Search results for: Daniel Icaza Alvarez
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 154

Search results for: Daniel Icaza Alvarez

4 Towards End-To-End Disease Prediction from Raw Metagenomic Data

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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3 Resolving a Piping Vibration Problem by Installing Viscous Damper Supports

Authors: Carlos Herrera Sierralta, Husain M. Muslim, Meshal T. Alsaiari, Daniel Fischer

Abstract:

The vast majority of piping vibration problems in the Oil & Gas industry are provoked by the process flow characteristics which are basically related to the fluid properties, the type of service and its different operational scenarios. In general, the corrective actions recommended for flow induced vibration in piping systems can be grouped in two major areas: those which affect the excitation mechanisms typically associated to process variables, and those which affect the response mechanism of the pipework per se. Where possible the first option is to try to solve the flow induced problem from the excitation mechanism perspective. However, in producing facilities the approach of changing process parameters might not always be convenient as it could lead to reduction of production rates or it may require the shutdown of the system. That impediment might lead to a second option, which is to modify the response of the piping system to excitation generated by the process flow. In principle, the action of shifting the natural frequency of the system well above the frequency inherent to the process always favours the elimination, or considerably reduces the level of vibration experienced by the piping system. Tightening up the clearances at the supports (ideally zero gap) and adding new static supports at the system, are typical ways of increasing the natural frequency of the piping system. However, only stiffening the piping system may not be sufficient to resolve the vibration problem, and in some cases, it might not be feasible to implement it at all, as the available piping layout could create limitations on adding supports due to thermal expansion/contraction requirements. In these cases, utilization of viscous damper supports could be recommended as these devices can allow relatively large quasi-static movement of piping while providing sufficient capabilities of dissipating the vibration. Therefore, when correctly selected and installed, viscous damper supports can provide a significant effect on the response of the piping system over a wide range of frequencies. Viscous dampers cannot be used to support sustained, static loads. This paper shows over a real case example, a methodology which allows to determine the selection of the viscous damper supports via a dynamic analysis model. By implementing this methodology, it is possible to resolve piping vibration problems by adding new viscous dampers supports to the system. The methodology applied on this paper can be used to resolve similar vibration issues.

Keywords: dynamic analysis, flow induced vibration, piping supports, turbulent flow, slug flow, viscous damper

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2 Piezoelectric Bimorph Harvester Based on Different Lead Zirconate Titanate Materials to Enhance Energy Collection

Authors: Irene Perez-Alfaro, Nieves Murillo, Carlos Bernal, Daniel Gil-Hernandez

Abstract:

Nowadays, the increasing applicability of internet of things (IoT) systems has changed the way that the world around is perceived. The massive interconnection of systems by means of sensing, processing and communication, allows multitude of data to be at our fingertips. In this way, countless advances have been made in different fields such as personal care, predictive maintenance in industry, quality control in production processes, security, and in everything imaginable. However, all these electronic systems have in common the need to be electrically powered. In this context, batteries and wires are the most commonly used solutions, but they are not a definitive solution in some applications, because of the attainability, the serviceability, or the performance requirements. Therefore, the need arises to look for other types of solutions based on energy harvesting and long-life electronics. Energy Harvesting can be defined as the action of capturing energy from the environment and store it for an instantaneous use or later use. Among the materials capable of harvesting energy from the environment, such as thermoelectrics, electromagnetics, photovoltaics or triboelectrics, the most suitable is the piezoelectric material. The phenomenon of piezoelectricity is one of the most powerful sources for energy harvesting, ranging from a few micro wats to hundreds of wats, depending on certain factors such as material type, geometry, excitation frequency, mechanical and electrical configurations, among others. In this research work, an exhaustive study is carried out on how different types of piezoelectric materials and electrical configurations influence the maximum power that a bimorph harvester is able to extract from mechanical vibrations. A series of experiments has been carried out in which the manufactured bimorph specimens are excited under fixed inertial vibrational conditions. In addition, in order to evaluate the dependence of the maximum transferred power, different load resistors are tested. In this way, the pure active power that achieves the maximum power transfer can be approximated. In this paper, we present the design of low-cost energy harvesting solutions based on piezoelectric smart materials with tunable frequency. The results obtained show the differences in energy extraction between the PZT materials studied and their electrical configurations. The aim of this work is to gain a better understanding of the behavior of piezoelectric materials, and the design process of bimorph PZT harvesters to optimize environmental energy extraction.

Keywords: Bimorph harvesters, electrical impedance, energy harvesting, piezoelectric, smart material.

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1 Socio-Economic Determinants of Physical Activity of Non-Manual Workers, Including the Early Senior Group, from the City of Wroclaw in Poland

Authors: Daniel Puciato, Piotr Oleśniewicz, Julita Markiewicz-Patkowska, Krzysztof Widawski, Michał Rozpara, Władysław Mynarski, Agnieszka Gawlik, Małgorzata Dębska, Soňa Jandová

Abstract:

Physical activity as a part of people’s everyday life reduces the risk of many diseases, including those induced by lifestyle, e.g. obesity, type 2 diabetes, osteoporosis, coronary heart disease, degenerative arthritis, and certain types of cancer. That refers particularly to professionally active people, including the early senior group working on non-manual positions. The aim of the study is to evaluate the relationship between physical activity and the socio-economic status of non-manual workers from Wroclaw—one of the biggest cities in Poland, a model setting for such investigations in this part of Europe. The crucial problem in the research is to find out the percentage of respondents who meet the health-related recommendations of the World Health Organization (WHO) concerning the volume, frequency, and intensity of physical activity, as well as to establish if the most important socio-economic factors, such as gender, age, education, marital status, per capita income, savings and debt, determine the compliance with the WHO physical activity recommendations. During the research, conducted in 2013, 1,170 people (611 women and 559 men) aged 21–60 years were examined. A diagnostic poll method was applied to collect the data. Physical activity was measured with the use of the short form of the International Physical Activity Questionnaire with extended socio-demographic questions, i.e. concerning gender, age, education, marital status, income, savings or debts. To evaluate the relationship between physical activity and selected socio-economic factors, logistic regression was used (odds ratio statistics). Statistical inference was conducted on the adopted ex ante probability level of p<0.05. The majority of respondents met the volume of physical effort recommended for health benefits. It was particularly noticeable in the case of the examined men. The probability of compliance with the WHO physical activity recommendations was highest for workers aged 21–30 years with secondary or higher education who were single, received highest incomes and had savings. The results indicate the relations between physical activity and socio-economic status in the examined women and men. People with lower socio-economic status (e.g. manual workers) are physically active primarily at work, whereas those better educated and wealthier implement physical effort primarily in their leisure time. Among the investigated subjects, the youngest group of non-manual workers have the best chances to meet the WHO standards of physical activity. The study also confirms that secondary education has a positive effect on the public awareness on the role of physical activity in human life. In general, the analysis of the research indicates that there is a relationship between physical activity and some socio-economic factors of the respondents, such as gender, age, education, marital status, income per capita, and the possession of savings. Although the obtained results cannot be applied for the general population, they show some important trends that will be verified in subsequent studies conducted by the authors of the paper.

Keywords: International physical activity questionnaire, non-manual workers, physical activity, socio-economic factors, WHO.

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