Search results for: evolutionary bioinformatics

Authors: Taleb L., Benarbia M., Brahmi M., Belmiloud H., Boukerche A.

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Introduction and purpose of the study: Cavum cancer in children and adolescents is rare and represents 8% of all nasopharyngeal cancers treated in our department. Our objective is to study its epidemiological, clinical, therapeutic, and evolutionary particularities. Material and methods: Retrospective study of 39 patients under 20 years old, treated for undifferentiated non-metastatic carcinoma of the nasopharynx at the Emir Abdelkader Cancer Center between 2014 and 2020. Results and statistical analysis: Median age was 14 years [7-19 years], with a sex ratio of 2.9. The median time to diagnosis was 5.6 months [1 to 14 months], the circumstances of the discovery of which were dominated by lymph node syndrome in 43.6% of cases (n=17) followed by a rhinological syndrome in 30.8% of cases (n=13). The tumor stage was T1 for two patients (5.1%), T2 for 8 (20.5%), T3 for 9 (23.1%), T4 for 20 (51.3%), N0 for 2 (5 .1%) N1 for 4 (10.3%), N2 for 28 (71.8%) and N3 for 5 (12.8%). All patients received induction chemotherapy followed by concomitant radiotherapy with cisplatin. The dose of irradiation delivered to the cavum and adenopathies was 66 Gy with fractionation of 2 Gy per session in 69.2% of cases (n=27) and 1.8 Gy in 30.8% of cases (n=12). With a median follow-up of 51 months (15 to 97 months), the locoregional, metastatic, specific, and overall relapse-free survival rates at five years were 91.1%, 73.5%, 66.1%, and 68.4, respectively. Conclusion: Chemotherapy and radiotherapy treatment of cavum cancer in children and adolescents has allowed excellent locoregional control despite the advanced stage of the disease. However, the frequency of metastatic relapses could justify the possible use of systemic maintenance treatment.

Keywords: cancer, nasopharynx, radiotherapy, chemotherapy, survival

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Authors: Antonin Ponsich, Eric Alfredo Rincon Garcia, Roman Anselmo Mora Gutierrez, Miguel Angel Gutierrez Andrade, Sergio Gerardo De Los Cobos Silva, Pedro Lara Velzquez

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The electoral zone design problem consists in redrawing the boundaries of legislative districts for electoral purposes in such a way that federal or state requirements are fulfilled. In Mexico, this process has been historically carried out by the National Electoral Institute (INE), by optimizing an integer nonlinear programming model, in which population equality and compactness of the designed districts are considered as two conflicting objective functions, while contiguity is included as a hard constraint. The solution technique used by the INE is a Simulated Annealing (SA) based algorithm, which handles the multi-objective nature of the problem through an aggregation function. The present work represents the first intent to apply a classical Multi-Objective Evolutionary Algorithm (MOEA), the second version of the Non-dominated Sorting Genetic Algorithm (NSGA-II), to this hard combinatorial problem. First results show that, when compared with the SA algorithm, the NSGA-II obtains promising results. The MOEA manages to produce well-distributed solutions over a wide-spread front, even though some convergence troubles for some instances constitute an issue, which should be corrected in future adaptations of MOEAs to the redistricting problem.

Keywords: multi-objective optimization, NSGA-II, redistricting, zone design problem

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Authors: Natasha Hazarika, Xiaoling Zhang

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Eco- innovations, unlike regular innovations, are not self-enforcing and are associated with the double externality problem. Therefore, it is emphasized that eco-innovations need government. intervention in the form of supportive policies on priority. Off late, factors like consumer demand, technological advancement as well as the competitiveness of the firms have been considered as equally important. However, the interaction among these driving forces has not been fully traced out. Also, the theory on eco-innovation is found to be at a nascent stage which does not resonate with its dynamics as it is traditionally studied under the neo- classical economics theory. Therefore, to begin with, insights for this research have been derived from the merits of ‘neo- classical economics’, ‘evolutionary approach’, and the ‘resource based view’ which revealed the issues pertaining to technological system lock- ins and firm- based capacities which usually remained undefined by the neo classical approach; it would be followed by determining how the policies (in the national level) and their instruments are designed in order to motivate firms to eco-innovate, by analyzing the innovation ‘friendliness’ of the policy style and the policy instruments as per the indicators provided in innovation literature by means of document review (content analysis) of the relevant policies introduced by the Chinese government. The significance of theoretical analysis lies in its ability to show why certain practices become dominant irrespective of gains or losses, and that of the policy analysis lies in its ability to demonstrate the credibility of govt.’s sticks, carrots and sermons for eco-innovation.

Keywords: firm competency, eco-innovation, policy, theory

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Authors: Johann Van Niekerk

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The disciplines of conducting (instrumental or choral) and of singing presume a willingness toward an open posture and, in many cases, demand it for effective communication and technique. Yet, this very openness, with the "spread-eagle" gesture as an extreme, is oftentimes counterintuitive for musicians and within the trajectory of human evolution. Conversely, it is in this very gesture of "taking up space" that confidence-gaining techniques such as the popular "power pose" are based. This paper consists primarily of a literature review, exploring the topics of physical openness and vulnerability, considering the semiotics of the "spread-eagle" and its accompanying letter X. A major finding of this research is the discrepancy between evolutionary instinct towards physical self-protection and “folding in” and the demands of the discipline of physical and gestural openness, expansiveness and vulnerability. A secondary finding is ways in which encouragement of confidence-gaining techniques may be more effective in obtaining the required results than insistence on vulnerability, which is influenced by various cultural contexts and socialization. Choral conductors and music educators are constantly seeking ways to promote engagement and healthy singing. Much of the information and direction toward this goal is gleaned by students from conducting gestures and other pedagogies employed in the rehearsal. The findings of this research provide yet another avenue toward reaching the goals required for sufficient and effective teaching and artistry on the part of instructors and students alike.

Keywords: conducting, gesture, music, pedagogy, posture, vulnerability

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Authors: Hui-Ling Huang, Tamara Vasylenko, Phasit Charoenkwan, Shih-Hsiang Chiu, Shinn-Ying Ho

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The knowledge of the human transporters is still limited due to technically demanding procedure of crystallization for the structural characterization of transporters by spectroscopic methods. It is desirable to develop bioinformatics tools for effective analysis of available sequences in order to identify human transmembrane transporter proteins (HMTPs). This study proposes a scoring card method (SCM) based method for predicting HMTPs. We estimated a set of propensity scores of dipeptides to be HMTPs using SCM from the training dataset (HTS732) consisting of 366 HMTPs and 366 non-HMTPs. SCM using the estimated propensity scores of 20 amino acids and 400 dipeptides -as HMTPs, has a training accuracy of 87.63% and a test accuracy of 66.46%. The five top-ranked dipeptides include LD, NV, LI, KY, and MN with scores 996, 992, 989, 987, and 985, respectively. Five amino acids with the highest propensity scores are Ile, Phe, Met, Gly, and Leu, that hydrophobic residues are mostly highly-scored. Furthermore, obtained propensity scores were used to analyze physicochemical properties of human transporters.

Keywords: dipeptide composition, physicochemical property, human transmembrane transporter proteins, human transmembrane transporters binding propensity, scoring card method

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Authors: Iryna P. Dzieciuch, Michael D. Putman

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Humidity is known to degrade Navy ship electronic equipment, especially in hot moist environments. If left untreated, it can cause significant and permanent damage. Even rigorous inspection and frequent clean-up would not prevent further equipment contamination and degradation because of the constant presence of favorable growth conditions for many microorganisms. Generally, relative humidity levels of less than 60% will inhibit corrosion in electronic equipment, but because NAVY electronics often operate in hot and humid environments, prevention via dehumidification is not always possible. Currently, there is no defined research that fully describes key mechanisms which cause electronics and its coating degradation. The corrosive action of most bacteria is mainly developed through (i) mycelium adherence to the metal plates, (ii) facilitation the formation of pitting areas, (iii) production of organic acids such as citric, iso-citric, cis-aconitic, alpha-ketoglutaric, which are corrosive to electronic equipment and its components. Our approach studies corrosive action in electronic equipment: circuit-board, wires and connections that are exposed in the humid environment that gets worse during condensation. In our new approach the technical task is built on work with the bacterial communities in public areas, bacterial genetics, bioinformatics, biostatistics and Scanning Electron Microscopy (SEM) of corroded circuit boards. Based on these methods, we collect and examine environmental samples from biofilms of the corroded and non-corroded sites, where bacterial contamination of electronic equipment, such as machine racks and shore boats, is an ongoing concern. Sample collection and sample analysis is focused on addressing the key questions identified above through the following tasks: laboratory sample processing and evaluation under scanning electron microscopy, initial sequencing and data evaluation; bioinformatics and data analysis. Preliminary results from scanning electron microscopy (SEM) have revealed that metal particulates and alloys in corroded samples consists mostly of Tin ( < 40%), Silicon ( < 4%), Sulfur ( < 1%), Aluminum ( < 2%), Magnesium ( < 2%), Copper ( < 1%), Bromine ( < 2%), Barium ( <1%) and Iron ( < 2%) elements. We have also performed X 12000 magnification of the same sites and that proved existence of undisrupted biofilm organelles and crystal structures. Non-corrosion sites have revealed high presence of copper ( < 47%); other metals remain at the comparable level as on the samples with corrosion. We have performed X 1000 magnification on the non-corroded at the sites and have documented formation of copper crystals. The next step of this study, is to perform metagenomics sequencing at all sites and to compare bacterial composition present in the environment. While copper is nontoxic to the living organisms, the process of bacterial adhesion creates acidic environment by releasing citric, iso-citric, cis-aconitic, alpha-ketoglutaric acidics, which in turn release copper ions Cu++, which that are highly toxic to the bacteria and higher order living organisms. This phenomenon, might explain natural “antibiotic” properties that are lacking in elements such as tin. To prove or deny this hypothesis we will use next - generation sequencing (NGS) methods to investigate types and growth cycles of bacteria that from bacterial biofilm the on corrosive and non-corrosive samples.

Keywords: bacteria, biofilm, circuit board, copper, corrosion, electronic equipment, organic acids, tin

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Authors: P. Pasomboon, P. Chumnanpuen, T. E-kobon

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Hyaluronic acid (HA) consists of linear heteropolysaccharides repeat of D-glucuronic acid and N-acetyl-D-glucosamine. HA has various useful properties to maintain skin elasticity and moisture, reduce inflammation, and lubricate the movement of various body parts without causing immunogenic allergy. HA can be found in several animal tissues as well as in the capsule component of some bacteria including Pasteurella multocida. This study aimed to modify a genome-scale metabolic model of Escherichia coli using computational simulation and flux analysis methods to predict HA productivity under different carbon sources and nitrogen supplement by the addition of two enzymes (GLMU2 and HYAD) from P. multocida to improve the HA production under the specified amount of carbon sources and nitrogen supplements. Result revealed that threonine and aspartate supplement raised the HA production by 12.186%. Our analyses proposed the genome-scale metabolic model is useful for improving the HA production and narrows the number of conditions to be tested further.

Keywords: Pasteurella multocida, Escherichia coli, hyaluronic acid, genome-scale metabolic model, bioinformatics

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Authors: Phanida Phukoetphim, Asaad Y. Shamseldin

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In this study, the novel Stochastic Gradient Boosting (SGB) combination method is addressed for producing daily river flows from four different rain-runoff models of Ohinemuri catchment, New Zealand. The selected rainfall-runoff models are two empirical black-box models: linear perturbation model and linear varying gain factor model, two conceptual models: soil moisture accounting and routing model and Nedbør-Afrstrømnings model. In this study, the simple average combination method and the weighted average combination method were used as a benchmark for comparing the results of the novel SGB combination method. The models and combination results are evaluated using statistical and graphical criteria. Overall results of this study show that the use of combination technique can certainly improve the simulated river flows of four selected models for Ohinemuri catchment, New Zealand. The results also indicate that the novel SGB combination method is capable of accurate prediction when used in a combination method of the simulated river flows in New Zealand.

Keywords: multi-model combination, rainfall-runoff modeling, stochastic gradient boosting, bioinformatics

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Authors: Olatunbosun Samuel Adekogbe

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This paper addresses the question of musical signification, revolving around nature and its natural divides; the paper tends to examine the roles of the dispositional apparatus of listeners to react to sounding environments through music as coordinated sound that focuses on the powerful strain between vibrational occurrences of sound and potentials of being structured. This paper sets out to examine music as a simple conventional design that does not allude to something beyond music and sound as a vehicle to communicate through production, perception, translation, and reaction with regard to melodic and semiotic functions of sounds. This paper adopts the application of questionnaire and evolutionary approach methods to probe musical adaptation, reproduction, and natural selection as the basis for explaining specific human behavioural responses to musical sense-making beyond the above-sketched dichotomies, with a major focus on the transition from acoustic-emotional sensibilities to musical meaning in the selected soundscapes. It was observed that music has emancipated itself from the level of mere acoustic processing of sounds to a functional description in terms of allowing music users to share experiences and interact with the soundscaping environment. The paper, therefore, concludes that the audience as music participants and listeners in the selected soundscapes have been conceived as adaptive devices in the paradigm shift, which can build up new semiotic linkages with the sounding environments in southwestern Nigeria.

Keywords: semiotics, sound, music, soundscape, environment

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Authors: Jaswinder Kaur, Nitika, Navneet Kaur, Rajesh Khanna

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A hand-fan shaped microstrip patch antenna (MPA) for L-band and S-band applications is designed, and its characteristics have been reconnoitered. The proposed microstrip patch antenna with double U-slot defected ground structure (DGS) is fabricated on an FR4 substrate which is a very readily available and inexpensive material. The suggested antenna is optimized using Orthogonal Design Method (ODM) of Design of Experiments (DOE) to cover the frequency range from 0.91-2.82 GHz for L-band and S-band applications. The L-band covers the frequency range of 1-2 GHz, which is allocated to telemetry, aeronautical, and military systems for passive satellite sensors, weather radars, radio astronomy, and mobile communication. The S-band covers the frequency range of 2-3 GHz, which is used by weather radars, surface ship radars and communication satellites and is also reserved for various wireless applications such as Worldwide Interoperability for Microwave Access (Wi-MAX), super high frequency radio frequency identification (SHF RFID), industrial, scientific and medical bands (ISM), Bluetooth, wireless broadband (Wi-Bro) and wireless local area network (WLAN). The proposed method of optimization is very time efficient and accurate as compared to the conventional evolutionary algorithms due to its statistical strategy. Moreover, the antenna is tested, followed by the comparison of simulated and measured results.

Keywords: design of experiments, hand fan shaped MPA, L-Band, orthogonal design method, S-Band

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Authors: Hue Dinh, Binh Nguyen, Vivian Mendez, Phillip W. Taylor, Fleur Ponton

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Better understanding of how parental diet affects offspring traits is an important ecological and evolutionary question. In this study, we explored how maternal diet influences offspring physiology and resistance to infection using Bactrocera tryoni (Q-fly) as a system model. Female Q-flies were fed one of six single diets varying in their yeast-to-sugar ratio yielding six protein-to-carbohydrate ratios. As controls, we used females that were given a choice between yeast and sugar. Males were reared on a choice diet and allowed to mate with females 14 days post-emergence. Results showed that while maternal diet does not influence offspring developmental time, it has a strong effect on larval body weight. Mother fed either high-protein or high-sugar diet produced larger progeny. By challenging offspring with the bacterium Serratia marcescens, we found that female offspring from mothers fed high-sugar diet survived better the infection compared to those from mothers fed low-sugar diet. In contrast, male offspring produced by mother fed high-protein diet showed better resistance to the infection compared to those produced by mother fed low-protein diet. These results suggested sex-dependent transgenerational effects of maternal nutrition on offspring physiology and immunity.

Keywords: bacterial infection, Bactrocera tryoni, maternal diet, offspring, Serretia marcescens

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Authors: Jin Ho Kim, Yujeong Shin, Seong-Jin Cho, Dong-Jin Kim, U-Syn Ha

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Due to the development of the information industry and technologies, cellular phones have must not only function to communicate, but also have functions such as the Internet, e-banking, entertainment, etc. These phones are called smartphones. The performance of smartphones has improved, because of the various functions of smartphones, and the capacity of the battery has been increased gradually. Recently, linear generators have been embedded in smartphones in order to recharge the smartphone's battery. In this study, optimization is performed and an array change of permanent magnets is examined in order to increase efficiency. We propose an optimal design using design of experiments (DOE) to maximize the generated induced voltage. The thickness of the poleshoe and permanent magnet (PM), the height of the poleshoe and PM, and the thickness of the coil are determined to be design variables. We made 25 sampling points using an orthogonal array according to four design variables. We performed electromagnetic finite element analysis to predict the generated induced voltage using the commercial electromagnetic analysis software ANSYS Maxwell. Then, we made an approximate model using the Kriging algorithm, and derived optimal values of the design variables using an evolutionary algorithm. The commercial optimization software PIAnO (Process Integration, Automation, and Optimization) was used with these algorithms. The result of the optimization shows that the generated induced voltage is improved.

Keywords: smartphone, linear generator, design of experiment, approximate model, optimal design

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Authors: Aleksandr S. Ermolenko

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Allometry is an important factor of morphological integration, contributing to the organization of the phenotype and its variability. The allometric change in the shape of the hand is particularly important in primate evolution, as the hand has important taxonomic features. Some of these features are known to parts with the shape, especially the ratio of the lengths of the index and ring fingers (2d: 4d ratio). The hand is a fairly well-studied system in the context of the evolutionary development of complex morphological structures since it consists of various departments (basipodium, metapodium, acropodium) that form a single structure –autopodium. In the present study, we examined the allometric variability of acropodium. We tested the null hypothesis that there would be no difference in allometric variation between the two components. Geometric morphometry based on a procrustation of 16 two-dimensional (2D) landmarks was analyzed using multivariate shape-by-size regressions in samples from 100 people (50 men and 50 women). The results obtained show that men have significantly greater allometric variability for the ring finger (variability in the transverse axis prevails), while women have significantly greater allometric variability for the index finger (variability in the longitudinal axis prevails). The influence of the middle finger on the shape of the hand is typical for both men and women. The influence of the little finger on the shape of the hand, regardless of gender, was not revealed. The results of this study support the hypothesis that allometry contributes to the organization of variation in the human hand.

Keywords: human hand, size and shape, 2d:4d ratio, geometric morphometry

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Authors: Ryadi Adityavarman

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The study is an analysis by using the postcolonial theoretical lens on the search for a distinctive architectural identity by architect Maclaine Pont in Indonesia in the early twentieth century. Influenced by progressive architectural thinking and enlightened humanism at the time, Pont applied the fundamental principles of Structural Rationalism by using a creative combination of traditional Indonesian architectural typology and innovative structural application. The interpretive design strategy also celebrated creative use of local building materials with sensible tropical climate design response. Moreover, his holistic architectural scheme, including inclusion of local custom of building construction, represents the notion of Gesamkunstwerk. By using such hybrid strategy, Maclaine Pont intended to preserve the essential cultural identity and vernacular architecture of the indigenous. The study will chronologically investigate the evolution of Structural Rationalism architecture philosophy of Viollet-le-Duc to Hendrik Berlage’s influential design thinking in the Dutch modern architecture, and subsequently to the Maclaine Pont’s innovative design in Indonesia. Consequently, the morphology analysis on his exemplary design works of ITB campus (1923) and Pohsarang Church (1936) is to understand the evolutionary influence of Structural Rationalism theory. The postmodern analysis method is to highlight the validity of Pont’s idea in the contemporary Indonesian architecture within the culture of globalism era.

Keywords: Indonesian modern architecture, postcolonial, structural rationalism, critical regionalism

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Authors: Ruchi Yadav, Shivani Pandey, Prachi Srivastava

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Microarrays provide a rich source of data on the molecular working of cells. Each microarray reports on the abundance of tens of thousands of mRNAs. Virtually every human disease is being studied using microarrays with the hope of finding the molecular mechanisms of disease. Bioinformatics analysis plays an important part of processing the information embedded in large-scale expression profiling studies and for laying the foundation for biological interpretation. A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project based on the R programming language. This paper describes specific procedures for conducting quality assessment, visualization and preprocessing of Affymetrix Gene Chip and also details the different bioconductor packages used to analyze affymetrix microarray data and describe the analysis and outcome of each plots.

Keywords: microarray analysis, R language, affymetrix visualization, bioconductor

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Authors: Amira, A. Goma, U. E. Mahrous

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Welfare may be considered to be a subjective experience; it has a biological function that is related to the fitness and survival of the animal accordingly, researches have suggested that welfare is compromised when the animal's evolutionary fitness is reduced. This study was carried out to explain the effect of some managerial stressors as handling and restraint on behavioral patterns and biochemical parameters of rats. A total of 24 (12 males and 12 females) Sprague-Dawley rats (12 months and 150-180g) were allotted into 3 groups, handled group (4 male and 4 female), restrained group (4 male and 4 female) and control group (4 males and 4 females). The obtained results revealed that time spent feeding, drinking frequency, movement and cage exploration increased significantly in handled rats than other groups, while lying time and licking increased significantly in restrained rats than handled and controls. Moreover, social behavior decreased in both stressed groups than control. Triglycerides were significantly increased in handled rats than other groups, while total lipid, total protein and globulin significantly increased in both treated groups than control. Corticosterone increased in restrained and handled rats than control ones. Moreover, there was an increment in packed cell volume significantly in restrained rats than others. These deducted that if we want to study the effect of stress on animal welfare it is necessary to study the effect of such stressors on animal’s behavior and physiological responses.

Keywords: handling, restraint, welfare, rat, behavior, physiology

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Authors: Anmar Dulaimi, Hassan Al Nageim, Felicite Ruddock, Linda Seton

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Cold bituminous asphalt mixture (CBEM) provide a sustainable, cost effective and energy efficiency alternative to traditional hot mixtures. However, these mixtures have a comparatively low initial strength and as it is considered as evolutionary materials, mainly in the early life where the initial cohesion is low and builds up slowly. On the other hand, asphalt concrete is, by far, the most common mixtures in use as binder course and base in road pavement in the UK having a continuous grade offer a good aggregate interlock results in this material having very good load-spreading properties as well as a high resistance to permanent deformation. This study aims at developing a novel fast curing cold asphalt concrete binder course mixtures by using Ordinary Portland Cement (OPC) as a replacement to conventional mineral filler (0%-100%) while new by-product material (LJMU-A2) was used as a supplementary cementitious material. With this purpose, cold asphalt concrete binder course mixtures with cationic emulsions were studied by means of stiffness modulus whereas water sensitivity was approved by assessing the stiffness modulus ratio before and after sample conditioning. The results indicate that a substantial enhancement in the stiffness modulus and a considerable improvement of water sensitivity resistance by adding of LJMU-A2 to the cold asphalt mixtures as a supplementary cementitious material. Moreover, the addition of LJMU-A2 to those mixtures leads to stiffness modulus after 2- day curing comparable to those obtained with Portland cement after 7-day curing.

Keywords: cold mix asphalt, binder course, cement, stiffness modulus, water sensitivity

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Authors: A. Iaaly, O. Jadayel, R. Jadayel

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This paper explores the effectiveness of approaches used for the implementation of technology within central governments specifically Geographic Information Systems (GIS). It examines the extent to which various strategies to GIS implementation and its roll out to users within an organization is crucial for its long term assimilation. Depending on the contextual requirements, various implementation strategies exist spanning from the most revolutionary to the most evolutionary, which have an influence on the success of GIS projects and the realization of resulting business benefits within the central governments. This research compares between two strategies of GIS implementation within the Lebanese Municipalities. The first strategy is the “Technological Approach” which is focused on technology acquisition, overlaid on existing governmental frameworks. This approach gives minimal attention to capability building and the long term sustainability of the implemented program. The second strategy, referred to as the “Ecological Approach”, is naturally oriented to the function of the organization. This approach stresses on fostering the evolution of the program and on building the human capabilities. The Union of the Joumeh Municipalities will be presented as a case study under the “Ecological Approach” and the role of the GIS Center at the University of Balamand will be highlighted. Thus, this research contributes to the development of knowledge on technology implementation and the vital role of academia in the specific context of the Lebanese public sector so that this experience may pave the way for further applications.

Keywords: ecological approach GIS, low income countries, technological approach

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Authors: Roslina Che Soh

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Best interest of the child has been the prevailing principle of the custody legislations of most nations in the world. The tremendous shift from parental rights to parental responsibilities throughout the centuries had made the principle of best interests of the child as the utmost matter which parents must uphold in child upbringing. Despite the commitment to this principle is significantly enshrined in the United Nation Convention on Rights of the Child, the content and application of the principle differs across borders. Differences persist notwithstanding many countries have experienced a substantial shift over the last several decades in the types of custodial arrangements that are thought to best serve children’s interests. The laws in Malaysia similarly uphold this principle but do not provide further deliberation on the principle itself. The principle is entirely developed by the courts through decided cases. Thus, this paper seeks to discuss the extent of the application of best interest of the child principle in custody disputes. In doing so, it attempts to provide an overview of the current laws and the approach of the Civil and the Shariah courts in Malaysia in applying the principle in determining custody disputes. For purposes of comparison, it briefly examines the legislations and the courts practices in Australia and England on this matter. The purpose is to determine the best standard to be adopted by Malaysia and to propose improvement to the laws whenever appropriate.

Keywords: child custody, best interest, Malaysian law, bioinformatics, biomedicine

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Authors: Daria Grechishnikova, Maria Poptsova

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Transposable elements play an important role in the evolution of various species from bacteria to human. Long Interspersed Nuclear Elements (LINEs) and Short Interspersed Nuclear Elements (SINEs) are two major classes of retrotransposons that occupy a considerable part of any genome and their copy numbers can range form several hundreds to a million. Both LINEs and SINEs multiply through a copy-and-paste mechanism. LINEs encode proteins, which make them capable of self-propagation while SINEs are parasitic and require the machinery of LINEs to multiply. The mechanisms how LINE and SINE RNA is recognized by the LINE-encoded reverse transcriptase (RT) remain unclear. For some SINE-LINE pairs, it was shown that they share a common 3’-end with a stem-loop structure. Majority of the SINE-LINE pairs do not have a common 3’-end. Recently we have shown that in the human genome Alu-L1 pairs have structurally similar stem-loop structure at the 3’-end. Here we extended our analysis to a wide range of species and analyzed LINEs from 161 different species from Repbase and 217 SINE sequences from SINEBase. It appeared that all of the analyzed sequences contained stem-loop structures at the 3’-end. Here we conclude that it is very likely that a common evolutionary mechanism of transposon RNA recognition requires the presence of stem-loop structures at their 3’-end.

Keywords: LINE, SINE, mechanisms of retrotransposition, retrotransposons, stem-loop, stem-loop structures, transposons

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Authors: Xiao Zhou, Jianlin Cheng

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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: María Araya Léon, Ainoa Abella, Aura Murillo, Ricardo Guasch, Laura Clèries

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Objectives: This article aims to examine scientific theory framed within the term hospitals of the future from a multidisciplinary and cross-sectional perspective. To understand the connection that the various cross-sectional areas we studied have with architectural spaces and to determine the future outlook of the works examined and how they can be classified into the categories of need/solution, evolution/revolution, collective/individual, and preventive/corrective. Background: The changes currently taking place within the context of healthcare demonstrate how important these projects are and the need for companies to face future changes. Method: A systematic review has been carried out focused on what will the hospitals of the future be like in relation to the elements that form part of their use, design, and architectural space experience, using the WOS database from 2016 to 2019. Results: The large number of works about sensoring & big data and the scarce amount related to the area of materials is worth highlighting. Furthermore, no growth concerning future issues is envisaged over time. Regarding classifications, the articles we reviewed address evolutionary and collective solutions more, and in terms of preventive and corrective solutions, they were found at a similar level. Conclusions: Although our research focused on the future of hospitals, there is little evidence representing this approach. We also detected that, given the relevance of the research on how the built environment influences human health and well-being, these studies should be promoted within the context of healthcare.

Keywords: hospitals, future, architectural space, disruptive approach

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Authors: Adesoji Tunbosun Jaiyeola, Josiah Adeyemo

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Sediment yield can be considered to be the total sediment load that leaves a drainage basin. The knowledge of the quantity of sediments present in a river at a particular time can lead to better flood capacity in reservoirs and consequently help to control over-bane flooding. Furthermore, as sediment accumulates in the reservoir, it gradually loses its ability to store water for the purposes for which it was built. The development of hydrological models to forecast the quantity of sediment present in a reservoir helps planners and managers of water resources systems, to understand the system better in terms of its problems and alternative ways to address them. The application of artificial intelligence models and technique to such real-life situations have proven to be an effective approach of solving complex problems. This paper makes an extensive review of literature relevant to the theories and applications of evolutionary algorithms, and most especially genetic programming. The successful applications of genetic programming as a soft computing technique were reviewed in sediment modelling and other branches of knowledge. Some fundamental issues such as benchmark, generalization ability, bloat and over-fitting and other open issues relating to the working principles of GP, which needs to be addressed by the GP community were also highlighted. This review aim to give GP theoreticians, researchers and the general community of GP enough research direction, valuable guide and also keep all stakeholders abreast of the issues which need attention during the next decade for the advancement of GP.

Keywords: benchmark, bloat, generalization, genetic programming, over-fitting, sediment yield

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Authors: Gareth Baxter

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We use a mathematical model of language change to examine two recently observed patterns of language change: one in which most speakers change gradually, following the mean of the community change, and one in which most individuals use predominantly one variant or another, and change rapidly if they change at all. The model is based on Croft’s Utterance Selection account of language change, which views language change as an evolutionary process, in which different variants (different ‘ways of saying the same thing’) compete for usage in a population of speakers. Language change occurs when a new variant replaces an older one as the convention within a given population. The present model extends a previous simpler model to include effects related to speaker aging and interspeaker variation in behaviour. The two patterns of individual change (one more centralized and the other more polarized) were recently observed in historical language changes, and it was further observed that slower changes were more associated with the centralized pattern, while quicker changes were more polarized. Our model suggests that the two patterns of change can be explained by different balances between the preference of speakers to use one variant over another and the degree of accommodation to (propensity to adapt towards) other speakers. The correlation with the rate of change appears naturally in our model, and results from the fact that both differential weighting of variants and the degree of accommodation affect the time for change to occur, while also determining the patterns of change. This work represents part of an ongoing effort to examine phenomena in language change through the use of mathematical models. This offers another way to evaluate qualitative explanations that cannot be practically tested (or cannot be tested at all) in a real-world, large-scale speech community.

Keywords: agent based modeling, cultural evolution, language change, social behavior modeling, social influence

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Authors: William Michael Short

Abstract:

Semantic Web’ technologies such as the Unified Medical Language System Metathesaurus, SNOMED-CT, and MeSH have been touted as transformational for the way users access online medical and health information, enabling both the automated analysis of natural-language data and the integration of heterogeneous healthrelated resources distributed across the Internet through the use of standardized terminologies that capture concepts and relationships between concepts that are expressed differently across datasets. However, the approaches that have so far characterized ‘semantic bioinformatics’ have not yet fulfilled the promise of the Semantic Web for medical and health information retrieval applications. This paper argues within the perspective of cognitive linguistics and cognitive anthropology that four features of human meaning-making must be taken into account before the potential of semantic technologies can be realized for this domain. First, many semantic technologies operate exclusively at the level of the word. However, texts convey meanings in ways beyond lexical semantics. For example, transitivity patterns (distributions of active or passive voice) and modality patterns (configurations of modal constituents like may, might, could, would, should) convey experiential and epistemic meanings that are not captured by single words. Language users also naturally associate stretches of text with discrete meanings, so that whole sentences can be ascribed senses similar to the senses of words (so-called ‘discourse topics’). Second, natural language processing systems tend to operate according to the principle of ‘one token, one tag’. For instance, occurrences of the word sound must be disambiguated for part of speech: in context, is sound a noun or a verb or an adjective? In syntactic analysis, deterministic annotation methods may be acceptable. But because natural language utterances are typically characterized by polyvalency and ambiguities of all kinds (including intentional ambiguities), such methods leave the meanings of texts highly impoverished. Third, ontologies tend to be disconnected from everyday language use and so struggle in cases where single concepts are captured through complex lexicalizations that involve profile shifts or other embodied representations. More problematically, concept graphs tend to capture ‘expert’ technical models rather than ‘folk’ models of knowledge and so may not match users’ common-sense intuitions about the organization of concepts in prototypical structures rather than Aristotelian categories. Fourth, and finally, most ontologies do not recognize the pervasively figurative character of human language. However, since the time of Galen the widespread use of metaphor in the linguistic usage of both medical professionals and lay persons has been recognized. In particular, metaphor is a well-documented linguistic tool for communicating experiences of pain. Because semantic medical knowledge-bases are designed to help capture variations within technical vocabularies – rather than the kinds of conventionalized figurative semantics that practitioners as well as patients actually utilize in clinical description and diagnosis – they fail to capture this dimension of linguistic usage. The failure of semantic technologies in these respects degrades the efficiency and efficacy not only of medical research, where information retrieval inefficiencies can lead to direct financial costs to organizations, but also of care provision, especially in contexts of patients’ self-management of complex medical conditions.

Keywords: ambiguity, bioinformatics, language, meaning, metaphor, ontology, semantic web, semantics

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Authors: Mohammed Muzafar, Darshan Ruikar

Abstract:

BIM, an acronym for Building Information Modelling relates to the practice of creating a computer generated model which is capable of displaying the planning, design, construction and operation of a structure. The resulting simulation is a data-rich, object-oriented, intelligent and parametric digital representation of the facility, from which views and data, appropriate to various users needs can be extracted and analysed to generate information that can be used to make decisions and to improve the process of delivering the facility. BIM also refers to a shift in culture that will influence the way the built environment and infrastructure operates and how it is delivered. One of the main issues of concern in the construction industry at present in the UK is its record on Health & Safety (H&S). It is, therefore, important that new technologies such as BIM are developed to help improve the quality of health and safety. Historically the H&S record of the construction industry in the UK is relatively poor as compared to the manufacturing industries. BIM and the digital environment it operates within now allow us to use design and construction data in a more intelligent way. It allows data generated by the design process to be re-purposed and contribute to improving efficiencies in other areas of a project. This evolutionary step in design is not only creating exciting opportunities for the designers themselves but it is also creating opportunity for every stakeholder in any given project. From designers, engineers, contractors through to H&S managers, BIM is accelerating a cultural change. The paper introduces the concept behind a research project that mitigates the H&S risks associated with the construction, operation and maintenance of assets through the adoption of BIM.

Keywords: building information modeling, BIM levels, health, safety, integration

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Authors: Karolina Pietras, Joanna Fryt, Aleksandra Gronostaj, Tomasz Smolen

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Young women and men differ from their parents in preferred values. Those differences enable their adaptability to a new socio-cultural context and help with fulfilling developmental tasks specific to young adulthood. At the same time core values, with special importance to family members, are transmitted within families. Intergenerational similarities in values may thus be both an effect of value transmission within a family and a consequence of sharing the same socio-cultural context. These processes are difficult to separate. In our study we assessed similarities and differences in values within four intergenerational family dyads (mothers-daughters, fathers-daughters, mothers-sons, fathers-sons). Sixty Polish young adults (30 women and 30 men aged 19-25) along with their parents (a total of 180 participants) completed the Schwartz’ Portrait Value Questionnaire (PVQ-21). To determine which values may be transmitted within families, we used a correlation analysis and pseudo dyad analysis that allows for the estimation of a baseline likeness between all tested subjects and consequently makes it possible to determine if similarities between actual family members are greater than chance. We also assessed whether different strategies of measuring similarity between family members render different results, and checked whether resemblances in family dyads are influenced by child’s and parent’s gender. Reported similarities were interpreted in light of the evolutionary and the value salience perspective.

Keywords: intergenerational differences in values, gender differences, pseudo dyad analysis, transmission of values

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Authors: Dulanjali Ranasinghe, Isuru Supasan, Kaushalya Premachandra, Ranjan Dissanayake, Ajith Rajapaksha, Eustace Fernando

Abstract:

Proteomics studies of organisms are considered to be significantly information-rich compared to their genomic counterparts because proteomes of organisms represent the expressed state of all proteins of an organism at a given time. In modern top-down and bottom-up proteomics workflows, the primary analysis methods employed are gel–based methods such as two-dimensional (2D) electrophoresis and mass spectrometry based methods. Machine learning (ML) and artificial intelligence (AI) have been used increasingly in modern biological data analyses. In particular, the fields of genomics, DNA sequencing, and bioinformatics have seen an incremental trend in the usage of ML and AI techniques in recent years. The use of aforesaid techniques in the field of proteomics studies is only beginning to be materialised now. Although there is a wealth of information available in the scientific literature pertaining to proteomics workflows, no comprehensive review addresses various aspects of the combined use of proteomics and machine learning. The objective of this review is to provide a comprehensive outlook on the application of machine learning into the known proteomics workflows in order to extract more meaningful information that could be useful in a plethora of applications such as medicine, agriculture, and biotechnology.

Keywords: proteomics, machine learning, gel-based proteomics, mass spectrometry

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Authors: Jihye Hwang, Eun Hwa Choi, Su Youn Baek, Bia Park, Gyeongmin Kim, Chorong Shin, Joon Ha Lee, Jae-Sam Hwang, Ui Wook Hwang

Abstract:

White-spotted flower chafers are widely distributed in Asian countries and traditionally used for the treatment of chronic fatigue, blood circulation, and paralysis in the oriental medicine field. The evolution and development of insect wings and metamorphosis remain under-discovered subjects in arthropod evolutionary researches. Gene expression abundance analyses along with developmental stages based on the large-scale RNA-seq data are also still rarely done. Here we report the de novo assembly of a Protestia brevitarsis seulensis transcriptome along four different developmental stages (egg, larva, pupa, and adult) to explore its development and evolution of wings and metamorphosis. The de novo transcriptome assembly consists of 23,551 high-quality transcripts and is approximately 96.7% complete. Out of 8,545 transcripts, 5,183 correspond to the possible orthologs with Drosophila melanogaster. As a result, we could found 265 genes related to wing development and 19 genes related to metamorphosis. The comparison of transcript expression abundance with different developmental stages revealed developmental stage-specific transcripts especially working at the stage of wing development and metamorphosis of P. b. seulensis. This transcriptome quantification along the developmental stages may provide some meaningful clues to elucidate the genetic modulation mechanism of wing development and metamorphosis obtained during the insect evolution.

Keywords: white-spotted flower chafers, transcriptomics, RNA-seq, network biology, wing development, metamorphosis

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Authors: Ravinder Singh, C Rajesh, Saroj Badhan, Shailendra Mishra, Ranjit Singh Kataria

Abstract:

Heat shock protein 60 and 70 are crucial chaperones that guide appropriate folding of denatured proteins under heat stress conditions. HSP60 and HSP70 provide assistance in correct folding of a multitude of denatured proteins. The heat shock factors are the family of some transcription factors which controls the regulation of gene expression of proteins involved in folding of damaged or improper folded proteins during stress conditions. Under normal condition heat shock proteins bind with HSF-1 and act as its repressor as well as aids in maintaining the HSF-1’s nonactive and monomeric confirmation. The experimental protein structure for all these proteins in Bubalus bubalis is not known till date. Therefore computational approach was explored to identify three-dimensional structure analysis of all these proteins. In this study, an extensive in silico analysis has been performed including sequence comparison among species to comparative modeling of Bubalus bubalis HSP60, HSP70 and HSF-1 protein. The stereochemical properties of proteins were assessed by utilizing several scrutiny bioinformatics tools to ensure model accuracy. Further docking approach was used to study interactions between Heat shock proteins and HSF-1.

Keywords: Bubalus bubalis, comparative modelling, docking, heat shock protein

Procedia PDF Downloads 322