Search results for: sequence diagram

Authors: N. D'Amico, E. Grossi, B. Colombo, F. Rigiroli, M. Buscema, D. Fazzini, G. Cornalba, S. Papa

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Purpose: To characterize, through a radiomic approach, the nature of nodules considered non-specific by expert radiologists, recognized in magnetic resonance mammography (MRm) with T1-weighted (T1w) sequences with paramagnetic contrast. Material and Methods: 47 cases out of 1200 undergoing MRm, in which the MRm assessment gave uncertain classification (non-specific nodules), were admitted to the study. The clinical outcome of the non-specific nodules was later found through follow-up or further exams (biopsy), finding 35 benign and 12 malignant. All MR Images were acquired at 1.5T, a first basal T1w sequence and then four T1w acquisitions after the paramagnetic contrast injection. After a manual segmentation of the lesions, done by a radiologist, and the extraction of 150 radiomic features (30 features per 5 subsequent times) a machine learning (ML) approach was used. An evolutionary algorithm (TWIST system based on KNN algorithm) was used to subdivide the dataset into training and validation test and to select features yielding the maximal amount of information. After this pre-processing, different machine learning systems were applied to develop a predictive model based on a training-testing crossover procedure. 10 cases with a benign nodule (follow-up older than 5 years) and 18 with an evident malignant tumor (clear malignant histological exam) were added to the dataset in order to allow the ML system to better learn from data. Results: NaiveBayes algorithm working on 79 features selected by a TWIST system, resulted to be the best performing ML system with a sensitivity of 96% and a specificity of 78% and a global accuracy of 87% (average values of two training-testing procedures ab-ba). The results showed that in the subset of 47 non-specific nodules, the algorithm predicted the outcome of 45 nodules which an expert radiologist could not identify. Conclusion: In this pilot study we identified a radiomic approach allowing ML systems to perform well in the diagnosis of a non-specific nodule at MR mammography. This algorithm could be a great support for the early diagnosis of malignant breast tumor, in the event the radiologist is not able to identify the kind of lesion and reduces the necessity for long follow-up. Clinical Relevance: This machine learning algorithm could be essential to support the radiologist in early diagnosis of non-specific nodules, in order to avoid strenuous follow-up and painful biopsy for the patient.

Keywords: breast, machine learning, MRI, radiomics

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Authors: Markus Rütten, Olaf Wünsch

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Non-Newtonian fluid properties can change the flow behaviour significantly, its prediction is more difficult when thermal effects come into play. Hence, the focal point of this work is the wake flow behind a heated circular cylinder in the laminar vortex shedding regime for thermo-viscous shear thinning fluids. In the case of isothermal flows of Newtonian fluids the vortex shedding regime is characterised by a distinct Reynolds number and an associated Strouhal number. In the case of thermo-viscous shear thinning fluids the flow regime can significantly change in dependence of the temperature of the viscous wall of the cylinder. The Reynolds number alters locally and, consequentially, the Strouhal number globally. In the present CFD study the temperature dependence of the Reynolds and Strouhal number is investigated for the flow of a Carreau fluid around a heated cylinder. The temperature dependence of the fluid viscosity has been modelled by applying the standard Williams-Landel-Ferry (WLF) equation. In the present simulation campaign thermal boundary conditions have been varied over a wide range in order to derive a relation between dimensionless heat transfer, Reynolds and Strouhal number. Together with the shear thinning due to the high shear rates close to the cylinder wall this leads to a significant decrease of viscosity of three orders of magnitude in the nearfield of the cylinder and a reduction of two orders of magnitude in the wake field. Yet the shear thinning effect is able to change the flow topology: a complex K´arm´an vortex street occurs, also revealing distinct characteristic frequencies associated with the dominant and sub-dominant vortices. Heating up the cylinder wall leads to a delayed flow separation and narrower wake flow, giving lesser space for the sequence of counter-rotating vortices. This spatial limitation does not only reduce the amplitude of the oscillating wake flow it also shifts the dominant frequency to higher frequencies, furthermore it damps higher harmonics. Eventually the locally heated wake flow smears out. Eventually, the CFD simulation results of the systematically varied thermal flow parameter study have been used to describe a relation for the main characteristic order parameters.

Keywords: heat transfer, thermo-viscous fluids, shear thinning, vortex shedding

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Authors: Kumar Divyendra

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Underwater Sensor Networks (UWSNs) have wide applications in areas such as water quality monitoring, marine wildlife management etc. A typical UWSN system consists of a set of sensors deployed randomly underwater which communicate with each other using acoustic links. RF communication doesn't work underwater, and GPS too isn't available underwater. Additionally Automated Underwater Vehicles (AUVs) are deployed to collect data from some special nodes called Cluster Heads (CHs). These CHs aggregate data from their neighboring nodes and forward them to the AUVs using optical links when an AUV is in range. This helps reduce the number of hops covered by data packets and helps conserve energy. We consider the three-dimensional model of the UWSN. Nodes are initially deployed randomly underwater. They attach themselves to the surface using a rod and can only move upwards or downwards using a pump and bladder mechanism. We use graph theory concepts to maximize the coverage volume while every node maintaining connectivity with at least one surface node. We treat the surface nodes as landmarks and each node finds out its hop distance from every surface node. We treat these hop-distances as coordinates and use them for AUV navigation. An AUV intending to move closer to a node with given coordinates moves hop by hop through nodes that are closest to it in terms of these coordinates. In absence of GPS, multiple different approaches like Inertial Navigation System (INS), Doppler Velocity Log (DVL), computer vision-based navigation, etc., have been proposed. These systems have their own drawbacks. INS accumulates error with time, vision techniques require prior information about the environment. We propose a method that makes use of the earth's magnetic field values for navigation and combines it with other methods that simultaneously increase the coverage volume under the UWSN. The AUVs are fitted with magnetometers that measure the magnetic intensity (I), horizontal inclination (H), and Declination (D). The International Geomagnetic Reference Field (IGRF) is a mathematical model of the earth's magnetic field, which provides the field values for the geographical coordinateson earth. Researchers have developed an inverse deep learning model that takes the magnetic field values and predicts the location coordinates. We make use of this model within our work. We combine this with with the hop-by-hop movement described earlier so that the AUVs move in such a sequence that the deep learning predictor gets trained as quickly and precisely as possible We run simulations in MATLAB to prove the effectiveness of our model with respect to other methods described in the literature.

Keywords: clustering, deep learning, network backbone, parallel computing

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Authors: Falana Yetunde Olaitan, Ijah U. J. J, Solebo Shakirat O.

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Genetically modified crops are already phenomenally successful and are grown worldwide in more than eighteen countries on more than 67 million hectares. Nigeria, in October 2018, approved Bacillus thuringiensis (Bt) cotton and maize; therefore, the need to carry out environmental risk assessment studies. A total of 15 4L octagonal ceramic pots were filled with 4kg of soil and placed on the bench in 2 rows of 10 pots each and the 3rd row of 5 pots, 1st-row pots were used to plant GM cotton seeds, while the 2nd-row pots were used for non-GM cotton seeds and the 3rd row of 5 pots served as control, all in the screen house. Soil samples for metagenomic DNA extraction were collected at random and at the monthly interval after planting at a distance of 2mm from the plant’s root and at a depth of 10cm using a sterile spatula. Soil samples for physicochemical analysis were collected before planting and after harvesting the GM and non-GM crops as well as from the control soil. The DNA was extracted, quantified and sequenced; Sample 1A (DNA from GM cotton Soil at 1st interval) gave the lowest sequence read with 0.853M while sample 2B (DNA from GM cotton Soil at 2nd interval) gave the highest with 5.785M, others gave between 1.8M and 4.7M. The samples treatment were grouped into four, Group 1 (GM cotton soil from 1 to 3 intervals) had between 800,000 and 5,700,000 strains of microbes (SOM), Group 2 (non GM cotton soil from 1 to 3 intervals) had between 1,400,600 and 4,200,000 SOM, Group 3 (control soil) had between 900,000 and 3,600,000 SOM and Group 4 (initial soil) had between 3,700,000 and 4,000,000 SOM. The microbes observed were predominantly bacteria (including archaea), fungi, dark matter alongside protists and phages. The predominant bacterial groups were the Terrabacteria (Bacillus funiculus, Bacillus sp.), the Proteobacteria (Microvirga massiliensis, sphingomonas sp.) and the Archaea (Nitrososphaera sp.), while the fungi were Aspergillus fischeri and Fusarium falciforme. The comparative analysis between groups was done using JACCARD PERMANOVA beta diversity analysis at P-value not more than 0.76 and there was no significant pair found. The pH for initial, GM cotton, non-GM cotton and control soil were 6.28, 6.26, 7.25, 8.26 and the percentage moisture was 0.63, 0.78, 0.89 and 0.82, respectively, while the percentage Nitrogen was observed to be 17.79, 1.14, 1.10 and 0.56 respectively. Other parameters include, varying concentrations of Potassium (0.46, 1,284.47, 1,785.48, 1,252.83 mg/kg) and Phosphorus (18.76, 17.76, 16.87, 15.23 mg/kg) were recorded for the four treatments respectively. The soil consisted mainly of silt (32.09 to 34.66%) and clay (58.89 to 60.23%), reflecting the soil texture as silty – clay. The results were then tested with ANOVA at less than 0.05 P-value and no pair was found to be significant as well. The results suggest that the GM crops have no significant effect on microbial ecology and physicochemical properties of the soil and, in turn, no direct or indirect effects on human health.

Keywords: genetically modified crop, microbial ecology, physicochemical properties, metagenomics, DNA, soil

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Authors: Rui Wang, Luodi Yu, Dan Huang, Hsuan-Chih Chen, Yang Zhang, Suiping Wang

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Enhanced discrimination of pure tones but diminished discrimination of speech pitch (i.e., lexical tone) were found in children with autism who speak a tonal language (Mandarin), suggesting a speech-specific impairment of pitch perception in these children. However, in tonal languages, both lexical tone and vowel are phonemic cues and integrally dependent on each other. Therefore, it is unclear whether the presence of phonemic vowel dimension contributes to the observed lexical tone deficits in Mandarin-speaking children with autism. The current study employed a multi-feature oddball paradigm to examine how vowel and tone dimensions contribute to the neural responses for syllable change detection and involuntary attentional orienting in school-age Mandarin-speaking children with autism. In the oddball sequence, syllable /da1/ served as the standard stimulus. There were three deviant stimulus conditions, representing tone-only change (TO, /da4/), vowel-only change (VO, /du1/), and change of tone and vowel simultaneously (TV, /du4/). EEG data were collected from 25 children with autism and 20 age-matched normal controls during passive listening to the stimulation. For each deviant condition, difference waveform measuring mismatch negativity (MMN) was derived from subtracting the ERP waveform to the standard sound from that to the deviant sound for each participant. Additionally, the linear summation of TO and VO difference waveforms was compared to the TV difference waveform, to examine whether neural sensitivity for TV change detection reflects simple summation or nonlinear integration of the two individual dimensions. The MMN results showed that the autism group had smaller amplitude compared with the control group in the TO and VO conditions, suggesting impaired discriminative sensitivity for both dimensions. In the control group, amplitude of the TV difference waveform approximated the linear summation of the TO and VO waveforms only in the early time window but not in the late window, suggesting a time course from dimensional summation to nonlinear integration. In the autism group, however, the nonlinear TV integration was already present in the early window. These findings suggest that speech perception atypicality in children with autism rests not only in the processing of single phonemic dimensions, but also in the dimensional integration process.

Keywords: autism, event-related potentials , mismatch negativity, speech perception

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Authors: Emma Avoyan

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The safety standards for flood protection in the Netherlands have been revised recently. It is expected that all major flood-protection structures will have to be reinforced to meet the new standards. The Dutch Flood Protection Programme aims at accomplishing this task through innovative integrated projects such as construction of multi-functional flood defenses. In these projects, flood safety purposes will be combined with spatial planning, nature development, emergency management or other sectoral objectives. Therefore, implementation of dike reinforcement projects requires early involvement and collaboration between public and private sectors, different governmental actors and agencies. The development and implementation of such integrated projects has been an issue in Dutch flood risk management since long. Therefore, this article analyses how cross-sector collaboration within flood risk governance in the Netherlands has evolved over time, and how this development can be explained. The integrative framework for collaborative governance is applied as an analytical tool to map external factors framing possibilities as well as constraints for cross-sector collaboration in Dutch flood risk domain. Supported by an extensive document and literature analysis, the paper offers insights on how the system context and different drivers changing over time either promoted or hindered cross-sector collaboration between flood protection sector, urban development, nature conservation or any other sector involved in flood risk governance. The system context refers to the multi-layered and interrelated suite of conditions that influence the formation and performance of complex governance systems, such as collaborative governance regimes, whereas the drivers initiate and enable the overall process of collaboration. In addition, by applying a method of process tracing we identify a causal and chronological chain of events shaping cross-sectoral interaction in Dutch flood risk management. Our results indicate that in order to evaluate the performance of complex governance systems, it is important to firstly study the system context that shapes it. Clear understanding of the system conditions and drivers for collaboration gives insight into the possibilities of and constraints for effective performance of complex governance systems. The performance of the governance system is affected by the system conditions, while at the same time the governance system can also change the system conditions. Our results show that the sequence of changes within the system conditions and drivers over time affect how cross-sector interaction in Dutch flood risk governance system happens now. Moreover, we have traced the potential of this governance system to shape and change the system context.

Keywords: collaborative governance, cross-sector interaction, flood risk management, the Netherlands

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Authors: Martina Marinelli, Samanta Vellante, Francesco Pilotti, Daniele Di Valerio, Gaetanino Paolone

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Any development in web marketing technology requires changes in information engineering to identify instruments and techniques suitable for the production of software applications for informative marketing. Moreover, for large web solutions, designing an interface that enables human interactions is a complex process that must bridge between informative marketing requirements and the developed solution. A user-friendly interface in web marketing applications is crucial for a successful business. The paper introduces mkInfo - a software platform that implements informative marketing. Informative marketing is a new interpretation of marketing which places the information at the center of every marketing action. The creative team includes software engineering researchers who have recently authored an article on automatic code generation. The authors have created the mkInfo software platform to generate informative marketing web applications. For each web application, it is possible to automatically implement an opt in page, a landing page, a sales page, and a thank you page: one only needs to insert the content. mkInfo implements an autoresponder to send mail according to a predetermined schedule. The mkInfo platform also includes e-commerce for a product or service. The stakeholder can access any opt-in page and get basic information about a product or service. If he wants to know more, he will need to provide an e-mail address to access a landing page that will generate an e-mail sequence. It will provide him with complete information about the product or the service. From this point on, the stakeholder becomes a user and is now able to purchase the product or related services through the mkInfo platform. This paper suggests a possible definition for Informative Marketing, illustrates its basic principles, and finally details the mkInfo platform that implements it. This paper also offers some Informative Marketing models, which are implemented in the mkInfo platform. Informative marketing can be applied to products or services. It is necessary to realize a web application for each product or service. The mkInfo platform enables the product or the service producer to send information concerning a specific product or service to all stakeholders. In conclusion, the technical contributions of this paper are: a different interpretation of marketing based on information; a modular architecture for web applications, particularly for one with standard features such as information storage, exchange, and delivery; multiple models to implement informative marketing; a software platform enabling the implementation of such models in a web application. Future research aims to enable stakeholders to provide information about a product or a service so that the information gathered about a product or a service includes both the producer’s and the stakeholders' point of view. The purpose is to create an all-inclusive management system of the knowledge regarding a specific product or service: a system that includes everything about the product or service and is able to address even unexpected questions.

Keywords: informative marketing, opt in page, software platform, web application

Procedia PDF Downloads 127

Authors: Panupong Lohrattanarungrot, Falan Srisuriyachai

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Polymer flooding is a well-known technique used for controlling mobility ratio in heterogeneous reservoirs, leading to improvement of sweep efficiency as well as wellbore profile. However, low injectivity of viscous polymer solution attenuates oil recovery rate and consecutively adds extra operating cost. An attempt of this study is to improve injectivity of polymer solution while maintaining recovery factor, enhancing effectiveness of polymer flooding method. This study is performed by using reservoir simulation program to modify conventional single polymer slug into sequential polymer flooding, emphasizing on increasing of injectivity and also reduction of polymer amount. Selection of operating conditions for single slug polymer including pre-injected water, polymer concentration and polymer slug size is firstly performed for a layered-heterogeneous reservoir with Lorenz coefficient (Lk) of 0.32. A selected single slug polymer flooding scheme is modified into sequential polymer flooding with reduction of polymer concentration in two different modes: Constant polymer mass and reduction of polymer mass. Effects of Residual Resistance Factor (RRF) is also evaluated. From simulation results, it is observed that first polymer slug with the highest concentration has the main function to buffer between displacing phase and reservoir oil. Moreover, part of polymer from this slug is also sacrificed for adsorption. Reduction of polymer concentration in the following slug prevents bypassing due to unfavorable mobility ratio. At the same time, following slugs with lower viscosity can be injected easily through formation, improving injectivity of the whole process. A sequential polymer flooding with reduction of polymer mass shows great benefit by reducing total production time and amount of polymer consumed up to 10% without any downside effect. The only advantage of using constant polymer mass is slightly increment of recovery factor (up to 1.4%) while total production time is almost the same. Increasing of residual resistance factor of polymer solution yields a benefit on mobility control by reducing effective permeability to water. Nevertheless, higher adsorption results in low injectivity, extending total production time. Modifying single polymer slug into sequence of reduced polymer concentration yields major benefits on reducing production time as well as polymer mass. With certain design of polymer flooding scheme, recovery factor can even be further increased. This study shows that application of sequential polymer flooding can be certainly applied to reservoir with high value of heterogeneity since it requires nothing complex for real implementation but just a proper design of polymer slug size and concentration.

Keywords: polymer flooding, sequential, heterogeneous reservoir, residual resistance factor

Procedia PDF Downloads 478

Authors: Epaminondas G. Kyriakidis, Theodosis D. Dimitrakos, Constantinos C. Karamatsoukis

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The vehicle routing problem (VRP) is a well-known problem in Operations Research and has been widely studied during the last fifty-five years. The context of the VRP is that of delivering products located at a central depot to customers who are scattered in a geographical area and have placed orders for these products. A vehicle or a fleet of vehicles start their routes from the depot and visit the customers in order to satisfy their demands. Special attention has been given to the capacitated VRP in which the vehicles have limited carrying capacity of the goods that must be delivered. In the present work, we present a specific capacitated stochastic vehicle routing problem which has realistic applications to distributions of materials to shops or to healthcare facilities or to military units. A vehicle starts its route from a depot loaded with items of two similar but not identical products. We name these products, product 1 and product 2. The vehicle must deliver the products to N customers according to a predefined sequence. This means that first customer 1 must be serviced, then customer 2 must be serviced, then customer 3 must be serviced and so on. The vehicle has a finite capacity and after servicing all customers it returns to the depot. It is assumed that each customer prefers either product 1 or product 2 with known probabilities. The actual preference of each customer becomes known when the vehicle visits the customer. It is also assumed that the quantity that each customer demands is a random variable with known distribution. The actual demand is revealed upon the vehicle’s arrival at customer’s site. The demand of each customer cannot exceed the vehicle capacity and the vehicle is allowed during its route to return to the depot to restock with quantities of both products. The travel costs between consecutive customers and the travel costs between the customers and the depot are known. If there is shortage for the desired product, it is permitted to deliver the other product at a reduced price. The objective is to find the optimal routing strategy, i.e. the routing strategy that minimizes the expected total cost among all possible strategies. It is possible to find the optimal routing strategy using a suitable stochastic dynamic programming algorithm. It is also possible to prove that the optimal routing strategy has a specific threshold-type structure, i.e. it is characterized by critical numbers. This structural result enables us to construct an efficient special-purpose dynamic programming algorithm that operates only over those routing strategies having this structure. The findings of the present study lead us to the conclusion that the dynamic programming method may be a very useful tool for the solution of specific vehicle routing problems. A problem for future research could be the study of a similar stochastic vehicle routing problem in which the vehicle instead of delivering, it collects products from ordered customers.

Keywords: collection of similar products, dynamic programming, stochastic demands, stochastic preferences, vehicle routing problem

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Authors: Ankita Singh, Chandan Gorain, Amirul I. Mallick

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Successful adherence of the mucosal epithelial cells is the key early step for Campylobacter jejuni pathogenesis (C. jejuni). A set of Surface Exposed Colonization Proteins (SECPs) are among the major factors involved in host cell adherence and invasion of C. jejuni. Among them, constitutively expressed surface-exposed lipoprotein adhesin of C. jejuni, JlpA, interacts with intestinal heat shock protein 90 (hsp90α) and contributes in disease progression by triggering pro-inflammatory response via activation of NF-κB and p38 MAP kinase pathway. Together with its ability to express in the bacterial surface, higher sequence conservation and predicted predominance of several B cells epitopes, JlpA protein reserves its potential to become an effective vaccine candidate against wide range of Campylobacter sps including C. jejuni. Given that chickens are the primary sources for C. jejuni and persistent gut colonization remain as major cause for foodborne pathogenesis to humans, present study explicitly used chickens as model to test the immune-protective efficacy of JlpA protein. Taking into account that gastrointestinal tract is the focal site for C. jejuni colonization, to extrapolate the benefit of mucosal (intragastric) delivery of JlpA protein, a food grade Nisin inducible Lactic acid producing bacteria, Lactococcus lactis (L. lactis) was engineered to express recombinant JlpA protein (rJlpA) in the surface of the bacteria. Following evaluation of optimal surface expression and functionality of recombinant JlpA protein expressed by recombinant L. lactis (rL. lactis), the immune-protective role of intragastric administration of live rL. lactis was assessed in commercial broiler chickens. In addition to the significant elevation of antigen specific mucosal immune responses in the intestine of chickens that received three doses of rL. lactis, marked upregulation of Toll-like receptor 2 (TLR2) gene expression in association with mixed pro-inflammatory responses (both Th1 and Th17 type) was observed. Furthermore, intragastric delivery of rJlpA expressed by rL. lactis, but not the injectable form, resulted in a significant reduction in C. jejuni colonization in chickens suggesting that mucosal delivery of live rL. lactis expressing JlpA serves as a promising vaccine platform to induce strong immune-protective responses against C. jejuni in chickens.

Keywords: chickens, lipoprotein adhesion of Campylobacter jejuni, immuno-protection, Lactococcus lactis, mucosal delivery

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Authors: Wael M. Rabeh, Cesar Carrasco-Lopez, Juliana C. Ferreira, Pance Naumov

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Bioluminescence, the emission of light from a biological process, is found in various living organisms including bacteria, fireflies, beetles, fungus and different marine organisms. Luciferase is an enzyme that catalyzes a two steps oxidation of luciferin in the presence of Mg2+ and ATP to produce oxyluciferin and releases energy in the form of light. The luciferase assay is used in biological research and clinical applications for in vivo imaging, cell proliferation, and protein folding and secretion analysis. The luciferase enzyme consists of two domains, a large N-terminal domain (1-436 residues) that is connected to a small C-terminal domain (440-544) by a flexible loop that functions as a hinge for opening and closing the active site. The two domains are separated by a large cleft housing the active site that closes after binding the substrates, luciferin and ATP. Even though all insect luciferases catalyze the same chemical reaction and share 50% to 90% sequence homology and high structural similarity, they emit light of different colors from green at 560nm to red at 640 nm. Currently, the majority of the structural and biochemical studies have been conducted on green-emitting firefly luciferases. To address the color emission mechanism, we expressed and purified two luciferase enzymes with blue-shifted green and red emission from indigenous Brazilian species Amydetes fanestratus and Phrixothrix, respectively. The two enzymes naturally emit light of different colors and they are an excellent system to study the color-emission mechanism of luciferases, as the current proposed mechanisms are based on mutagenesis studies. Using a vapor-diffusion method and a high-throughput approach, we crystallized and solved the crystal structure of both enzymes, at 1.7 Å and 3.1 Å resolution respectively, using X-ray crystallography. The free enzyme adopted two open conformations in the crystallographic unit cell that are different from the previously characterized firefly luciferase. The blue-shifted green luciferase crystalized as a monomer similar to other luciferases reported in literature, while the red luciferases crystalized as an octamer and was also purified as an octomer in solution. The octomer conformation is the first of its kind for any insect’s luciferase, which might be relate to the red color emission. Structurally designed mutations confirmed the importance of the transition between the open and close conformations in the fine-tuning of the color and the characterization of other interesting mutants is underway.

Keywords: bioluminescence, enzymology, structural biology, x-ray crystallography

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Authors: Auzair Mehmood, Mohammad Arif

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The LCT (Li, Cs and Ta rich)-type pegmatites, genetically related to peraluminous S-type granites, are being mined for strategic metals (SMs) and rare earth elements (REEs) around the world. This study investigates the SMs and REEs potentials of pegmatites that are spatially associated with an S-type granitic suite of the Himalayan sequence, specifically Mansehra Granitic Complex (MGC), northwest Pakistan. Geochemical signatures of the pegmatites and some of their mineral extracts were analyzed using Inductive Coupled Plasma Mass Spectroscopy (ICP-MS) technique to explore and generate potential prospects (if any) for SMs and REEs. In general, the REE patterns of the studied whole-rock pegmatite samples show tetrad effect and possess low total REE abundances, strong positive Europium (Eu) anomalies, weak negative Cesium (Cs) anomalies and relative enrichment in heavy REE. Similar features have been observed on the REE patterns of the feldspar extracts. However, the REE patterns of the muscovite extracts reflect preferential enrichment and possess negative Eu anomalies. The trace element evaluation further suggests that the MGC pegmatites have undergone low levels of fractionation. Various trace elements concentrations (and their ratios) including Ta versus Cs, K/Rb (Potassium/Rubidium) versus Rb and Th/U (Thorium/Uranium) versus K/Cs, were used to analyze the economically viable mineral potential of the studied rocks. On most of the plots, concentrations fall below the dividing line and confer either barren or low-level mineralization potential of the studied rocks for both SMs and REEs. The results demonstrate paucity of the MGC pegmatites with respect to Ta-Nb (Tantalum-Niobium) mineralization, which is in sharp contrast to many Pan-African S-type granites around the world. The MGC pegmatites are classified as muscovite pegmatites based on their K/Rb versus Cs relationship. This classification is consistent with the occurrence of rare accessory minerals like garnet, biotite, tourmaline, and beryl. Furthermore, the classification corroborates with an earlier sorting of the MCG pegmatites into muscovite-bearing, biotite-bearing, and subordinate muscovite-biotite types. These types of pegmatites lack any significant SMs and REEs mineralization potentials. Field relations, such as close spatial association with parent granitic rocks and absence of internal zonation structure, also reflect the barren character and hence lack of any potential prospects of the MGC pegmatites.

Keywords: exploration, fractionation, Himalayas, pegmatites, rare earth elements

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Authors: Sven Tackenberg, Sönke Duckwitz, Andreas Petz, Christopher M. Schlick

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This paper introduces an extension to the well-established Resource-Constrained Project Scheduling Problem (RCPSP) to apply it to complex maintenance problems. The problem is to assign technicians to a team which has to process several tasks with multi-level skill requirements during a work shift. Here, several alternative activities for a task allow both, the temporal shift of activities or the reallocation of technicians and tools. As a result, switches from one valid work process variant to another can be considered and may be selected by the developed evolutionary algorithm based on the present skill level of technicians or the available tools. An additional complication of the observed scheduling problem is that the locations of the construction sites are only temporarily accessible during a day. Due to intensive rail traffic, the available time slots for maintenance and repair works are extremely short and are often distributed throughout the day. To identify efficient working periods, a first concept of a Bayesian network is introduced and is integrated into the extended RCPSP with pre-emptive and non-pre-emptive tasks. Thereby, the Bayesian network is used to calculate the probability of a maintenance task to be processed during a specific period of the shift. Focusing on the domain of maintenance of the railway infrastructure in metropolitan areas as the most unproductive implementation process at construction site, the paper illustrates how the extended RCPSP can be applied for maintenance planning support. A multi-criteria evolutionary algorithm with a problem representation is introduced which is capable of revising technician-task allocations, whereas the duration of the task may be stochastic. The approach uses a novel activity list representation to ensure easily describable and modifiable elements which can be converted into detailed shift schedules. Thereby, the main objective is to develop a shift plan which maximizes the utilization of each technician due to a minimization of the waiting times caused by rail traffic. The results of the already implemented core algorithm illustrate a fast convergence towards an optimal team composition for a shift, an efficient sequence of tasks and a high probability of the subsequent implementation due to the stochastic durations of the tasks. In the paper, the algorithm for the extended RCPSP is analyzed in experimental evaluation using real-world example problems with various size, resource complexity, tightness and so forth.

Keywords: maintenance management, scheduling, resource constrained project scheduling problem, genetic algorithms

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Authors: S. Jurado, E. Pazmino

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Determination of the medial axis of a porous media sample is a non-trivial problem of interest for several disciplines, e.g., hydrology, fluid dynamics, contaminant transport, filtration, oil extraction, etc. However, the computational tools available for researchers are limited and restricted. The primary aim of this work was to develop a series of algorithms to extract porosity, medial axis structure, and pore-throat size distributions from porous media domains. A complementary objective was to provide the algorithms as free computational software available to the academic community comprising researchers and students interested in 3D data processing. The burn algorithm was tested on porous media data obtained from High-Resolution X-Ray Microtomography (HRXMT) and idealized computer-generated domains. The real data and idealized domains were discretized in voxels domains of 550³ elements and binarized to denote solid and void regions to determine porosity. Subsequently, the algorithm identifies the layer of void voxels next to the solid boundaries. An iterative process removes or 'burns' void voxels in sequence of layer by layer until all the void space is characterized. Multiples strategies were tested to optimize the execution time and use of computer memory, i.e., segmentation of the overall domain in subdomains, vectorization of operations, and extraction of single burn layer data during the iterative process. The medial axis determination was conducted identifying regions where burnt layers collide. The final medial axis structure was refined to avoid concave-grain effects and utilized to determine the pore throat size distribution. A graphic user interface software was developed to encompass all these algorithms, including the generation of idealized porous media domains. The software allows input of HRXMT data to calculate porosity, medial axis, and pore-throat size distribution and provide output in tabular and graphical formats. Preliminary tests of the software developed during this study achieved medial axis, pore-throat size distribution and porosity determination of 100³, 320³ and 550³ voxel porous media domains in 2, 22, and 45 minutes, respectively in a personal computer (Intel i7 processor, 16Gb RAM). These results indicate that the software is a practical and accessible tool in postprocessing HRXMT data for the academic community.

Keywords: medial axis, pore-throat distribution, porosity, porous media

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Authors: Dhouha Laribi Galalou, Najla Allani Bouhoula, Atef Hammouda

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This research delves into the fundamental question of the morphological restitution of built archaeology in order to place it in its paradigmatic context and to seek answers to it. Indeed, the understanding of the object of the study, its analysis, and the methodology of solving the morphological problem posed, are manageable aspects only by means of a thoughtful strategy that draws on well-defined epistemological scaffolding. In this stream, the crisis of natural reasoning in archaeology has generated multiple changes in this field, ranging from the use of new tools to the integration of an archaeological information system where urbanization involves the interplay of several disciplines. The built archaeological topic is also an architectural and morphological object. It is also a set of articulated elementary data, the understanding of which is about to be approached from a logicist point of view. Morphological restitution is no exception to the rule, and the inter-exchange between the different disciplines uses the capacity of each to frame the reflection on the incomplete elements of a given architecture or on its different phases and multiple states of existence. The logicist sequence is furnished by the set of scattered or destroyed elements found, but also by what can be called a rule base which contains the set of rules for the architectural construction of the object. The knowledge base built from the archaeological literature also provides a reference that enters into the game of searching for forms and articulations. The choice of the Roman Forum in North Africa is justified by the great urban and architectural characteristics of this entity. The research on the forum involves both a fairly large knowledge base but also provides the researcher with material to study - from a morphological and architectural point of view - starting from the scale of the city down to the architectural detail. The experimentation of the knowledge deduced on the paradigmatic level, as well as the deduction of an analysis model, is then carried out on the basis of a well-defined context which contextualises the experimentation from the elaboration of the morphological information container attached to the rule base and the knowledge base. The use of logicist analysis and artificial intelligence has allowed us to first question the aspects already known in order to measure the credibility of our system, which remains above all a decision support tool for the morphological restitution of Roman Fora in North Africa. This paper presents a first experimentation of the model elaborated during this research, a model framed by a paradigmatic discussion and thus trying to position the research in relation to the existing paradigmatic and experimental knowledge on the issue.

Keywords: classical reasoning, logicist reasoning, archaeology, architecture, roman forum, morphology, calculation

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Authors: Zohar Manber, Ran Elkon

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Accumulation of somatic mutations (SMs) in the genome is a major driving force of cancer development. Most SMs in the tumor's genome are functionally neutral; however, some cause damage to critical processes and provide the tumor with a selective growth advantage (termed cancer driver mutations). Current research on functional significance of SMs is mainly focused on finding alterations in protein coding sequences. However, the exome comprises only 3% of the human genome, and thus, SMs in the noncoding genome significantly outnumber those that map to protein-coding regions. Although our understanding of noncoding driver SMs is very rudimentary, it is likely that disruption of regulatory elements in the genome is an important, yet largely underexplored mechanism by which somatic mutations contribute to cancer development. The expression of most human genes is controlled by multiple enhancers, and therefore, it is conceivable that regulatory SMs are distributed across different enhancers of the same target gene. Yet, to date, most statistical searches for regulatory SMs have considered each regulatory element individually, which may reduce statistical power. The first challenge in considering the cumulative activity of all the enhancers of a gene as a single unit is to map enhancers to their target promoters. Such mapping defines for each gene its set of regulating enhancers (termed "set of regulatory elements" (SRE)). Considering multiple enhancers of each gene as one unit holds great promise for enhancing the identification of driver regulatory SMs. However, the success of this approach is greatly dependent on the availability of comprehensive and accurate enhancer-promoter (E-P) maps. To date, the discovery of driver regulatory SMs has been hindered by insufficient sample sizes and statistical analyses that often considered each regulatory element separately. In this study, we analyzed more than 2,500 whole-genome sequence (WGS) samples provided by The Cancer Genome Atlas (TCGA) and The International Cancer Genome Consortium (ICGC) in order to identify such driver regulatory SMs. Our analyses took into account the combinatorial aspect of gene regulation by considering all the enhancers that control the same target gene as one unit, based on E-P maps from three genomics resources. The identification of candidate driver noncoding SMs is based on their recurrence. We searched for SREs of genes that are "hotspots" for SMs (that is, they accumulate SMs at a significantly elevated rate). To test the statistical significance of recurrence of SMs within a gene's SRE, we used both global and local background mutation rates. Using this approach, we detected - in seven different cancer types - numerous "hotspots" for SMs. To support the functional significance of these recurrent noncoding SMs, we further examined their association with the expression level of their target gene (using gene expression data provided by the ICGC and TCGA for samples that were also analyzed by WGS).

Keywords: cancer genomics, enhancers, noncoding genome, regulatory elements

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Authors: Yew Mun Yip, Dawei Zhang

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Proteins are the biological machinery that executes specific vital functions in every cell of the human body by folding into their 3D structures. When a protein misfolds from its native structure, the machinery will malfunction and lead to misfolding diseases. Although in vitro experiments are able to conclude that the mutations of the amino acid sequence lead to incorrectly folded protein structures, these experiments are unable to decipher the folding process. Therefore, molecular dynamic (MD) simulations are employed to simulate the folding process so that our improved understanding of the folding process will enable us to contemplate better treatments for misfolding diseases. MD simulations make use of force fields to simulate the folding process of peptides. Secondary structures are formed via the hydrogen bonds formed between the backbone atoms (C, O, N, H). It is important that the hydrogen bond energy computed during the MD simulation is accurate in order to direct the folding process to the native structure. Since the atoms involved in a hydrogen bond possess very dissimilar electronegativities, the more electronegative atom will attract greater electron density from the less electronegative atom towards itself. This is known as the polarization effect. Since the polarization effect changes the electron density of the two atoms in close proximity, the atomic charges of the two atoms should also vary based on the strength of the polarization effect. However, the fixed atomic charge scheme in force fields does not account for the polarization effect. In this study, we introduce the polarized structure-specific backbone charge (PSBC) model. The PSBC model accounts for the polarization effect in MD simulation by updating the atomic charges of the backbone hydrogen bond atoms according to equations derived between the amount of charge transferred to the atom and the length of the hydrogen bond, which are calculated from quantum-mechanical calculations. Compared to other polarizable models, the PSBC model does not require quantum-mechanical calculations of the peptide simulated at every time-step of the simulation and maintains the dynamic update of atomic charges, thereby reducing the computational cost and time while accounting for the polarization effect dynamically at the same time. The PSBC model is applied to two different β-peptides, namely the Beta3s/GS peptide, a de novo designed three-stranded β-sheet whose structure is folded in vitro and studied by NMR, and the trpzip peptides, a double-stranded β-sheet where a correlation is found between the type of amino acids that constitute the β-turn and the β-propensity.

Keywords: hydrogen bond, polarization effect, protein folding, PSBC

Procedia PDF Downloads 270

Authors: Farahnaz Amini, Woo Yun Kin, Lazwani Kolandaiveloo

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Availability of different genetic tests after completion of Human Genome Project increases the physicians’ responsibility to keep themselves update on the potential implementation of these genetic tests in their daily practice. However, due to numbers of barriers, still many of physicians are not either aware of these tests or are not willing to offer or refer their patients for genetic tests. This study was conducted an anonymous, cross-sectional, mailed-based survey to develop a primary data of Malaysian physicians’ level of knowledge and perception of gene profiling. Questionnaire had 29 questions. Total scores on selected questions were used to assess the level of knowledge. The highest possible score was 11. Descriptive statistics, one way ANOVA and chi-squared test was used for statistical analysis. Sixty three completed questionnaires was returned by 27 general practitioners (GPs) and 36 medical specialists. Responders’ age range from 24 to 55 years old (mean 30.2 ± 6.4). About 40% of the participants rated themselves as having poor level of knowledge in genetics in general whilst 60% believed that they have fair level of knowledge. However, almost half (46%) of the respondents felt that they were not knowledgeable about available genetic tests. A majority (94%) of the responders were not aware of any lab or company which is offering gene profiling services in Malaysia. Only 4% of participants were aware of using gene profiling for detection of dosage of some drugs. Respondents perceived greater utility of gene profiling for breast cancer (38%) compared to the colorectal familial cancer (3%). The score of knowledge ranged from 2 to 8 (mean 4.38 ± 1.67). Non-significant differences between score of knowledge of GPs and specialists were observed, with score of 4.19 and 4.58 respectively. There was no significant association between any demographic factors and level of knowledge. However, those who graduated between years 2001 to 2005 had higher level of knowledge. Overall, 83% of participants showed relatively high level of perception on value of gene profiling to detect patient’s risk of disease. However, low perception was observed for both statements of using gene profiling for general population in order to alter their lifestyle (25%) as well as having the full sequence of a patient genome for the purpose of determining a patient’s best match for treatment (18%). The lack of clinical guidelines, limited provider knowledge and awareness, lack of time and resources to educate patients, lack of evidence-based clinical information and cost of tests were the most barriers of ordering gene profiling mentioned by physicians. In conclusion Malaysian physicians who participate in this study had mediocre level of knowledge and awareness in gene profiling. The low exposure to the genetic questions and problems might be a key predictor of lack of awareness and knowledge on available genetic tests. Educational and training workshop might be useful in helping Malaysian physicians incorporate genetic profiling into practice for eligible patients.

Keywords: gene profiling, knowledge, Malaysia, physician

Procedia PDF Downloads 326

Authors: Man Fung Ho, Lap So, Jiaqi Zhang, Yuheng Zhao, Huiyang Lu, Tat Shing Choi, K. Y. Michael Wong

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Nowadays, a tremendous amount of data is available in the transportation system, enabling the development of various machine learning approaches to make short-term latency predictions. A natural question is then the choice of relevant information to enable accurate predictions. Using traffic data collected from the Taiwan Freeway System, we consider the prediction of short-term latency of a freeway segment with a length of 17 km covering 5 measurement points, each collecting vehicle-by-vehicle data through the electronic toll collection system. The processed data include the past latencies of the freeway segment with different time lags, the traffic conditions of the individual segments (the accumulations, the traffic fluxes, the entrance and exit rates), the total accumulations, and the weekday latency profiles obtained by Gaussian process regression of past data. We arrive at several important conclusions about how data should be refined to obtain accurate predictions, which have implications for future system-wide latency predictions. (1) We find that the prediction of median latency is much more accurate and meaningful than the prediction of average latency, as the latter is plagued by outliers. This is verified by machine-learning prediction using XGBoost that yields a 35% improvement in the mean square error of the 5-minute averaged latencies. (2) We find that the median latency of the segment 15 minutes ago is a very good baseline for performance comparison, and we have evidence that further improvement is achieved by machine learning approaches such as XGBoost and Long Short-Term Memory (LSTM). (3) By analyzing the feature importance score in XGBoost and calculating the mutual information between the inputs and the latencies to be predicted, we identify a sequence of inputs ranked in importance. It confirms that the past latencies are most informative of the predicted latencies, followed by the total accumulation, whereas inputs such as the entrance and exit rates are uninformative. It also confirms that the inputs are much less informative of the average latencies than the median latencies. (4) For predicting the latencies of segments composed of two or three sub-segments, summing up the predicted latencies of each sub-segment is more accurate than the one-step prediction of the whole segment, especially with the latency prediction of the downstream sub-segments trained to anticipate latencies several minutes ahead. The duration of the anticipation time is an increasing function of the traveling time of the upstream segment. The above findings have important implications to predicting the full set of latencies among the various locations in the freeway system.

Keywords: data refinement, machine learning, mutual information, short-term latency prediction

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Authors: Michelle Rippy

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Medicolegal death investigation historically is a field that does not receive much research attention or advancement, as all of the subjects are deceased. Public health threats, drug epidemics and contagious diseases are typically recognized in decedents first, with thorough and accurate death investigations able to assist in epidemiology research and prevention programs. One vital component of medicolegal death investigation is determining the decedent’s time of death. An accurate time of death can assist in corroborating alibies, determining sequence of death in multiple casualty circumstances and provide vital facts in civil situations. Popular television portrays an unrealistic forensic ability to provide the exact time of death to the minute for someone found deceased with no witnesses present. The actuality of unattended decedent time of death determination can generally only be narrowed to a 4-6 hour window. In the mid- to late-20th century, liver temperatures were an invasive action taken by death investigators to determine the decedent’s core temperature. The core temperature was programmed into an equation to determine an approximate time of death. Due to many inconsistencies with the placement of the thermometer and other variables, the accuracy of the liver temperatures was dispelled and this once common place action lost scientific support. Currently, medicolegal death investigators utilize three major after death or post-mortem changes at a death scene. Many factors are considered in the subjective determination as to the time of death, including the cooling of the decedent, stiffness of the muscles, release of blood internally, clothing, ambient temperature, disease and recent exercise. Current research is utilizing non-invasive hospital grade tympanic thermometers to measure the temperature in the each of the decedent’s ears. This tool can be used at the scene and in conjunction with scene indicators may provide a more accurate time of death. The research is significant and important to investigations and can provide an area of accuracy to a historically inaccurate area, considerably improving criminal and civil death investigations. The goal of the research is to provide a scientific basis to unwitnessed deaths, instead of the art that the determination currently is. The research is currently in progress with expected termination in December 2018. There are currently 15 completed case studies with vital information including the ambient temperature, decedent height/weight/sex/age, layers of clothing, found position, if medical intervention occurred and if the death was witnessed. This data will be analyzed with the multiple variables studied and available for presentation in January 2019.

Keywords: algor mortis, forensic pathology, investigations, medicolegal, time of death, tympanic

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Authors: Ekaterina G. Lipatova

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The developing potential of a video task in teaching foreign languages involves the opportunities to improve four aspects of speech production process: listening, reading, speaking and writing. A video represents the sequence of actions, realized in the pictures logically connected and verbalized speech flow that simplifies and stimulates the process of perception. In this connection listening skills of students are developed effectively as well as their intellectual properties such as synthesizing, analyzing and generalizing the information. In terms of teaching capacity, a video task, in our opinion, is more stimulating than a traditional listening, since it involves the student into the plot of the communicative situation, emotional background and potentially makes them react to the gist in the cognitive and communicative ways. To be an effective method of teaching the video task should be structured in the way of psycho-linguistic characteristics of speech production process, in other words, should include three phases: before-watching, while-watching and after-watching. The system of tasks provided to each phase might involve the situations on reflecting to the video content in the forms of filling-the-gap tasks, multiple choice, True-or-False tasks (reading skills), exercises on expressing the opinion, project fulfilling (writing and speaking skills). In the before-watching phase we offer the students to adjust their perception mechanism to the topic and the problem of the chosen video by such task as “what do you know about such a problem?”, “is it new for you?”, “have you ever faced the situation of…?”. Then we proceed with the lexical and grammatical analysis of language units that form the body of a speech sample to lessen the perception and develop the student’s lexicon. The goal of while-watching phase is to build the student’s awareness about the problem presented in the video and challenge their inner attitude towards what they have seen by identifying the mistakes in the statements about the video content or making the summary, justifying their understanding. Finally, we move on to development of their speech skills within the communicative situation they observed and learnt by stimulating them to search the similar ideas in their backgrounds and represent them orally or in the written form or express their own opinion on the problem. It is compulsory to highlight, that a video task should contain the urgent, valid and interesting event related to the future profession of the student, since it will help to activate cognitive, emotional, verbal and ethic capacity of students. Also, logically structured video tasks are easily integrated into the system of e-learning and can provide the opportunity for the students to work with the foreign language on their own.

Keywords: communicative situation, perception mechanism, speech production process, speech skills

Procedia PDF Downloads 245

Authors: Daniel Todorov, Anton Hinkov, Petya Angelova, Kalina Shishkova, Venelin Tsvetkov, Stoyan Shishkov

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Human herpes viruses (HHV) are ubiquitous pathogens with a pandemic spread across the globe. HHV type 1 is the main causative agent of cold sores and fever blisters around the mouth and on the face, whereas HHV type 2 is generally responsible for genital herpes outbreaks. The treatment of both viruses is more or less successful with antivirals from the nucleoside analogues group. Their wide application increasingly leads to the emergence of resistant mutants In the past, medicinal plants have been used to treat a number of infectious and non-infectious diseases. Their diversity and ability to produce the vast variety of secondary metabolites according to the characteristics of the environment give them the potential to help us in our warfare with viral infections. The variable chemical characteristics and complex composition is an advantage in the treatment of herpes since the emergence of resistant mutants is significantly complicated. The screening process is difficult due to the lack of standardization. That is why it is especially important to follow the mechanism of antiviral action of plants. On the one hand, it may be expected to interact with its compounds, resulting in enhanced antiviral effects, and the most appropriate environmental conditions can be chosen to maximize the amount of active secondary metabolites. During our study, we followed the activity of various plant extracts on the viral replication cycle as well as their effect on the extracellular virion. We obtained our results following the logical sequence of the experimental settings - determining the cytotoxicity of the extracts, evaluating the overall effect on viral replication and extracellular virion.During our research, we have screened a variety of plant extracts for their antiviral activity against both virus replication and the virion itself. We investigated the effect of the extracts on the individual stages of the viral replication cycle - viral adsorption, penetration and the effect on replication depending on the time of addition. If there are positive results in the later experiments, we had studied the activity over viral adsorption, penetration and the effect of replication according to the time of addition. Our results indicate that some of the extracts from the Lamium album have several targets. The first stages of the viral life cycle are most affected. Several of our active antiviral agents have shown an effect on extracellular virion and adsorption and penetration processes. Our research over the last decade has shown several curative antiviral plants - some of which are from the Lamiacea family. The rich set of active ingredients of the plants in this family makes them a good source of antiviral preparation.

Keywords: human herpes virus, antiviral activity, Lamium album, Nepeta nuda

Procedia PDF Downloads 157

Authors: Alsu F. Saifitdinova, Alexey S. Komissarov, Svetlana A. Galkina, Elena I. Koshel, Maria M. Kulak, Stephen J. O'Brien, Elena R. Gaginskaya

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The mystery of sex determination is one of the most ancient and still not solved until the end so far. In many species, sex determination is genetic and often accompanied by the presence of dimorphic sex chromosomes in the karyotype. Genomic sequencing gave the information about the gene content of sex chromosomes which allowed to reveal their origin from ordinary autosomes and to trace their evolutionary history. Female-specific W chromosome in birds as well as mammalian male-specific Y chromosome is characterized by the degeneration of gene content and the accumulation of repetitive DNA. Tandem repeats complicate the analysis of genomic data. Despite the best efforts chicken W chromosome assembly includes only 1.2 Mb from expected 55 Mb. Supplementing the information on the sex chromosome composition not only helps to complete the assembly of genomes but also moves us in the direction of understanding of the sex-determination systems evolution. A whole-genome survey to the assembly Gallus_gallus WASHUC 2.60 was applied for repeats search in assembled genome and performed search and assembly of high copy number repeats in unassembled reads of SRR867748 short reads datasets. For cytogenetic analysis conventional methods of fluorescent in situ hybridization was used for previously cloned W specific satellites and specifically designed directly labeled synthetic oligonucleotide DNA probe was used for bioinformatically identified repetitive sequence. Hybridization was performed with mitotic chicken chromosomes and manually isolated giant meiotic lampbrush chromosomes from growing oocytes. A novel chicken W specific satellite (GGAAA)n which is not co-localizes with any previously described classes of W specific repeats was identified and mapped with high resolution. In the composition of autosomes this repeat units was found as a part of upstream regions of gonad specific protein coding sequences. These findings may contribute to the understanding of the role of tandem repeats in sex specific differentiation regulation in birds and sex chromosome evolution. This work was supported by the postdoctoral fellowships from St. Petersburg State University (#1.50.1623.2013 and #1.50.1043.2014), the grant for Leading Scientific Schools (#3553.2014.4) and the grant from Russian foundation for basic researches (#15-04-05684). The equipment and software of Research Resource Center “Chromas” and Theodosius Dobzhansky Center for Genome Bioinformatics of Saint Petersburg State University were used.

Keywords: birds, lampbrush chromosomes, sex chromosomes, tandem repeats

Procedia PDF Downloads 389

Authors: Christofas Stergianos, Jason Atkin, Herve Morvan

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As air traffic increases, more airports are interested in utilizing optimization methods. Many processes happen in parallel at an airport, and complex models are needed in order to have a reliable solution that can be implemented for ground movement operations. The ground movement for aircraft in an airport, allocating a path to each aircraft to follow in order to reach their destination (e.g. runway or gate), is one process that could be optimized. The Quickest Path Problem with Time Windows (QPPTW) algorithm has been developed to provide a conflict-free routing of vehicles and has been applied to routing aircraft around an airport. It was subsequently modified to increase the accuracy for airport applications. These modifications take into consideration specific characteristics of the problem, such as: the pushback process, which considers the extra time that is needed for pushing back an aircraft and turning its engines on; stand holding where any waiting should be allocated to the stand; and runway sequencing, where the sequence of the aircraft that take off is optimized and has to be respected. QPPTW involves searching for the quickest path by expanding the search in all directions, similarly to Dijkstra’s algorithm. Finding a way to direct the expansion can potentially assist the search and achieve a better performance. We have further modified the QPPTW algorithm to use a heuristic approach in order to guide the search. This new algorithm is based on the A-star search method but estimates the remaining time (instead of distance) in order to assess how far the target is. It is important to consider the remaining time that it is needed to reach the target, so that delays that are caused by other aircraft can be part of the optimization method. All of the other characteristics are still considered and time windows are still used in order to route multiple aircraft rather than a single aircraft. In this way the quickest path is found for each aircraft while taking into account the movements of the previously routed aircraft. After running experiments using a week of real aircraft data from Zurich Airport, the new algorithm (A-star QPPTW) was found to route aircraft much more quickly, being especially fast in routing the departing aircraft where pushback delays are significant. On average A-star QPPTW could route a full day (755 to 837 aircraft movements) 56% faster than the original algorithm. In total the routing of a full week of aircraft took only 12 seconds with the new algorithm, 15 seconds faster than the original algorithm. For real time application, the algorithm needs to be very fast, and this speed increase will allow us to add additional features and complexity, allowing further integration with other processes in airports and leading to more optimized and environmentally friendly airports.

Keywords: a-star search, airport operations, ground movement optimization, routing and scheduling

Procedia PDF Downloads 231

Authors: Nazish Badar

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In early 2009, Pandemic type A (H1N1) Influenza virus emerged globally. Since then, it has continued circulation causing considerable morbidity and mortality. The purpose of this study was to evaluate the evolutionary changes in Influenza A (H1N1) pdm09 viruses from 2009-15 and their relevance with the current vaccine viruses. Methods: Respiratory specimens were collected with influenza-like illness and Severe Acute Respiratory Illness. Samples were processed according to CDC protocol. Sequencing and phylogenetic analysis of Haemagglutinin (HA) and neuraminidase (NA) genes was carried out comparing representative isolates from Pakistan viruses. Results: Between Jan2009 - Feb 2016, 1870 (13.2%) samples were positive for influenza A out of 14086. During the pandemic period (2009–10), Influenza A/ H1N1pdm 09 was the dominant strain with 366 (45%) of total influenza positives. In the post-pandemic period (2011–2016), a total of 1066 (59.6%) cases were positive Influenza A/ H1N1pdm 09 with co-circulation of different Influenza A subtypes. Overall, the Pakistan A(H1N1) pdm09 viruses grouped in two genetic clades. Influenza A(H1N1)pdm09 viruses only ascribed to Clade 7 during the pandemic period whereas viruses belong to clade 7 (2011) and clade 6B (2015) during the post-pandemic years. Amino acid analysis of the HA gene revealed mutations at positions S220T, I338V and P100S specially associated with outbreaks in all the analyzed strains. Sequence analyses of post-pandemic A(H1N1)pdm09 viruses showed additional substitutions at antigenic sites; S179N,K180Q (SA), D185N, D239G (CA), S202A (SB) and at receptor binding sites; A13T, S200P when compared with pandemic period. Substitution at Genetic markers; A273T (69%), S200P/T (15%) and D239G (7.6%) associated with severity and E391K (69%) associated with virulence was identified in viruses isolated during 2015. Analysis of NA gene revealed outbreak markers; V106I (23%) among pandemic and N248D (100%) during post-pandemic Pakistan viruses. Additional N-Glycosylation site; HA S179N (23%), NA I23T(7.6%) and N44S (77%) in place of N386K(77%) were only found in post-pandemic viruses. All isolates showed histidine (H) at position 275 in NA indicating sensitivity to neuraminidase inhibitors. Conclusion: This study shows that the Influenza A(H1N1)pdm09 viruses from Pakistan clustered into two genetic clades, with co-circulation of some variants. Certain key substitutions in the receptor binding site and few changes indicative of virulence were also detected in post-pandemic strains. Therefore, it is imperative to continue monitoring of the viruses for early identification of potential variants of high virulence or emergence of drug-resistant variants.

Keywords: Influenza A (H1N1) pdm09, evolutionary analysis, post pandemic period, Pakistan

Procedia PDF Downloads 207

Authors: Zhe Li, Tao Ju, Liguo Zhang, Zehong Zhang, Baoshun Zhang

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In-grow stacking-faults (IGSFs) in 4H-SiC epilayers can cause increased leakage current and reduce the blocking voltage of 4H-SiC power devices. Double Shockley stacking fault (2SSF) is a common type of IGSF with double slips on the basal planes. In this study, a 2SSF in the 4H-SiC epilayer grown by chemical vaper deposition (CVD) is characterized. The nucleation site of the 2SSF is discussed, and a model for the 2SSF nucleation is proposed. Homo-epitaxial 4H-SiC is grown on a commercial 4 degrees off-cut substrate by a home-built hot-wall CVD. Defect-selected-etching (DSE) is conducted with melted KOH at 500 degrees Celsius for 1-2 min. Room temperature cathodoluminescence (CL) is conducted at a 20 kV acceleration voltage. Low-temperature photoluminescence (LTPL) is conducted at 3.6 K with the 325 nm He-Cd laser line. In the CL image, a triangular area with bright contrast is observed. Two partial dislocations (PDs) with a 20-degree angle in between show linear dark contrast on the edges of the IGSF. CL and LTPL spectrums are conducted to verify the IGSF’s type. The CL spectrum shows the maximum photoemission at 2.431 eV and negligible bandgap emission. In the LTPL spectrum, four phonon replicas are found at 2.468 eV, 2.438 eV, 2.420 eV and 2.410 eV, respectively. The Egx is estimated to be 2.512 eV. A shoulder with a red-shift to the main peak in CL, and a slight protrude at the same wavelength in LTPL are verified as the so called Egx- lines. Based on the CL and LTPL results, the IGSF is identified as a 2SSF. Back etching by neutral loop discharge and DSE are conducted to track the origin of the 2SSF, and the nucleation site is found to be a threading screw dislocation (TSD) in this sample. A nucleation mechanism model is proposed for the formation of the 2SSF. Steps introduced by the off-cut and the TSD on the surface are both suggested to be two C-Si bilayers height. The intersections of such two types of steps are along [11-20] direction from the TSD, while a four-bilayer step at each intersection. The nucleation of the 2SSF in the growth is proposed as follows. Firstly, the upper two bilayers of the four-bilayer step grow down and block the lower two at one intersection, and an IGSF is generated. Secondly, the step-flow grows over the IGSF successively, and forms an AC/ABCABC/BA/BC stacking sequence. Then a 2SSF is formed and extends by the step-flow growth. In conclusion, a triangular IGSF is characterized by CL approach. Base on the CL and LTPL spectrums, the estimated Egx is 2.512 eV and the IGSF is identified to be a 2SSF. By back etching, the 2SSF nucleation site is found to be a TSD. A model for the 2SSF nucleation from an intersection of off-cut- and TSD- introduced steps is proposed.

Keywords: cathodoluminescence, defect-selected-etching, double Shockley stacking fault, low-temperature photoluminescence, nucleation model, silicon carbide

Procedia PDF Downloads 317

Authors: Abduladim Maitieg, Kevin Lynch, Mark Johnson

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The goal of the Libyan Environmental General Authority (EGA) and National Oil Corporation (Department of Health, Safety & Environment) during the last 5 years has been to adopt a common approach to coastal and marine spatial planning. Protection and planning of the coastal zone is a significant for Libya, due to the length of coast and, the high rate of oil export, and spills’ potential negative impacts on coastal and marine habitats. Coastal resource scenarios constitute an important tool for exploring the long-term and short-term consequences of oil spill impact and available response options that would provide an integrated perspective on mitigation. To investigate that, this paper reviews the Misratah coastal parameters to present the physical and human controls and attributes of coastal habitats as the first step in understanding how they may be damaged by an oil spill. This paper also investigates costal resources, providing a better understanding of the resources and factors that impact the integrity of the ecosystem. Therefore, the study described the potential spatial distribution of oil spill risk and the coastal resources value, and also created spatial maps of coastal resources and their vulnerability to oil spills along the coast. This study proposes an analysis of coastal resources condition at a local level in the Misratah region of the Mediterranean Sea, considering the implementation of coastal and marine spatial planning over time as an indication of the will to manage urban development. Oil spill contamination analysis and their impact on the coastal resources depend on (1) oil spill sequence, (2) oil spill location, (3) oil spill movement near the coastal area. The resulting maps show natural, socio-economic activity, environmental resources along of the coast, and oil spill location. Moreover, the study provides significant geodatabase information which is required for coastal sensitivity index mapping and coastal management studies. The outcome of study provides the information necessary to set an Environmental Sensitivity Index (ESI) for the Misratah shoreline, which can be used for management of coastal resources and setting boundaries for each coastal sensitivity sectors, as well as to help planners measure the impact of oil spills on coastal resources. Geographic Information System (GIS) tools were used in order to store and illustrate the spatial convergence of existing socio-economic activities such as fishing, tourism, and the salt industry, and ecosystem components such as sea turtle nesting area, Sabkha habitats, and migratory birds feeding sites. These geodatabases help planners investigate the vulnerability of coastal resources to an oil spill.

Keywords: coastal and marine spatial planning advancement training, GIS mapping, human uses, ecosystem components, Misratah coast, Libyan, oil spill

Procedia PDF Downloads 362

Authors: E. Zafeiraki, P. Nisianakis, K. Machera

Abstract:

Cannabis plant contains 113 cannabinoids and it is commonly known for its psychoactive substance tetrahydrocannabinol or as a source of narcotic substances. The recent years’ cannabis cultivation also increases due to its wide use both for medical and industrial purposes as well as for uses as para-pharmaceuticals, cosmetics and food commodities. Depending on the final product, different parts of the plant are utilized, with the leaves and bud (seeds) being the most frequently used. Cannabis can accumulate various contaminants, including heavy metals, both from the soil and the water in which the plant grows. More specifically, metals may occur naturally in the soil and water, or they can enter into the environment through fertilizers, pesticides and fungicides that are commonly applied to crops. The high probability of metals accumulation in cannabis, combined with the latter growing use, raise concerns about the potential health effects in humans and consequently lead to the need for the implementation of safety measures for cannabis products, such as guidelines for regulating contaminants, including metals, and especially the ones characterized by high toxicity in cannabis. Acknowledging the above, the aim of the current study was first to investigate metals contamination in cannabis samples collected from Greece, and secondly to examine potential differences in metals accumulation among the different parts of the plant. To our best knowledge, this is the first study presenting information on elements in cannabis cultivated in Greece, and also on the distribution pattern of the former in the plant body. To this end, the leaves and the seeds of all the samples were initially separated and dried and then digested with Nitric acid (HNO₃) and Hydrochloric acid (HCl). For the analysis of these samples, an Inductive Coupled Plasma-Mass Spectrometry (ICP-MS) method was developed, able to quantify 28 elements. Internal standards were added at a constant rate and concentration to all calibration standards and unknown samples, while two certified reference materials were analyzed in every batch to ensure the accuracy of the measurements. The repeatability of the method and the background contamination were controlled by the analysis of quality control (QC) standards and blank samples in every sequence, respectively. According to the results, essential metals, such as Ca, Zn and Mg, were detected at high levels. On the contrary, the concentration of high toxicity metals, like As (average: 0.10ppm), Pb (average: 0.36ppm), Cd (average: 0.04ppm), and Hg (average: 0.012ppm) were very low in all the samples, indicating that no harmful effects on human health can be caused by the analyzed samples. Moreover, it appears that the pattern of contamination of metals is very similar in all the analyzed samples, which could be attributed to the same origin of the analyzed cannabis, i.e., the common soil composition, use of fertilizers, pesticides, etc. Finally, as far as the distribution pattern between the different parts of the plant is concerned, it was revealed that leaves present a higher concentration in comparison to seeds for all metals examined.

Keywords: cannabis, heavy metals, ICP-MS, leaves and seeds, elements

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Authors: Nick Woodier, Iain Moppett

Abstract:

Background: It is estimated that one in ten patients admitted to hospital will suffer an adverse event in their care. While the majority of these will result in low harm, patients are being significantly harmed by the processes meant to help them. Healthcare, therefore, seeks to make improvements in patient safety by taking learning from other industries that are perceived to be more mature in their management of safety events. Of particular interest to healthcare are ‘near misses,’ those events that almost happened but for an intervention. Healthcare does not have any guidance as to how best to manage and learn from near misses to reduce the chances of harm to patients. The authors, as part of a larger study of near-miss management in healthcare, sought to learn from the UK nuclear sector to develop principles for how healthcare can identify, report, and learn from near misses to improve patient safety. The nuclear sector was chosen as an exemplar due to its status as an ultra-safe industry. Methods: A Grounded Theory (GT) methodology, augmented by a scoping review, was used. Data collection included interviews, scenario discussion, field notes, and the literature. The review protocol is accessible online. The GT aimed to develop theories about how nuclear manages near misses with a focus on defining them and clarifying how best to support reporting and analysis to extract learning. Near misses related to radiation release or exposure were focused on. Results: Eightnuclear interviews contributed to the GT across nuclear power, decommissioning, weapons, and propulsion. The scoping review identified 83 articles across a range of safety-critical industries, with only six focused on nuclear. The GT identified that nuclear has a particular focus on precursors and low-level events, with regulation supporting their management. Exploration of definitions led to the recognition of the importance of several interventions in a sequence of events, but that do not solely rely on humans as these cannot be assumed to be robust barriers. Regarding reporting and analysis, no consistent methods were identified, but for learning, the role of operating experience learning groups was identified as an exemplar. The safety culture across nuclear, however, was heard to vary, which undermined reporting of near misses and other safety events. Some parts of the industry described that their focus on near misses is new and that despite potential risks existing, progress to mitigate hazards is slow. Conclusions: Healthcare often sees ‘nuclear,’ as well as other ultra-safe industries such as ‘aviation,’ as homogenous. However, the findings here suggest significant differences in safety culture and maturity across various parts of the nuclear sector. Healthcare can take learning from some aspects of management of near misses in nuclear, such as how they are defined and how learning is shared through operating experience networks. However, healthcare also needs to recognise that variability exists across industries, and comparably, it may be more mature in some areas of safety.

Keywords: culture, definitions, near miss, nuclear safety, patient safety

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Authors: Epaminondas G. Kyriakidis, Theodosis D. Dimitrakos, Constantinos C. Karamatsoukis

Abstract:

The vehicle routing problem (VRP) is a well-known problem in Operations Research and has been widely studied during the last fifty-five years. The context of the VRP is that of delivering or collecting products to or from customers who are scattered in a geographical area and have placed orders for these products. A vehicle or a fleet of vehicles start their routes from a depot and visit the customers in order to satisfy their demands. Special attention has been given to the capacitated VRP in which the vehicles have limited carrying capacity for the goods that are delivered or collected. In the present work, we present a specific capacitated stochastic vehicle routing problem which has many realistic applications. We develop and analyze a mathematical model for a specific vehicle routing problem in which a vehicle starts its route from a depot and visits N customers according to a particular sequence in order to collect from them two similar but not identical products. We name these products, product 1 and product 2. Each customer possesses items either of product 1 or product 2 with known probabilities. The number of the items of product 1 or product 2 that each customer possesses is a discrete random variable with known distribution. The actual quantity and the actual type of product that each customer possesses are revealed only when the vehicle arrives at the customer’s site. It is assumed that the vehicle has two compartments. We name these compartments, compartment 1 and compartment 2. It is assumed that compartment 1 is suitable for loading product 1 and compartment 2 is suitable for loading product 2. However, it is permitted to load items of product 1 into compartment 2 and items of product 2 into compartment 1. These actions cause costs that are due to extra labor. The vehicle is allowed during its route to return to the depot to unload the items of both products. The travel costs between consecutive customers and the travel costs between the customers and the depot are known. The objective is to find the optimal routing strategy, i.e. the routing strategy that minimizes the total expected cost among all possible strategies for servicing all customers. It is possible to develop a suitable dynamic programming algorithm for the determination of the optimal routing strategy. It is also possible to prove that the optimal routing strategy has a specific threshold-type strategy. Specifically, it is shown that for each customer the optimal actions are characterized by some critical integers. This structural result enables us to design a special-purpose dynamic programming algorithm that operates only over these strategies having this structural property. Extensive numerical results provide strong evidence that the special-purpose dynamic programming algorithm is considerably more efficient than the initial dynamic programming algorithm. Furthermore, if we consider the same problem without the assumption that the customers are ordered, numerical experiments indicate that the optimal routing strategy can be computed if N is smaller or equal to eight.

Keywords: dynamic programming, similar products, stochastic demands, stochastic preferences, vehicle routing problem

Procedia PDF Downloads 257