Search results for: miRNA:mRNA target prediction

Authors: Yake Zhang, Peng Xu

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The development of building energy models (BEM) required for architectural design and analysis is a time-consuming and complex process, demanding a deep understanding and proficient use of simulation software. To streamline the generation of complex building energy models, this study proposes an automated method for generating building energy models using a large language model and the BEM library aimed at improving the efficiency of model generation. This method leverages a large language model to parse user-specified requirements for target building models, extracting key features such as building location, window-to-wall ratio, and thermal performance of the building envelope. The BEM library is utilized to retrieve energy models that match the target building’s characteristics, serving as reference information for the large language model to enhance the accuracy and relevance of the generated model, allowing for the creation of a building energy model that adapts to the user’s modeling requirements. This study enables the automatic creation of building energy models based on natural language inputs, reducing the professional expertise required for model development while significantly decreasing the time and complexity of manual configuration. In summary, this study provides an efficient and intelligent solution for building energy analysis and simulation, demonstrating the potential of a large language model in the field of building simulation and performance modeling.

Keywords: artificial intelligence, building energy modelling, building simulation, large language model

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Authors: Koe Han Beng, Khoo Boo Cheong

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The rising interest of stepped hull design has been led by the demand of more efficient high-speed boat. At the same time, the need of accurate prediction method for stepped planing hull is getting more important. By understanding the flow at high Froude number is the key in designing a practical step hull, the study surrounding stepped hull has been done mainly in the towing tank which is time-consuming and costly for initial design phase. Here the feasibility of predicting hydrodynamics of high-speed planing hull both with and without step using computational fluid dynamics (CFD) with the volume of fluid (VOF) methodology is studied in this work. First the flow around the prismatic body is analyzed, the force generated and its center of pressure are compared with available experimental and empirical data from the literature. The wake behind the transom on the keel line as well as the quarter beam buttock line are then compared with the available data, this is important since the afterbody flow of stepped hull is subjected from the wake of the forebody. Finally the calm water performance prediction of a conventional planing hull and its stepped version is then analyzed. Overset mesh methodology is employed in solving the dynamic equilibrium of the hull. The resistance, trim, and heave are then compared with the experimental data. The resistance is found to be predicted well and the dynamic equilibrium solved by the numerical method is deemed to be acceptable. This means that computational fluid dynamics will be very useful in further study on the complex flow around stepped hull and its potential usage in the design phase.

Keywords: planing hulls, stepped hulls, wake shape, numerical simulation, hydrodynamics

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Authors: Nikita Katyal, Shaurya Uppal

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This paper tackles the significant challenge of accurately classifying customers within a retailer’s customer base. Accurate classification is essential for developing targeted marketing strategies that effectively engage this important demographic. To address this issue, we propose a method that utilizes Large Language Models (LLMs). By employing LLMs, we analyze the metadata associated with product purchases derived from historical data to identify key product categories that act as distinguishing factors. These categories, such as baby food, eldercare products, or family-sized packages, offer valuable insights into the likely household composition of customers, including families with babies, families with kids/teenagers, families with pets, households caring for elders, or mixed households. We segment high-confidence customers into distinct categories by integrating historical purchase behavior with LLM-powered product classification. This paper asserts that life stage segmentation can significantly enhance e-commerce businesses’ ability to target the appropriate customers with tailored products and campaigns, thereby augmenting sales and improving customer retention. Additionally, the paper details the data sources, model architecture, and evaluation metrics employed for the segmentation task.

Keywords: LLMs, segmentation, product tags, fine-tuning, target segments, marketing communication

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Authors: Muhammad Luthfi, Sutikno Sutikno, Purhadi Purhadi

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Weather forecast has necessarily been improved to provide the communities an accurate and objective prediction as well. To overcome such issue, the numerical-based weather forecast was extensively developed to reduce the subjectivity of forecast. Yet the Numerical Weather Predictions (NWPs) outputs are unfortunately issued without taking dynamical weather behavior and local terrain features into account. Thus, NWPs outputs are not able to accurately forecast the weather quantities, particularly for medium and long range forecast. The aim of this research is to aid and extend the development of ensemble forecast for Meteorology, Climatology, and Geophysics Agency of Indonesia. Ensemble method is an approach combining various deterministic forecast to produce more reliable one. However, such forecast is biased and uncalibrated due to its underdispersive or overdispersive nature. As one of the parametric methods, Bayesian Model Averaging (BMA) generates the calibrated ensemble forecast and constructs predictive PDF for specified period. Such method is able to utilize ensemble of any size but does not take spatial correlation into account. Whereas space dependencies involve the site of interest and nearby site, influenced by dynamic weather behavior. Meanwhile, Geostatistical Output Perturbation (GOP) reckons the spatial correlation to generate future weather quantities, though merely built by a single deterministic forecast, and is able to generate an ensemble of any size as well. This research conducts both BMA and GOP to generate the calibrated ensemble forecast for the daily temperature at few meteorological sites nearby Indonesia international airport.

Keywords: Bayesian Model Averaging, ensemble forecast, geostatistical output perturbation, numerical weather prediction, temperature

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Authors: Manuela Villani, Anila Xhahysa, Christopher Brooks, Marco Pagani

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The geological structure of Western Balkans is strongly affected by the collision between Adria microplate and the southwestern Euroasia margin, resulting in a considerably active seismic region. The Harmonization of Seismic Hazard Maps in the Western Balkan Countries Project (BSHAP) (2007-2011, 2012-2015) by NATO supported the preparation of new seismic hazard maps of the Western Balkan, but when inspecting the seismic hazard models produced later by these countries on a national scale, significant differences in design PGA values are observed in the border, for instance, North Albania-Montenegro, South Albania- Greece, etc. Considering the fact that the catalogues were unified and seismic sources were defined within BSHAP framework, obviously, the differences arise from the Ground Motion Prediction Equations selection, which are generally the component with highest impact on the seismic hazard assessment. At the time of the project, a modest database was present, namely 672 three-component records, whereas nowadays, this strong motion database has increased considerably up to 20,939 records with Mw ranging in the interval 3.7-7 and epicentral distance distribution from 0.47km to 490km. Statistical analysis of the strong motion database showed the lack of recordings in the moderate-to-large magnitude and short distance ranges; therefore, there is need to re-evaluate the Ground Motion Prediction Equation in light of the recently updated database and the new generations of GMMs. In some cases, it was observed that some events were more extensively documented in one database than the other, like the 1979 Montenegro earthquake, with a considerably larger number of records in the BSHAP Analogue SM database when compared to ESM23. Therefore, the strong motion flat-file provided from the Harmonization of Seismic Hazard Maps in the Western Balkan Countries Project was merged with the ESM23 database for the polygon studied in this project. After performing the preliminary residual analysis, the candidate GMPE-s were identified. This process was done using the GMPE performance metrics available within the SMT in the OpenQuake Platform. The Likelihood Model and Euclidean Distance Based Ranking (EDR) were used. Finally, for this study, a GMPE logic tree was selected and following the selection of candidate GMPEs, model weights were assigned using the average sample log-likelihood approach of Scherbaum.

Keywords: residual analysis, GMPE, western balkan, strong motion, openquake

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Authors: Marina Passero, Tianhua Zhai, Zuyi (Jacky) Huang

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Alzheimer’s disease has become a major public health issue, as indicated by the increasing populations of Americans living with Alzheimer’s disease. After decades of extensive research in Alzheimer’s disease, only seven drugs have been approved by Food and Drug Administration (FDA) to treat Alzheimer’s disease. Five of these drugs were designed to treat the dementia symptoms, and only two drugs (i.e., Aducanumab and Lecanemab) target the progression of Alzheimer’s disease, especially the accumulation of amyloid-b plaques. However, controversial comments were raised for the accelerated approvals of either Aducanumab or Lecanemab, especially with concerns on safety and side effects of these two drugs. There is still an urgent need for further drug discovery to target the biological processes involved in the progression of Alzheimer’s disease. Excessive cholesterol has been found to accumulate in the brain of those with Alzheimer’s disease. Cholesterol can be synthesized in both the blood and the brain, but the majority of biosynthesis in the adult brain takes place in astrocytes and is then transported to the neurons via ApoE. The blood brain barrier separates cholesterol metabolism in the brain from the rest of the body. Various proteins contribute to the metabolism of cholesterol in the brain, which offer potential targets for Alzheimer’s treatment. In the astrocytes, SREBP cleavage-activating protein (SCAP) binds to Sterol Regulatory Element-binding Protein 2 (SREBP2) in order to transport the complex from the endoplasmic reticulum to the Golgi apparatus. Cholesterol is secreted out of the astrocytes by ATP-Binding Cassette A1 (ABCA1) transporter. Lipoprotein receptors such as triggering receptor expressed on myeloid cells 2 (TREM2) internalize cholesterol into the microglia, while lipoprotein receptors such as Low-density lipoprotein receptor-related protein 1 (LRP1) internalize cholesterol into the neuron. Cytochrome P450 Family 46 Subfamily A Member 1 (CYP46A1) converts excess cholesterol to 24S-hydroxycholesterol (24S-OHC). Cholesterol has been approved for its direct effect on the production of amyloid-beta and tau proteins. The addition of cholesterol to the brain promotes the activity of beta-site amyloid precursor protein cleaving enzyme 1 (BACE1), secretase, and amyloid precursor protein (APP), which all aid in amyloid-beta production. The reduction of cholesterol esters in the brain have been found to reduce phosphorylated tau levels in mice. In this work, a computational pipeline was developed to identify the protein targets involved in cholesterol regulation in brain and further to identify chemical compounds as the inhibitors of a selected protein target. Since extensive evidence shows the strong correlation between brain cholesterol regulation and Alzheimer’s disease, a detailed literature review on genes or pathways related to the brain cholesterol synthesis and regulation was first conducted in this work. An interaction network was then built for those genes so that the top gene targets were identified. The involvement of these genes in Alzheimer’s disease progression was discussed, which was followed by the investigation of existing clinical trials for those targets. A ligand-protein docking program was finally developed to screen 1.5 million chemical compounds for the selected protein target. A machine learning program was developed to evaluate and predict the binding interaction between chemical compounds and the protein target. The results from this work pave the way for further drug discovery to regulate brain cholesterol to combat Alzheimer’s disease.

Keywords: Alzheimer’s disease, drug discovery, ligand-protein docking, gene-network analysis, cholesterol regulation

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Authors: Yezli-Touiker Samira, Amrani-Kirane Leila, Soltani Mazouni Nadia

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Due to secondary effects of conventional insecticides on the environment, the agrochemical research has resulted in the discovery of novel molecules. That research work will help in the development of a new group of pesticides that may be cheaper and less hazardous to the environment and non-target organisms which is the main desired outcome of the present work. Angiotensin-converting enzyme as a target for the development of novel insect growth regulators. Captopril is an inhibitor of angiotensin converting enzyme (ACE) it was tested in vivo by topical application on reproduction of Ephestia kuehniella Zeller (Lepidoptera: Pyralidae). The compound is diluted in acetone and applied topically to newly emerged pupae (10µg/ 2µl). The effects of this molecule was studied,on the biochemistry of ovary (on amounts nucleic acid, proteins, the qualitative analysis of the ovarian proteins and the reproductive potential (duration of the pre-oviposition, duration of the oviposition, number of eggs laid and hatching percentage). Captopril reduces significantly quantity of ovarian proteins and nucleic acid. The electrophoresis profile reveals the absence of tree bands at the treated series. This molecule reduced the duration of the oviposition period, the fecundity and the eggviability.

Keywords: environment, ephestia kuehniella, captopril, reproduction, the agrochemical research

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Authors: Tie-Gang Wang, De-Qiang Meng, Yan-Mei Liu

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Ternary AlCrN coatings were widely used to prolong cutting tool life because of their high hardness and excellent abrasion resistance. However, the friction between the workpiece and cutter surface was increased remarkably during machining difficult-to-cut materials (such as superalloy, titanium, etc.). As a result, a lot of cutting heat was generated and cutting tool life was shortened. In this work, an appropriate amount of solid lubricant MoS₂ was added into the AlCrN coating to reduce the friction between the tool and the workpiece. A series of Al-Cr-N/MoS₂ self-lubricating coatings with different MoS₂ contents were prepared by high power impulse magnetron sputtering (HiPIMS) and pulsed direct current magnetron sputtering (Pulsed DC) compound system. The MoS₂ content in the coatings was changed by adjusting the sputtering power of the MoS₂ target. The composition, structure and mechanical properties of the Al-Cr-N/MoS2 coatings were systematically evaluated by energy dispersive spectrometer, scanning electron microscopy, X-ray photoelectron spectroscopy, X-ray diffractometer, nano-indenter tester, scratch tester, and ball-on-disk tribometer. The results indicated the lubricant content played an important role in the coating properties. As the sputtering power of the MoS₂ target was 0.1 kW, the coating possessed the highest hardness 14.1GPa, the highest critical load 44.8 N, and the lowest wear rate 4.4×10−3μm2/N.

Keywords: self-lubricating coating, Al-Cr-N/MoS₂ coating, wear rate, friction coefficient

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Authors: Abdolghani Ebrahimi, Diego Klabjan, Chenxi Ge, Daniela Ladner, Parker Stride

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In this work, we use machine learning and novel data analysis techniques to predict the one-year mortality of cirrhotic patients. Data from 2,322 patients with liver cirrhosis are collected at a single medical center. Different machine learning models are applied to predict one-year mortality. A comprehensive feature space including demographic information, comorbidity, clinical procedure and laboratory tests is being analyzed. A temporal pattern mining technic called Frequent Subgraph Mining (FSM) is being used. Model for End-stage liver disease (MELD) prediction of mortality is used as a comparator. All of our models statistically significantly outperform the MELD-score model and show an average 10% improvement of the area under the curve (AUC). The FSM technic itself does not improve the model significantly, but FSM, together with a machine learning technique called an ensemble, further improves the model performance. With the abundance of data available in healthcare through electronic health records (EHR), existing predictive models can be refined to identify and treat patients at risk for higher mortality. However, due to the sparsity of the temporal information needed by FSM, the FSM model does not yield significant improvements. To the best of our knowledge, this is the first work to apply modern machine learning algorithms and data analysis methods on predicting one-year mortality of cirrhotic patients and builds a model that predicts one-year mortality significantly more accurate than the MELD score. We have also tested the potential of FSM and provided a new perspective of the importance of clinical features.

Keywords: machine learning, liver cirrhosis, subgraph mining, supervised learning

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Authors: Yan Zhang

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Predictive maintenance is a technique to predict when an in-service machine will fail so that maintenance can be planned in advance. Analytics-driven predictive maintenance is gaining increasing attention in many industries such as manufacturing, utilities, aerospace, etc., along with the emerging demand of Internet of Things (IoT) applications and the maturity of technologies that support Big Data storage and processing. This study aims to build an end-to-end analytics solution that includes both real-time machine condition monitoring and machine learning based predictive analytics capabilities. The goal is to showcase a general predictive maintenance solution architecture, which suggests how the data generated from field machines can be collected, transmitted, stored, and analyzed. We use a publicly available aircraft engine run-to-failure dataset to illustrate the streaming analytics component and the batch failure prediction component. We outline the contributions of this study from four aspects. First, we compare the predictive maintenance problems from the view of the traditional reliability centered maintenance field, and from the view of the IoT applications. When evolving to the IoT era, predictive maintenance has shifted its focus from ensuring reliable machine operations to improve production/maintenance efficiency via any maintenance related tasks. It covers a variety of topics, including but not limited to: failure prediction, fault forecasting, failure detection and diagnosis, and recommendation of maintenance actions after failure. Second, we review the state-of-art technologies that enable a machine/device to transmit data all the way through the Cloud for storage and advanced analytics. These technologies vary drastically mainly based on the power source and functionality of the devices. For example, a consumer machine such as an elevator uses completely different data transmission protocols comparing to the sensor units in an environmental sensor network. The former may transfer data into the Cloud via WiFi directly. The latter usually uses radio communication inherent the network, and the data is stored in a staging data node before it can be transmitted into the Cloud when necessary. Third, we illustrate show to formulate a machine learning problem to predict machine fault/failures. By showing a step-by-step process of data labeling, feature engineering, model construction and evaluation, we share following experiences: (1) what are the specific data quality issues that have crucial impact on predictive maintenance use cases; (2) how to train and evaluate a model when training data contains inter-dependent records. Four, we review the tools available to build such a data pipeline that digests the data and produce insights. We show the tools we use including data injection, streaming data processing, machine learning model training, and the tool that coordinates/schedules different jobs. In addition, we show the visualization tool that creates rich data visualizations for both real-time insights and prediction results. To conclude, there are two key takeaways from this study. (1) It summarizes the landscape and challenges of predictive maintenance applications. (2) It takes an example in aerospace with publicly available data to illustrate each component in the proposed data pipeline and showcases how the solution can be deployed as a live demo.

Keywords: Internet of Things, machine learning, predictive maintenance, streaming data

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Authors: Sharon Yunger, Liat Altman, Yuval Garini, Yaron Shav-Tal

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Understanding the dynamics of transcription in living cells has improved since the development of quantitative fluorescence-based imaging techniques. We established a method for following transcription from a single copy gene in living cells. A gene tagged with MS2 repeats, used for mRNA tagging, in its 3' UTR was integrated into a single genomic locus. The actively transcribing gene was detected and analyzed by fluorescence in situ hybridization (FISH) and live-cell imaging. Several cell clones were created that differed in the promoter regulating the gene. Thus, comparative analysis could be obtained without the risk of different position effects at each integration site. Cells in S/G2 phases could be detected exhibiting two adjacent transcription sites on sister chromatids. A sharp reduction in the transcription levels was observed as cells progressed along the cell cycle. We hypothesized that a change in chromatin structure acts as a general mechanism during the cell cycle leading to down-regulation in the activity of some genes. We addressed this question by treating the cells with chromatin decondensing agents. Quantifying and imaging the treated cells suggests that chromatin structure plays a role both in regulating transcriptional levels along the cell cycle, as well as in limiting an active gene from reaching its maximum transcription potential at any given time. These results contribute to understanding the role of chromatin as a regulator of gene expression.

Keywords: cell cycle, living cells, nucleus, transcription

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Authors: Juan Jose Filgueira, Daniela Londono-Serna, Liliana Maria Hoyos

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Carnation (Dianthus caryophyllus) is one of the most important products of exportation in the floriculture industry worldwide. Fusariosis is the disease that causes the highest losses on farms, in particular the one produced by Fusarium oxysporum f.sp. dianthi, called vascular wilt. Gene identification and metabolic routes of the genes that participate in the building of the plant response to Fusarium are some of the current targets in the carnation breeding industry. The techniques for the identifying of resistant genes in the plants, is the analysis of the transcriptome obtained during the host-pathogen interaction. In this work, we report the cell transcriptome of different varieties of carnation that present differential response from Fusarium oxysporum f.sp. dianthi attack. The cells of the different hybrids produced in the outbreeding program were cultured in vitro and elicited with the parasite in a dual culture. The isolation and purification of mRNA was achieved by using affinity chromatography Oligo dT columns and the transcriptomes were obtained by using Illumina NGS techniques. A total of 85,669 unigenes were detected in all the transcriptomes analyzed and 31,000 annotations were found in databases, which correspond to 36.2%. The library construction of genic expression techniques used, allowed to recognize the variation in the expression of genes such as Germin-like protein, Glycosyl hydrolase family and Cinnamate 4-hydroxylase. These have been reported in this study for the first time as part of the response mechanism to the presence of Fusarium oxysporum.

Keywords: Carnation, Fusarium, vascular wilt, transcriptome

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Authors: Jingsong Ma

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In political translation, ideology plays an important role in conveying implications accurately. Ideological collisions can occur in political translation when there existdifferences of political environments embedded in the translingual political texts in both source and target languages. To reach an accurate translationrequires the translatorto understand the ideologies implied in (and often transcending) the texts. This paper explores the conditions, procedure, and purpose of processingideological collision and resolution of such issues in political translation. These points will be elucidated by case studies of translating English and Chinese political texts. First, there are specific political terminologies in certain political environments. These terminological peculiarities in one language are often determined by ideological elements rather than by syntactical and semantical understanding. The translation of these ideological-loaded terminologiesis a process and operation consisting of understanding the ideological context, including cultural, historical, and political situations. This will be explained with characteristic Chinese political terminologies and their renderings in English. Second, when the ideology in the source language fails to match with the ideology in the target language, the decisions to highlight or disregard these conflicts are shaped by power relations, political engagement, social context, etc. It thus is necessary to go beyond linguisticanalysis of the context by deciphering ideology in political documents to provide a faithful or equivalent rendering of certain messages. Finally, one of the practical issues is about equivalence in political translation by redefining the notion of faithfulness and retainment of ideological messages in the source language in translations of political texts. To avoid distortion, the translator should be liberated from grip the literal meaning, instead diving into functional meanings of the text.

Keywords: translation, ideology, politics, society

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Authors: Priyal Motwani

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The current market for bamboo products in India is about Rs. 21000 crores and is highly unorganised and fragmented. In this study, we have closely analysed the structure and functions of a major bamboo craft based organisation in Kerela, India and elaborated about its value chain, product mix, pricing strategy and supply chain, collaborations and competitive landscape. We have identified six major bottlenecks that are prevalent in such organisations, based on the Indian context, in relation to their product mix, asset management, and supply chain- corresponding waste management and retail network. The study has identified that the target customers for the bamboo based products and alternative revenue streams (eco-tourism, microenterprises, training), by carrying out secondary and primary research (5000 sample space), that can boost the existing revenue by 150%. We have then recommended an optimum product mix-covering premium, medium and low valued processing, for medium sized bamboo based organisations, in accordance with their capacity to maximize their revenue potential. After studying such organisations and their counter parts, the study has established an optimum retail network, considering B2B, B2C physical and online retail, to maximize their sales to their target groups. On the basis of the results obtained from the analysis of the future and present trends, our study gives recommendations to improve the revenue potential of bamboo based organisation in India and promote sustainability.

Keywords: bamboo, bottlenecks, optimization, product mix, retail network, value chain

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Authors: Cristian Pauna

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Trading the financial markets is a widespread activity today. A large number of investors, companies, public of private funds are buying and selling every day in order to make profit. Algorithmic trading is the prevalent method to make the trade decisions after the electronic trading release. The orders are sent almost instantly by computers using mathematical models. This paper will present a price prediction methodology based on a multi-dimensional neural network. Using the Fisher transform, the neural network will be instructed for a low-latency auto-adaptive process in order to predict the price evolution for the next period of time. The model is designed especially for algorithmic trading and uses the real-time price series. It was found that the characteristics of the Fisher function applied at the nodes scale level can generate reliable trading signals using the neural network methodology. After real time tests it was found that this method can be applied in any timeframe to trade the financial markets. The paper will also include the steps to implement the presented methodology into an automated trading system. Real trading results will be displayed and analyzed in order to qualify the model. As conclusion, the compared results will reveal that the neural network methodology applied together with the Fisher transform at the nodes level can generate a good price prediction and can build reliable trading signals for algorithmic trading.

Keywords: algorithmic trading, automated trading systems, financial markets, high-frequency trading, neural network

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Authors: Aadiv Shah, Hari Nair, Vedant Mittal, Alice Cheeran

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Present-day agricultural practices such as blanket spraying not only lead to excessive usage of pesticides but also harm the overall crop yield. This paper introduces an algorithm to optimize the traversal of an unmanned aerial vehicle (UAV) in constrained environments. The proposed system focuses on the agricultural application of targeted spraying for locust elimination. Given a satellite image of a farm, target zones that are prone to locust swarm formation are detected through the calculation of the normalized difference vegetation index (NDVI). This is followed by determining the optimal path for traversal of a UAV through these target zones using the proposed algorithm in order to perform pesticide spraying in the most efficient manner possible. Unlike the classic travelling salesman problem involving point-to-point optimization, the proposed algorithm determines an optimal path for multiple regions, independent of its geometry. Finally, the paper explores the idea of implementing reinforcement learning to model complex environmental behaviour and make the path planning mechanism for UAVs agnostic to external environment changes. This system not only presents a solution to the enormous losses incurred due to locust attacks but also an efficient way to automate agricultural practices across the globe in order to improve farmer ergonomics.

Keywords: locust, NDVI, optimization, path planning, reinforcement learning, UAV

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Authors: Fatemeh Zeinali Sehrig

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Background: miRNAs play an important role in the post-transcriptional regulation of genes, including genes involved in DNA methylation (DNMTs), and are also important regulators of oncogenic pathways. The study of microRNAs and DNMTs in breast cancer allows the development of targeted treatments and early detection of this cancer. Methods and Materials: Clinical Patients and Samples: Institutional guidelines, including ethical approval and informed consent, were followed by the Ethics Committee (Ethics code: IR.IAU.TABRIZ.REC.1401.063) of Tabriz Azad University, Tabriz, Iran. In this study, tissues of 100 patients with breast cancer and tissues of 100 healthy women were collected from Noor Nejat Hospital in Tabriz. The basic characteristics of the patients with breast cancer included: 1)Tumor grade(Grade 3 = 5%, Grade 2 = 87.5%, Grade 1 = 7.5%), 2)Lymph node(Yes = 87.5%, No = 12.5%), 3)Family cancer history(Yes = 47.5%, No = 41.3%, Unknown = 11.2%), 4) Abortion history(Yes = 36.2%).In silico methods (data gathering, process, and build networks): Gene Expression Omnibus (GEO), a high-throughput genomic database, was queried for miRNAs expression profiles in breast cancer. For Experimental protocol Tissue Processing, Total RNA isolation, complementary DNA(cDNA) synthesis, and quantitative real time PCR (QRT-PCR) analysis were performed. Results: In the present study, we found significant (p.value<0.05) changes in the expression level of miRNAs and DNMTs in patients with breast cancer. In bioinformatics studies, the GEO microarray data set, similar to qPCR results, showed a decreased expression of miRNAs and increased expression of DNMTs in breast cancer. Conclusion: According to the results of the present study, which showed a decrease in the expression of miRNAs and DNMTs in breast cancer, it can be said that these genes can be used as important diagnostic and therapeutic biomarkers in breast cancer.

Keywords: gene expression omnibus, microarray dataset, breast cancer, miRNA, DNMT (DNA methyltransferases)

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Authors: Pawel Kiper, Alfonc Baba, Mahmoud Alhelou, Giorgia Pregnolato, Michela Agostini, Andrea Turolla

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Impairment of cervical spine mobility is often related to pain triggered by musculoskeletal disorders or direct traumatic injuries of the spine. To date, these disorders are assessed with goniometers and inclinometers, which are the most popular devices used in clinical settings. Nevertheless, these technologies usually allow measurement of no more than two-dimensional range of motion (ROM) quotes in static conditions. Conversely, the wide use of motion tracking systems able to measure 3 to 6 degrees of freedom dynamically, while performing standard ROM assessment, are limited due to technical complexities in preparing the setup and high costs. Thus, motion tracking systems are primarily used in research. These systems are an integral part of virtual reality (VR) technologies, which can be used for measuring spine mobility. To our knowledge, the accuracy of VR measure has not yet been studied within virtual environments. Thus, the aim of this study was to test the reliability of a protocol for the assessment of sensorimotor function of the cervical spine in a population of healthy subjects and to compare whether using immersive or non-immersive VR for visualization affects the performance. Both VR assessments consisted of the same five exercises and random sequence determined which of the environments (i.e. immersive or non-immersive) was used as first assessment. Subjects were asked to perform head rotation (right and left), flexion, extension and lateral flexion (right and left side bending). Each movement was executed five times. Moreover, the participants were invited to perform head reaching movements i.e. head movements toward 8 targets placed along a circular perimeter each 45°, visualized one-by-one in random order. Finally, head repositioning movement was obtained by head movement toward the same 8 targets as for reaching and following reposition to the start point. Thus, each participant performed 46 tasks during assessment. Main measures were: ROM of rotation, flexion, extension, lateral flexion and complete kinematics of the cervical spine (i.e. number of completed targets, time of execution (seconds), spatial length (cm), angle distance (°), jerk). Thirty-five healthy participants (i.e. 14 males and 21 females, mean age 28.4±6.47) were recruited for the cervical spine assessment with immersive and non-immersive VR environments. Comparison analysis demonstrated that: head right rotation (p=0.027), extension (p=0.047), flexion (p=0.000), time (p=0.001), spatial length (p=0.004), jerk target (p=0.032), trajectory repositioning (p=0.003), and jerk target repositioning (p=0.007) were significantly better in immersive than non-immersive VR. A regression model showed that assessment in immersive VR was influenced by height, trajectory repositioning (p<0.05), and handedness (p<0.05), whereas in non-immersive VR performance was influenced by height, jerk target (p=0.002), head extension, jerk target repositioning (p=0.002), and by age, head flex/ext, trajectory repositioning, and weight (p=0.040). The results of this study showed higher accuracy of cervical spine assessment when executed in immersive VR. The assessment of ROM and kinematics of the cervical spine can be affected by independent and dependent variables in both immersive and non-immersive VR settings.

Keywords: virtual reality, cervical spine, motion analysis, range of motion, measurement validity

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Authors: Soujanya Pasumarthi

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Inverse docking is a relatively new technique that has been used to identify potential receptor targets of small molecules. Our docking software package MDock is well suited for such an application as it is both computationally efficient, yet simultaneously shows adequate results in binding affinity predictions and enrichment tests. As a validation study, we present the first stage results of an inverse-docking study which seeks to identify potential direct targets of PRIMA-1. PRIMA-1 is well known for its ability to restore mutant p53's tumor suppressor function, leading to apoptosis in several types of cancer cells. For this reason, we believe that potential direct targets of PRIMA-1 identified in silico should be experimentally screened for their ability to inhibitcancer cell growth. The highest-ranked human protein of our PRIMA-1 docking results is oxidosqualene cyclase (OSC), which is part of the cholesterol synthetic pathway. The results of two followup experiments which treat OSC as a possible anti-cancer target are promising. We show that both PRIMA-1 and Ro 48-8071, a known potent OSC inhibitor, significantly reduce theviability of BT-474 breast cancer cells relative to normal mammary cells. In addition, like PRIMA-1, we find that Ro 48-8071 results in increased binding of mutant p53 to DNA in BT- 474cells (which highly express p53). For the first time, Ro 48-8071 is shown as a potent agent in killing human breast cancer cells. The potential of OSC as a new target for developing anticancer therapies is worth further investigation.

Keywords: inverse docking, in silico screening, protein-ligand interactions, molecular docking

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Authors: Aid Abdelkrim

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A method of fatigue damage accumulation based upon application of energy parameters of the fatigue process is proposed in the paper. Using this model is simple, it has no parameter to be determined, it requires only the knowledge of the curve W–N (W: strain energy density N: number of cycles at failure) determined from the experimental Wöhler curve. To examine the performance of nonlinear models proposed in the estimation of fatigue damage and fatigue life of components under random loading, a batch of specimens made of 6082 T 6 aluminium alloy has been studied and some of the results are reported in the present paper. The paper describes an algorithm and suggests a fatigue cumulative damage model, especially when random loading is considered. This work contains the results of uni-axial random load fatigue tests with different mean and amplitude values performed on 6082T6 aluminium alloy specimens. The proposed model has been formulated to take into account the damage evolution at different load levels and it allows the effect of the loading sequence to be included by means of a recurrence formula derived for multilevel loading, considering complex load sequences. It is concluded that a ‘damaged stress interaction damage rule’ proposed here allows a better fatigue damage prediction than the widely used Palmgren–Miner rule, and a formula derived in random fatigue could be used to predict the fatigue damage and fatigue lifetime very easily. The results obtained by the model are compared with the experimental results and those calculated by the most fatigue damage model used in fatigue (Miner’s model). The comparison shows that the proposed model, presents a good estimation of the experimental results. Moreover, the error is minimized in comparison to the Miner’s model.

Keywords: damage accumulation, energy model, damage indicator, variable loading, random loading

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Authors: Rohit Dey, Sailendra Karra

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This paper aims at solving the problem of multi-target searching in a Global Positioning System (GPS) denied environment using swarm robots with limited sensing and communication abilities. Typically, existing swarm-based search algorithms rely on the presence of a global coordinate system (vis-à-vis, GPS) that is shared by the entire swarm which, in turn, limits its application in a real-world scenario. This can be attributed to the fact that robots in a swarm need to share information among themselves regarding their location and signal from targets to decide their future course of action but this information is only meaningful when they all share the same coordinate frame. The paper addresses this very issue by eliminating any dependency of a search algorithm on the need of a predetermined global coordinate frame by the unification of the relative coordinate of individual robots when within the communication range, therefore, making the system more robust in real scenarios. Our algorithm assumes that all the robots in the swarm are equipped with range and bearing sensors and have limited sensing range and communication abilities. Initially, every robot maintains their relative coordinate frame and follow Levy walk random exploration until they come in range with other robots. When two or more robots are within communication range, they share sensor information and their location w.r.t. their coordinate frames based on which we unify their coordinate frames. Now they can share information about the areas that were already explored, information about the surroundings, and target signal from their location to make decisions about their future movement based on the search algorithm. During the process of exploration, there can be several small groups of robots having their own coordinate systems but eventually, it is expected for all the robots to be under one global coordinate frame where they can communicate information on the exploration area following swarm search techniques. Using the proposed method, swarm-based search algorithms can work in a real-world scenario without GPS and any initial information about the size and shape of the environment. Initial simulation results show that running our modified-Particle Swarm Optimization (PSO) without global information we can still achieve the desired results that are comparable to basic PSO working with GPS. In the full paper, we plan on doing the comparison study between different strategies to unify the coordinate system and to implement them on other bio-inspired algorithms, to work in GPS denied environment.

Keywords: bio-inspired search algorithms, decentralized control, GPS denied environment, swarm robotics, target searching, unifying coordinate systems

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Authors: Shilpa Khobragade, Carlos Da Silva Granja, Niklas Sandström, Igor Efimov, Victor P. Ostanin, Wouter van der Wijngaart, David Klenerman, Sourav K. Ghosh

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Rapid, label-free and direct detection of pathogenic bacteria is critical for the prevention of disease outbreaks. This paper for the first time attempts to probe the nonlinear acoustic response of quartz crystal resonator (QCR) functionalized with specific DNA aptamers for direct detection and quantification of viable E. coli KCTC 2571 bacteria. DNA aptamers were immobilized through biotin and streptavidin conjugation, onto the gold surface of QCR to capture the target bacteria and the detection was accomplished by shift in amplitude of the peak 3f signal (3 times the drive frequency) upon binding, when driven near fundamental resonance frequency. The developed nonlinear acoustic aptasensor system demonstrated better reliability than conventional resonance frequency shift and energy dissipation monitoring that were recorded simultaneously. This sensing system could directly detect 10⁽⁵⁾ cells/mL target bacteria within 30 min or less and had high specificity towards E. coli KCTC 2571 bacteria as compared to the same concentration of S.typhi bacteria. Aptasensor response was observed for the bacterial suspensions ranging from 10⁽⁵⁾-10⁽⁸⁾ cells/mL. Conclusively, this nonlinear acoustic aptasensor is simple to use, gives real-time output, cost-effective and has the potential for rapid, specific, label-free direction detection of bacteria.

Keywords: acoustic, aptasensor, detection, nonlinear

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Authors: Zoran Šverko, Saša Vlahinić, Nino Stojković, Ivan Markovinović

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In this article, the classification of target letters is performed using data from the EEG P300 Speller paradigm. Neural networks trained with the results of dynamic connectivity analysis between different brain regions are used for classification. Dynamic connectivity analysis is based on the adaptive window size and the imaginary part of the complex Pearson correlation coefficient. Brain dynamics are analysed using the relative intersection of confidence intervals for the imaginary component of the complex Pearson correlation coefficient method (RICI-imCPCC). The RICI-imCPCC method overcomes the shortcomings of currently used dynamical connectivity analysis methods, such as the low reliability and low temporal precision for short connectivity intervals encountered in constant sliding window analysis with wide window size and the high susceptibility to noise encountered in constant sliding window analysis with narrow window size. This method overcomes these shortcomings by dynamically adjusting the window size using the RICI rule. This method extracts information about brain connections for each time sample. Seventy percent of the extracted brain connectivity information is used for training and thirty percent for validation. Classification of the target word is also done and based on the same analysis method. As far as we know, through this research, we have shown for the first time that dynamic connectivity can be used as a parameter for classifying EEG signals.

Keywords: dynamic connectivity analysis, EEG, neural networks, Pearson correlation coefficients

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Authors: Mustafa Salman, Nurcan Cetinkaya, Zehra Selcuk, Bugra Genc

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The objectives of the present study were to estimate the microbial-N flow to the small intestine and to predict the digestible organic matter intake (DOMI) in grazing Karayaka sheep based on urinary excretion of purine derivatives (xanthine, hypoxanthine, uric acid, and allantoin) by the use of spot urine sampling under field conditions. In the trial, 10 Karayaka sheep from 2 to 3 years of age were used. The animals were grazed in a pasture for ten months and fed with concentrate and vetch plus oat hay for the other two months (January and February) indoors. Highly significant linear and cubic relationships (P<0.001) were found among months for purine derivatives index, purine derivatives excretion, purine derivatives absorption, microbial-N and DOMI. Through urine sampling and the determination of levels of excreted urinary PD and Purine Derivatives / Creatinine ratio (PDC index), microbial-N values were estimated and they indicated that the protein nutrition of the sheep was insufficient. In conclusion, the prediction of protein nutrition of sheep under the field conditions may be possible with the use of spot urine sampling, urinary excreted PD and PDC index. The mean purine derivative levels in spot urine samples from sheep were highest in June, July and October. Protein nutrition of pastured sheep may be affected by weather changes, including rainfall. Spot urine sampling may useful in modeling the feed consumption of pasturing sheep. However, further studies are required under different field conditions with different breeds of sheep to develop spot urine sampling as a model.

Keywords: Karayaka sheep, spot sampling, urinary purine derivatives, PDC index, microbial-N, feed intake

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Authors: Jelena S. Kiurski, Vesna S. Kecić, Snežana M. Aksentijević

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The identification and evaluation of organic and inorganic pollutants were performed in a flexographic facility in Novi Sad, Serbia. Air samples were collected and analyzed in situ, during 4-hours working time at five sampling points by the mobile gas chromatograph and ozonometer at the printing of collagen casing. Experimental results showed that the concentrations of isopropyl alcohol, acetone, total volatile organic compounds and ozone varied during the sampling times. The highest average concentrations of 94.80 ppm and 102.57 ppm were achieved at 200 minutes from starting the production for isopropyl alcohol and total volatile organic compounds, respectively. The mutual dependences between target hazardous and microclimate parameters were confirmed using a multiple linear regression model with software package STATISTICA 10. Obtained multiple coefficients of determination in the case of ozone and acetone (0.507 and 0.589) with microclimate parameters indicated a moderate correlation between the observed variables. However, a strong positive correlation was obtained for isopropyl alcohol and total volatile organic compounds (0.760 and 0.852) with microclimate parameters. Higher values of parameter F than F_critical for all examined dependences indicated the existence of statistically significant difference between the concentration levels of target pollutants and microclimates parameters. Given that, the microclimate parameters significantly affect the emission of investigated gases and the application of eco-friendly materials in production process present a necessity.

Keywords: flexographic printing, indoor air, multiple regression analysis, pollution emission

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Authors: M. D. Haneef, R. B. Randall, Z. Peng

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Journal bearings used in IC engines are prone to premature failures and are likely to fail earlier than the rated life due to highly impulsive and unstable operating conditions and frequent starts/stops. Vibration signature extraction and wear debris analysis techniques are prevalent in the industry for condition monitoring of rotary machinery. However, both techniques involve a great deal of technical expertise, time and cost. Limited literature is available on the application of these techniques for fault detection in reciprocating machinery, due to the complex nature of impact forces that confounds the extraction of fault signals for vibration based analysis and wear prediction. This work is an extension of a previous study, in which an engine simulation model was developed using a MATLAB/SIMULINK program, whereby the engine parameters used in the simulation were obtained experimentally from a Toyota 3SFE 2.0 litre petrol engines. Simulated hydrodynamic bearing forces were used to estimate vibrations signals and envelope analysis was carried out to analyze the effect of speed, load and clearance on the vibration response. Three different loads 50/80/110 N-m, three different speeds 1500/2000/3000 rpm, and three different clearances, i.e., normal, 2 times and 4 times the normal clearance were simulated to examine the effect of wear on bearing forces. The magnitude of the squared envelope of the generated vibration signals though not affected by load, but was observed to rise significantly with increasing speed and clearance indicating the likelihood of augmented wear. In the present study, the simulation model was extended further to investigate the bearing wear behavior, resulting as a consequence of different operating conditions, to complement the vibration analysis. In the current simulation, the dynamics of the engine was established first, based on which the hydrodynamic journal bearing forces were evaluated by numerical solution of the Reynold’s equation. Also, the essential outputs of interest in this study, critical to determine wear rates are the tangential velocity and oil film thickness between the journal and bearing sleeve, which if not maintained appropriately, have a detrimental effect on the bearing performance. Archard’s wear prediction model was used in the simulation to calculate the wear rate of bearings with specific location information as all determinative parameters were obtained with reference to crank rotation. Oil film thickness obtained from the model was used as a criterion to determine if the lubrication is sufficient to prevent contact between the journal and bearing thus causing accelerated wear. A limiting value of 1 µm was used as the minimum oil film thickness needed to prevent contact. The increased wear rate with growing severity of operating conditions is analogous and comparable to the rise in amplitude of the squared envelope of the referenced vibration signals. Thus on one hand, the developed model demonstrated its capability to explain wear behavior and on the other hand it also helps to establish a correlation between wear based and vibration based analysis. Therefore, the model provides a cost-effective and quick approach to predict the impending wear in IC engine bearings under various operating conditions.

Keywords: condition monitoring, IC engine, journal bearings, vibration analysis, wear prediction

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Authors: Muhsin Kizhisseri, Jorg Schluter, Saleh Gharie

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Atherosclerosis is the main reason of stroke, which is one of the deadliest diseases in the world. The carotid artery in the brain is the prominent location for atherosclerotic progression, which hinders the blood flow into the brain. The inclusion of computational fluid dynamics (CFD) into the diagnosis cycle to understand the hemodynamics of the patient-specific carotid artery can give insights into stroke prediction. Realistic outlet boundary conditions are an inevitable part of the numerical simulations, which is one of the major factors in determining the accuracy of the CFD results. The Windkessel model-based outlet boundary conditions can give more realistic characteristics of the distal vascular branches of the carotid artery, such as the resistance to the blood flow and compliance of the distal arterial walls. This study aims to find the most influential distal branches of the carotid artery by using the Windkessel model parameters in the outlet boundary conditions. The parametric study approach to Windkessel model parameters can include the geometrical features of the distal branches, such as radius and length. The incorporation of the variations of the geometrical features of the major distal branches such as the middle cerebral artery, anterior cerebral artery, and ophthalmic artery through the Windkessel model can aid in identifying the most influential distal branch in the carotid artery. The results from this study can help physicians and stroke neurologists to have a more detailed and accurate judgment of the patient's condition.

Keywords: stroke, carotid artery, computational fluid dynamics, patient-specific, Windkessel model, distal vascular branches

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Authors: Laura Gantley, Vanessa M. Conn, Stuart Webb, Kirsty Kirk, Marta Gabryelska, Duncan Holds, Brett W. Stringer, Simon J. Conn

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Trinucleotide repeat disorders comprise ~20 severe, inherited human neuromuscular and neurodegenerative disorders, which are a result of an abnormal expansion of repetitive sequences in the DNA. The most common of these, Huntington’s disease, results from the expansion of the CAG repeat region in exon 1 of the HTT gene via an unknown mechanism. Non-coding RNAs have been implicated in the initiation and progression of many diseases; thus, we focus on one circular RNA (circRNA) molecule arising from non-canonical splicing (back splicing) of HTT pre-mRNA. This circRNA and its mouse orthologue were transgenically overexpressed in human cells (SHSY-5Y and HEK293T) and mouse cells (Mb1), respectively. High-content imaging and flow cytometry demonstrated the overexpression of this circRNA reduces cell proliferation, reduces nuclear size independent of cellular size, and alters cell cycle progression. Analysis of protein by western blot and immunofluorescence demonstrated no change to HTT protein levels but altered nuclear-cytoplasmic distribution without impacting the expansion of the HTT repeat region. As these phenotypic and genotypic changes are found in Huntington’s disease patients, these results may suggest that this circRNA may play a functional role in the progression of Huntington’s disease.

Keywords: cell biology, circular RNAs, Huntington’s disease, molecular biology, neurodegenerative disorders

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Authors: Pei Yi Lin

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Objective: The objective of this study is to use machine learning methods to build an early prediction classifier model for acute delirium to improve the quality of medical care for intensive care patients. Background: Delirium is a common acute and sudden disturbance of consciousness in critically ill patients. After the occurrence, it is easy to prolong the length of hospital stay and increase medical costs and mortality. In 2021, the incidence of delirium in the intensive care unit of internal medicine was as high as 59.78%, which indirectly prolonged the average length of hospital stay by 8.28 days, and the mortality rate is about 2.22% in the past three years. Therefore, it is expected to build a delirium prediction classifier through big data analysis and machine learning methods to detect delirium early. Method: This study is a retrospective study, using the artificial intelligence big data database to extract the characteristic factors related to delirium in intensive care unit patients and let the machine learn. The study included patients aged over 20 years old who were admitted to the intensive care unit between May 1, 2022, and December 31, 2022, excluding GCS assessment <4 points, admission to ICU for less than 24 hours, and CAM-ICU evaluation. The CAMICU delirium assessment results every 8 hours within 30 days of hospitalization are regarded as an event, and the cumulative data from ICU admission to the prediction time point are extracted to predict the possibility of delirium occurring in the next 8 hours, and collect a total of 63,754 research case data, extract 12 feature selections to train the model, including age, sex, average ICU stay hours, visual and auditory abnormalities, RASS assessment score, APACHE-II Score score, number of invasive catheters indwelling, restraint and sedative and hypnotic drugs. Through feature data cleaning, processing and KNN interpolation method supplementation, a total of 54595 research case events were extracted to provide machine learning model analysis, using the research events from May 01 to November 30, 2022, as the model training data, 80% of which is the training set for model training, and 20% for the internal verification of the verification set, and then from December 01 to December 2022 The CU research event on the 31st is an external verification set data, and finally the model inference and performance evaluation are performed, and then the model has trained again by adjusting the model parameters. Results: In this study, XG Boost, Random Forest, Logistic Regression, and Decision Tree were used to analyze and compare four machine learning models. The average accuracy rate of internal verification was highest in Random Forest (AUC=0.86), and the average accuracy rate of external verification was in Random Forest and XG Boost was the highest, AUC was 0.86, and the average accuracy of cross-validation was the highest in Random Forest (ACC=0.77). Conclusion: Clinically, medical staff usually conduct CAM-ICU assessments at the bedside of critically ill patients in clinical practice, but there is a lack of machine learning classification methods to assist ICU patients in real-time assessment, resulting in the inability to provide more objective and continuous monitoring data to assist Clinical staff can more accurately identify and predict the occurrence of delirium in patients. It is hoped that the development and construction of predictive models through machine learning can predict delirium early and immediately, make clinical decisions at the best time, and cooperate with PADIS delirium care measures to provide individualized non-drug interventional care measures to maintain patient safety, and then Improve the quality of care.

Keywords: critically ill patients, machine learning methods, delirium prediction, classifier model

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Authors: Eda Üstünel, Seval Karacabey

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The students, who are enrolled in German Preparatory Language Programme at the School of Foreign Languages, Muğla Sıtkı Koçman University, Turkey, learn German as a foreign language for two semesters in an academic year. Although the language programme is a skills-based one, the students lack German speaking skills due to their fear of making language mistakes while speaking in German. This problem of incompetency in German speaking skills exists also in their four-year departmental study at the Faculty of Education. In order to address this problem we design German speaking activities, which are extra-curricular activities. With the help of these activities, we aim to lead Turkish students of German language to speak in the target language, to improve their speaking skills in the target language and to create a stress-free atmosphere and a meaningful learning environment to communicate in the target language. In order to achieve these aims, an ERASMUS+ exchange staff (a German trainee teacher of German as a foreign language), who is from Schwabisch Gmünd University, Germany, conducted out-of-class German speaking activities once a week for three weeks in total. Each speaking activity is lasted for one and a half hour per week. 7 volunteered students of German preparatory language programme attended the speaking activity for three weeks. The activity took place at a cafe in the university campus, that’s the reason, we call it as an out-of-class activity. The content of speaking activity is not related to the topics studied at the units of coursebook, that’s the reason, we call this activity as extra-curricular one. For data collection, three tools are used. A questionnaire, which is an adapted version of Sabo’s questionnaire, is applied to seven volunteers. An interview session is then held with each student on individual basis. The interview questions are developed so as to ask students to expand their answers that are given at the questionnaires. The German trainee teacher wrote fieldnotes, in which the teacher described the activity in the light of her thoughts about what went well and which areas were needed to be improved. The results of questionnaires show that six out of seven students note that such an acitivity must be conducted by a native speaker of German. Four out of seven students emphasize that they like the way that the activities are designed in a learner-centred fashion. All of the students point out that they feel motivated to talk to the trainee teacher in German. Six out of seven students note that the opportunity to communicate in German with the teacher and the peers enable them to improve their speaking skills, the use of grammatical rules and the use of vocabulary.

Keywords: Learning a Foreign Language, Speaking Skills, Teaching German as a Foreign Language, Turkish Learners of German Language

Procedia PDF Downloads 321