Search results for: sequence alignment problem

Authors: Guillaume Bélanger, Jean-Philippe Fontaine, Clémence Hauduc

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There is an undeniable thirst from organic chemists and from the pharmaceutical industry to access complex alkaloids with short syntheses. While medicinal chemists are interested in the fascinating wide range of biological properties of alkaloids, synthetic chemists are rather interested in finding new routes to access these challenging natural products of often low availability from nature. To synthesize complex polycyclic cores of natural products, reaction cascades or sequences performed one-pot offer a neat advantage over classical methods for their rapid increase in molecular complexity in a single operation. In counterpart, reaction cascades need to be run on substrates bearing all the required functional groups necessary for the key cyclizations. Chemoselectivity is thus a major issue associated with such a strategy, in addition to diastereocontrol and regiocontrol for the overall transformation. In the pursuit of synthetic efficiency, our research group developed an innovative one-pot transformation of linear substrates into bi- and tricyclic adducts applied to the construction of Aspidospermatan-type alkaloids. The latter is a rich class of indole alkaloids bearing a unique bridged azatricyclic core. Despite many efforts toward the synthesis of members of this family, efficient and versatile synthetic routes are still coveted. Indeed, very short, non-racemic approaches are rather scarce: for example, in the cases of aspidospermidine and aspidospermine, syntheses are all fifteen steps and over. We envisaged a unified approach to access several members of the Aspidospermatan alkaloids family. The key sequence features a highly chemoselective formamide activation that triggers a Vilsmeier-Haack cyclization, followed by an azomethine ylide generation and intramolecular cycloaddition. Despite the high density and variety of functional groups on the substrates (electron-rich and electron-poor alkenes, nitrile, amide, ester, enol ether), the sequence generated three new carbon-carbon bonds and three rings in a single operation with good yield and high chemoselectivity. A detailed study of amide, nucleophile, and dipolarophile variations to finally get to the successful combination required for the key transformation will be presented. To complete the indoline fragment of the natural products, we developed an original approach. Indeed, all reported routes to Aspidospermatan alkaloids introduce the indoline or indole early in the synthesis. In our work, the indoline needs to be installed on the azatricyclic core after the key cyclization sequence. As a result, typical Fischer indolization is not suited since this reaction is known to fail on such substrates. We thus envisaged a unique photocatalyzed decarboxylative radical cyclization. The development of this reaction as well as the scope and limitations of the methodology, will also be presented. The original Vilsmeier-Haack and azomethine ylide cyclization sequence as well as the new photocatalyzed decarboxylative radical cyclization will undoubtedly open access to new routes toward polycyclic indole alkaloids and derivatives of pharmaceutical interest in general.

Keywords: Aspidospermatan alkaloids, azomethine ylide cycloaddition, decarboxylative radical cyclization, indole and indoline synthesis, one-pot sequential cyclizations, photocatalysis, Vilsmeier-Haack Cyclization

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Authors: Srijata Mitra, Mobina Parveen, Pranab Roy, Narayan Chandra Chattopadhyay

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Chlorinated hydrocarbon can be a major pollution problem in groundwater as well as soil. Many people interact with these chemicals on daily accidentally or by professionally in the laboratory. One of the most common sources for Chlorinated hydrocarbon contamination of soil and groundwater are industrial effluents. The wide use and discharge of Trichloroethylene (TCE), a volatile chlorohydrocarbon from chemical industry, led to major water pollution in rural areas. TCE is an mainly used as an industrial metal degreaser in industries. Biotransformation of TCE to the potent carcinogen vinyl chloride (VC) by consortia of anaerobic bacteria might have role for the above purpose. For these reasons, the aim of current study was to isolate and characterized the genes involved in TCE metabolism and also to investigate the in silico study of those genes. To our knowledge, only one aromatic dioxygenase system, the toluene dioxygenase in Pseudomonas putida F1 has been shown to be involved in TCE degradation. This is first instance where Bacillus cereus group being used in biodegradation of trichloroethylene. A novel bacterial strain 2479 was isolated from oil depot site at Rajbandh, Durgapur (West Bengal, India) by enrichment culture technique. It was identified based on polyphasic approach and ribotyping. The bacterium was gram positive, rod shaped, endospore forming and capable of degrading trichloroethylene as the sole carbon source. On the basis of phylogenetic data and Fatty Acid Methyl Ester Analysis, strain 2479 should be placed within the genus Bacillus and species cereus. However, the present isolate (strain 2479) is unique and sharply different from the usual Bacillus strains in its biodegrading nature. Fujiwara test was done to estimate that the strain 2479 could degrade TCE efficiently. The gene for TCE biodegradation was PCR amplified from genomic DNA of Bacillus cereus 2479 by using todC1 gene specific primers. The 600bp amplicon was cloned into expression vector pUC I8 in the E. coli host XL1-Blue and expressed under the control of lac promoter and nucleotide sequence was determined. The gene sequence was deposited at NCBI under the Accession no. GU183105. In Silico approach involved predicting the physico-chemical properties of deduced Tce1 protein by using ProtParam tool. The tce1 gene contained 342 bp long ORF encoding 114 amino acids with a predicted molecular weight 12.6 kDa and the theoretical pI value of the polypeptide was 5.17, molecular formula: C559H886N152O165S8, total number of atoms: 1770, aliphatic index: 101.93, instability index: 28.60, Grand Average of Hydropathicity (GRAVY): 0.152. Three differentially expressed proteins (97.1, 40 and 30 kDa) were directly involved in TCE biodegradation, found to react immunologically to the antibodies raised against TCE inducible proteins in Western blot analysis. The present study suggested that cloned gene product (TCE1) was capable of degrading TCE as verified chemically.

Keywords: cloning, Bacillus cereus, in silico analysis, TCE

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Authors: Seyed Reza Aghili, Tahereh Shokohi, Shirin Sadat Hashemi Fesharaki, Mohammad Ali Boroumand, Bahar Salmanian

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Introduction: Intravenous catheter-associated fungal infection as nosocomial infection continue to be a deep problem among hospitalized patients, decreasing quality of life and adding healthcare costs. The capacity of catheters in the spread of candidemia in heart failure patients is obvious. The aim of this study was to evaluate the prevalence and genetic identification of Candida species in heart disorder patients. Material and Methods: This study was conducted in Tehran Hospital of Cardiology Center (Tehran, Iran, 2014) during 1.5 years on the patients hospitalized for at least 7 days and who had central or peripheral vein catheter. Culture of catheters, blood and skin of the location of catheter insertion were applied for detecting Candida colonies in 223 patients. Identification of Candida species was made on the basis of a combination of various phenotypic methods and confirmed by sequencing the ITS1-5.8S-ITS2 region amplified from the genomic DNA using PCR and the NCBI BLAST. Results: Of the 223 patients samples tested, we identified totally 15 Candida isolates obtained from 9 (4.04%) catheter cultures, 3 (1.35%) blood cultures and 2 (0.90%) skin cultures of the catheter insertion areas. On the base of ITS region sequencing, out of nine Candida isolates from catheter, 5(55.6%) C. albicans, 2(22.2%) C. glabrata, 1(11.1%) C. membranifiaciens and 1 (11.1%) C. tropicalis were identified. Among three Candida isolates from blood culture, C. tropicalis, C. carpophila and C. membranifiaciens were identified. Non-candida yeast isolated from one blood culture was Cryptococcus albidus. One case of C. glabrata and one case of Candida albicans were isolated from skin culture of the catheter insertion areas in patients with positive catheter culture. In these patients, ITS region of rDNA sequence showed a similarity between Candida isolated from the skin and catheter. However, the blood samples of these patients were negative for fungal growth. We report two cases of catheter-related candidemia caused by C. membranifiaciens and C. tropicalis on the base of genetic similarity of species isolated from blood and catheter which were treated successfully with intravenous fluconazole and catheter removal. In phenotypic identification methods, we could only identify C. albicans and C. tropicalis and other yeast isolates were diagnosed as Candida sp. Discussion: Although more than 200 species of Candida have been identified, only a few cause diseases in humans. There is some evidence that non-albicans infections are increasing. Many risk factors, including prior antibiotic therapy, use of a central venous catheter, surgery, and parenteral nutrition are considered to be associated with candidemia in hospitalized heart failure patients. Identifying the route of infection in candidemia is difficult. Non-albicans candida as the cause of candidemia is increasing dramatically. By using conventional method, many non-albicans isolates remain unidentified. So, using more sensitive and specific molecular genetic sequencing to clarify the aspects of epidemiology of the unknown candida species infections is essential. The positive blood and catheter cultures for candida isolates and high percentage of similarity of their ITS region of rDNA sequence in these two patients confirmed the diagnosis of intravenous catheter-associated candidemia.

Keywords: catheter-associated infections, heart failure patient, molecular genetic sequencing, ITS region of rDNA, Candidemia

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Authors: Tuba Bagatarhan, Digdem Muge Siyez

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The aim of this research is to examine the effects of the psycho-education program on problem-solving skills of parents of high school students in the risk group for Internet addiction. A quasi-experimental design based on the pre-test, post-test and follow up test including experimental and control groups was used in the research. The independent variable of the study was the parent psycho-education program on problem-solving skills; the dependent variable was the problem-solving skills of parents. The research was conducted with the parents of 52 tenth-grade students in the risk group for Internet addiction from two high schools and volunteer to participate research on evaluation of the effectiveness of internet addiction prevention psycho-education program within the scope of another study. In this study, as 26 students were in the experimental groups in the first-high school, the parents of these 26 students were asked if they would like to participate in the parent psycho-education program on parental problem-solving skills. The parents were volunteer to participate in parent psycho-education program assigned experimental group (n=13), the other parents assigned control group 1 (n=13) in the first high school. The parents of the 26 students were randomly assigned to the control group 2 (n=13) and control group 3 (n=13) in the second high school. The data of the research was obtained via the problem behavior scale - coping - parents form and demographic questionnaire. Four-session parent psycho-education program to cope with Internet addiction and other problem behaviors in their children was applied to the experimental group. No program was applied to the control group 1, control group 2 and control group 3. In addition, an internet addiction prevention psycho-education program was applied to the children of the parents in experimental group and control group 1 within the scope of another study. In the analysis of the obtained data, two-factor variance analysis for repeated measures on one factor was used. Bonferroni post-hoc test was used to find the source of intergroup difference. According to the findings, the psycho-education program significantly increases parents’ problem-solving abilities, and the increase has continued throughout the follow-up test.

Keywords: internet addiction, parents, prevention, psyho-education

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Authors: Shavindrie Cooray

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It is vital that students are supported in having balanced conversations about topics that might be controversial. This process is crucial to the development of critical thinking skills. This can be difficult to attain in e-learning environments, with some research finding students report a perceived loss in the quality of knowledge exchange and performance. This research investigated if Systems Theory could be applied to structure the discussion, improve information sharing, and reduce conflicts when students are working in online environments. This research involved 160 participants across four categories of student groups at a college in the Northeastern US. Each group was provided with a shared problem, and each group was expected to make a proposal for a solution. Two groups worked face-to-face; the first face to face group engaged with the problem and each other with no intervention from a facilitator; a second face to face group worked on the problem using Systems tools to facilitate problem structuring, group discussion, and decision-making. There were two types of virtual teams. The first virtual group also used Systems tools to facilitate problem structuring and group discussion. However, all interactions were conducted in a synchronous virtual environment. The second type of virtual team also met in real time but worked with no intervention. Findings from the study demonstrated that the teams (both virtual and face-to-face) using Systems tools shared more information with each other than the other teams; additionally, these teams reported an increased level of disagreement amongst their members, but also expressed more confidence and satisfaction with the experience and resulting decision compared to the other groups.

Keywords: e-learning, virtual teams, systems approach, conflicts

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Authors: Stepan Papacek, Jiri Jablonsky, Radek Kana, Ctirad Matonoha, Stefan Kindermann

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FRAP (Fluorescence Recovery After Photobleaching) is a widely used measurement technique to determine the mobility of fluorescent molecules within living cells. While the experimental setup and protocol for FRAP experiments are usually fixed, data processing part is still under development. In this paper, we formulate and solve the problem of data selection which enhances the processing of FRAP images. We introduce the concept of the irrelevant data set, i.e., the data which are almost not reducing the confidence interval of the estimated parameters and thus could be neglected. Based on sensitivity analysis, we both solve the problem of the optimal data space selection and we find specific conditions for optimizing an important experimental design factor, e.g., the radius of bleach spot. Finally, a theorem announcing less precision of the integrated data approach compared to the full data case is proven; i.e., we claim that the data set represented by the FRAP recovery curve lead to a larger confidence interval compared to the spatio-temporal (full) data.

Keywords: FRAP, inverse problem, parameter identification, sensitivity analysis, optimal experimental design

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Authors: Dirk Briskorn, Michael Dienstknecht

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Cranes are a key element in construction projects as they are the primary lifting equipment and among the most expensive construction equipment. Thus, selecting cranes and locating them on-site is an important factor for a project's profitability. We focus on a site with supply and demand areas that have to be connected by tower cranes. There are several types of tower cranes differing in certain specifications such as costs or operating radius. The objective is to select cranes and determine their locations such that each demand area is connected to its supply area at minimum cost. We detail the problem setting and show how to obtain a discrete set of candidate locations for each crane type without losing optimality. This discretization allows us to reduce our problem to the classic set cover problem. Despite its NP-hardness, we achieve good results employing a standard solver and a greedy heuristic, respectively.

Keywords: positioning, selection, standard solver, tower cranes

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Authors: Aigul Manapova

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We consider an optimal control problem in the higher coefficient of nonlinear equations with a divergent elliptic operator and unbounded nonlinearity, and the Dirichlet boundary condition. The conditions imposed on the coefficients of the state equation are assumed to hold only in a small neighborhood of the exact solution to the original problem. This assumption suggests that the state equation involves nonlinearities of unlimited growth and considerably expands the class of admissible functions as solutions of the state equation. We obtain formulas for the first partial derivatives of the objective functional with respect to the control functions. To calculate the gradients the numerical solutions of the state and adjoint problems are used. We also prove that the gradient of the cost function is Lipchitz continuous.

Keywords: cost functional, differentiability, divergent elliptic operator, optimal control, unbounded nonlinearity

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Authors: Hanieh Tarbiat Khosrowshahi, Mojtaba Shakeri

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Wireless Sensor Networks (WSNs) consist of a set of sensor nodes with limited capability. WSNs may suffer from multiple node failures when they are exposed to harsh environments such as military zones or disaster locations and lose connectivity by getting partitioned into disjoint segments. Relay nodes (RNs) are alternatively introduced to restore connectivity. They cost more than sensors as they benefit from mobility, more power and more transmission range, enforcing a minimum number of them to be used. This paper addresses the problem of RN placement in a multiple disjoint network by developing a genetic algorithm (GA). The problem is reintroduced as the Steiner tree problem (which is known to be an NP-hard problem) by the aim of finding the minimum number of Steiner points where RNs are to be placed for restoring connectivity. An upper bound to the number of RNs is first computed to set up the length of initial chromosomes. The GA algorithm then iteratively reduces the number of RNs and determines their location at the same time. Experimental results indicate that the proposed GA is capable of establishing network connectivity using a reasonable number of RNs compared to the best existing work.

Keywords: connectivity restoration, genetic algorithms, multiple-node failure, relay nodes, wireless sensor networks

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Authors: Varsha Shinde, Belle Damodara Shenoy

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Tarballs are crude oil remnants found in oceans after long term weathering process and are a global concern since several decades as potential marine pollutant. Being complicated in structure microbial remediation of tarballs in natural environment is a slow process. They are rich in high molecular weight alkanes and poly aromatic hydrocarbons which are resistant to microbial attack and other environmental factors, therefore remain in environment for long time. However, it has been found that many bacteria and fungi inhabit on tarballs for nutrients and shelter. Many of them are supposed to be oil degraders, while others are supposed to be getting benefited by byproducts formed during hydrocarbon metabolism. Thus tarballs are forming special interesting ecological niche of microbes. This work aimed to study diversity of bacteria and fungi from tarballs and to see their potential application in crude oil degradation. The samples of tarballs were collected from Betul beach of south Goa (India). Different methods were used to isolate culturable fraction of bacteria and fungi from it. Those were sequenced for 16S rRNA gene and ITS for molecular level identification. The 16S rRNA gene sequence analysis revealed the presence of 13 bacterial genera/clades (Alcanivorax, Brevibacterium, Bacillus, Cellulomonas, Enterobacter, Klebsiella, Marinobacter, Nitratireductor, Pantoea, Pseudomonas, Pseudoxanthomonas, Tistrella and Vibrio), while the ITS sequence analysis placed the fungi in 8 diverse genera/ clades (Aspergillus, Byssochlamys, Monascus, Paecilomyces, Penicillium, Scytalidium/ Xylogone, Talaromyces and Trichoderma). All bacterial isolates were screened for oil degradation capacity. Potential strains were subjected to crude oil degradation experiment for quantification. Results were analyzed by GC-MS-MS.

Keywords: bacteria, biodegradation, crude oil, diversity, fungi, tarballs

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Authors: Helen Frialde-Dupale

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Critical thinking Index (CTI) of 150 third year college students from five State Colleges and Universities (SUCs) in Region I were determined. Only students with Grade Point Average (GPA) of at least 2.0 from four general classification of degree courses, namely: Education, Arts and Sciences, Engineering and Agriculture were included. Specific problem No.1 dealt with the profile variables, namely: age, sex, degree course, monthly family income, number of siblings, high school graduated from, grade point average, personality type, highest educational attainment of parents, and occupation of parents. Problem No. 2 determined the critical thinking index among the respondents. Problem No. 3 investigated whether or not there are significant differences in the critical thinking index among the respondents across the profile variables. While problem No.4 determined whether or not there are significant relationship between the critical thinking index and selected profile variables, namely: age, monthly family income, number of siblings, and grade point average of the respondents. Finally, on problem No. 5, the critical thinking instrument which obtained the lowest rates, were used as basis for outlining an intervention program for enhancing critical thinking index (CTI) of students. The following null hypotheses were tested at 0.05 level of significance: there are no significant differences in the critical thinking index of the third college students across the profile variables; there are no significant relationships between the critical thinking index of the respondents and selected variables, namely: age, monthly family income, number of siblings, and grade point average.

Keywords: attitude as critical thinker, critical thinking applied, critical thinking index, self-perception as critical thinker

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Authors: Tien-Ling Yeh, Jo-Han Chan

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The percentage of dual-earner couples has become higher and higher each year. Family lifestyles in Taiwan have also been changing. This fact reflects the importance of family communication and parent-child relationship. This study aimed to explore the influences of family lifestyles and accompany forms on children’s capability to solve problems. The research process included two phases: (1) literature review, to explore the characteristics of children’s capability to solve problems and methods to measure this capability; and (2) questionnaire analyses, to explore the influences of lifestyles and accompany time and forms of modern families on their children’s capability to solve problems. The questionnaires were issued in October and November, 2016. A total of 300 questionnaires were retrieved, among which 250 were valid. The findings are summarized below: -The linguistic performances of the children from families of the busy and haggling lifestyle or the intermittent childcare lifestyle were rather good. Besides being interested in learning, these children could solve problems or difficulties independently. -The capability to ‘analyze problems’ of children from families with accompanying time during 19:00-19:30 (family dinner time) or 22:00-23:30 (before bedtime) was good. When facing a complex problem, these children could identify the most important factor in the problem. When seeing a problem, they would first look for the cause. If they encountered a bottleneck while solving a problem, they would review the context of the problem and related conditions to come up with another solution. -According to the literature, learning toys with numbers and symbols to learn to read can help develop children’s logic thinking, which is helpful to solve problems. Interestingly, some study suggested that children playing with fluid constructive toys are less likely to give up what they are doing and more likely to identify problems in their daily life. Some of them can even come up with creative and effective solutions.

Keywords: accompany, lifestyle, parent-child, problem-solving

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Authors: Shimeles Terefe Mengistue, Ascensión Del Olmo, Paola Marziani, Mirjana Pović, María Angeles Martínez-Carballo, Jaime Perea, Isabel M. Árquez

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Quasars have historically been classified into two distinct classes, radio-loud (RL) and radio-quiet (RQ), taking into account the presence and absence of relativistic radio jets, respectively. The absence of spectra with a high S/N ratio led to the impression that all quasars (QSOs) are spectroscopically similar. Although different attempts were made to unify these two classes, there is a long-standing open debate involving the possibility of a real physical dichotomy between RL and RQ quasars. In this work, we present new high S/N spectra of 11 extremely powerful jetted quasars with radio-to-optical flux density ratio > 1000 that concomitantly cover the low-ionization emission of Mgii𝜆2800 and Hbeta𝛽 as well as the Feii blends in the redshift range 0.35 < z < 1, observed at Calar Alto Observatory (Spain). This work aims to quantify broad emission line differences between RL and RQ quasars by using the four-dimensional eigenvector 1 (4DE1) parameter space and its main sequence (MS) and to check the effect of powerful radio ejection on the low ionization broad emission lines. Emission lines are analysed by making two complementary approaches, a multicomponent non-linear fitting to account for the individual components of the broad emission lines and by analysing the full profile of the lines through parameters such as total widths, centroid velocities at different fractional intensities, asymmetry, and kurtosis indices. It is found that broad emission lines show large reward asymmetry both in Hbeta𝛽 and Mgii2800A. The location of our RL sources in a UV plane looks similar to the optical one, with weak Feii UV emission and broad Mgii2800A. We supplement the 11 sources with large samples from previous work to gain some general inferences. The result shows, compared to RQ, our extreme RL quasars show larger median Hbeta full width at half maximum (FWHM), weaker Feii emission, larger 𝑀BH, lower 𝐿bol/𝐿Edd, and a restricted space occupation in the optical and UV MS planes. The differences are more elusive when the comparison is carried out by restricting the RQ population to the region of the MS occupied by RL quasars, albeit an unbiased comparison matching 𝑀BH and 𝐿bol/𝐿Edd suggests that the most powerful RL quasars show the highest redward asymmetries in Hbeta.

Keywords: galaxies, active, line, profiles, quasars, emission lines, supermassive black holes

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Authors: Abir Derouiche, Abdesslem Layeb

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Association Rule Mining (ARM) is one of the most popular data mining tasks and it is widely used in various areas. The search for association rules is an NP-complete problem that is why metaheuristics have been widely used to solve it. The present paper presents the ARM as an optimization problem and surveys the proposed approaches in the literature based on metaheuristics.

Keywords: Optimization, Metaheuristics, Data Mining, Association rules Mining

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Authors: Hamzeh Alipour, Masoumeh Bagheri, Tahereh Karamzadeh, Abbasali Raz, Kourosh Azizi

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Netrin-A, a protein identified for conducting commissural axons, has a similar role in angiogenesis. In addition, studies have shown that one of the netrin-A receptors is expressed in the growing cells of small capillaries. It will be interesting to study this new group of molecules because their role in wound healing will become clearer in the future due to angiogenesis. The greenbottle blowfly Luciliasericata (L. sericata) larvae are increasingly used in maggot therapy of chronic wounds. This aim of this was the identification of moleculareatures of Netrin-A in L. sericata larvae. Larvae were reared under standard maggotarium conditions. The nucleic acid sequence of L. sericataNetrin-A (LSN-A) was then identified using Rapid Amplification of cDNA Ends (RACE) and Rapid Amplification of Genomic Ends (RAGE). Parts of the Netrin-A gene, including the middle, 3′-, and 5′-ends were identified, TA cloned in pTG19 plasmid, and transferred into DH5ɑ Escherichia coli. Each part was sequenced and assembled using SeqMan software. This gene structure was further subjected to in silico analysis. The DNA of LSN-A was identified to be 2407 bp, while its mRNA sequence was recognized as 2115 bp by Oligo0.7 software. It translated the Netrin-A protein with 704 amino acid residues. Its molecular weight is estimated to be 78.6 kDa. The 3-D structure ofNetrin-A drawn by SWISS-MODEL revealed its similarity to the Netrin-1 of humans with 66.8% identity. The LSN-A protein conduces to repair the myelin membrane in neuronal cells. Ultimately, it can be an effective candidate in neural regeneration and wound healing. Furthermore, our next attempt is to deplore recombinant proteins for use in medical sciences.

Keywords: maggot therapy, netrin-A, RACE, RAGE, lucilia sericata

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Authors: Sofia Sehli, Zainab El Ouafi, Casey Eddington, Soumaya Jbara, Kasambula Arthur Shem, Islam El Jaddaoui, Ayorinde Afolayan, Olaitan I. Awe, Allissa Dillman, Hassan Ghazal

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The ability to promptly sequence whole genomes at a relatively low cost has revolutionized the way we study the microbiome. Microbiologists are no longer limited to studying what can be grown in a laboratory and instead are given the opportunity to rapidly identify the makeup of microbial communities in a wide variety of environments. Analyzing whole genome sequencing (WGS) data is a complex process that involves multiple moving parts and might be rather unintuitive for scientists that don’t typically work with this type of data. Thus, to help lower the barrier for less-computationally inclined individuals, TAXAPRO was developed at the first Omics Codeathon held virtually by the African Society for Bioinformatics and Computational Biology (ASBCB) in June 2021. TAXAPRO is an advanced metagenomics pipeline that accurately assembles organelle genomes from whole-genome sequencing data. TAXAPRO seamlessly combines WGS analysis tools to create a pipeline that automatically processes raw WGS data and presents organism abundance information in both a tabular and graphical format. TAXAPRO was evaluated using COVID-19 patient gut microbiome data. Analysis performed by TAXAPRO demonstrated a high abundance of Clostridia and Bacteroidia genera and a low abundance of Proteobacteria genera relative to others in the gut microbiome of patients hospitalized with COVID-19, consistent with the original findings derived using a different analysis methodology. This provides crucial evidence that the TAXAPRO workflow dispenses reliable organism abundance information overnight without the hassle of performing the analysis manually.

Keywords: metagenomics, shotgun metagenomic sequence analysis, COVID-19, pipeline, bioinformatics

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Authors: Parul Johri, Mala Trivedi

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Major Intrinsic proteins (MIPs), actively involved in the passive transport of small polar molecules across the membranes of almost all living organisms. MIPs that specifically transport water molecules are named aquaporins (AQPs). The permeability of membranes is actively controlled by the regulation of the amount of different MIPs present but also in some cases by phosphorylation and dephosphorylation of the channel. Based on sequence similarity, MIPs have been classified into many categories. All of the proteins are made up of the 20 amino acids, the only difference is there in their orientations. Again all the 20 amino acids are made up of the basic five elements namely: carbon, hydrogen, oxygen, sulphur and nitrogen. These elements are responsible for giving the amino acids the properties of hydrophilicity/hydrophobicity which play an important role in protein interactions. The hydrophobic amino acids characteristically have greater number of carbon atoms as carbon is the main element which contributes to hydrophobic interactions in proteins. It is observed that the carbon level of proteins in different species is different. In the present work, we have taken a sample set of 150 aquaporins proteins from Uniprot database and a dynamic programming code was written to calculate the carbon percentage for each sequence. This carbon percentage was further used to barcode the aqauporins of animals and plants. The protein taken from Oryza sativa, Zea mays and Arabidopsis thaliana preferred to have carbon percentage of 31.8 to 35, whereas on the other hand sequences taken from Mus musculus, Saccharomyces cerevisiae, Homo sapiens, Bos Taurus, and Rattus norvegicus preferred to have carbon percentage of 31 to 33.7. This clearly demarks the carbon range in the aquaporin proteins from plant and animal origin. Hence the atom level analysis of protein sequences can provide us with better results as compared to the residue level comparison.

Keywords: aquaporins, carbon, dynamic prgramming, MIPs

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Authors: Adam Marks, Munir Majdalawieh, Maytha Al Ali

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While research is rich with what criteria could be included in the academic program review processes, there is rarely any mention of how this significant and complex process should be managed. This paper proposes using project management methodology in alignment with the program review criteria of the Dickeson’s Prioritizing Academic Programs model. Project management and academic program review share two distinct characteristics; one is their life cycle, and the second is the core knowledge areas they use. This aligned and structured approach offers academic administrators a step-by-step guide that can help them manage this process and effectively assess academic programs.

Keywords: project management, academic program, program review, education, higher education institution, strategic management

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Authors: Debjani Chakraborty, Abhijit Chatterjee, Aishwaryaprajna

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Posynomials, a special type of polynomials, having singularities, pose difficulties while solving geometric programming problems. In this paper, a methodology has been proposed and used to obtain extreme values for geometric programming problems by nth degree polynomial interpolation technique. Here the main idea to optimise the posynomial is to fit a best polynomial which has continuous gradient values throughout the range of the function. The approximating polynomial is smoothened to remove the discontinuities present in the feasible region and the objective function. This spatial interpolation method is capable to optimise univariate and multivariate geometric programming problems. An example is solved to explain the robustness of the methodology by considering a bivariate nonlinear geometric programming problem. This method is also applicable for signomial programming problem.

Keywords: geometric programming problem, multivariate optimisation technique, posynomial, spatial interpolation

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Authors: Ming Liu, Zhihui Sun, Xiaoning Zhang

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This paper studies a deterministic container transportation problem, jointly optimizing the berth allocation, quay crane assignment and yard storage allocation at container ports. The problem is formulated as an integer program to coordinate the decisions. Because of the large scale, it is then transformed into a set partitioning formulation, and a framework of branchand- price algorithm is provided to solve it.

Keywords: branch-and-price, container terminal, joint scheduling, maritime logistics

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Authors: A. V. Varfolomeeva, N. S. Tkachenko, A. G. Tishchenko

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The problem of violation of internal validity in studies of psychological structures is considered. The role of epistemological attitudes of researchers in the planning of research within the methodology of the system-evolutionary approach is assessed. Alternative programs of psychological research involving representatives of different biological species are presented. On the example of the results of two research series the variants of solving the problem are discussed.

Keywords: epistemological attitudes, experimental design, validity, psychological structure, learning

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Authors: Harun Aydilek, Asiye Aydilek, Ali Allahverdi

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Our objective is to minimize the total tardiness in an m-machine two-stage assembly flowshop scheduling problem. The objective is an important performance measure because of the fact that the fulfillment of due dates of customers has to be taken into account while making scheduling decisions. In the literature, the problem is considered with zero setup times which may not be realistic and appropriate for some scheduling environments. Considering separate setup times from processing times increases machine utilization by decreasing the idle time and reduces total tardiness. We propose two new algorithms and adapt four existing algorithms in the literature which are different versions of simulated annealing and genetic algorithms. Moreover, a dominance relation is developed based on the mathematical formulation of the problem. The developed dominance relation is incorporated in our proposed algorithms. Computational experiments are conducted to investigate the performance of the newly proposed algorithms. We find that one of the proposed algorithms performs significantly better than the others, i.e., the error of the best algorithm is less than those of the other algorithms by minimum 50%. The newly proposed algorithm is also efficient for the case of zero setup times and performs better than the best existing algorithm in the literature.

Keywords: algorithm, assembly flowshop, scheduling, simulation, total tardiness

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Authors: Othman E. Othman, Agnés Germot, Daniel Petit, Abderrahman Maftah

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Threats to the biodiversity are increasing due to the loss of genetic diversity within the species utilized in agriculture. Due to the progressive substitution of the less productive, locally adapted and native breeds by highly productive breeds, the number of threatened breeds is increased. In these conditions, it is more strategically important than ever to preserve as much the farm animal diversity as possible, to ensure a prompt and proper response to the needs of future generations. Mitochondrial (mtDNA) sequencing has been used to explain the origins of many modern domestic livestock species. Studies based on sequencing of sheep mitochondrial DNA showed that there are five maternal lineages in the world for domestic sheep breeds; A, B, C, D and E. Because of the eastern location of Egypt in the Mediterranean basin and the presence of fat-tailed sheep breeds- character quite common in Turkey and Syria- where genotypes that seem quite primitive, the phylogenetic studies of Egyptian sheep breeds become particularly attractive. We aimed in this work to clarify the genetic affinities, biodiversity and phylogeny of five Egyptian sheep breeds using cytochrome B sequencing. Blood samples were collected from 63 animals belonging to the five tested breeds; Barki, Rahmani, Ossimi, Saidi and Sohagi. The total DNA was extracted and the specific primer allowed the conventional PCR amplification of the cytochrome B region of mtDNA (approximately 1272 bp). PCR amplified products were purified and sequenced. The alignment of Sixty-three samples was done using BioEdit software. DnaSP 5.00 software was used to identify the sequence variation and polymorphic sites in the aligned sequences. The result showed that the presence of 34 polymorphic sites leading to the formation of 18 haplotypes. The haplotype diversity in five tested breeds ranged from 0.676 in Rahmani breed to 0.894 in Sohagi breed. The genetic distances (D) and the average number of pairwise differences (Dxy) between breeds were estimated. The lowest distance was observed between Rahmani and Saidi (D: 1.674 and Dxy: 0.00150) while the highest distance was observed between Ossimi and Sohagi (D: 5.233 and Dxy: 0.00475). Neighbour-joining (Phylogeny) tree was constructed using Mega 5.0 software. The sequences of the 63 analyzed samples were aligned with references sequences of different haplogroups. The phylogeny result showed the presence of three haplogroups (HapA, HapB and HapC) in the 63 examined samples. The other two haplogroups described in literature (HapD and HapE) were not found. The result showed that 50 out of 63 tested animals cluster with haplogroup B (79.37%) whereas 7 tested animals cluster with haplogroup A (11.11%) and 6 animals cluster with haplogroup C (9.52%). In conclusion, the phylogenetic reconstructions showed that the majority of Egyptian sheep breeds belonging to haplogroup B which is the dominant haplogroup in Eastern Mediterranean countries like Syria and Turkey. Some individuals are belonging to haplogroups A and C, suggesting that the crosses were done with other breeds for characteristic selection for growth and wool quality.

Keywords: cytochrome B, diversity, phylogheny, Egyptian sheep breeds

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Authors: Giuseppe Maria Russo, Patrícia Amélia Tomei, Antônio Linhares, André Moreira Santos

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Alignment between management strategies, policies and practices with organizational cultures holds great potential to meet the challenges of retaining professionals and maintaining their commitment. In this article, authors consider that when it is aligned with company strategy, compensation acts as an incentive for developing common visions within the organizational culture. This article verified the correlation between types of culture and compensation’s strategic components and provided inputs for the definition of strategies aligned with cultural typologies. We conclude that the impact of compensation variables varies according to the type of organizational culture. This result reinforces the theory that different cultures define different organizational strategies. Thus, compensation strategies may explain types of organizational culture.

Keywords: compensation, Handy’s cultural typology, organizational culture, rewards

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Authors: Isaac K. E. Ampomah, Seong-Bae Park, Sang-Jo Lee

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Over the past decade, there have been promising developments in Natural Language Processing (NLP) with several investigations of approaches focusing on Recognizing Textual Entailment (RTE). These models include models based on lexical similarities, models based on formal reasoning, and most recently deep neural models. In this paper, we present a sentence encoding model that exploits the sentence-to-sentence relation information for RTE. In terms of sentence modeling, Convolutional neural network (CNN) and recurrent neural networks (RNNs) adopt different approaches. RNNs are known to be well suited for sequence modeling, whilst CNN is suited for the extraction of n-gram features through the filters and can learn ranges of relations via the pooling mechanism. We combine the strength of RNN and CNN as stated above to present a unified model for the RTE task. Our model basically combines relation vectors computed from the phrasal representation of each sentence and final encoded sentence representations. Firstly, we pass each sentence through a convolutional layer to extract a sequence of higher-level phrase representation for each sentence from which the first relation vector is computed. Secondly, the phrasal representation of each sentence from the convolutional layer is fed into a Bidirectional Long Short Term Memory (Bi-LSTM) to obtain the final sentence representations from which a second relation vector is computed. The relations vectors are combined and then used in then used in the same fashion as attention mechanism over the Bi-LSTM outputs to yield the final sentence representations for the classification. Experiment on the Stanford Natural Language Inference (SNLI) corpus suggests that this is a promising technique for RTE.

Keywords: deep neural models, natural language inference, recognizing textual entailment (RTE), sentence-to-sentence relation

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Authors: Nkwanyang L. Takem, Christopher M. Agyingi

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Background and aim: An integrated interpretation of wireline logs and lithology of two selected wells (KF-1 and KF-2) of Kribi oil field within the southeastern offshore Douala/Kribi Campo Basin was carried out for sequence stratigraphic analysis of sediments penetrated by the wells. Methods: The stratigraphic units within the wells were subdivided into depositional sequences using characteristic well log patterns that were deposited between Tertiary Miocene to lower Cretaceous. Results: Nine (9) and eight (8) depositional sequences were identified respectively for KF-1 and KF-2. The sequences comprise LST (progradational packages), TSTs (retrogradational packages) and HSTs (aggradational packages), which reflect depositional systems deposited during different phases of base-level changes. The (LST) consists of Basin Floor Fans (BFF), Slope Fans and Channel Sands deposited when sea level was low and accommodation space lower than rate of sediment influx. TST consists of retrogradational marine shales deposited during high relative sea levels and when accommodation space was higher than rate of sediment influx. HST consisted of shoreface sands displaying mostly aggradational to progradational stacking patterns. Conclusion: The rapid facies changes between successive systems tracts provide potential stratigraphic traps. Reservoir stratification and continuity vary greatly between systems tracts and this enhanced development of stratigraphic traps in the area. Basin floor fans comprise sandstone of good reservoir quality, thus huge accumulation of HC can be trapped in this reservoirs.

Keywords: Douala-Kribi-Campo Basin, reservoirs, sequence strastigraphyy, system tracks

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Authors: Y. Wang

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The Traveling salesman problem (TSP) is NP-hard in combinatorial optimization. The research shows the algorithms for TSP on the sparse graphs have the shorter computation time than those for TSP according to the complete graphs. We present an improved iterative algorithm to compute the sparse graphs for TSP by frequency graphs computed with frequency quadrilaterals. The iterative algorithm is enhanced by adjusting two parameters of the algorithm. The computation time of the algorithm is O(CN_maxn²) where C is the iterations, N_max is the maximum number of frequency quadrilaterals containing each edge and n is the scale of TSP. The experimental results showed the computed sparse graphs generally have less than 5n edges for most of these Euclidean instances. Moreover, the maximum degree and minimum degree of the vertices in the sparse graphs do not have much difference. Thus, the computation time of the methods to resolve the TSP on these sparse graphs will be greatly reduced.

Keywords: frequency quadrilateral, iterative algorithm, sparse graph, traveling salesman problem

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Authors: César Garza

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In supervised binary classification and regression problems, it is well-known that learnability is equivalent to a uniform convergence of the hypothesis class, and if a problem is learnable, it is learnable by empirical risk minimization. For the general learning setting of unsupervised learning tasks, there are non-trivial learning problems where uniform convergence does not hold. We present here the task of learning centers of mass with an extra feature that “activates” some of the coordinates over the unit ball in a Hilbert space. We show that the learning problem is learnable under a stable RLM rule. We introduce a family of distributions over the domain space with some mild restrictions for which the sample complexity of uniform convergence for these problems must grow logarithmically with the dimension of the Hilbert space. If we take this dimension to infinity, we obtain a learnable problem for which the uniform convergence property fails for a vast family of distributions.

Keywords: statistical learning theory, learnability, uniform convergence, stability, regularized loss minimization

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Authors: Karen Odendaal

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Accounting transactions are becoming more complex, and more extensive accounting guidance is provided on a continuous basis. It is widely perceived that conceptual teaching of accounting contributes to lifelong learning. Such a conceptual teaching approach also contributes to effective accounting problem-solving. This framework-based approach is rooted in educational psychologies such as constructivism and Ausubel’s subsumption theory. This study aimed at investigating the ability of students to solve complex accounting problems by using only concepts underlying the Conceptual Framework. An assignment was administered to pre-graduate students at a South African university and this study made use of an interpretative research design which implemented multiple research instruments to investigate the ability of students to solve complex accounting problems using only concepts underlying the Conceptual Framework. Student perceptions were analysed and were aided by a related reflective questionnaire. The importance of the study indicates the necessity of Accounting educators to enhance a conceptual understanding among students as a mechanism for problem-solving of accounting issues. The results indicate that the ability of students to solve accounting problems effectively using only the Conceptual Framework depends on the complexity of the scenario and the students’ familiarity with the problem. The study promotes a balanced and more conceptual (rather than only technical) preference to the problem-solving of complex accounting problems. The study indubitably promotes considerable emphasis on the importance of the Conceptual Framework in accounting education and the promotion of life-long learning in the subject field.

Keywords: accounting education, conceptual teaching, constructivism, framework-based, problem-solving

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Authors: Sanchai Ratthanakwan

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This research aims to study situations and characteristics of the problems facing the urban poor. The data and information are collected by focus group and in-depth interview leader and members of Four Regions Slum Network, community representatives and the social welfare officer. The research can be concluded that the problems of the urban poor faced with three major problems: Firstly, the shortage of housing and stability issues in housing; secondly, the problem of substandard quality of life; and thirdly, the debt problem. The study found that a solution will be found in two ways: First way is the creation of housing for the urban poor in slums or community intrusion by the state. Second way is the stability in the housing and subsistence provided by the community center called “housing stability”.

Keywords: urban poor, social welfare, Bangkok metropolis, housing stability

Procedia PDF Downloads 405