, Dimitar Karastojanov, Ivan Altaparmakov

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For briquetting of metal chips are used hydraulic and mechanical presses. The density of the briquettes in this case is about 60% - 70 % on the density of solid metal. In this work are presented the results of experimental studies for briquetting of metal chips, by using a new technology for impact briquetting. The used chips are by Armco iron, steel, cast iron, copper, aluminum and brass. It has been found that: (i) in a controlled impact the density of the briquettes can be increases up to 30%; (ii) at the same specific impact energy Es (J/sm3) the density of the briquettes increases with increasing of the impact velocity; (iii), realization of the repeated impact leads to decrease of chips density, which can be explained by distribution of elastic waves in the briquette.

Keywords: briquetting, chips briquetting, impact briquetting, controlled impact

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Authors: Rodrigo S. Fonseca, Antônio C. P. Veiga

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Aiming at helping people with some movement limitation that makes typing and communication difficult, there is a need to customize an assistive tool with a learning environment that helps the user in order to optimize text input, identifying the error and providing the correction and possibilities of choice in the Portuguese language. The work presents an Orthographic and Grammatical System that can be incorporated into writing environments, improving and facilitating the use of an alphanumeric keyboard, using a prototype built using a genetic algorithm in addition to carrying out the prediction, which can occur based on the quantity and position of the inserted letters and even placement in the sentence, ensuring the sequence of ideas using a Long Short Term Memory (LSTM) neural network. The prototype optimizes data entry, being a component of assistive technology for the textual formulation, detecting errors, seeking solutions and informing the user of accurate predictions quickly and effectively through machine learning.

Keywords: genetic algorithm, neural networks, word prediction, machine learning

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Authors: O. M. Couto Junior, I. Matos, I. M. Fonseca, P. A. Arroyo, E. A. Silva, M. A. S. D. Barros

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This study was the adsorption of paracetamol from aqueous solutions on fixed beds of activated carbon from babassy coconut shell. Several operation conditions on the shape of breakthrough curves were investigated and proposed model is successfully validated with the literature data and obtained experimental data. The initial paracetamol concentration increases from 20 to 50 mg.L-1, and the break point time decreases, tb, from 18.00 to 10.50 hours. The fraction of unused bed length, HUNB, at break-through point is obtained in the range of 1.62 to 2.81 for 20 to 50 mg.L-1 of initial paracetamol concentration. The presence of Ca+2 and Mg+2 are responsible for increasing the hardness of the water, affects significantly the adsorption kinetics, and lower removal efficiency by adsorption of paracetamol on activated carbons. The axial dispersion coefficients, DL, was constants for concentrated feed solution, but this parameter has different values for deionized and hardness water. The mass transfer coefficient, Ks, was increasing with concentrated feed solution.

Keywords: paracetamol, adsorption, water hardness, activated carbon.

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Authors: Jose A. Romero, Frank Otremba, Alejandro A. Lozano-Guzman

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Road safety is affected by many factors, involving the vehicle, the infrastructure, and the environment. Many efforts have been thus made to improve road safety through rational standards for the different systems involved in freight transportation. Cargo shifting and falling have been recognized as critical and contributive effects for road crashes. To avoid such situations, regional and international standards have been implemented, aiming to prevent such types of cargo-related accidents. In particular, there are specific compulsory standard requirements to maintain the cargo on the vehicle without shifting, when the vehicle performs an emergency braking maneuver. In this paper, a simulation is presented to analyze the effect of the vibration of the cargo on the braking distance of the vehicle. Such vibration can lead to a poor cargo restraining, and higher braking efficiency, as a result of the decoupling of the cargo mass from the vehicle mass. Such higher braking efficiency, on the order of 4.4%, further suggests a greater demand for the current braking standards.

Keywords: road safety, cargo securement, shifting cargo, vehicle dynamics, ABS

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Authors: D. Romero Espitia

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Research on peacebuilding has taken a critical turn into examining the neoliberal and hegemonic conception of peace operations. Alternative peacebuilding models have been analyzed, but the scholarly discussion fails to bring them together or form connections between them. The objective of this paper is to rethink peacebuilding by extracting the positive aspects of the various peacebuilding models, connecting them with the local context, and therefore promote emancipation in contemporary peacebuilding efforts. Moreover, local ownership has been widely labelled as one, if not the core principle necessary for a successful peacebuilding project. Yet, definitions of what constitutes the 'local' remain debated. Through a qualitative review of literature, this paper unpacks the contemporary conception of peacebuilding in nexus with 'local ownership' as manifested through civil society. Using Colombia as a case study, this paper argues that a new peacebuilding framework, one that reconsiders the terms of engagement between international and national actors, is needed in order to foster effective peacebuilding efforts in contested transitional states.

Keywords: civil society, Colombia, emancipation, peacebuilding

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Authors: Marina Kljaković-Gašpić Batinjan, Tea Petrović, Frano Vučković, Irzal Hadžibegović, Barbara Radovani, Ivana Jurin, Lovorka Đerek, Eva Huljev, Alemka Markotić, Ivica Lukšić, Irena Trbojević-Akmačić, Gordan Lauc, Ivan Gudelj, Rok Čivljak

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Immunoglobulin G has essential role in defense against infectious diseases, but its role cannot be fully recognized without understanding of changes in its N-glycans attached to the Fc domain. We analyzed and compared total IgG glycome in plasma samples of patients with influenza, patients with COVID-19 and healthy controls. We found similarities in IgG glycosylation changes in COVID-19 survivors and influenza patients that could be the consequence of adequate immune response to enveloped viruses, while observed changes in deceased COVID-19 patients may indicate its deviation.

Keywords: COVID-19, glycosylation, immunoglobulin G, influenza, pneumonia, viral infection

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Authors: Coline Bretz, Andrea Vaccaro, Dario Leumann

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The food, personal care, and cosmetic industries are seeing increased consumer demand for more sustainable and innovative ingredients. When developing new formulations incorporating such ingredients, stability is one of the first criteria that must be assessed, and it is thus of great importance to have a method that can detect instabilities early and quickly. Diffusing Wave Spectroscopy (DWS) is a light scattering technique that probes the motion,i.e., the mean square displacement (MSD), of colloids, such as nanoparticles in a suspension or droplets in emulsions. From the MSD, the rheological properties of the surrounding medium can be determined via the so-called microrheology approach. In the case of purely viscous media, it is also possible to obtain information about particle size. DWS can thus be used to monitor the size evolution of particles, droplets, or bubbles in aging dispersions, emulsions, or foams. In the context of early instability detection in emulsions, DWS offers considerable advantages, as the samples are measured in a contact-free manner, using only small quantities of samples loaded in a sealable cuvette. The sensitivity and rapidity of the technique are key to detecting and following the ageing of emulsions reliably. We present applications of DWS focused on the characterization of emulsions. In particular, we demonstrate the ability to record very subtle changes in the structural properties early on. We also discuss the various mechanisms at play in the destabilization of emulsions, such as coalescence or Ostwald ripening, and how to identify them through this technique.

Keywords: instrumentation, emulsions, stability, DWS

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Authors: Ivan Stanev, Maria Koleva

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A common platform for automated programming (CPAP) is defined in details. Two versions of CPAP are described: Cloud-based (including the set of components for classic programming, and the set of components for combined programming) and KBASE based (including the set of components for automated programming, and the set of components for ontology programming). Four KBASE products (module for automated programming of robots, intelligent product manual, intelligent document display, and intelligent form generator) are analyzed and CPAP contributions to automated programming are presented.

Keywords: automated programming, cloud computing, knowledge based software engineering, service oriented architecture

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Authors: Dmitry V. Pasynkov, Ivan A. Egoshin, Alexey A. Kolchev, Ivan V. Kliouchkin

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In most cases, typical cysts are easily recognized at ultrasonography. The specificity of this method for typical cysts reaches 98%, and it is usually considered as gold standard for typical cyst diagnosis. However, it is necessary to have all the following features to conclude the typical cyst: clear margin, the absence of internal echoes and dorsal acoustic enhancement. At the same time, not every breast cyst is typical. It is especially characteristic for protein-contained cysts that may have significant internal echoes. On the other hand, some solid lesions (predominantly malignant) may have cystic appearance and may be falsely accepted as cysts. Therefore we tried to develop the automatic method of cystic and solid breast lesions differentiation. Materials and methods. The input data were the ultrasonography digital images with the 256-gradations of gray color (Medison SA8000SE, Siemens X150, Esaote MyLab C). Identification of the lesion on these images was performed in two steps. On the first one, the region of interest (or contour of lesion) was searched and selected. Selection of such region is carried out using the sigmoid filter where the threshold is calculated according to the empirical distribution function of the image brightness and, if necessary, it was corrected according to the average brightness of the image points which have the highest gradient of brightness. At the second step, the identification of the selected region to one of lesion groups by its statistical characteristics of brightness distribution was made. The following characteristics were used: entropy, coefficients of the linear and polynomial regression, quantiles of different orders, an average gradient of brightness, etc. For determination of decisive criterion of belonging to one of lesion groups (cystic or solid) the training set of these characteristics of brightness distribution separately for benign and malignant lesions were received. To test our approach we used a set of 217 ultrasonic images of 107 cystic (including 53 atypical, difficult for bare eye differentiation) and 110 solid lesions. All lesions were cytologically and/or histologically confirmed. Visual identification was performed by trained specialist in breast ultrasonography. Results. Our system correctly distinguished all (107, 100%) typical cysts, 107 of 110 (97.3%) solid lesions and 50 of 53 (94.3%) atypical cysts. On the contrary, with the bare eye it was possible to identify correctly all (107, 100%) typical cysts, 96 of 110 (87.3%) solid lesions and 32 of 53 (60.4%) atypical cysts. Conclusion. Automatic approach significantly surpasses the visual assessment performed by trained specialist. The difference is especially large for atypical cysts and hypoechoic solid lesions with the clear margin. This data may have a clinical significance.

Keywords: breast cyst, breast solid lesion, differentiation, ultrasonography

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Authors: Ivan Belik, Kurt Jornsten

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We construct the coauthorship network based on the scientific collaboration between the faculty members at the Norwegian School of Economics (NHH) and based on their international academic publication experience. The network structure is based on the NHH faculties’ publications recognized by the ISI Web of Science for the period 1950 – Spring, 2014. The given network covers the publication activities of the NHH faculty members (over six departments) based on the information retrieved from the ISI Web of Science in Spring, 2014. In this paper we analyse the constructed coauthorship network in different aspects of the theory of social networks analysis.

Keywords: coauthorship networks, social networks analysis, Norwegian School of Economics, ISI

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Authors: Kalaumari Mayoral-Peña, Ana I. Montejano-Montelongo, Josué Reyes-Muñoz, Gonzalo A. Ortiz-Mancilla, Mayrin Rodríguez-Cruz, Víctor Hernández-Villalobos, Jesús A. Guzmán-López, Santiago García-Jacobo, Iván Licona-Vázquez, Grisel Fierros-Romero, Rosario Flores-Vallejo

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The group B-lactamic antibiotics include some of the most frequently used small drug molecules against bacterial infections. Nevertheless, an alarming decrease in their efficacy has been reported due to the emergence of antibiotic-resistant bacteria. Infections caused by bacteria expressing extended Spectrum B-lactamases (ESBLs) are difficult to treat and account for higher morbidity and mortality rates, delayed recovery, and high economic burden. According to the Global Report on Antimicrobial Resistance Surveillance, it is estimated that mortality due to resistant bacteria will ascend to 10 million cases per year worldwide. These facts highlight the importance of developing low-cost and readily accessible detection methods of drug-resistant ESBLs bacteria to prevent their spread and promote accurate and fast diagnosis. Bacterial detection is commonly done using molecular diagnostic techniques, where PCR stands out for its high performance. However, this technique requires specialized equipment not available everywhere, is time-consuming, and has a high cost. Loop-Mediated Isothermal Amplification (LAMP) is an alternative technique that works at a constant temperature, significantly decreasing the equipment cost. It yields double-stranded DNA of several lengths with repetitions of the target DNA sequence as a product. Although positive and negative results from LAMP can be discriminated by colorimetry, fluorescence, and turbidity, there is still a large room for improvement in the point-of-care implementation. DNA origami is a technique that allows the formation of 3D nanometric structures by folding a large single-stranded DNA (scaffold) into a determined shape with the help of short DNA sequences (staples), which hybridize with the scaffold. This research aimed to generate DNA origami structures using LAMP products as scaffolds to improve the sensitivity to detect ESBLs in point-of-care diagnosis. For this study, the coding sequence of the CTM-X-15 ESBL of E. coli was used to generate the LAMP products. The set of LAMP primers were designed using PrimerExplorerV5. As a result, a target sequence of 200 nucleotides from CTM-X-15 ESBL was obtained. Afterward, eight different DNA origami structures were designed using the target sequence in the SDCadnano and analyzed with CanDo to evaluate the stability of the 3D structures. The designs were constructed minimizing the total number of staples to reduce costs and complexity for point-of-care applications. After analyzing the DNA origami designs, two structures were selected. The first one was a zig-zag flat structure, while the second one was a wall-like shape. Given the sequence repetitions in the scaffold sequence, both were able to be assembled with only 6 different staples each one, ranging between 18 to 80 nucleotides. Simulations of both structures were performed using scaffolds of different sizes yielding stable structures in all the cases. The generation of the LAMP products were tested by colorimetry and electrophoresis. The formation of the DNA structures was analyzed using electrophoresis and colorimetry. The modeling of novel detection methods through bioinformatics tools allows reliable control and prediction of results. To our knowledge, this is the first study that uses LAMP products and DNA-origami in combination to delect ESBL-producing bacterial strains, which represent a promising methodology for diagnosis in the point-of-care.

Keywords: beta-lactamases, antibiotic resistance, DNA origami, isothermal amplification, LAMP technique, molecular diagnosis

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Authors: Georgi I. Petkov, Ivan I. Vankov, Yolina A. Petrova

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A structure-based model of category learning and categorization at different levels of abstraction is presented. The model compares different structures and expresses their similarity implicitly in the forms of mappings. Based on this similarity, the model can categorize different targets either as members of categories that it already has or creates new categories. The model is novel using two threshold parameters to evaluate the structural correspondence. If the similarity between two structures exceeds the higher threshold, a new sub-ordinate category is created. Vice versa, if the similarity does not exceed the higher threshold but does the lower one, the model creates a new category on higher level of abstraction.

Keywords: analogy-making, categorization, learning of categories, abstraction, hierarchical structure

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Authors: Adam Abate, Elham Rasti, Philip Romero

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Beta-glucosidase is the key enzyme component present in cellulase and completes the final step during cellulose hydrolysis by converting the cellobiose to glucose. The regulatory properties of beta-glucosidases are most commonly found for the retaining and inverting enzymes. Hydrolysis of a glycoside typically occurs with general acid and general base assistance from two amino acid side chains, normally glutamic or aspartic acids. In order to obtain more detailed information on the dynamic events origination from the interaction with enzyme active site, we carried out molecular dynamics simulations of beta-glycosidase in protonated state (Glu-H178) and deprotonated state (Glu178). The theoretical models generated from our molecular dynamics simulations complement and advance the structural information currently available, leading to a more detailed understanding of Beta-glycosidase structure and function. This article presents the important role of Asn307 in enzyme activity of beta-glucosidase

Keywords: Beta-glucosidase, GROMACS, molecular dynamics simulation, structural parameters

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