Search results for: miRNA:mRNA target prediction

Authors: Mohamed Aly, Aliaa Rehan Youssef, Emad Sawerees, Mounir Guirgis

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Relevance: Osteoarthritis (OA) is the most common degenerative disease seen in all populations. It causes disability and substantial socioeconomic burden. Evidence supports that exercise are the most effective conservative treatment for patients with OA. Therapists experience and clinical judgment play major role in exercise prescription and scientific evidence for this regard is lacking. The development of clinical prediction rules to identify patients who are most likely benefit from exercise may help solving this dilemma. Purpose: This study investigated whether body mass index and functional ability at baseline can predict patients’ response to a selected exercise program. Approach: Fifty-six patients, aged 35 to 65 years, completed an exercise program consisting of open kinetic chain strengthening and passive stretching exercises. The program was given for 3 sessions per week, 45 minutes per session, for 6 weeks Evaluation: At baseline and post treatment, pain severity was assessed using the numerical pain rating scale, whereas functional ability was being assessed by step test (ST), time up and go test (TUG) and 50 feet time walk test (50 FTW). After completing the program, global rate of change (GROC) score of greater than 4 was used to categorize patients as successful and non-successful. Thirty-eight patients (68%) had successful response to the intervention. Logistic regression showed that BMI and 50 FTW test were the only significant predictors. Based on the results, patients with BMI less than 34.71 kg/m2 and 50 FTW test less than 25.64 sec are 68% to 89% more likely to benefit from the exercise program. Conclusions: Clinicians should consider the described strengthening and flexibility exercise program for patents with BMI less than 34.7 Kg/m2 and 50 FTW faster than 25.6 seconds. The validity of these predictors should be investigated for other exercise.

Keywords: clinical prediction rule, knee osteoarthritis, physical therapy exercises, validity

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Authors: Sukhbir Singh

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This paper describes the modeling of novel solar air collector (NSAC) system by using artificial neural network (ANN) model. The objective of the study is to demonstrate the application of the ANN model to predict the performance of the NSAC with acetamide as a phase change material (PCM) storage. Input data set consist of time, solar intensity and ambient temperature wherever as outlet air temperature of NSAC was considered as output. Experiments were conducted between 9.00 and 24.00 h in June and July 2014 underneath the prevailing atmospheric condition of Kurukshetra (city of the India). After that, experimental results were utilized to train the back propagation neural network (BPNN) to predict the outlet air temperature of NSAC. The results of proposed algorithm show that the BPNN is effective tool for the prediction of responses. The BPNN predicted results are 99% in agreement with the experimental results.

Keywords: Evacuated tube solar air collector, Artificial neural network, Phase change material, solar air collector

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Authors: Jacques Lamarche, Juhani Dickinson

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This paper introduces a computational model of a Grammar as Logic of Labeling (GLL), where the lexical primitives of morphosyntax are phonological matrixes, the form of words, understood as labels that apply to realities (or targets) assumed to be outside of grammar altogether. The hypothesis is that even though a lexical label relates to its target arbitrarily, this label in a complex (constituent) label is part of a labeling pattern which, depending on its value (i.e., N, V, Adj, etc.), imposes language-specific restrictions on what it targets outside of grammar (in the world/semantics or in cognitive knowledge). Lexical forms categorized as nouns, verbs, adjectives, etc., are effectively targets of labeling patterns in use. The paper illustrates GLL through a computer model of basic patterns in English NPs. A constituent label is a binary object that encodes: i) alignment of input forms so that labels occurring at different points in time are understood as applying at once; ii) endocentric structuring - every grammatical constituent has a head label that determines the target of the constituent, and a limiter label (the non-head) that restricts this target. The N or A values are restricted to limiter label, the two differing in terms of alignment with a head. Consider the head initial DP ‘the dog’: the label ‘dog’ gets an N value because it is a limiter that is evenly aligned with the head ‘the’, restricting application of the DP. Adapting a traditional analysis of ‘the’ to GLL – apply label to something familiar – the DP targets and identifies one reality familiar to participants by applying to it the label ‘dog’ (singular). Consider next the DP ‘the large dog’: ‘large dog’ is nominal by even alignment with ‘the’, as before, and since ‘dog’ is the head of (head final) ‘large dog’, it is also nominal. The label ‘large’, however, is adjectival by narrow alignment with the head ‘dog’: it doesn’t target the head but targets a property of what dog applies to (a property or value of attribute). In other words, the internal composition of constituents determines that a form targets a property or a reality: ‘large’ and ‘dog’ happen to be valid targets to realize this constituent. In the presentation, the computer model of the analysis derives the 8 possible sequences of grammatical values with three labels after the determiner (the x y z): 1- D [ N [ N N ]]; 2- D [ A [ N N ] ]; 3- D [ N [ A N ] ]; 4- D [ A [ A N ] ]; 5- D [ [ N N ] N ]; 5- D [ [ A N ] N ]; 6- D [ [ N A ] N ] 7- [ [ N A ] N ] 8- D [ [ Adv A ] N ]. This approach that suggests that a computer model of these grammatical patterns could be used to construct ontologies/knowledge using speakers’ judgments about the validity of lexical meaning in grammatical patterns.

Keywords: syntactic theory, computational linguistics, logic and grammar, semantics, knowledge and grammar

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Authors: Jan Henrik Wosnitza

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The logistic regression has developed into a standard approach for estimating conditional probabilities in a wide range of applications including credit risk prediction. The article at hand contributes to the current literature on logistic regression fourfold: First, it is demonstrated that the binary logistic regression automatically meets its model assumptions under very general conditions. This result explains, at least in part, the logistic regression's popularity. Second, the requirement of homoscedasticity in the context of binary logistic regression is theoretically substantiated. The variances among the groups of defaulted and non-defaulted obligors have to be the same across the level of the aggregated default indicators in order to achieve linear logits. Third, this article sheds some light on the question why nonlinear logits might be superior to linear logits in case of a small amount of data. Fourth, an innovative methodology for estimating correlations between obligor-specific log-odds is proposed. In order to crystallize the key ideas, this paper focuses on the example of credit risk prediction. However, the results presented in this paper can easily be transferred to any other field of application.

Keywords: correlation, credit risk estimation, default correlation, homoscedasticity, logistic regression, nonlinear logistic regression

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Authors: Feride Sumbul

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Drama is a literary genre that mirrors the people and society and transfers the human nature and life to the reader or the audience within its own social-cultural structure. Each play takes on a new reality in the time and culture of the staging, and each performance actually brings a new interpretation to the play. Similarly, each translation adds a new meaning to the source text. In other words, the translated theatrical text transcends the boundaries of its language and culture and finds a new interpretation. Thus the translation of drama takes place as a transfer from one culture to another as a cross cultural communication. In this context, translating culture specific references play a key role in terms of reflecting cultural aspects of a target society. This study aims to explore the use of Venuti's translation principles of domestication and foreignization in the transfer of culture specific references in the Turkish translation of Shakespeare's Macbeth. Macbeth is to be compared with its Turkish version in terms of the transference of culture specific references such as religious, witchcraft, and mythological, which have no equivalent in the target language and culture. To evaluate these principles of Venuti, Davies’s translation strategies are also conducted. As a method, for the most part, he predominantly uses Davies’ method of ‘addition’ through adding extra information in the notes. For instance, rather than finding the Turkish renderings of them, the translator mostly chooses to transfer witchcraft references through retaining them in the target text, but he mainly adds extra information about the references in the notes. Therefore, the translator Nutku mostly uses Venuti’s translation principle of foreignization so that he preserves the foreignness of the theatrical text.

Keywords: drama translation, theatrical texts, culture specific references, Macbeth

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Authors: Mohammad Reza Dahmardeh Ghaleno, Mohammad Nohtani, Saeedeh Khaledi

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Hydrological models are applied to simulation and prediction floods in watersheds. WetSpa is a distributed, continuous and physically model with daily or hourly time step that explains of precipitation, runoff and evapotranspiration processes for both simple and complex contexts. This model uses a modified rational method for runoff calculation. In this model, runoff is routed along the flow path using Diffusion-Wave Equation which depend on the slope, velocity and flow route characteristics. Garmabrood watershed located in Mazandaran province in Iran and passing over coordinates 53° 10´ 55" to 53° 38´ 20" E and 36° 06´ 45" to 36° 25´ 30"N. The area of the catchment is about 1133 km2 and elevations in the catchment range from 213 to 3136 m at the outlet, with average slope of 25.77 %. Results of the simulations show a good agreement between calculated and measured hydrographs at the outlet of the basin. Drawing upon Nash-Sutcliffe Model Efficiency Coefficient for calibration periodic model estimated daily hydrographs and maximum flow rate with an accuracy up to 61% and 83.17 % respectively.

Keywords: watershed simulation, WetSpa, runoff, flood prediction

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Authors: Adam Abdullahi Mohammed

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Performance appraisal is an assessment made to ensure the level of a worker’s productivity in a given period of time. The appraisal system is divided into two categories that are traditional methods and modern methods, with emphasis based on the evaluation of work results. In the traditional approach of staff appraisal, which puts more emphasis on individual traits, supervisors are required to measure employees through interactions based on what they achieved with reference to job descriptions, as well as rating them based on questionnaires without staff interaction. These methods are not effective because staff may give biased information. The study will attempt to assess the effect of performance appraisal on employee productivity at Yobe State University, Damaturu. It is aimed at assessing the process, methods, and objectives of performance appraisal and its feedback to know how they affect the success of the appraisal, its results, and employee productivity. In this study, a quantitative research method is adopted in collecting and analyzing data, and a questionnaire will be used as data collecting instrument. As it is a case study, the target population is the staff of the department of Islamic Studies. The research will employ a census sampling technique where all the subjects in the target populations are given a chance to participate in the study. This sampling method was considered because the entire target population is considered researchable. The expected findings are that staff performance appraisal in the department of Islamic Studies has effects on employee productivity; this is to say if it is given due consideration and the needful being done will improve employee productivity.

Keywords: performance appraisal, employee productivity, Yobe state University, appraisal feedback

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Authors: Morteza Habibi, Reza Amrollahi

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The Aluminum made targets were placed at the central part of a Fillipov type (90KJ) plasma focus cathode. These targets were exposed to perpendicular dense plasma stream incidence. Melt layer erosion by melt motion, surface smoothing, and bubble formation were some of different effects caused by diverse working conditions. Micro hardness of surface layer tends to decrease particularly in the central region of the sample where destruction is more intense. The most pronouced melt motion is registered in the region of the maximum gradient of pressure and the etching of aluminium surface is noticeable in the central part of target. The crater with a maximum depth of 200µm, and the diameter of about 8.5mm is observed close to the mountains. Adding Krypton admixture to the Deuterium gas lead to collapsing bubbles and greater surface damage.

Keywords: fillipov type plasma focus, al target interaction, bubbling effect, melt layer motion, surface smoothing

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Authors: Robert Caulk

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A generalized framework for adaptive machine learning deployments in algorithmic trading is introduced, tested, and released as open-source code. The presented software aims to test the hypothesis that recent data contains enough information to form a probabilistically favorable short-term price prediction. Further, the framework contains various adaptive machine learning techniques that are geared toward generating profit during strong trends and minimizing losses during trend changes. Results demonstrate that this adaptive machine learning approach is capable of capturing trends and generating profit. The presentation also discusses the importance of defining the parameter space associated with the dynamic training data-set and using the parameter space to identify and remove outliers from prediction data points. Meanwhile, the generalized architecture enables common users to exploit the powerful machinery while focusing on high-level feature engineering and model testing. The presentation also highlights common strengths and weaknesses associated with the presented technique and presents a broad range of well-tested starting points for feature set construction, target setting, and statistical methods for enforcing risk management and maintaining probabilistically favorable entry and exit points. The presentation also describes the end-to-end data processing tools associated with FreqAI, including automatic data fetching, data aggregation, feature engineering, safe and robust data pre-processing, outlier detection, custom machine learning and statistical tools, data post-processing, and adaptive training backtest emulation, and deployment of adaptive training in live environments. Finally, the generalized user interface is also discussed in the presentation. Feature engineering is simplified so that users can seed their feature sets with common indicator libraries (e.g. TA-lib, pandas-ta). The user also feeds data expansion parameters to fill out a large feature set for the model, which can contain as many as 10,000+ features. The presentation describes the various object-oriented programming techniques employed to make FreqAI agnostic to third-party libraries and external data sources. In other words, the back-end is constructed in such a way that users can leverage a broad range of common regression libraries (Catboost, LightGBM, Sklearn, etc) as well as common Neural Network libraries (TensorFlow, PyTorch) without worrying about the logistical complexities associated with data handling and API interactions. The presentation finishes by drawing conclusions about the most important parameters associated with a live deployment of the adaptive learning framework and provides the road map for future development in FreqAI.

Keywords: machine learning, market trend detection, open-source, adaptive learning, parameter space exploration

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Authors: Misuk Kim, Seokho Kang, Jehyuk Lee, Hyunchang Cho, Sungzoon Cho

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In semiconductor manufacturing, virtual metrology (VM) refers to methods to predict properties of a wafer based on machine parameters and sensor data of the production equipment, without performing the (costly) physical measurement of the wafer properties (Wikipedia). Additional benefits include avoidance of human bias and identification of important factors affecting the quality of the process which allow improving the process quality in the future. It is however rare to find VM applied to other areas of manufacturing. In this work, we propose to use VM to copper clad laminate (CCL) manufacturing. CCL is a core element of a printed circuit board (PCB) which is used in smartphones, tablets, digital cameras, and laptop computers. The manufacturing of CCL consists of three processes: Treating, lay-up, and pressing. Treating, the most important process among the three, puts resin on glass cloth, heat up in a drying oven, then produces prepreg for lay-up process. In this process, three important quality factors are inspected: Treated weight (T/W), Minimum Viscosity (M/V), and Gel Time (G/T). They are manually inspected, incurring heavy cost in terms of time and money, which makes it a good candidate for VM application. We developed prediction models of the three quality factors T/W, M/V, and G/T, respectively, with process variables, raw material, and environment variables. The actual process data was obtained from a CCL manufacturer. A variety of variable selection methods and learning algorithms were employed to find the best prediction model. We obtained prediction models of M/V and G/T with a high enough accuracy. They also provided us with information on “important” predictor variables, some of which the process engineers had been already aware and the rest of which they had not. They were quite excited to find new insights that the model revealed and set out to do further analysis on them to gain process control implications. T/W did not turn out to be possible to predict with a reasonable accuracy with given factors. The very fact indicates that the factors currently monitored may not affect T/W, thus an effort has to be made to find other factors which are not currently monitored in order to understand the process better and improve the quality of it. In conclusion, VM application to CCL’s treating process was quite successful. The newly built quality prediction model allowed one to reduce the cost associated with actual metrology as well as reveal some insights on the factors affecting the important quality factors and on the level of our less than perfect understanding of the treating process.

Keywords: copper clad laminate, predictive modeling, quality control, virtual metrology

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Authors: Ammar Alali, Mahmoud Abughaban

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Cost reduction and drilling optimization is the goal of many drilling operators. Historically, stuck pipe incidents were a major segment of non-productive time (NPT) associated costs. Traditionally, stuck pipe problems are part of the operations and solved post-sticking. However, the real key to savings and success is in predicting the stuck pipe incidents and avoiding the conditions leading to its occurrences. Previous attempts in stuck-pipe predictions have neglected the local geology of the problem. The proposed predictive tool utilizes geophysical data processing techniques and Machine Learning (ML) algorithms to predict drilling activities events in real-time using surface drilling data with minimum computational power. The method combines two types of analysis: (1) real-time prediction, and (2) cause analysis. Real-time prediction aggregates the input data, including historical drilling surface data, geological formation tops, and petrophysical data, from wells within the same field. The input data are then flattened per the geological formation and stacked per stuck-pipe incidents. The algorithm uses two physical methods (stacking and flattening) to filter any noise in the signature and create a robust pre-determined pilot that adheres to the local geology. Once the drilling operation starts, the Wellsite Information Transfer Standard Markup Language (WITSML) live surface data are fed into a matrix and aggregated in a similar frequency as the pre-determined signature. Then, the matrix is correlated with the pre-determined stuck-pipe signature for this field, in real-time. The correlation used is a machine learning Correlation-based Feature Selection (CFS) algorithm, which selects relevant features from the class and identifying redundant features. The correlation output is interpreted as a probability curve of stuck pipe incidents prediction in real-time. Once this probability passes a fixed-threshold defined by the user, the other component, cause analysis, alerts the user of the expected incident based on set pre-determined signatures. A set of recommendations will be provided to reduce the associated risk. The validation process involved feeding of historical drilling data as live-stream, mimicking actual drilling conditions, of an onshore oil field. Pre-determined signatures were created for three problematic geological formations in this field prior. Three wells were processed as case studies, and the stuck-pipe incidents were predicted successfully, with an accuracy of 76%. This accuracy of detection could have resulted in around 50% reduction in NPT, equivalent to 9% cost saving in comparison with offset wells. The prediction of stuck pipe problem requires a method to capture geological, geophysical and drilling data, and recognize the indicators of this issue at a field and geological formation level. This paper illustrates the efficiency and the robustness of the proposed cross-disciplinary approach in its ability to produce such signatures and predicting this NPT event.

Keywords: drilling optimization, hazard prediction, machine learning, stuck pipe

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Authors: Subhamita Chakraborty, Shubhabrata Datta, Sujay Kumar Mukherjea, Partha Protim Chattopadhyay

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Manufacturing of multiphase high strength steel in hot strip mill have drawn significant attention due to the possibility of forming low temperature transformation product of austenite under continuous cooling condition. In such endeavor, reliable prediction of temperature profile of hot strip coil is essential in order to accesses the evolution of microstructure at different location of hot strip coil, on the basis of corresponding Continuous Cooling Transformation (CCT) diagram. Temperature distribution profile of the hot strip coil has been determined by using finite volume method (FVM) vis-à-vis finite difference method (FDM). It has been demonstrated that FVM offer greater computational reliability in estimation of contact pressure distribution and hence the temperature distribution for curved and irregular profiles, owing to the flexibility in selection of grid geometry and discrete point position, Moreover, use of finite volume concept allows enforcing the conservation of mass, momentum and energy, leading to enhanced accuracy of prediction.

Keywords: simulation, modeling, thermal analysis, coil cooling, contact pressure, finite volume method

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Authors: Patarasuda Chaisupa, R. Clay Wright

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The selection of appropriate biomolecular targets is a crucial aspect of biopharmaceutical development. The Auxin-Inducible Degron Degradation (AID) technology has demonstrated remarkable potential in efficiently and rapidly degrading target proteins, thereby enabling the identification and acquisition of drug targets. The AID system also offers a viable method to deplete specific proteins, particularly in cases where the degradation pathway has not been exploited or when the adaptation of proteins, including the cell environment, occurs to compensate for the mutation or gene knockout. In this study, we have engineered an improved AID system tailored to deplete proteins of interest. This AID construct combines the auxin-responsive E3 ubiquitin ligase binding domain, AFB2, and the substrate degron, IAA17, fused to the target genes. Essential genes of fungi with the lowest percent amino acid similarity to human and plant orthologs, according to the Basic Local Alignment Search Tool (BLAST), were cloned into the AID construct in S. cerevisiae (AID-tagged strains) using a modular yeast cloning toolkit for multipart assembly and direct genetic modification. Each E3 ubiquitin ligase and IAA17 degron was fused to a fluorescence protein, allowing for real-time monitoring of protein levels in response to different auxin doses via cytometry. Our AID system exhibited high sensitivity, with an EC50 value of 0.040 µM (SE = 0.016) for AFB2, enabling the specific promotion of IAA17::target protein degradation. Furthermore, we demonstrate how this improved AID system enhances quantitative functional studies of various proteins in fungi. The advancements made in auxin-inducible protein degradation in this study offer a powerful approach to investigating critical target protein viability in fungi, screening protein targets for drugs, and regulating intracellular protein abundance, thus revolutionizing the study of protein function underlying a diverse range of biological processes.

Keywords: synthetic biology, bioengineering, molecular biology, biotechnology

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Authors: M.Rüştü Karaman, İsmail İşeri, Kadir Saltalı, A.Reşit Brohi, Ayhan Horuz, Mümin Dizman

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Considerable relations has recently been given to the environmental hazardous caused by agricultural chemicals such as excess fertilizers. In this study, a neural network approach was investigated in the prediction of potential nitrate pollution across different land-use patterns by using a feedforward multilayered computer model of artificial neural network (ANN) with proper training. Periodical concentrations of some anions, especially nitrate (NO3-), and cations were also detected in drainage waters collected from the drain pipes placed in irrigated tomato field, unirrigated wheat field, fallow and pasture lands. The soil samples were collected from the irrigated tomato field and unirrigated wheat field on a grid system with 20 m x 20 m intervals. Site specific nitrate concentrations in the soil samples were measured for ANN based simulation of nitrate leaching potential from the land profiles. In the application of ANN model, a multi layered feedforward was evaluated, and data sets regarding with training, validation and testing containing the measured soil nitrate values were estimated based on spatial variability. As a result of the testing values, while the optimal structures of 2-15-1 was obtained (R2= 0.96, P < 0.01) for unirrigated field, the optimal structures of 2-10-1 was obtained (R2= 0.96, P < 0.01) for irrigated field. The results showed that the ANN model could be successfully used in prediction of the potential leaching levels of nitrate, based on different land use patterns. However, for the most suitable results, the model should be calibrated by training according to different NN structures depending on site specific soil parameters and varied agricultural managements.

Keywords: artificial intelligence, ANN, drainage water, nitrate pollution

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Authors: M. Paraipan, V. M. Javadova, S. I. Tyutyunnikov

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The concept of energy amplifier or accelerator driven system (ADS) involves the use of a particle accelerator coupled with a nuclear reactor. The accelerated particle beam generates a supplementary source of neutrons, which allows the subcritical functioning of the reactor, and consequently a safe exploitation. The harder neutron spectrum realized ensures a better incineration of the actinides. The almost generalized opinion is that the optimal beam for ADS is represented by protons with energy around 1 GeV (gigaelectronvolt). In the present work, a systematic analysis of the energy gain for proton beams with energy from 0.5 to 3 GeV and ion beams from deuteron to neon with energies between 0.25 and 2 AGeV is performed. The target is an assembly of metallic U-Pu-Zr fuel rods in a bath of lead-bismuth eutectic coolant. The rods length is 150 cm. A beryllium converter with length 110 cm is used in order to maximize the energy released in the target. The case of a linear accelerator is considered, with a beam intensity of 1.25‧10¹⁶ p/s, and a total accelerator efficiency of 0.18 for proton beam. These values are planned to be achieved in the European Spallation Source project. The energy gain G is calculated as the ratio between the energy released in the target to the energy spent to accelerate the beam. The energy released is obtained through simulation with the code Geant4. The energy spent is calculating by scaling from the data about the accelerator efficiency for the reference particle (proton). The analysis concerns the G values, the net power produce, the accelerator length, and the period between refueling. The optimal energy for proton is 1.5 GeV. At this energy, G reaches a plateau around a value of 8 and a net power production of 120 MW (megawatt). Starting with alpha, ion beams have a higher G than 1.5 GeV protons. A beam of 0.25 AGeV(gigaelectronvolt per nucleon) ⁷Li realizes the same net power production as 1.5 GeV protons, has a G of 15, and needs an accelerator length 2.6 times lower than for protons, representing the best solution for ADS. Beams of ¹⁶O or ²⁰Ne with energy 0.75 AGeV, accelerated in an accelerator with the same length as 1.5 GeV protons produce approximately 900 MW net power, with a gain of 23-25. The study of the evolution of the isotopes composition during irradiation shows that the increase in power production diminishes the period between refueling. For a net power produced of 120 MW, the target can be irradiated approximately 5000 days without refueling, but only 600 days when the net power reaches 1 GW (gigawatt).

Keywords: accelerator driven system, ion beam, electrical power, energy gain

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Authors: Fahimeh Palizban, Farshad Noravesh, Amir Hossein Saeidian, Mahya Mehrmohamadi

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In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the blood and contribute to a pool of circulating fragments called cell-free DNA. Accordingly, identifying the tissue origin of these DNA fragments from the plasma can result in more accurate and fast disease diagnosis and precise treatment protocols. Open chromatin regions are important epigenetic features of DNA that reflect cell types of origin. Profiling these features by DNase-seq, ATAC-seq, and histone ChIP-seq provides insights into tissue-specific and disease-specific regulatory mechanisms. There have been several studies in the area of cancer liquid biopsy that integrate distinct genomic and epigenomic features for early cancer detection along with tissue of origin detection. However, multimodal analysis requires several types of experiments to cover the genomic and epigenomic aspects of a single sample, which will lead to a huge amount of cost and time. To overcome these limitations, the idea of predicting OCRs from WGS is of particular importance. In this regard, we proposed a computational approach to target the prediction of open chromatin regions as an important epigenetic feature from cell-free DNA whole genome sequence data. To fulfill this objective, local sequencing depth will be fed to our proposed algorithm and the prediction of the most probable open chromatin regions from whole genome sequencing data can be carried out. Our method integrates the signal processing method with sequencing depth data and includes count normalization, Discrete Fourie Transform conversion, graph construction, graph cut optimization by linear programming, and clustering. To validate the proposed method, we compared the output of the clustering (open chromatin region+, open chromatin region-) with previously validated open chromatin regions related to human blood samples of the ATAC-DB database. The percentage of overlap between predicted open chromatin regions and the experimentally validated regions obtained by ATAC-seq in ATAC-DB is greater than 67%, which indicates meaningful prediction. As it is evident, OCRs are mostly located in the transcription start sites (TSS) of the genes. In this regard, we compared the concordance between the predicted OCRs and the human genes TSS regions obtained from refTSS and it showed proper accordance around 52.04% and ~78% with all and the housekeeping genes, respectively. Accurately detecting open chromatin regions from plasma cell-free DNA-seq data is a very challenging computational problem due to the existence of several confounding factors, such as technical and biological variations. Although this approach is in its infancy, there has already been an attempt to apply it, which leads to a tool named OCRDetector with some restrictions like the need for highly depth cfDNA WGS data, prior information about OCRs distribution, and considering multiple features. However, we implemented a graph signal clustering based on a single depth feature in an unsupervised learning manner that resulted in faster performance and decent accuracy. Overall, we tried to investigate the epigenomic pattern of a cell-free DNA sample from a new computational perspective that can be used along with other tools to investigate genetic and epigenetic aspects of a single whole genome sequencing data for efficient liquid biopsy-related analysis.

Keywords: open chromatin regions, cancer, cell-free DNA, epigenomics, graph signal processing, correlation clustering

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Authors: Mohammed Hassan Alshaikhi

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Vocabulary is essential factor of learning and mastering any languages, and it helps learners to communicate with others and to be understood. The aim of this study was to examine whether semantic mapping technique was helpful in terms of improving student's English vocabulary learning comparing to the traditional technique. The students’ age was between 11 and 13 years old. There were 60 students in total who participated in this study. 30 students were in the treatment group (target vocabulary items were taught with semantic mapping). The other 30 students were in the control group (the target vocabulary items were taught by a traditional technique). A t-test was used with the results of pre-test and post-test in order to examine the outcomes of using semantic mapping when teaching vocabulary. The results showed that the vocabulary mastery in the treatment group was increased more than the control group.

Keywords: English language, learning vocabulary, Saudi teachers, semantic mapping, teaching vocabulary strategies

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Authors: Amin Salighehdar, Ziwen Ye, Mingzhe Liu, Ionut Florescu, Alan F. Blumberg

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Storm surge is an abnormal water level caused by a storm. Accurate prediction of a storm surge is a challenging problem. Researchers developed various ensemble modeling techniques to combine several individual forecasts to produce an overall presumably better forecast. There exist some simple ensemble modeling techniques in literature. For instance, Model Output Statistics (MOS), and running mean-bias removal are widely used techniques in storm surge prediction domain. However, these methods have some drawbacks. For instance, MOS is based on multiple linear regression and it needs a long period of training data. To overcome the shortcomings of these simple methods, researchers propose some advanced methods. For instance, ENSURF (Ensemble SURge Forecast) is a multi-model application for sea level forecast. This application creates a better forecast of sea level using a combination of several instances of the Bayesian Model Averaging (BMA). An ensemble dressing method is based on identifying best member forecast and using it for prediction. Our contribution in this paper can be summarized as follows. First, we investigate whether the ensemble models perform better than any single forecast. Therefore, we need to identify the single best forecast. We present a methodology based on a simple Bayesian selection method to select the best single forecast. Second, we present several new and simple ways to construct ensemble models. We use correlation and standard deviation as weights in combining different forecast models. Third, we use these ensembles and compare with several existing models in literature to forecast storm surge level. We then investigate whether developing a complex ensemble model is indeed needed. To achieve this goal, we use a simple average (one of the simplest and widely used ensemble model) as benchmark. Predicting the peak level of Surge during a storm as well as the precise time at which this peak level takes place is crucial, thus we develop a statistical platform to compare the performance of various ensemble methods. This statistical analysis is based on root mean square error of the ensemble forecast during the testing period and on the magnitude and timing of the forecasted peak surge compared to the actual time and peak. In this work, we analyze four hurricanes: hurricanes Irene and Lee in 2011, hurricane Sandy in 2012, and hurricane Joaquin in 2015. Since hurricane Irene developed at the end of August 2011 and hurricane Lee started just after Irene at the beginning of September 2011, in this study we consider them as a single contiguous hurricane event. The data set used for this study is generated by the New York Harbor Observing and Prediction System (NYHOPS). We find that even the simplest possible way of creating an ensemble produces results superior to any single forecast. We also show that the ensemble models we propose generally have better performance compared to the simple average ensemble technique.

Keywords: Bayesian learning, ensemble model, statistical analysis, storm surge prediction

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Authors: Rezvan Najafi, Korosh Heydari, Massoud Saidijam

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5-FU is a chemotherapeutic agent that has been used in colorectal cancer (CRC) treatment. However, it is usually associated with the acquired resistance, which decreases the therapeutic effects of 5-FU. miR-200c is involved in chemotherapeutic drug resistance, but its mechanism is not fully understood. In this study, the effect of inhibition of miR-200c in sensitivity of HCT-116 CRC cells to 5-FU was evaluated. HCT-116 cells were transfected with LNA-anti- miR-200c for 48 h. mRNA expression of miR-200c was evaluated using quantitative real- time PCR. The protein expression of phosphatase and tensin homolog (PTEN) and E-cadherin were analyzed by western blotting. Annexin V and propidium iodide staining assay were applied for apoptosis detection. The caspase-3 activation was evaluated by an enzymatic assay. The results showed LNA-anti-miR-200c inhibited the expression of PTEN and E-cadherin protein, apoptosis and activation of caspase 3 compared with control cells. In conclusion, these results suggest that miR-200c as a prognostic marker can overcome to 5-FU chemoresistance in CRC.

Keywords: colorectal cancer, miR-200c, 5-FU resistance, E-cadherin, PTEN

Procedia PDF Downloads 166

Authors: Naima Jannat, Ariful Islam, Sharafat Hossain

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Due to the involvement of the large target volume, Craniospinal Irradiation makes it challenging to achieve a uniform dose, and it requires different isocenters. This isocentric junction needs to shift after every five fractions to overcome the possibility of hot and cold spots. This study aims to evaluate the Planning Target Volume coverage & sparing Organ at Risk between two techniques and shows that the Field Alignment Technique does not need replanning and resetting. Planning method for Craniospinal Irradiation by Eclipse treatment planning system Field Alignment and Extended Source to Surface Distance technique was developed where 36 Gy in 20 Fraction at the rate of 1.8 Gy was prescribed. The patient was immobilized in the prone position. In the Field Alignment technique, the plan consists of half beam blocked parallel opposed cranium and a single posterior cervicospine field was developed by sharing the same isocenter, which obviates divergence matching. Further, a single field was created to treat the remaining lumbosacral spine. Matching between the inferior diverging edge of the cervicospine field and the superior diverging edge of a lumbosacral field, the field alignment option was used, which automatically matches the field edge divergence as per the field alignment rule in Eclipse Treatment Planning System where the couch was set to 2700. In the Extended Source to Surface Distance technique, two parallel opposed fields were created for the cranium, and a single posterior cervicospine field was created where the Source to Surface Distance was from 120-140 cm. Dose Volume Histograms were obtained for each organ contoured and for each technique used. In all, the patient’s maximum dose to Planning Target Volume is higher for the Extended Source to Surface Distance technique to Field Alignment technique. The dose to all surrounding structures was increased with the use of a single Extended Source to Surface Distance when compared to the Field Alignment technique. The average mean dose to Eye, Brain Steam, Kidney, Oesophagus, Heart, Liver, Lung, and Ovaries were respectively (58% & 60 %), (103% & 98%), (13% & 15%), (10% & 63%), (12% & 16%), (33% & 30%), (14% & 18%), (69% & 61%) for Field Alignment and Extended Source to Surface Distance technique. However, the clinical target volume at the spine junction site received a less homogeneous dose with the Field Alignment technique as compared to Extended Source to Surface Distance. We conclude that, although the use of a single field Extended Source to Surface Distance delivered a more homogenous, but its maximum dose is higher than the Field Alignment technique. Also, a huge advantage of the Field Alignment technique for Craniospinal Irradiation is that it doesn’t need replanning and resetting up of patients after every five fractions and 95% prescribed dose was received by more than 95% of the Planning Target Volume in all the plane with the acceptable hot spot.

Keywords: craniospinalirradiation, cranium, cervicospine, immobilize, lumbosacral spine

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Authors: Krishna Pal Singh, Shailendra Kumar Gupta, Olaf Wolkenhauer

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Background: Our study aimed to identify common genes and potential targets across the four diseases, which include rheumatoid arthritis, melanoma metastasis, ulcerative colitis, and Crohn’s disease. We used a network and systems biology approach to identify the hub gene, which can act as a potential target for all four disease conditions. The regulatory network was extracted from the PPI using the MCODE module present in Cytoscape. Our objective was to investigate the significance of hub genes in these diseases using gene ontology and KEGG pathway enrichment analysis. Methods: Our methodology involved collecting disease gene-related information from DisGeNET databases and performing protein-protein interaction (PPI) network and core genes screening. We then conducted gene ontology and KEGG pathway enrichment analysis. Results: We found that IL6 plays a critical role in all disease conditions and in different pathways that can be associated with the development of all four diseases. Conclusions: The theoretical importance of our research is that we employed various systems and structural biology techniques to identify a crucial protein that could serve as a promising target for treating multiple diseases. Our data collection and analysis procedures involved rigorous scrutiny, ensuring high-quality results. Our conclusion is that IL6 plays a significant role in all four diseases, and it can act as a potential target for treating them. Our findings may have important implications for the development of novel therapeutic interventions for these diseases.

Keywords: melanoma metastasis, rheumatoid arthritis, inflammatory bowel diseases, integrated bioinformatics analysis

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Authors: Tea Poklepović, Zdravka Aljinović, Branka Marasović

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Due to the importance of yield curve and its estimation it is inevitable to have valid methods for yield curve forecasting in cases when there are scarce issues of securities and/or week trade on a secondary market. Therefore in this paper, after the estimation of weekly yield curves on Croatian financial market from October 2011 to August 2012 using Nelson-Siegel and Svensson models, yield curves are forecasted using Vector auto-regressive model and Neural networks. In general, it can be concluded that both forecasting methods have good prediction abilities where forecasting of yield curves based on Nelson Siegel estimation model give better results in sense of lower Mean Squared Error than forecasting based on Svensson model Also, in this case Neural networks provide slightly better results. Finally, it can be concluded that most appropriate way of yield curve prediction is neural networks using Nelson-Siegel estimation of yield curves.

Keywords: Nelson-Siegel Model, neural networks, Svensson Model, vector autoregressive model, yield curve

Procedia PDF Downloads 337

Authors: Bosiacki Mateusz, Anna Lubkowska, Dariusz Chlubek, Irena Baranowska-Bosiacka

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Exposure to cold temperatures can be considered a stressor that can lead to adaptive responses. The present study hypothesized the possibility of a positive effect of cold water exercise on mitochondrial biogenesis and muscle energy metabolism in aging rats. The purpose of this study was to evaluate the effects of cold water exercise on energy status, purine compounds, and mitochondrial biogenesis in the muscles of aging rats as indicators of the effects of cold water exercise and their usefulness in monitoring adaptive changes. The study was conducted on 64 aging rats of both sexes, 15 months old at the time of the experiment. The rats (male and female separately) were randomly assigned to the following study groups: control, sedentary animals; 5°C groups animals - training swimming in cold water at 5°C; 36°C groups - animals training swimming in water at thermal comfort temperature. The study was conducted with the approval of the Local Ethical Committee for Animal Experiments. The animals in the experiment were subjected to swimming training for 9 weeks. During the first week of the study, the duration of the first swimming training was 2 minutes (on the first day), increasing daily by 0.5 minutes up to 4 minutes on the fifth day of the first week. From the second to the eighth week, the swimming training was 4 minutes per day, five days a week. At the end of the study, forty-eight hours after the last swim training, the animals were dissected. In the skeletal muscle tissue of the thighs of the rats, we determined the concentrations of ATP, ADP, AMP, Ado (HPLC), PGC-1a protein expression (Western blot), PGC1A, Mfn1, Mfn2, Opa1, and Drp1 gene expression (qRT PCR). The study showed that swimming in water at a thermally comfortable temperature improved the energy metabolism of the aging rat muscles by increasing the metabolic rate (increase in ATP, ADP, TAN, AEC) and enhancing mitochondrial fusion (increase in mRNA expression of regulatory proteins Mfn1 and Mfn2). Cold water swimming improved muscle energy metabolism in aging rats by increasing the rate of muscle energy metabolism (increase in ATP, ADP, TAN, AEC concentrations) and enhancing mitochondrial biogenesis and dynamics (increase in the mRNA expression of proteins of fusion-regulating factors – Mfn1, Mfn2, and Opa1, and the factor regulating mitochondrial fission – Drp1). The concentration of high-energy compounds and the expression of proteins regulating mitochondrial dynamics in the muscle may be a useful indicator in monitoring adaptive changes occurring in aging muscles under the influence of exercise in cold water. It represents a short-term adaptation to changing environmental conditions and has a beneficial effect on maintaining the bioenergetic capacity of muscles in the long term. Conclusion: exercise in cold water can exert positive effects on energy metabolism, biogenesis and dynamics of mitochondria in aging rat muscles. Enhancement of mitochondrial dynamics under cold water exercise conditions can improve mitochondrial function and optimize the bioenergetic capacity of mitochondria in aging rat muscles.

Keywords: cold water immersion, adaptive responses, muscle energy metabolism, aging

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Authors: Prateeksha Mahamallik, Anjali Pal

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In the present study, Co(II)-adsolubilized surfactant modified alumina (SMA) was prepared, and methylene blue (MB) degradation was carried out on Co-SMA surface by visible light photo-Fenton process. The entire reaction proceeded on solid surface as MB was embedded on Co-SMA surface. The reaction followed zero order kinetics. Response surface methodology (RSM) and artificial neural network (ANN) were used for modeling the decolorization of MB by photo-Fenton process as a function of dose of Co-SMA (10, 20 and 30 g/L), initial concentration of MB (10, 20 and 30 mg/L), concentration of H2O2 (174.4, 348.8 and 523.2 mM) and reaction time (30, 45 and 60 min). The prediction capabilities of both the methodologies (RSM and ANN) were compared on the basis of correlation coefficient (R2), root mean square error (RMSE), standard error of prediction (SEP), relative percent deviation (RPD). Due to lower value of RMSE (1.27), SEP (2.06) and RPD (1.17) and higher value of R2 (0.9966), ANN was proved to be more accurate than RSM in order to predict decolorization efficiency.

Keywords: adsolubilization, artificial neural network, methylene blue, photo-fenton process, response surface methodology

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Authors: Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Y. Rafii

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A huge revolution has emerged in genome engineering by the discovery of CRISPR (clustered regularly interspaced palindromic repeats) and CRISPR-associated system genes (Cas) in bacteria. The function of type II Streptococcus pyogenes (Sp) CRISPR/Cas9 system has been confirmed in various species. Other S. thermophilus (St) CRISPR-Cas systems, CRISPR1-Cas and CRISPR3-Cas, have been also reported for preventing phage infection. The CRISPR1-Cas system interferes by cleaving foreign dsDNA entering the cell in a length-specific and orientation-dependant manner. The S. thermophilus CRISPR3-Cas system also acts by cleaving phage dsDNA genomes at the same specific position inside the targeted protospacer as observed in the CRISPR1-Cas system. It is worth mentioning, for the effective DNA cleavage activity, RNA-guided Cas9 orthologs require their own specific PAM (protospacer adjacent motif) sequences. Activity levels are based on the sequence of the protospacer and specific combinations of favorable PAM bases. Therefore, based on the specific length and sequence of PAM followed by a constant length of target site for the three orthogonals of Cas9 protein, a well-organized procedure will be required for high-throughput and accurate mining of possible target sites in a large genomic dataset. Consequently, we created a reliable procedure to explore potential gRNA sequences for type I (Streptococcus thermophiles), II (Streptococcus pyogenes), and III (Streptococcus thermophiles) CRISPR/Cas systems. To mine CRISPR target sites, four different searching modes of sgRNA binding to target DNA strand were applied. These searching modes are as follows: i) coding strand searching, ii) anti-coding strand searching, iii) both strand searching, and iv) paired-gRNA searching. The output of such procedure highlights the power of comparative genome mining for different CRISPR/Cas systems. This could yield a repertoire of Cas9 variants with expanded capabilities of gRNA design, and will pave the way for further advance genome and epigenome engineering.

Keywords: CRISPR/Cas systems, gRNA mining, Streptococcus pyogenes, Streptococcus thermophiles

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Authors: Andrii Natochii

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We are currently presenting the recent results from the CERN accelerator facilities obtained in the frame of the UA9 Collaboration. The UA9 experiment investigates how a tiny silicon bent crystal (few millimeters long) can be used for various high-energy physics applications. Due to the huge electrostatic field (tens of GV/cm) between crystalline planes, there is a probability for charged particles, impinging the crystal, to be trapped in the channeling regime. It gives a possibility to steer a high intensity and momentum beam by bending the crystal: channeled particles will follow the crystal curvature and deflect on the certain angle (from tens microradians for LHC to few milliradians for SPS energy ranges). The measurements at SPS, performed in 2017 and 2018, confirmed that the protons deflected by the first crystal, inserted in the primary beam halo, can be caught and channeled by the second crystal. In this configuration, we measure the single pass deflection efficiency of the second crystal and prove our opportunity to perform the fixed target experiment at SPS accelerator (LHC in the future).

Keywords: channeling, double-crystal setup, fixed target experiment, Timepix detector

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Authors: Siddiq Ahmed

Abstract:

The current study aimed to investigate the effectiveness of a Peer-Mediated Intervention (PMI) on writing skills for a student with autism spectrum disorders in inclusive classrooms. The participants in this study were two students, one as a tutor and another as a tutee who was diagnosed with autism spectrum disorder (ASD). The target participant struggled with writing skills and was paired with a student with high academic outcomes. The Tutor had a readiness to act as a tutor for his peer and was trained on how to assist his peer and how to identify and guide his peer’s writing mistakes. Multiple baseline design across behaviors was implemented to monitor the student’s progress in writing skills. The results of the present study showed that PMI yielded significant improvements in academic achievements for the target student. This study suggests that further studies should replicate the current study with an intensive focus on other academic skills such as reading comprehension, writing social stories, and math.

Keywords: peer tutoring, writing skills, autism, inclusion

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Authors: Moustafa Osman

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Modeling of air pollutants from the accidental release is performed for quantifying the impact of industrial facilities into the ambient air. The mathematical methods are requiring for the prediction of the accidental scenario in probability of failure-safe mode and analysis consequences to quantify the environmental damage upon human health. The initial statement of mitigation plan is supporting implementation during production and maintenance periods. In a number of mathematical methods, the flow rate at which gaseous and liquid pollutants might be accidentally released is determined from various types in term of point, line and area sources. These emissions are integrated meteorological conditions in simplified stability parameters to compare dispersion coefficients from non-continuous air pollution plumes. The differences are reflected in concentrations levels and greenhouse effect to transport the parcel load in both urban and rural areas. This research reveals that the elevation effect nearby buildings with other structure is higher 5 times more than open terrains. These results are agreed with Sutton suggestion for dispersion coefficients in different stability classes.

Keywords: air pollutants, dispersion modeling, GIS, health effect, urban planning

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Authors: Sanja Pfeifer, Nataša Šarlija, Marina Jeger, Ana Bilandžić

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The purpose of this study is to explore the different facets of growth among micro, small and medium-sized firms in Croatia and to analyze the differences between models designed for all micro, small and medium-sized firms and those in creative industries. Three growth prediction models were designed and tested using the growth of sales, employment and assets of the company as dependent variables. The key drivers of sales growth are: prudent use of cash, industry affiliation and higher share of intangible assets. Growth of assets depends on retained profits, internal and external sources of financing, as well as industry affiliation. Growth in employment is closely related to sources of financing, in particular, debt and it occurs less frequently than growth in sales and assets. The findings confirm the assumption that growth strategies of small and medium-sized enterprises (SMEs) in creative industries have specific differences in comparison to SMEs in general. Interestingly, only 2.2% of growing enterprises achieve growth in employment, assets and sales simultaneously.

Keywords: creative industries, growth prediction model, growth determinants, growth measures

Procedia PDF Downloads 332

Authors: Babak Bahri, Fatemeh Yassaee Meybodi, Changiz Eslahchi

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In the pursuit of effective cancer therapies, the exploration of combinatorial drug regimens is crucial to leverage synergistic interactions between drugs, thereby improving treatment efficacy and overcoming drug resistance. However, identifying synergistic drug pairs poses challenges due to the vast combinatorial space and limitations of experimental approaches. This study introduces ClusterSyn, a machine learning (ML)-powered framework for classifying anti-cancer drug synergy scores. ClusterSyn employs a two-step approach involving drug clustering and synergy score prediction using a fully connected deep neural network. For each cell line in the training dataset, a drug graph is constructed, with nodes representing drugs and edge weights denoting synergy scores between drug pairs. Drugs are clustered using the Markov clustering (MCL) algorithm, and vectors representing the similarity of drug pairs to each cluster are input into the deep neural network for synergy score prediction (synergy or antagonism). Clustering results demonstrate effective grouping of drugs based on synergy scores, aligning similar synergy profiles. Subsequently, neural network predictions and synergy scores of the two drugs on others within their clusters are used to predict the synergy score of the considered drug pair. This approach facilitates comparative analysis with clustering and regression-based methods, revealing the superior performance of ClusterSyn over state-of-the-art methods like DeepSynergy and DeepDDS on diverse datasets such as Oniel and Almanac. The results highlight the remarkable potential of ClusterSyn as a versatile tool for predicting anti-cancer drug synergy scores.

Keywords: drug synergy, clustering, prediction, machine learning., deep learning

Procedia PDF Downloads 81