Search results for: sequence dependent setup time

Authors: Sobiya George, Anna Dora Gudmundsdottir

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The 2-hydroxychalcones form an important group of organic compounds not only because of their pharmacological properties but also because they are intermediates in the biosynthesis of flavanones. We studied the photoreactivity of 2-hydroxychalcone derivatives in aprotic solvent acetonitrile and found that their photochemistry is concentration-dependent. Irradiation of 2-hydroxychalcone derivatives with 365 nm light emitting diode (LED) in dilute concentration selectively forms flavanones, whereas, at higher concentrations, an additional photoproduct is observed. However, the application of the continuous photo-flow method resulted in the selective formation of flavanones even at higher concentrations. To understand the reaction mechanism and explain the concentration-dependent photoreactivity of 2-hydroxychalcones, we preformed trapping studies with tris(trimethylsilyl)silane, nanosecond laser flash photolysis, and time dependent-density functional theory (TD-DFT) calculations.

Keywords: flavanones, hydroxychalcones, laser flash photolysis, TD-DFT calculations

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Authors: Palanisamy Sivanandy, Tan Tyng Wei, Tan Wee Loon, Lim Chong Yee

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Background: Patient safety has become a major concern over recent years with elevated medication errors; particularly prescribing and dispensing errors. Meticulous prescription screening and diligent drug dispensing is therefore important to prevent drug-related adverse events from inflicting harm to patients. Hence, pharmacists play a significant role in this scenario. The evaluation of patient safety in a pharmacy setup is crucial to contemplate current practices, attitude and perception of pharmacists towards patient safety. Method: The questionnaire for Pharmacy Survey on Patient Safety Culture developed by the Agency for Healthcare and Research Quality (AHRQ) was used to assess patient safety. Main objectives of the study was to evaluate the attitude and perception of pharmacists towards patient safety in retail pharmacies setup in Malaysia. Results: 417 questionnaire were distributed via convenience sampling in three different states of Malaysia, where 390 participants were responded and the response rate was 93.52%. The overall positive response rate (PRR) was ranged from 31.20% to 87.43% and the average PRR was found to be 67%. The overall patient safety grade for our pharmacies was appreciable and it ranges from good to very good. The study found a significant difference in the perception of senior and junior pharmacists towards patient safety. The internal consistency of the questionnaire contents /dimensions was satisfactory (Cronbach’s alpha - 0.92). Conclusion: Our results reflect that there was positive attitude and perception of retail pharmacists towards patient safety. Despite this, various efforts can be implemented in the future to amplify patient safety in retail pharmacies setup.

Keywords: patient safety, attitude, perception, positive response rate, medication errors

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Authors: Gurjit Kaur, Shashank Johri, Arpit Mehrotra

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In this paper we have analyzed and compared the performance of various coding schemes. The basic ID prime sequence codes are unique in only dimension i.e. time slots whereas 2D coding techniques are not unique by their time slots but with their wavelengths also. In this research we have evaluated and compared the performance of 1D and 2D coding techniques constructed using prime sequence coding pattern for OCDMA system on a single platform. Results shows that 1D Extended Prime Code (EPC) can support more number of active users compared to other codes but at the expense of larger code length which further increases the complexity of the code. Modified Prime Code (MPC) supports lesser number of active users at λc=2 but it has a lesser code length as compared to 1D prime code. Analysis shows that 2D prime code supports lesser number of active users than 1D codes but they are having large code family and are the most secure codes compared to other codes. The performance of all these codes is analyzed on basis of number of active users supported at a Bit Error Rate (BER) of 10-9.

Keywords: CDMA, OCDMA, BER, OOC, PC, EPC, MPC, 2-D PC/PC, λc, λa

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Authors: Himanshu Kumar Gupta

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The Jaisalmer Basin is one of the parts of the Rajasthan basin in northwestern India. The presence of five major unconformities/hiatuses of varying span i.e. at the top of Archean basement, Cambrian, Jurassic, Cretaceous, and Eocene have created the foundation for constructing a sequence stratigraphic framework. Based on basin formative tectonic events and their impact on sedimentation processes three first-order sequences have been identified in Rajasthan Basin. These are Proterozoic-Early Cambrian rift sequence, Permian to Middle-Late Eocene shelf sequence and Pleistocene - Recent sequence related to Himalayan Orogeny. The Permian to Middle Eocene I order sequence is further subdivided into three-second order sequences i.e. Permian to Late Jurassic II order sequence, Early to Late Cretaceous II order sequence and Paleocene to Middle-Late Eocene II order sequence. In this study, Late Jurassic to Early Cretaceous sequence was identified and log-based interpretation of smaller order T-R cycles have been carried out. A log profile from eastern margin to western margin (up to Shahgarh depression) has been taken. The depositional environment penetrated by the wells interpreted from log signatures gave three major facies association. The blocky and coarsening upward (funnel shape), the blocky and fining upward (bell shape) and the erratic (zig-zag) facies representing distributary mouth bar, distributary channel and marine mud facies respectively. Late Jurassic Formation (Baisakhi-Bhadasar) and Early Cretaceous Formation (Pariwar) shows a lesser number of T-R cycles in shallower and higher number of T-R cycles in deeper bathymetry. Shallowest well has 3 T-R cycles in Baisakhi-Bhadasar and 2 T-R cycles in Pariwar, whereas deeper well has 4 T-R cycles in Baisakhi-Bhadasar and 8 T-R cycles in Pariwar Formation. The Maximum Flooding surfaces observed from the stratigraphy analysis indicate major shale break (high shale content). The study area is dominated by the alternation of shale and sand lithologies, which occurs in an approximate ratio of 70:30. A seismo-geological cross section has been prepared to understand the stratigraphic thickness variation and structural disposition of the strata. The formations are quite thick to the west, the thickness of which reduces as we traverse towards the east. The folded and the faulted strata indicated the compressional tectonics followed by the extensional tectonics. Our interpretation is supported with seismic up to second order sequence indicates - Late Jurassic sequence is a Highstand Systems Tract (Baisakhi - Bhadasar formations), and the Early Cretaceous sequence is Regressive to Lowstand System Tract (Pariwar Formation).

Keywords: Jaisalmer Basin, sequence stratigraphy, system tract, T-R cycle

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Authors: Mustafa Yorgancılar, Emine Atalay, Necdet Akgün, Ali Topal

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In this study, polymerase chain reaction based Inter-simple sequence repeat (ISSR) from DNA fingerprinting techniques were used to investigate the genetic relationships among barley crossbreed genotypes in Turkey. It is important that selection based on the genetic base in breeding programs via ISSR, in terms of breeding time. 14 ISSR primers generated a total of 97 bands, of which 81 (83.35%) were polymorphic. The highest total resolution power (RP) value was obtained from the F2 (0.53) and M16 (0.51) primers. According to the ISSR result, the genetic similarity index changed between 0.64–095; Lane 3 with Line 6 genotypes were the closest, while Line 36 were the most distant ones. The ISSR markers were found to be promising for assessing genetic diversity in barley crossbreed genotypes.

Keywords: barley, crossbreed, genetic similarity, ISSR

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Authors: S. Nasri, H. Bouziri

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Disasters are quite experienced in our days. They are caused by floods, landslides, and building fires that is the main objective of this study. To cope with these unexpected events, precautions must be taken to protect human lives. The emphasis on disposal work focuses on the resolution of the evacuation problem in case of no-notice disaster. The problem of evacuation is listed as a dynamic network flow problem. Particularly, we model the evacuation problem as an earliest arrival flow problem with load dependent transit time. This problem is classified as NP-Hard. Our challenge here is to propose a metaheuristic solution for solving the evacuation problem. We define our objective as the maximization of evacuees during earliest periods of a time horizon T. The objective provides the evacuation of persons as soon as possible. We performed an experimental study on emergency evacuation from the tunisian children’s hospital. This work prompts us to look for evacuation plans corresponding to several situations where the network dynamically changes.

Keywords: dynamic network flow, load dependent transit time, evacuation strategy, earliest arrival flow problem, tabu search metaheuristic

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Authors: Harsh Panchal, Saurabh Amrutkar

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Quality management is an essential part of any project that has directly related to the performance of a project. Quality management is depended on multiple factors at different stages in a project, right from time management to construction logistics. A project is a mixture of various components that include iternary management, health and safety, crew productivity, and many more. From the survey conducted, we came to the conclusion that advancement in technology and indigenous approach to any project will result in maximum quality standards and better project performance. In this paper, we discuss various components of the factors above that lead to compromise the quality of a project and how it can be controlled in order to achieve maximum quality assurance using quality planning and total quality management. The paper also focuses on limitations and problems faced in each factor responsible for quality management and to tackle them using techniques and processes based on activities and identifying the sequence, approaching critical path, and duration. The project management concept that deals with the sequence of scope cost time give us an overview regarding the ongoing quality management, in a nutshell, giving us hints to regulate the current procedure for maximum achievable quality. It also deals with the problems faced by engineers that make the mundane work process slow, reducing the quality outcome drastically.

Keywords: management, performance, project, quality

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Authors: Farzad Hosseini Hossein Abadi, Cristina Prieto Sierra, Cesar Álvarez Díaz

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Predicting streamflow accurately in flashy catchments prone to floods is a major research and operational challenge in hydrological modeling. Recent advancements in deep learning, particularly Long Short-Term Memory (LSTM) networks, have shown to be promising in achieving accurate hydrological predictions at daily and hourly time scales. In this work, a multi-timescale LSTM (MTS-LSTM) network was applied to the context of regional hydrological predictions at an hourly time scale in flashy catchments. The case study includes 40 catchments allocated in the Basque Country, north of Spain. We explore the impact of hyperparameters on the performance of streamflow predictions given by regional deep learning models through systematic hyperparameter tuning - where optimal regional values for different catchments are identified. The results show that predictions are highly accurate, with Nash-Sutcliffe (NSE) and Kling-Gupta (KGE) metrics values as high as 0.98 and 0.97, respectively. A principal component analysis reveals that a hyperparameter related to the length of the input sequence contributes most significantly to the prediction performance. The findings suggest that input sequence lengths have a crucial impact on the model prediction performance. Moreover, employing catchment-scale analysis reveals distinct sequence lengths for individual basins, highlighting the necessity of customizing this hyperparameter based on each catchment’s characteristics. This aligns with well known “uniqueness of the place” paradigm. In prior research, tuning the length of the input sequence of LSTMs has received limited focus in the field of streamflow prediction. Initially it was set to 365 days to capture a full annual water cycle. Later, performing limited systematic hyper-tuning using grid search, revealed a modification to 270 days. However, despite the significance of this hyperparameter in hydrological predictions, usually studies have overlooked its tuning and fixed it to 365 days. This study, employing a simultaneous systematic hyperparameter tuning approach, emphasizes the critical role of input sequence length as an influential hyperparameter in configuring LSTMs for regional streamflow prediction. Proper tuning of this hyperparameter is essential for achieving accurate hourly predictions using deep learning models.

Keywords: LSTMs, streamflow, hyperparameters, hydrology

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Authors: Joseph C. Chen

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Machine vision system provides automatic inspection to reduce manufacturing costs considerably. However, only a few principles have been found to optimize machine vision system and help it function more accurately in industrial practice. Mostly, there were complicated and impractical design techniques to improve the accuracy of machine vision system. This paper discusses implementing the Six Sigma Define, Measure, Analyze, Improve, and Control (DMAIC) approach to optimize the setup parameters of machine vision system when it is used as a direct measurement technique. This research follows a case study showing how Six Sigma DMAIC methodology has been put into use.

Keywords: DMAIC, machine vision system, process capability, Taguchi Parameter Design

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Authors: H. Y. Jung, Jing Wang, J. H. Park, Hao Shen

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This brief addresses the passivity problem for neural networks with time-varying delays. The aim is focus on establishing the passivity condition of the considered neural networks.

Keywords: neural networks, passivity analysis, time-varying delays, linear matrix inequality

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Authors: Matthew John F. Sino Cruz, Sarah Jane M. Ferrer, Janice C. Francisco

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COVID-19 pandemic has affected more than 114 countries all over the world since it was considered a global health concern in 2020. Different sectors, including education, have shifted to remote/distant setups to follow the guidelines set to prevent the spread of the disease. One of the higher education institutes which shifted to remote setup is the Pangasinan State University (PSU). In order to continue providing quality instructions to the students, PSU designed Flexible Learning Model to still provide services to its stakeholders amidst the pandemic. The model covers the redesigning of delivering instructions in remote setup and the technology needed to support these adjustments. The primary goal of this study is to determine the insights of the PSU – Bayambang students towards the remote setup implemented during the pandemic and how they perceived the initiatives employed in relation to their experiences in flexible learning. In this study, the topic modelling approach was implemented using Latent Dirichlet Allocation. The dataset used in the study. The results show that the most common concern of the students includes time and resource management, poor internet connection issues, and difficulty coping with the flexible learning modality. Furthermore, the findings of the study can be used as one of the bases for the administration to review and improve the policies and initiatives implemented during the pandemic in relation to remote service delivery. In addition, further studies can be conducted to determine the overall sentiment of the other stakeholders in the policies implemented at the University.

Keywords: COVID-19, topic modelling, students’ sentiment, flexible learning, Latent Dirichlet allocation

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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: Sanjoy Barua Chowdhury

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This research is an attempt to examine psychological aspect of the Buddha’s most cardinal and fundamental doctrine of Dependent Origination (paṭiccasamuppāda) along with drawing out a clear picture of the constituents from the law of causation and analyzes the mental states and motivational factors behind each constituent among twelvefold links. Meticulous research into the doctrine of Dependent Origination reveals how the main links from the doctrine of dependent origination provide a framework for psychological analysis through volitional formation (saṅkhāra), consciousness (viññāna), mentality and materiality (nāma-rūpa), contact (phassa), feeling (vedanā), craving (tanhā) and clinging (upādāna). This paper further illustrates the notion of perception (saññā) which can be found in the function of volitional formation (saṅkhāra) - a contributing factor, according to modern psychology, in the role of understanding human (puggala) motivation. The psychological analysis of dependent origination expounds the concept of personality highlighting present existence through the inter-relationship of the five faculties (pañcaupadānakkhandhā), viz., form (rūpa), feeling (vedanā), perception (saññā), volitional formation (saṅkhārā) and consciousness (viññāṇa).

Keywords: dependent origination, perception, motivational factors, feelings

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Authors: Matteo Rossini, Alberto Portioli Staudacher

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The market competition is moving from the single firm to the whole supply chain one because of increasing competition and growing need for operational efficiencies and customer orientation. Supply chain management allows companies to look beyond their organizational boundaries to develop and leverage resources and capabilities of their supply chain partners. This leads to create competitive advantages in the marketplace and because of this SCM has acquired strategic importance. Lean Approach is a management strategy that focuses on reducing every type of waste present in an organization. This approach is becoming more and more popular among supply chain managers. The supply chain application of lean approach is low diffused. It is not well studied which are the impacts of lean approach principles in a supply chain context. In literature there are only few studies simulating the lean approach performance in single products supply chain. This research work studies the impacts of lean principles implementation along a supply chain. To achieve this, a simulation model of a three-echelon multiproduct product supply chain has been built. Kanban system (and several priority policies) and setup time reduction degrees are implemented in the lean-configured supply chain to apply pull and lot-sizing decrease principles respectively. To evaluate the benefits of lean approach, lean supply chain is compared with an EOQ-configured supply chain. The simulation results show that Kanban system and setup-time reduction improve inventory stock level. They also show that logistics efforts are affected to lean implementation degree. The paper concludes describing performances of lean supply chain in different contexts.

Keywords: inventory policy, Kanban, lean supply chain, simulation study, supply chain management, planning

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Authors: Mudawamah Mudawamah, Muhammad Z. Fadli, Gatot Ciptadi, Aulanni’am

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Canary breeders have spread throughout Indonesian regions for the low-middle society and become an income source for them. The interesting phenomenon of the canary market is the feather colours become one of determining factor for the price. The advantages of this research were contributed to the molecular database as a base of selection and mating for the Indonesia canary breeder. The research method was experiment with the genome obtained from canary blood isolation. The genome did the PCR amplification with PMEL marker followed by sequencing. Canaries were used 24 heads of light and dark colour feathers. Research data analyses used BioEdit and Network 4.6.0.0 software. The results showed that all samples were amplification with PMEL gene with 500 bp fragment length. In base sequence of 40 was found Cytosine(C) in the light colour canaries, while the dark colour canaries was obtained Thymine (T) in same base sequence. Sequence results had 286-415 bp fragment and 10 haplotypes. The conclusions were the PMEL gene (gene of white pigment) was likely to be used PMEL gene to detect molecular genetic variation of dark and light colour feather.

Keywords: canary, haplotype, PMEL, sequence

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Authors: Ling Qi, Matloob Khushi, Josiah Poon

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This paper introduces a pre-trained Masked Candlestick Model (MCM) for trading time-series data. The pre-trained model is based on three core designs. First, we convert trading price data at each data point as a set of normalized elements and produce embeddings of each element. Second, we generate a masked sequence of such embedded elements as inputs for self-supervised learning. Third, we use the encoder mechanism from the transformer to train the inputs. The masked model learns the contextual relations among the sequence of embedded elements, which can aid downstream classification tasks. To evaluate the performance of the pre-trained model, we fine-tune MCM for three different downstream classification tasks to predict future price trends. The fine-tuned models achieved better accuracy rates for all three tasks than the baseline models. To better analyze the effectiveness of MCM, we test the same architecture for three currency pairs, namely EUR/GBP, AUD/USD, and EUR/JPY. The experimentation results demonstrate MCM’s effectiveness on all three currency pairs and indicate the MCM’s capability for signal extraction from trading data.

Keywords: masked language model, transformer, time series prediction, trading prediction, embedding, transfer learning, self-supervised learning

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Authors: G. Olamiti; TK. Takalani; D. Beswa, AIO Jideani

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The study investigated the effects of malting and fermentation times on some chemical, functional properties and microstructural behaviour of Agrigreen, Babala pearl millet cultivars and sorghum flours using response surface methodology (RSM). Central Composite Rotatable Design (CCRD) was performed on two independent variables: malting and fermentation times (h), at intervals of 24, 48, and 72, respectively. The results of dependent parameters such as pH, titratable acidity (TTA), Water absorption capacity (WAC), Oil absorption capacity (OAC), bulk density (BD), dispersibility and microstructural behaviour of the flours studied showed a significant difference in p < 0.05 upon malting and fermentation time. Babala flour exhibited a higher pH value at 4.78 at 48 h malted and 81.9 fermentation times. Agrigreen flour showed a higher TTA value at 0.159% at 81.94 h malted and 48 h fermentation times. WAC content was also higher in malted and fermented Babala flour at 2.37 ml g-1 for 81.94 h malted and 48 h fermentation time. Sorghum flour exhibited the least OAC content at 1.67 ml g-1 at 14 h malted and 48 h fermentation times. Agrigreen flour recorded the least bulk density, at 0.53 g ml-1 for 72 h malted and 24 h fermentation time. Sorghum flour exhibited a higher content of dispersibility, at 56.34%, after 24 h malted and 72 h fermented time. The response surface plots showed that increased malting and fermentation time influenced the dependent parameters. The microstructure behaviour of malting and fermentation times of pearl millet varieties and sorghum flours showed isolated, oval, spherical, or polygonal to smooth surfaces. The optimal processing conditions, such as malting and fermentation time for Agrigreen, were 32.24 h and 63.32 h; 35.18 h and 34.58 h for Babala; and 36.75 h and 47.88 h for sorghum with high desirability of 1.00. The validation of the optimum processing malting and fermentation times (h) on the dependent improved the experimented values. Food processing companies can use the study's findings to improve food processing and quality.

Keywords: Pearl millet, malting, fermentation, microstructural behaviour

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Authors: Wameed Alghazali, Shawn Kenny, Paul J. Van Geel

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Settlement of municipal solid waste (MSW) in landfills can be represented by mechanical settlement, which is instantaneous and time-dependent creep components, and biodegradation-induced settlement. Mechanical settlement is governed by the physical characteristics of MSW and the applied overburden pressure. Several research studies used oedometers and different size compression cells to evaluate the primary and mechanical creep compression indices/ratios. However, MSW is known for its heterogeneity, which means data obtained from laboratory testing are not necessary to be a good representation of the mechanical response observed in the field. Furthermore, most of the laboratory tests found in the literature were conducted on shredded samples of MSW to obtain specimens that are suitable for the testing setup. It is believed that shredding MSW samples changes the physical and mechanical properties of the waste. In this study, settlement field data was collected during the filling stage of Ste. Sophie landfill was used to estimate the primary and mechanical creep compression ratios. The field results from Ste. Sophie landfill indicated that both the primary and mechanical creep compression ratios of MSW are not constants but decrease with the increase in the applied vertical stress.

Keywords: mechanical creep compression ratio, municipal solid waste, primary compression ratio, stress level

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Authors: Rajkumar Ghosh

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The Out-of-Sequence Thrust (OOST) is a common phenomenon in collisional tectonic settings like the Himalayas. These OOSTs are activated in different locations at different time frames. These OOST are linked with the multiple Himalayan Thrusts. Apart from minimal documentation in geological mapping for OOST, there exists a lack of field data to establish OOST in the field. This work has considered three thrusts from NW Himalaya in Himachal Pradesh with published data from other sources, allowing a re-examination for correlation of OOST. For the Sutlej section, the approach has been to do fieldwork and microstructural studies. The information related to the cross-cut signature of S/C- and relative time relation could help to predict the nature of OOST. The activation timing, along with the basis of identification of OOST in Higher Himalayan, was documented in various literature. Compilation of the Grain Boundary Migration (GBM) associated temperature range (400–750 °C) was documented from microstructural studies along the Jhakri-Chaura section. No such significant temperature variation across thrusts was observed. Strain variation paths using S Ʌ C angle measurement were carried out along the Jeori-Wangtu transect to distinguish overprinting structures for OOSTs. Near the Chaura Thrust (CT), angular variation of S Ʌ C was documented, and it varies within a range of 15° - 28 °. Along the NH22 (National Highway, 22), all tectonic units of the orogen are exposed in NW Himalaya, INDIA. But there are inherent difficulties in finding field evidence of OOST, largely due to the lack of adequate surface morphology, including topography and drainage pattern.

Keywords: out-of-sequence thrust (OOST), main central thrust (MCT), south tibetan detachment system (STDS), jhakri thrust (JT), sarahan thrust (ST), chaura thrust (CT), higher himalaya (HH), greater himalayan crystalline (GHC)

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Qinglin Liu, Zhiyong Lin, Zongheng Wei, Jianfeng Wen, Congming Yi, Hai Liu

Abstract:

The multi-channel blind rendezvous problem in distributed cognitive radio networks (DCRNs) refers to how users in the network can hop to the same channel at the same time slot without any prior knowledge (i.e., each user is unaware of other users' information). The channel hopping (CH) technique is a typical solution to this blind rendezvous problem. In this paper, we propose a quinary coding and matrix structure-based CH algorithm called QCMS-CH. The QCMS-CH algorithm can guarantee the rendezvous of users using only one cognitive radio in the scenario of the asynchronous clock (i.e., arbitrary time drift between the users), heterogeneous channels (i.e., the available channel sets of users are distinct), and symmetric role (i.e., all users play a same role). The QCMS-CH algorithm first represents a randomly selected channel (denoted by R) as a fixed-length quaternary number. Then it encodes the quaternary number into a quinary bootstrapping sequence according to a carefully designed quaternary-quinary coding table with the prefix "R00". Finally, it builds a CH matrix column by column according to the bootstrapping sequence and six different types of elaborately generated subsequences. The user can access the CH matrix row by row and accordingly perform its channel, hoping to attempt rendezvous with other users. We prove the correctness of QCMS-CH and derive an upper bound on its Maximum Time-to-Rendezvous (MTTR). Simulation results show that the QCMS-CH algorithm outperforms the state-of-the-art in terms of the MTTR and the Expected Time-to-Rendezvous (ETTR).

Keywords: channel hopping, blind rendezvous, cognitive radio networks, quaternary-quinary coding

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Authors: Baris Can Yalcin

Abstract:

Motion sensors have been commonly used as a valuable component in mechatronic systems, however, many mechatronic designs and applications that need motion sensors cost enormous amount of money, especially high-tech systems. Design of a software for communication protocol between data acquisition card and motion sensor is another issue that has to be solved. This study presents how to design a low cost motion data acquisition setup consisting of MPU 6050 motion sensor (gyro and accelerometer in 3 axes) and Arduino Mega2560 microcontroller. Design parameters are calibration of the sensor, identification and communication between sensor and data acquisition card, interpretation of data collected by the sensor.

Keywords: design, mechatronics, motion sensor, data acquisition

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Authors: Aloke Bapli, Debabrata Seth

Abstract:

Graphene oxide (GO) is the two-dimensional (2D) nanoscale allotrope of carbon having several physiochemical properties such as high mechanical strength, high surface area, strong thermal and electrical conductivity makes it an important candidate in various modern applications such as drug delivery, supercapacitors, sensors etc. GO has been used in the photothermal treatment of cancers and Alzheimer’s disease etc. The main idea to choose GO in our work is that it is a surface active molecule, it has a large number of hydrophilic functional groups such as carboxylic acid, hydroxyl, epoxide on its surface and in basal plane. So it can easily interact with organic fluorophores through hydrogen bonding or any other kind of interaction and easily modulate the photophysics of the probe molecules. We have used different spectroscopic techniques for our work. The Ground-state absorption spectra and steady-state fluorescence emission spectra were measured by using UV-Vis spectrophotometer from Shimadzu (model-UV-2550) and spectrofluorometer from Horiba Jobin Yvon (model-Fluoromax 4P) respectively. All the fluorescence lifetime and anisotropy decays were collected by using time-correlated single photon counting (TCSPC) setup from Edinburgh instrument (model: LifeSpec-II, U.K.). Herein, we described the photophysics of a hydrophilic molecule 7-(n,n׀-diethylamino) coumarin-3-carboxylic acid (7-DCCA) in the reverse micelles containing GO. It was observed that photophysics of dye is modulated in the presence of GO compared to photophysics of dye in the absence of GO inside the reverse micelles. Here we have reported the solvent relaxation and rotational relaxation time in GO containing reverse micelle and compare our work with normal reverse micelle system by using 7-DCCA molecule. Normal reverse micelle means reverse micelle in the absence of GO. The absorption maxima of 7-DCCA were blue shifted and emission maxima were red shifted in GO containing reverse micelle compared to normal reverse micelle. The rotational relaxation time in GO containing reverse micelle is always faster compare to normal reverse micelle. Solvent relaxation time, at lower w₀ values, is always slower in GO containing reverse micelle compare to normal reverse micelle and at higher w₀ solvent relaxation time of GO containing reverse micelle becomes almost equal to normal reverse micelle. Here emission maximum of 7-DCCA exhibit bathochromic shift in GO containing reverse micelles compared to that in normal reverse micelles because in presence of GO the polarity of the system increases, as polarity increases the emission maxima was red shifted an average decay time of GO containing reverse micelle is less than that of the normal reverse micelle. In GO containing reverse micelle quantum yield, decay time, rotational relaxation time, solvent relaxation time at λₑₓ=375 nm is always higher than λₑₓ=405 nm, shows the excitation wavelength dependent photophysics of 7-DCCA in GO containing reverse micelles.

Keywords: photophysics, reverse micelle, rotational relaxation, solvent relaxation

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Authors: Xiao Zhou, Jianlin Cheng

Abstract:

A single amino acid mutation can have a significant impact on the stability of protein structure. Thus, the prediction of protein stability change induced by single site mutations is critical and useful for studying protein function and structure. Here, we presented a deep learning network with the dropout technique for predicting protein stability changes upon single amino acid substitution. While using only protein sequence as input, the overall prediction accuracy of the method on a standard benchmark is >85%, which is higher than existing sequence-based methods and is comparable to the methods that use not only protein sequence but also tertiary structure, pH value and temperature. The results demonstrate that deep learning is a promising technique for protein stability prediction. The good performance of this sequence-based method makes it a valuable tool for predicting the impact of mutations on most proteins whose experimental structures are not available. Both the downloadable software package and the user-friendly web server (DNpro) that implement the method for predicting protein stability changes induced by amino acid mutations are freely available for the community to use.

Keywords: bioinformatics, deep learning, protein stability prediction, biological data mining

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Authors: Dong Tran, Thanh Dac Van, Ly Le

Abstract:

Hemagglutinin (HA) and Neuraminidase (NA) play an important role in host immune evasion across influenza virus evolution process. The correlation between HA and NA evolution in respect to epitopic evolution and drug interaction has yet to be investigated. In this study, combining of sequence to structure evolution and statistical analysis on epitopic/binding site specificity, we identified potential therapeutic features of HA and NA that show specific antibody binding site of HA and specific binding distribution within NA active site of current inhibitors. Our approach introduces the use of sequence variation and molecular interaction to provide an effective strategy in establishing experimental based distributed representations of protein-protein/ligand complexes. The most important advantage of our method is that it does not require complete dataset of complexes but rather directly inferring feature interaction from sequence variation and molecular interaction. Using correlated sequence analysis, we additionally identified co-evolved mutations associated with maintaining HA/NA structural and functional variability toward immunity and therapeutic treatment. Our investigation on the HA binding specificity revealed unique conserved stalk domain interacts with unique loop domain of universal antibodies (CR9114, CT149, CR8043, CR8020, F16v3, CR6261, F10). On the other hand, NA inhibitors (Oseltamivir, Zaninamivir, Laninamivir) showed specific conserved residue contribution and similar to that of NA substrate (sialic acid) which can be exploited for drug design. Our study provides an important insight into rational design and identification of novel therapeutics targeting universally recognized feature of influenza HA/NA.

Keywords: influenza virus, hemagglutinin (HA), neuraminidase (NA), sequence evolution

Procedia PDF Downloads 147

Authors: Anahit Hakobjanyan, Zdenka Navratilova, Gabriela Strakova, Martin Petrek

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Aging has a suppressive influence on human immune cells. Apoptosis may play important role in age-dependent immunosuppression and lymphopenia. Prevention of apoptosis may be promoted by BCL2-dependent and BCL2-independent manner. BCL2 is an antiapoptotic factor that has an antioxidative role by locating the glutathione at mitochondria and repressing oxidative stress. STAT3 may suppress apoptosis in BCL2-independent manner and promote cell survival blocking cytochrome-c release and reducing ROS production. The aim of our study was to estimate the influence of aging on BCL2-dependent and BCL2-independent prevention of apoptosis via measurement of BCL2 and STAT3 mRNAs expressions. The study was done on Armenian population (2 groups: 37 healthy young (mean age±SE; min/max age, male/female: 37.6±1.1; 20/54, 15/22), 28 healthy aged (66.7±1.5; 57/85, 12/16)). mRNA expression in peripheral blood leukocytes (PBL) was determined by RT-PCR using PSMB2 as the reference gene. Statistical analysis was done with Graph-Pad Prism 5; P < 0.05 considered as significant. The expression of BCL2 mRNA was lower in aged group (0.199) compared with young ones (0.643)(p < 0.01). Decrease expression was also recorded for female and male subgroups (p < 0.01). The expression level of STAT3 mRNA was increased (young, 0.228; aged, 0.428) (p < 0.05) during aging (in the whole age group and male/female subgroups). Decreased level of BCL2 mRNA may indicate about the suppression of BCL2-dependent prevention of apoptosis during aging in peripheral blood leukocytes. At the same time increased the level of STAT3 may suggest about activation of BCL2-independent prevention of apoptosis during aging.

Keywords: BCL2, STAT3, aging, apoptosis

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Authors: Perdana Rakhmana Putra, Hansen Wijaya, Sri Budiyani, Muhamad Natsir, Alexis badai Samudra

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The Palembang Sub-Basin (PSB) located in southern part of South Sumatera basin (SSB) consist of half-graben complex trending N-S to NW-SE. These geometries are believe as an impact of strike-slip regime developed in Eocene-Oligocene. Generally, most of the wells in this area produced hydrocarbon from late stage of syn-rift sequences called Lower Talang Akar (LTAF) and post-rift sequences called Batu Raja Formation (BRF) and drilled to proved hydrocarbon on structural trap; three-way dip anticline, four-way dip anticline, dissected anticline, and stratigraphy trap; carbonate build-up and stratigraphic pinch out. Only a few wells reached the deeper syn-rift sequences called Lahat Formation (LAF) and Lemat Formation (LEF). The new interpretation of subsurface data was done by the tectonostratigraphy concept and focusing on syn-rift sequence. Base on seismic characteristic on basin centre, it divided into four sequences: pre-rift sequence, rift initiation, maximum rift and late rift. These sequences believed as a new exploration target on PSB mature basin. This paper will demonstrate the paleo depositional setting during Paleogene and exploration play concept of syn-rift sequence in PSB. The main play for this area consists of stratigraphic and structure play, where the stratigraphic play is Eocene-Oligocene sediment consist of LAF sandstone, LEF-Benakat formation, and LAF with pinch-out geometry. The pinch-out, lenses geometry and on-lap features can be seen on the seismic reflector and formed at the time of the syn-rift sequence. The structural play is dominated by a 3 Way Dip play related to reverse fault trap.

Keywords: syn-rift, tectono-stratigraphy, exploration play, basin center play, south sumatera basin

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Authors: Atef Ibrahim, Hamed Elsimary, Abdullah Aljumah, Fayez Gebali

Abstract:

This paper presents a novel semi-systolic array architecture for an optimized parallel sequence alignment algorithm. This architecture has the advantage that it can be modified to be reused for multiple pass processing in order to increase the number of processing elements that can be packed into a single FPGA and to increase the number of sequences that can be aligned in parallel in a single FPGA. This resolves the potential problem of many FPGA resources left unused for designs that have large values of short read length. When using the previously published conventional hardware design. FPGA implementation results show that, for large values of short read lengths (M>128), the proposed design has a slightly higher speed up and FPGA utilization over the the conventional one.

Keywords: bioinformatics, genome sequence alignment, re-sequencing applications, systolic array

Procedia PDF Downloads 515

Authors: Yuexi Xiong, Jingwu He

Abstract:

The structural components in an energy facility such as steam turbine machines are operated under high stress and elevated temperature in an endured time period and thus the creep deformation and creep rupture failure are important issues that need to be addressed in the design of such components. There are numerous creep models being used for creep analysis that have both advantages and disadvantages in terms of accuracy and efficiency. The Isochronous Creep Analysis is one of the simplified approaches in which a full-time dependent creep analysis is avoided and instead an elastic-plastic analysis is conducted at each time point. This approach has been established based on the rupture dependent creep equations using the well-known Larson-Miller parameter. In this paper, some fundamental aspects of creep deformation and the rupture dependent creep models are reviewed and the analysis procedures using isochronous creep curves are discussed. Four rupture failure criteria are examined from creep fundamental perspectives including criteria of Stress Damage, Strain Damage, Strain Rate Damage, and Strain Capability. The accuracy of these criteria in predicting creep life is discussed and applications of the creep analysis procedures and failure predictions of simple models will be presented. In addition, a new failure criterion is proposed to improve the accuracy and effectiveness of the existing criteria. Comparisons are made between the existing criteria and the new one using several examples materials. Both strain increase and stress relaxation form a full picture of the creep behaviour of a material under high temperature in an endured time period. It is important to bear this in mind when dealing with creep problems. Accordingly there are two sets of rupture dependent creep equations. While the rupture strength vs LMP equation shows how the rupture time depends on the stress level under load controlled condition, the strain rate vs rupture time equation reflects how the rupture time behaves under strain-controlled condition. Among the four existing failure criteria for rupture life predictions, the Stress Damage and Strain Damage Criteria provide the most conservative and non-conservative predictions, respectively. The Strain Rate and Strain Capability Criteria provide predictions in between that are believed to be more accurate because the strain rate and strain capability are more determined quantities than stress to reflect the creep rupture behaviour. A modified Strain Capability Criterion is proposed making use of the two sets of creep equations and therefore is considered to be more accurate than the original Strain Capability Criterion.

Keywords: creep analysis, high temperature mateials, rapture evalution, steam turbine machines

Procedia PDF Downloads 280