Search results for: genetic analysis

Authors: Baye Berihun Getahun, Mulugeta Atnaf Tiruneh, Richard G. F. Visser

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Resource-poor farmers practice low-input farming systems, and yet, most breeding programs give less attention to this huge farming system, which serves as a source of food and income for several people in developing countries. The high-input conventional breeding system appears to have failed to adequately meet the needs and requirements of 'difficult' environments operating under this system. Moreover, the unavailability of resources for crop production is getting for their peaks, the environment is maltreated by excessive use of agrochemicals, crop productivity reaches its plateau stage, particularly in the developed nations, the world population is increasing, and food shortage sustained to persist for poor societies. In various parts of the world, genetic gain at the farmers' level remains low which could be associated with low adoption of crop varieties, which have been developed under high input systems. Farmers usually use their local varieties and apply minimum inputs as a risk-avoiding and cost-minimizing strategy. This evidence indicates that the conventional high-input plant breeding system has failed to feed the world population, and the world is moving further away from the United Nations' goals of ending hunger, food insecurity, and malnutrition. In this review, we discussed the rationality of focused breeding programs for low-input farming systems and, the technical aspect of crop breeding that accommodates future food needs and its significance for developing countries in the decreasing scenario of resources required for crop production. To this end, the application of exotic introgression techniques like polyploidization, pan-genomics, comparative genomics, and De novo domestication as a pre-breeding technique has been discussed in the review to exploit the untapped genetic diversity of the crop wild relatives (CWRs). Desired recombinants developed at the pre-breeding stage are exploited through appropriate breeding approaches such as evolutionary plant breeding (EPB), rhizosphere-related traits breeding, and participatory plant breeding approaches. Populations advanced through evolutionary breeding like composite cross populations (CCPs) and rhizosphere-associated traits breeding approach that provides opportunities for improving abiotic and biotic soil stress, nutrient acquisition capacity, and crop microbe interaction in improved varieties have been reviewed. Overall, we conclude that low input farming system is a huge farming system that requires distinctive breeding approaches, and the exotic pre-breeding introgression techniques and the appropriate breeding approaches which deploy the skills and knowledge of both breeders and farmers are vital to develop heterogeneous landrace populations, which are effective for farmers practicing low input farming across the world.

Keywords: low input farming, evolutionary plant breeding, composite cross population, participatory plant breeding

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Authors: Huang Xiaoling, Liu Lufeng

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In this paper, we seek to determine one reasonable local hub port and optimal routes for a containership fleet, performing pick-ups and deliveries, between the hub and spoke ports in a same region. The relationship between a hub port, and traffic in feeder lines is analyzed. A new network planning method is proposed, an integrated hub port location and route design, a capacitated vehicle routing problem with pick-ups, deliveries and time deadlines are formulated and solved using an improved genetic algorithm for positioning the hub port and establishing routes for a containership fleet. Results on the performance of the algorithm and the feasibility of the approach show that a relatively small fleet of containerships could provide efficient services within deadlines.

Keywords: route planning, hub port location, container feeder service, regional transportation network

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Authors: Omar Dib, Alexandre Caminada, Marie-Ange Manier

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The purpose of this study is to introduce a novel approach to solve the one-to-one shortest path problem. A directed connected graph is assumed in which all edges’ weights are positive. Our method is based on a memetic algorithm in which we combine a genetic algorithm (GA) and a variable neighborhood search method (VNS). We compare our approximate method with two exact algorithms Dijkstra and Integer Programming (IP). We made experimentations using random generated, complete and real graph instances. In most case studies, numerical results show that our method outperforms exact methods with 5% average gap to the optimality. Our algorithm’s average speed is 20-times faster than Dijkstra and more than 1000-times compared to IP. The details of the experimental results are also discussed and presented in the paper.

Keywords: shortest path problem, Dijkstra’s algorithm, integer programming, memetic algorithm

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Authors: Leonard Lipovich, Pattaraporn Thepsuwan, Anton-Scott Goustin, Juan Cai, Donghong Ju, James B. Brown

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Two-thirds of human genes do not encode any known proteins. Aside from long non-coding RNA (lncRNA) genes with recently-discovered functions, the ~40,000 non-protein-coding human genes remain poorly understood, and a role for their transcripts as de-facto unconventional messenger RNAs has not been formally excluded. Ribosome profiling (Riboseq) predicts translational potential, but without independent evidence of proteins from lncRNA open reading frames (ORFs), ribosome binding of lncRNAs does not prove translation. Previously, we mass-spectrometrically documented translation of specific lncRNAs in human K562 and GM12878 cells. We now examined lncRNA translation in human MCF7 cells, integrating strand-specific Illumina RNAseq, Riboseq, and deep mass spectrometry in biological quadruplicates performed at two core facilities (BGI, China; City of Hope, USA). We excluded known-protein matches. UCSC Genome Browser-assisted manual annotation of imperfect (tryptic-digest-peptides)-to-(lncRNA-three-frame-translations) alignments revealed three peptides hypothetically explicable by 'stop-to-nonstop' in-frame replacement of stop codons by amino acids in two ORFs of the lncRNA MMP24-AS1. To search for this phenomenon genomewide, we designed and implemented a novel pipeline, matching tryptic-digest spectra to wildcard-instead-of-stop versions of repeat-masked, six-frame, whole-genome translations. Along with singleton putative stop-to-nonstop events affecting four other lncRNAs, we identified 24 additional peptides with stop-to-nonstop in-frame substitutions from multiple positive-strand MMP24-AS1 ORFs. Only UAG and UGA, never UAA, stop codons were impacted. All MMP24-AS1-matching spectra met the same significance thresholds as high-confidence known-protein signatures. Targeted resequencing of MMP24-AS1 genomic DNA and cDNA from the same samples did not reveal any mutations, polymorphisms, or sequencing-detectable RNA editing. This unprecedented apparent gene-specific violation of the genetic code highlights the importance of matching peptides to whole-genome, not known-genes-only, ORFs in mass-spectrometry workflows, and suggests a new mechanism enhancing the combinatorial complexity of the proteome. Funding: NIH Director’s New Innovator Award 1DP2-CA196375 to LL.

Keywords: genetic code, lncRNA, long non-coding RNA, mass spectrometry, proteogenomics, ribo-seq, ribosome, RNAseq

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Authors: Natalia Buderatskaya, Igor Ilyin, Julia Gontar, Sergey Lavrynenko, Olga Parnitskaya, Ekaterina Ilyina, Eduard Kapustin, Yana Lakhno

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Introduction: It is known that cryopreservation of oocytes has peculiar features due to the complex structure of the oocyte. One of the most important features is that mature oocytes contain meiotic division spindle which is very sensitive even to the slightest variation in temperature. Thus, the main objective of this study is to analyse the resulting euploid embryos obtained from thawed oocytes in comparison with the data of preimplantation genetic screening (PGS) in fresh embryo cycles. Material and Methods: The study was conducted at 'Medical Centre IGR' from January to July 2016. Data were analysed for 908 donor oocytes obtained in 67 cycles of assisted reproductive technologies (ART), of which 693 oocytes were used in the 51 'fresh' cycles (group A), and 215 oocytes - 16 ART programs with vitrification female gametes (group B). The average age of donors in the groups match 27.3±2.9 and 27.8±6.6 years. Stimulation of superovulation was conducted the standard way. Vitrification was performed in 1-2 hours after transvaginal puncture and thawing of oocytes were carried out in accordance with the standard protocol of Cryotech (Japan). Manipulation ICSI was performed 4-5 hours after transvaginal follicle puncture for fresh oocytes, or after defrosting - for vitrified female gametes. For the PGS, an embryonic biopsy was done on the third or on the fifth day after fertilization. Diagnostic procedures were performed using fluorescence in situ hybridization with the study of such chromosomes as 13, 16, 18, 21, 22, X, Y. Only morphologically quality blastocysts were used for the transfer, the estimation of which corresponded to the Gardner criteria. The statistical hypotheses were done using the criteria t, x^2 at a significance levels p<0.05, p<0.01, p<0.001. Results: The mean number of mature oocytes per cycle in group A was 13.58±6.65 and in group B - 13.44±6.68 oocytes for patient. The survival of oocytes after thawing totaled 95.3% (n=205), which indicates a highly effective quality of performed vitrification. The proportion of zygotes in the group A corresponded to 91.1%(n=631), in the group B – 80.5%(n=165), which shows statistically significant difference between the groups (p<0.001) and explained by non-viable oocytes elimination after vitrification. This is confirmed by the fact that on the fifth day of embryos development a statistically significant difference in the number of blastocysts was absent (p>0.05), and constituted respectively 61.6%(n=389) and 63.0%(n=104) in the groups. For the PGS performing 250 embryos analyzed in the group A and 72 embryos - in the group B. The results showed that euploidy in the studied chromosomes were 40.0%(n=100) embryos in the group A and 41.7% (n=30) - in the group B, which shows no statistical significant difference (p>0.05). The indicators of clinical pregnancies in the groups amounted to 64.7% (22 pregnancies per 34 embryo transfers) and 61.5% (8 pregnancies per 13 embryo transfers) respectively, and also had no significant difference between the groups (p>0.05). Conclusions: The results showed that the vitrification does not affect the resulting euploid embryos in assisted reproductive technologies and are not reflected in their morphological characteristics in ART programs.

Keywords: euploid embryos, preimplantation genetic screening, thawing oocytes, vitrification

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Authors: Samaneh Nadali, Masrah Azrifah Azmi Murad, Nurfadhlina Mohammad Sharef

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Sarcasm is a common phenomenon in social media which is a nuanced form of language for stating the opposite of what is implied. Due to the intentional ambiguity, analysis of sarcasm is a difficult task not only for a machine but even for a human. Although sarcasm detection has an important effect on sentiment, it is usually ignored in social media analysis because sarcasm analysis is too complicated. While there is a few systems exist which can detect sarcasm, almost no work has been carried out on a study and the review of the existing work in this area. This survey presents a nearly full image of sarcasm detection techniques and the related fields with brief details. The main contributions of this paper include the illustration of the recent trend of research in the sarcasm analysis and we highlight the gaps and propose a new framework that can be explored.

Keywords: sarcasm detection, sentiment analysis, social media, sarcasm analysis

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Authors: Sarpong Boateng, Rohit Balasundaram, Akua Afrah Amoah

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Introduction: Racial and Gender disparities have been found to be independently associated with Salivary Gland Cancers (SGCs) survival; however, to our best knowledge, there are no previous studies on the interplay of these social determinants on the prognosis of SGCs. The objective of this study was to examine the joint effect of race and gender on the survival of SGCs. Methods: We analyzed survival outcomes of 13,547 histologically confirmed cases of SGCs using the Surveillance Epidemiology and End Results (SEER) database (2004 to 2015). Multivariable Cox regression analysis and Kaplan-Meier curves were used to estimate hazard ratios (HR) after controlling for age, tumor characteristics, treatment type and year of diagnosis. Results: 73.5% of the participants were whites, 8.5% were blacks, 10.1% were Hispanics and 58.5% were males. Overall, males had poorer survival than females (HR = 1.16, p=0.003). In the adjusted multivariable model, there were no significant differences in survival by race. However, the interaction of gender and race was statistically significant (p=0.01) in Hispanic males. Thus, compared to White females (reference), Hispanic females had significantly better survival (HR=0.53), whiles Hispanic males had worse survival outcomes (HR=1.82) for SGCs. Conclusions: Our results show significant interactions between race and gender, with racial disparities varying across the different genders for SGCs survival. This study indicates that racial and gender differences are crucial factors to be considered in the prognostic counseling and management of patients with SGCs. Biologic factors, tumor genetic characteristics, chemotherapy, lifestyle, environmental exposures, and socioeconomic and dietary factors are potential yet proven reasons that could account for racial and gender differences in the survival of SGCs.

Keywords: salivary, cancer, survival, disparity, race, gender, SEER

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Authors: Salam N. Abdo, Orien L. Tulp, George P. Einstein

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The purpose of this exploratory study was to gather the insights into psoriasis etiology, treatment, and patient experience, for developing psoriasis and psoriatic arthritis diagnostic test. Data collection methods consisted of a comprehensive meta-analysis of relevant studies and psoriasis patient survey. Established meta-analysis guidelines were used for the selection and qualitative comparative analysis of psoriasis and psoriatic arthritis research studies. Only studies that clearly discussed psoriasis etiology, treatment, and patient experience were reviewed and analyzed, to establish a qualitative data base for the study. Using the insights gained from meta-analysis, an existing psoriasis patient survey was modified and administered to collect additional data as well as triangulate the results. The hypothesis is that specific types of psoriatic disease have specific etiology and pathophysiologic pattern. The following etiology categories were identified: bacterial, environmental/microbial, genetic, immune, infectious, trauma/stress, and viral. Additional results, obtained from meta-analysis and confirmed by patient survey, were the common age of onset (early to mid-20s) and type of psoriasis (plaque; mild; symmetrical; scalp, chest, and extremities, specifically elbows and knees). Almost 70% of patients reported no prescription drug use due to severe side effects and prohibitive cost. These results will guide the development of psoriasis and psoriatic arthritis diagnostic test. The significant number of medical publications classified psoriatic arthritis disease as inflammatory of an unknown etiology. Thus numerous meta-analyses struggle to report any meaningful conclusions since no definitive results have been reported to date. Therefore, return to the basics is an essential step to any future meaningful results. To date, medical literature supports the fact that psoriatic disease in its current classification could be misidentifying subcategories, which in turn hinders the success of studies conducted to date. Moreover, there has been an enormous commercial support to pursue various immune-modulation therapies, thus following a narrow hypothesis/mechanism of action that is yet to yield resolution of disease state. Recurrence and complications may be considered unacceptable in a significant number of these studies. The aim of the ongoing study is to focus on a narrow subgroup of patient population, as identified by this exploratory study via meta-analysis and patient survey, and conduct an exhaustive work up, aiming at mechanism of action and causality before proposing a cure or therapeutic modality. Remission in psoriasis has been achieved and documented in medical literature, such as immune-modulation, phototherapy, various over-the-counter agents, including salts and tar. However, there is no psoriasis and psoriatic arthritis diagnostic test to date, to guide the diagnosis and treatment of this debilitating and, thus far, incurable disease. Because psoriasis affects approximately 2% of population, the results of this study may affect the treatment and improve the quality of life of a significant number of psoriasis patients, potentially millions of patients in the United States alone and many more millions worldwide.

Keywords: biologics, early diagnosis, etiology, immune disease, immune modulation therapy, inflammation skin disorder, phototherapy, plaque psoriasis, psoriasis, psoriasis classification, psoriasis disease marker, psoriasis diagnostic test, psoriasis marker, psoriasis mechanism of action, psoriasis treatment, psoriatic arthritis, psoriatic disease, psoriatic disease marker, psoriatic patient experience, psoriatic patient quality of life, remission, salt therapy, targeted immune therapy

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Authors: Francesco Piluso

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Nowadays, to restore the deconstructive power of semiotics implies a critical analysis of neoliberal ideology, and, even more critically, a confrontation with materialist perspective. The theoretical path of Jean Baudrillard is crucial to understand the ambivalence of this intersection. A semiotic critique of Baudrillard’s work, through tools of both structuralism and interpretative semiotics, has the aim to give materialism a new consistent semiotic approach and vice-versa. According to Baudrillard, the commodity form is characterized by the same abstract and systemic logic of the sign-form, in which the production of the signified (use-value) is a mere ideological mean for the reproduction of the signifiers-chain (exchange-value). Nevertheless, this parallelism is broken by the author himself: if the use-value is deconstructed in its relative logic, the signified and the referent, both as discrete and positive elements, are collapsed on the same plane at the shadows of the signified forms. These divergent considerations lead Baudrillard to the same crucial point: the dismissal of the material world, replaced by the hyperreality as reproduction of a semiotic (genetic) Code. The stress on the concept of form, as an epistemological and semiotic tool to analyse the construction of values in the consumer society, has led to the Code as its ontological drift. In other words, Baudrillard seems to enclose consumer society (and reality) in this immanent and self-fetishized world of signs–an ideological perspective that mystifies the gravity of the material relationships between Northern-Western World and Third World. The notion of Encyclopaedia by Umberto Eco is the key to overturn the relationship of immanence/transcendence between the Code and the economic political of the sign, by understanding the former as an ideological plane within the encyclopedia itself. Therefore, rather than building semiotic (hyper)realities, semiotics has to deal with materialism in terms of material relationships of power which are mystified and reproduced through such ideological ontologies of signs.

Keywords: Baudrillard, Code, Eco, Encyclopaedia, epistemology vs. ontology, semiotics vs. materialism

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Authors: Chih-Fong Tsai, Ya-Han Hu

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The aim of feature selection (or dimensionality reduction) is to filter out unrepresentative features (or variables) making the classifier perform better than the one without feature selection. Since there are many well-known feature selection algorithms, and different classifiers based on different selection results may perform differently, very few studies consider examining the effect of performing different feature selection algorithms on the classification performances by different classifiers over different types of datasets. In this paper, two widely used algorithms, which are the genetic algorithm (GA) and information gain (IG), are used to perform feature selection. On the other hand, three well-known classifiers are constructed, which are the CART decision tree (DT), multi-layer perceptron (MLP) neural network, and support vector machine (SVM). Based on 14 different types of datasets, the experimental results show that in most cases IG is a better feature selection algorithm than GA. In addition, the combinations of IG with DT and IG with SVM perform best and second best for small and large scale datasets.

Keywords: data mining, feature selection, pattern classification, dimensionality reduction

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Authors: Arsyam Mawardi, Sony Suhandono, Azzania Fibriani, Fifi Fitriyah Masduki

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Malaria is an infectious disease caused by Plasmodium sp. This disease has a high prevalence in Indonesia, especially in Jayapura. The vaccine that is currently being developed has not been effective in overcoming malaria. This is due to the high polymorphism in the Plasmodium genome especially in areas that encode Plasmodium surface proteins. Merozoite Surface Protein 1 (MSP1) Plasmodium falciparum is a surface protein that plays a role in the invasion process in human erythrocytes through the interaction of Glycophorin A protein receptors and sialic acid in erythrocytes with Reticulocyte Binding Proteins (RBP) and Duffy Adhesion Protein (DAP) ligands in merozoites. MSP1 can be targeted to be a specific antigen and predicted epitope area which will be used for the development of diagnostic and malaria vaccine therapy. MSP1 consists of 17 blocks, each block is dimorphic, and has been marked as the K1 and MAD20 alleles. Exceptions only in block 2, because it has 3 alleles, among others K1, MAD20 and RO33. These polymorphisms cause allelic variations and implicate the severity of patients infected P. falciparum. In addition, polymorphism of MSP1 in Jayapura isolates has not been reported so it is interesting to be further identified and projected as a specific antigen. Therefore, in this study, we analyzed the allele polymorphism as well as detected the MSP1 epitope antigen candidate on block 2 P. falciparum. Clinical samples of selected malaria patients followed the consecutive sampling method, examining malaria parasites with blood preparations on glass objects observed through a microscope. Plasmodium DNA was isolated from the blood of malarial positive patients. The block 2 MSP1 gene was amplified using PCR method and cloned using the pGEM-T easy vector then transformed to TOP'10 E.coli. Positive colonies selection was performed with blue-white screening. The existence of target DNA was confirmed by PCR colonies and DNA sequencing methods. Furthermore, DNA sequence analysis was done through alignment and formation of a phylogenetic tree using MEGA 6 software and insilico analysis using IEDB software to predict epitope candidate for P. falciparum. A total of 15 patient samples have been isolated from Plasmodium DNA. PCR amplification results show the target gene size about ± 1049 bp. The results of MSP1 nucleotide alignment analysis reveal that block 2 MSP1 genes derived from the sample of malarial patients were distributed in four different allele family groups, K1 (7), MAD20 (1), RO33 (0) and MSP1_Jayapura (10) alleles. The most commonly appears of the detected allele is MSP1_Jayapura single allele. There was no significant association between sex variables, age, the density of parasitemia and alel variation (Mann Whitney, U > 0.05), while symptomatic signs have a significant difference as a trigger of detectable allele variation (U < 0.05). In this research, insilico study shows that there is a new epitope antigen candidate from the MSP1_Jayapura allele and it is predicted to be recognized by B cells with 17 amino acid lengths in the amino acid sequence 187 to 203.

Keywords: epitope candidate, insilico analysis, MSP1 P. falciparum, polymorphism

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Authors: Benito Minjarez, Jesse Haramati, Yury Rodriguez-Yanez, Florencio Recendiz-Hurtado, Juan-Pedro Luna-Arias, Salvador Mena-Munguia

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During the last decades, the world has experienced a rapid industrialization and an expanding economy favoring a demographic boom. As a consequence, countries around the world have focused on developing new strategies related to the production of different farm products in order to meet future demands. Consequently, different strategies have been developed seeking to improve the major food products for both humans and livestock. Corn, after wheat and rice, is the third most important crop globally and is the primary food source for both humans and livestock in many regions around the globe. In addition, maize (Zea mays) is an important source of protein accounting for up to 60% of the daily human protein supply. Generally, many of the cereal grains have proteins with relatively low nutritional value, when they are compared with proteins from meat. In the case of corn, much of the protein is found in the endosperm (75 to 85%) and is deficient in two essential amino acids, lysine, and tryptophan. This deficiency results in an imbalance of amino acids and low protein content; normal maize varieties have less than half of the recommended amino acids for human nutrition. In addition, studies have shown that this deficiency has been associated with symptoms of growth impairment, anemia, hypoproteinemia, and fatty liver. Due to the fact that most of the presently available maize varieties do not contain the quality and quantity of proteins necessary for a balanced diet, different countries have focused on the research of quality protein maize (QPM). Researchers have characterized QPM noting that these varieties may contain between 70 to 100% more residues of the amino acids essential for animal and human nutrition, lysine, and tryptophan, than common corn. Several countries in Africa, Latin America, as well as China, have incorporated QPM in their agricultural development plan. Large parts of these countries have chosen a specific QPM variety based on their local needs and climate. Reviews have described the breeding methods of maize and have revealed the lack of studies on genetic and proteomic diversity of proteins in QPM varieties, and their genetic relationships with normal maize varieties. Therefore, molecular marker identification using tools such as mass spectrometry may accelerate the selection of plants that carry the desired proteins with high lysine and tryptophan concentration. To date, QPM maize lines have played a very important role in alleviating the malnutrition, and better characterization of these lines would provide a valuable nutritional enhancement for use in the resource-poor regions of the world. Thus, the objectives of this study were to identify proteins in QPM maize in comparison with a common maize line as a control.

Keywords: corn, mass spectrometry, QPM, tryptophan

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Authors: Arshad Mehmood Ch, Riaz Ahmad, Imran Ali Ch, Waqas Durrani

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This study deals with the application of Ant Colony Optimization (ACO) approach to solve no-wait flowshop scheduling problem (NW-FSSP). ACO algorithm so developed has been coded on Matlab computer application. The paper covers detailed steps to apply ACO and focuses on judging the strength of ACO in relation to other solution techniques previously applied to solve no-wait flowshop problem. The general purpose approach was able to find reasonably accurate solutions for almost all the problems under consideration and was able to handle a fairly large spectrum of problems with far reduced CPU effort. Careful scrutiny of the results reveals that the algorithm presented results better than other approaches like Genetic algorithm and Tabu Search heuristics etc; earlier applied to solve NW-FSSP data sets.

Keywords: no-wait, flowshop, scheduling, ant colony optimization (ACO), makespan

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Authors: Shuai Liu

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In corporate social responsibility (CSR) reporting, companies are expected to present both the positive and negative parts of the social and environmental impacts of their performance. This study investigates how the companies that listed in fortune 500 respond to this challenge by analyzing the representations of negative part especially the safety performance. It has found that in the level of genre analysis, it presented 3 major moves and 11 steps in terms of the interdiscursivity analysis. It was made up of three dominant discourse.. The study calls for greater focus on the internal and external analysis of the negative aspect of aspects of companies’ self-disclosure.

Keywords: CSR reports, negative parts, critical genre analysis, interdiscursivity

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Authors: Jang-Hwan Jo

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Implementing sustainable island forest management policies requires categorizing islands into groups based on key indicators and establishing a consistent management system. Building on the results of previous studies, a typology of forested islands was established: Type 1 – connected islands with high natural vegetation cover; Type 2 – connected islands with moderate natural vegetation cover; Type 3 – connected islands with low natural vegetation cover; Type 4 – unconnected islands with high natural vegetation cover; Type 5 – unconnected islands with moderate natural vegetation cover; and Type 6 – unconnected islands with low natural vegetation cover. An AHP analysis was conducted with island forest experts to identify priority ecosystem services (ESs) for the sustainable management of each island type. In connected islands, provisioning services (natural resources, natural medicines, etc.) assumed greater importance than regulating (erosion control) and supporting services (genetic diversity). In unconnected islands, particularly those with a small proportion of natural vegetation, regulating services (erosion control) requires greater emphasis in management. Considering that Type 3 islands require urgent management as connectivity to the mainland makes natural vegetation-sparse island forest ecosystems vulnerable to anthropogenic activities, the land-use scoring method was carried out on Jin-do, a Type 3 forested island. Comparisons between AHP-derived expert demand for key island ESs and the spatial distribution of ES supply potential revealed mismatches between the supply and demand of erosion control, freshwater supply, and habitat provision. The framework developed in this study can help guide decisions and indicate where interventions should be focused to achieve sustainable island management.

Keywords: ecosystem service, sustainable management, forested islands, Analytic hierarchy process

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Authors: Quan Gu, Daniel Dimitrov

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BingleSeq was developed as a shiny-based, intuitive, and comprehensive application that enables the analysis of single-Cell RNA-Sequencing count data. This was achieved via incorporating three state-of-the-art software packages for each type of RNA sequencing analysis, alongside functional annotation analysis and a way to assess the overlap of differential expression method results. At its current state, the functionality implemented within BingleSeq is comparable to that of other applications, also developed with the purpose of lowering the entry requirements to RNA Sequencing analyses. BingleSeq is available on GitHub and will be submitted to R/Bioconductor.

Keywords: bioinformatics, functional annotation analysis, single-cell RNA-sequencing, transcriptomics

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Authors: Juliza Hidayati, Sawarni Hasibuan

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PT. XYZ is a manufacturing company that produces Crude Palm Oil (CPO). The fierce competition in the global markets not only between companies but also a competition between supply chains. This research aims to analyze the supply chain and value chain of Crude Palm Oil (CPO) in the company. Data analysis method used is qualitative analysis and quantitative analysis. The qualitative analysis describes supply chain and value chain, while the quantitative analysis is used to find out value added and the establishment of the value chain. Based on the analysis, the value chain of crude palm oil (CPO) in the company consists of four main actors that are suppliers of raw materials, processing, distributor, and customer. The value chain analysis consists of two actors; those are palm oil plantation and palm oil processing plant. The palm oil plantation activities include nurseries, planting, plant maintenance, harvesting, and shipping. The palm oil processing plant activities include reception, sterilizing, thressing, pressing, and oil classification. The value added of palm oil plantations was 72.42% and the palm oil processing plant was 10.13%.

Keywords: palm oil, value chain, value added, supply chain

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Authors: Alexiou Dimitra, Fragkaki Maria

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The objective of the paper is the study of geographic, economic and educational variables and their contribution to determine the position of each member-state among the EU-28 countries based on the values of seven variables as given by Eurostat. The Data Analysis methods of Multiple Factorial Correspondence Analysis (MFCA) Principal Component Analysis and Factor Analysis have been used. The cross tabulation tables of data consist of the values of seven variables for the 28 countries for 2014. The data are manipulated using the CHIC Analysis V 1.1 software package. The results of this program using MFCA and Ascending Hierarchical Classification are given in arithmetic and graphical form. For comparison reasons with the same data the Factor procedure of Statistical package IBM SPSS 20 has been used. The numerical and graphical results presented with tables and graphs, demonstrate the agreement between the two methods. The most important result is the study of the relation between the 28 countries and the position of each country in groups or clouds, which are formed according to the values of the corresponding variables.

Keywords: Multiple Factorial Correspondence Analysis, Principal Component Analysis, Factor Analysis, E.U.-28 countries, Statistical package IBM SPSS 20, CHIC Analysis V 1.1 Software, Eurostat.eu Statistics

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Authors: Jesmin Akter, Chang Hyuk Ahn, Ilho Kim, Jaiyeop Lee

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Global pandemic coronavirus disease (COVID-19) caused by Severe acute respiratory syndrome SARS-CoV-2, to control the spread of the COVID-19 pandemic, wastewater surveillance has been used to monitor SARS-CoV2 prevalence in the community. The challenging part is establishing wastewater surveillance; there is a need for a well-equipped laboratory for wastewater sample analysis. According to many previous studies, reverse transcription-polymerase chain reaction (RT-PCR) based molecular tests are the most widely used and popular detection method worldwide. However, the RT-qPCR based approaches for the detection or quantification of SARS-CoV-2 genetic fragments ribonucleic acid (RNA) from wastewater require a specialized laboratory, skilled personnel, expensive instruments, and a workflow that typically requires 6 to 8 hours to provide results for just minimum samples. Rapid and reliable alternative detection methods are needed to enable less-well-qualified practitioners to set up and provide sensitive detection of SARS-CoV-2 within wastewater at less-specialized regional laboratories. Therefore, scientists and researchers are conducting experiments for rapid detection methods of COVID-19; in some cases, the structural and molecular characteristics of SARS-CoV-2 are unknown, and various strategies for the correct diagnosis of COVID-19 have been proposed by research laboratories, which are presented in the present study. The ongoing research and development of these highly sensitive and rapid technologies, namely RT-LAMP, ELISA, Biosensors, GeneXpert, allows a wide range of potential options not only for SARS-CoV-2 detection but also for other viruses as well. The effort of this study is to discuss the above effective and regional rapid detection and quantification methods in community wastewater as an essential step in advancing scientific goals.

Keywords: rapid detection, SARS-CoV-2, sensitive detection, wastewater surveillance

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Authors: J. R. Wang, W. Y. Cheng, J. S. Yeh, S. W. Chen, Y. M. Ferng, J. H. Yang, W. S. Hsu, C. Shih

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To understand the risk for dry storage concrete casks in the cask loading, transfer, and storage phase, the purpose of this research is to establish the probabilistic risk assessment (PRA) analysis methodology for dry storage concrete casks by using SAPHIRE 8 code. This analysis methodology is used to perform the study of Taiwan nuclear power plants (NPPs) dry storage system. The process of research has three steps. First, the data of the concrete casks and Taiwan NPPs are collected. Second, the PRA analysis methodology is developed by using SAPHIRE 8. Third, the PRA analysis is performed by using this methodology. According to the analysis results, the maximum risk is the multipurpose canister (MPC) drop case.

Keywords: PRA, dry storage, concrete cask, SAPHIRE

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Authors: Dimitrios Binas, Marianna Konidari, Charis Bourgioti, Lia Angela Moulopoulou, Theodore Economopoulos, George Matsopoulos

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High grade ovarian epithelial cancer (OEC) is fatal gynecological cancer and the poor prognosis of this entity is closely related to considerable intratumoral genetic heterogeneity. By examining imaging data, it is possible to assess the heterogeneity of tumorous tissue. This study proposes a methodology for aligning, segmenting and finally visualizing information from various magnetic resonance imaging series in order to construct 3D models of heterogeneity maps from the same tumor in OEC patients. The proposed system may be used as an adjunct digital tool by health professionals for personalized medicine, as it allows for an easy visual assessment of the heterogeneity of the examined tumor.

Keywords: image segmentation, ovarian epithelial cancer, quantitative characteristics, image registration, tumor visualization

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Authors: Bongmun Kang, Kagnari Yamakawa, Yoshihisa Hagihara, Yuji Ito, Michimasa Kishimoto, Yoichi Kumada

Abstract:

The PMMA-tag was genetically fused with the C-terminal region of VHH molecules. This antibody, VHH, is known as a single-chain domain, which is devoid of light chains. The PMMA-tag, which could affect the isoelectric point (pI) changeable with a charge of amino acid in VHHs were closely related to the solubility of VHH molecules during refolding. The genetic fusion of PMMA-tag to C-terminal region of VHHs significantly affects the recovery of their soluble protein during refolding by 50 mM TAPS at pH 8.5. It could be refolded with a recovery of more than 95% by dialysis at pH 8.5. A marked difference in the antigen-binding activities in the adsorption state was significantly high in VHH-PM compared to the wild type of VHH. There are approximately 8-fold differences in the antigen-binding activities in the adsorption state between VHH-PM and VHH.

Keywords: VHH, PMMA-tag, isoelectric point, pH, Solubility, refolding, immobilization, ELISA

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Authors: Jeong-Hyun Park, Young-Sik Park, Hyo-Teag Jung

Abstract:

This paper presents static analysis deployment model for code quality on R&D Projects of SW Development. The proposed model includes the scope of R&D projects and index for static analysis of source code, operation model and execution process, environments and infrastructure system for R&D projects of SW development. There is the static analysis result of pilot project as case study based on the proposed deployment model and environment, and strategic considerations for success operation of the proposed static analysis deployment model for R&D Projects of SW Development. The proposed static analysis deployment model in this paper will be adapted and improved continuously for quality upgrade of R&D projects, and customer satisfaction of developed source codes and products.

Keywords: static analysis, code quality, coding rules, automation tool

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Authors: Ju-young Hwang, Hyo-Gyoung Kwak, Hong Jae Yim

Abstract:

This paper introduces a numerical analysis method for reinforced-concrete (RC) structures exposed to fire and compares the result with experimental results. The proposed analysis method for RC structure under the high temperature consists of two procedures. First step is to decide the temperature distribution across the section through the heat transfer analysis by using the time-temperature curve. After determination of the temperature distribution, the nonlinear analysis is followed. By considering material and geometrical non-linearity with the temperature distribution, nonlinear analysis predicts the behavior of RC structure under the fire by the exposed time. The proposed method is validated by the comparison with the experimental results. Finally, Prediction model to describe the status of after-cooling concrete can also be introduced based on the results of additional experiment. The product of this study is expected to be embedded for smart structure monitoring system against fire in u-City.

Keywords: RC structures, heat transfer analysis, nonlinear analysis, after-cooling concrete model

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Authors: Masoud Soltanialvar, Ali Bagherpour

Abstract:

Documented cases of human infection with H9N2 avian influenza viruses, first detected in 1999 in Hong Kong and China, indicate that these viruses can be directly transmitted from birds to humans. In this study, we characterized the mutation in the Hemagglutinin (HA) genes and proteins that correlates with a shift in affinity of the Hemagglutinin (HA) protein from the “avian” type sialic receptors to the “human” type in 10 Iranian isolates. We delineated the genomes and receptor binding profile of HA gene of some field isolates and established their phylogenetic relationship to the other Asian H9N2 sub lineages. A total of 1200 tissue samples collected from 40 farms located in various states of Iran during 2008 – 2010 as part of a program to monitor Avian Influenza Viruses (AIV) infection. To determine the genetic relationship of Iranian viruses, the Hemagglutinin (HA) genes from ten isolates were amplified and sequenced (by RT-PCR method). Nucleotide sequences (orf) of the (HA) genes were used for phylogenetic tree construction. Deduced amino acid sequences showed the presence of L226 (234 in H9 numbering) in all ten Iranian isolates which indicates a preference to binding of α (2–6) sialic acid receptors, so these Iranian H9N2 viruses have the potential to infect human beings. These isolates showed high degree of homology with 2 human H9N2 isolates A/HK/1073/99, A/HK/1074/99. Phylogenetic analysis of showed that all the HA genes of the Iranian H9N2 viruses fall into a single group within a G1-like sublineage which had contributed as donor of six internal genes to H5N1 highly pathogenic avian influenza. The results of this study indicated that all Iranian viruses have the potential to emerge as highly pathogenic influenza virus, and considering the homology of these isolates with human H9N2 strains, it seems that the potential of these avian influenza isolates to infect human should not be overlooked.

Keywords: influenza virus, hemagglutinin, neuraminidase, Iran

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Authors: Mrigakshi Das

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The private sector investments and quantum of money required in this sector critically hinges on the financial risk and returns the sector offers to providers of capital. Therefore, it becomes important to understand financial performance of hospitals. Financial Analysis is useful for decision makers in a variety of settings. Consider the small proprietary hospitals, say, Physicians Clinic. The managers of such clinic need the information that financial statements provide. Attention to Financial Statements of healthcare Organizations can provide answers to questions like: How are they doing? What is their rate of profit? What is their solvency and liquidity position? What are their sources and application of funds? What is their Operational Efficiency? The researcher has studied Financial Statements of 5 Private Healthcare Organizations in Guwahati City.

Keywords: not-for-profit organizations, financial analysis, ratio analysis, profitability analysis, liquidity analysis, operational efficiency, capital structure analysis

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Authors: Irina S. Kolesnikova, Alexander A. Dolskiy, Natalya A. Lemskaya, Yulia V. Maksimova, Asia R. Shorina, Alena S. Telepova, Alexander S. Graphodatsky, Dmitry V. Yudkin

Abstract:

A cytogenetic and molecular genetic study of the family with a male child who had mental retardation and autistic features revealed an abnormal chromosome 13 bearing an enlarged p-arm with amplified ribosomal DNA (rDNA) in a boy and his father. Cytogenetic analysis using standard G-banding and FISH with labeled rDNA probes revealed an abnormal chromosome 13 with an enlarged p-arms due to rDNA amplification in a male child, who had clinically confirmed mental retardation and an autistic behavior. This chromosome is evidently inherited from the father, who has morphologically the same chromosome, but is healthy. The karyotype of the mother was normal. Ag-NOR staining showed brightly stained large whole-p-arm nucleolus organizer regions (NORs) in a child and normal-sized NORs in his father with 13p+-NOR-amount mosaicism. qRT-PCR with specific primers showed highly increased levels of 18S, 28S and 5,8 S ribosomal RNA (rRNA) in the patient’s blood samples compared to a normal healthy control donor. Both patient’s father and mother had no elevated levels of rRNAs expression. Thus, in this case, rRNA level seems to correlate with mental retardation in familial individuals with 13p+. Our findings of rRNA overexpression in a patient with mental retardation and his parents may show a possible link between the karyotype (p-arm enlargement due to rDNA amplification), rDNA functionality (rRNA overexpression), functional changes in the brain and mental retardation. The study is supported by Russian Science Foundation Grant 15-15-10001.

Keywords: mental retardation, ribosomal DNA–rDNA, ribosomal RNA–rRNA, nucleolus organizer region–NOR, chromosome 13

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Authors: Deniz Dincel, Sena Ardicli, Hale Samli, Mustafa Ogan, Faruk Balci

Abstract:

The aim of the study was to determine the effects of some environmental and genetic factors on growth, fertility traits, milk yield and composition in Saanen goats. For this purpose, the total of 173 Saanen goats and kids were investigated for growth, fertility and milk traits in Marmara Region of Turkey. Fertility parameters (n=70) were evaluated during two years. Milk samples were collected during the lactation and the milk yield/components (n=59) of each goat were calculated. In terms of CSN3 and AGPAT6 gene; the genotypes were defined by PCR-RFLP. Saanen kids (n=86-112) were measured from birth to 6 months of life. The birth, weaning, 60ᵗʰ, 90ᵗʰ, 120ᵗʰ and 180tᵗʰ days of average live weights were calculated. The effects of maternal age on pregnancy rate (p < 0.05), birth rate (p < 0.05), infertility rate (p < 0.05), single born kidding (p < 0.001), twinning rate (p < 0.05), triplet rate (p < 0.05), survival rate of kids until weaning (p < 0.05), number of kids per parturition (p < 0.01) and number of kids per mating (p < 0.01) were found significant. The impacts of year on birth rate (p < 0.05), abortion rate (p < 0.001), single born kidding (p < 0.01), survival rate of kids until weaning (p < 0.01), number of kids per mating (p < 0.01) were found significant for fertility traits. The impacts of lactation length on all milk yield parameters (lactation milk, protein, fat, totally solid, solid not fat, casein and lactose yield) (p < 0.001) were found significant. The effects of age on all milk yield parameters (lactation milk, protein, fat, total solid, solid not fat, casein and lactose yield) (p < 0.001), protein rate (p < 0.05), fat rate (p < 0.05), total solid rate (p < 0.01), solid not fat rate (p < 0.05), casein rate (p < 0.05) and lactation length (p < 0.01), were found significant too. However, the effect of AGPAT6 gene on milk yield and composition was not found significant in Saanen goats. The herd was found monomorphic (FF) for CSN3 gene. The effects of sex on live weights until 90ᵗʰ days of life (birth, weaning and 60ᵗʰ day of average weight) were found significant statistically (p < 0.001). The maternal age affected only birth weight (p < 0,001). The effects month at birth on all of the investigated day [the birth, 120ᵗʰ, 180ᵗʰ days (p < 0.05); the weaning, 60ᵗʰ, 90ᵗʰ days (p < 0,001)] were found significant. The birth type was found significant on the birth (p < 0,001), weaning (p < 0,01), 60ᵗʰ (p < 0,01) and 90ᵗʰ (p < 0,01) days of average live weights. As a result, screening the other regions of CSN3, AGPAT6 gene and also investigation the phenotypic association of them should be useful to clarify the efficiency of target genes. Environmental factors such as maternal age, year, sex and birth type were found significant on some growth, fertility and milk traits in Saanen goats. So consideration of these factors could be used as selection criteria in dairy goat breeding.

Keywords: fertility, growth, milk yield, Saanen goats

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Authors: M. Chňapek, M. Tomka, R. Peroutková, Z. Gálová

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Processes of plant breeding, testing and licensing of new varieties, patent protection in seed production, relations in trade and protection of copyright are dependent on identification, differentiation and characterization of plant genotypes. Therefore, we focused our research on utilization of wheat storage proteins as genetic markers suitable not only for differentiation of individual genotypes, but also for identification and characterization of their considerable properties. We analyzed a collection of 102 genotypes of bread wheat (Triticum aestivum L.), 41 genotypes of spelt wheat (Triticum spelta L.), and 35 genotypes of durum wheat (Triticum durum Desf.), in this study. Our results show, that genotypes of bread wheat and durum wheat were homogenous and single line, but spelt wheat genotypes were heterogenous. We observed variability of HMW-GS composition according to environmental factors and level of breeding and predict technological quality on the basis of Glu-score calculation.

Keywords: genotype identification, HMW-GS, wheat quality, polymorphism

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Authors: Catherine K. Derow

Abstract:

Possibly a slime mold somehow mutated or already was mutated at progeniture and so stayed as a metazoan when it developed into the fruiting stage and so the slime mold(s) we are evolved and similar to are genetically differ from the slime molds in existence now. This may be why there are genetic links between humans and other metazoa now alive and slime molds now alive but we are now divergent branches of the evolutionary tree compared to the original slime mold, or perhaps slime mold-like organisms, that gave rise to metazoan animalia and perhaps algae and plantae as slime molds were undifferentiated enough in many ways that could allow their descendants to evolve into these three separate phylogenetic categories. Or it may be a slime mold was born or somehow progenated as multicellular, as the particular organism was mutated enough to have say divided in a a 'pseudo-embryonic' stage, and this could have happened for algae, plantae as well as animalia or all the branches may be from the same line but the missing link might be covered in 'phylogenetic sequence comparison noise'.

Keywords: metazoan evolution, unicellular bridge to metazoans, evolution, slime mold

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