Search results for: investigative genetic genealogy

Authors: Zhenyu Zhang, Hsi-Hsien Wei

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Highway networks play a vital role in post-disaster recovery for disaster-damaged areas. Damaged bridges in such networks can disrupt the recovery activities by impeding the transportation of people, cargo, and reconstruction resources. Therefore, rapid restoration of damaged bridges is of paramount importance to long-term disaster recovery. In the post-disaster recovery phase, the key to restoration scheduling for a highway network is prioritization of bridge-repair tasks. Resilience is widely used as a measure of the ability to recover with which a network can return to its pre-disaster level of functionality. In practice, highways will be temporarily blocked during the downtime of bridge restoration, leading to the decrease of highway-network functionality. The failure to take downtime effects into account can lead to overestimation of network resilience. Additionally, post-disaster recovery of highway networks is generally divided into emergency bridge repair (EBR) in the response phase and long-term bridge repair (LBR) in the recovery phase, and both of EBR and LBR are different in terms of restoration objectives, restoration duration, budget, etc. Distinguish these two phases are important to precisely quantify highway network resilience and generate suitable restoration schedules for highway networks in the recovery phase. To address the above issues, this study proposes a novel resilience quantification method for the optimization of long-term bridge repair schedules (LBRS) taking into account the impact of EBR activities and restoration downtime on a highway network’s functionality. A time-dependent integer program with recursive functions is formulated for optimally scheduling LBR activities. Moreover, since uncertainty always exists in the LBRS problem, this paper extends the optimization model from the deterministic case to the stochastic case. A hybrid genetic algorithm that integrates a heuristic approach into a traditional genetic algorithm to accelerate the evolution process is developed. The proposed methods are tested using data from the 2008 Wenchuan earthquake, based on a regional highway network in Sichuan, China, consisting of 168 highway bridges on 36 highways connecting 25 cities/towns. The results show that, in this case, neglecting the bridge restoration downtime can lead to approximately 15% overestimation of highway network resilience. Moreover, accounting for the impact of EBR on network functionality can help to generate a more specific and reasonable LBRS. The theoretical and practical values are as follows. First, the proposed network recovery curve contributes to comprehensive quantification of highway network resilience by accounting for the impact of both restoration downtime and EBR activities on the recovery curves. Moreover, this study can improve the highway network resilience from the organizational dimension by providing bridge managers with optimal LBR strategies.

Keywords: disaster management, highway network, long-term bridge repair schedule, resilience, restoration downtime

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Authors: Dali Gaganidze, Ekaterine Abashidze

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Potato is one of the main agricultural crops in Georgia. Georgia produces early and late potato varieties in almost all regions. In traditional potato growing regions (Svaneti, Samckhet javaheti and Tsalka), the yield is higher than 30-35 t/ha. Among the plant pests that limit potato production and quality, the potato cyst nematodes (PCN) are harmful around the world. Yield losses caused by PCN are estimated up to 30%. Rout surveys conducted in two geographically distinct regions of Georgia producing potatoes - Samtskhe - Javakheti and Svaneti revealed potato cyst nematode Globodera rostochiensi. The aim of the study was the Phylogenetic analyses of Globodera rostochiensi revealed in Georgia by the amplification and sequencing of 28S gen in the D3 region and intergenic ITS1-15.8S-ITS2 region. Identification of all the samples from the two Globodera populations (Samtskhe - Javakheti and Svaneti), i.e., G. rostochiensis (20 isolates) were confirmed by conventional multiplex PCR with ITS 5 universal and PITSp4, PITSr3 specific primers of the cyst nematodes’ (G. pallida, G. rostochiensis). The size of PCR fragment 434 bp confirms that PCN samples from two populations, Samtskhe- Javakheti and Svaneti, belong to G. rostochiensi . The ITS1–5.8S-ITS2 regions were amplified using prime pairs: rDNA1 ( 5’ -TTGATTACGTCCCTGCCCTTT-3’ and rDNA2( 5’ TTTCACTCGCCGTTACTAAGG-3’), D3 expansion regions were amplified using primer pairs: D3A (5’ GACCCCTCTTGAAACACGGA-3’) and D3B (5’-TCGGAAGGAACCAGCTACTA-3’. PCR products of each region were cleaned up and sequenced using an ABI 3500xL Genetic Analyzer. Obtained sequencing results were analyzed by computer program BLASTN (https://blast.ncbi.nlm.nih.gov/Blast.cg). Phylogenetic analyses to resolve the relationships between the isolates were conducted in MEGA7 using both distance- and character-based methods. Based on analysis of G.rostochiensis isolate`s D3 expansion regions are grouped in three major clades (A, B and C) on the phylogenetic tree. Clade A is divided into three subclades; clade C is divided into two subclades. Isolates from the Samtckhet-javakheti population are in subclade 1 of clade A and isolates in subclade 1 of clade C. Isolates) from Svaneti populations are in subclade 2 of clade A and in clad B. In Clade C, subclade two is presented by three isolates from Svaneti and by one isolate (GL17) from Samckhet-Javakheti. . Based on analysis of G.rostochiensis isolate`s ITS1–5.8S-ITS2 regions are grouped in two main clades, the first contained 20 Georgian isolates of Globodera rostochiensis from Svaneti . The second clade contained 15 isolates of Globodera rostochiensis from Samckhet javakheti. Our investigation showed of high genetic variation of D3 and ITS1–5.8S-ITS2 region of rDNA of the isolates of G. rostochiensis from different geographic origins (Svameti, Samckhet-Javakheti) of Georgia. Acknowledgement: The research has been supported by the Shota Rustaveli National Scientific Foundation of Georgia : Project # FR17_235

Keywords: globodera rostochiensi, PCR, phylogenetic tree, sequencing

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Authors: Cristina Felipeto, Catherine Bore, Eduardo Calil

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This work aims to analyze and compare the punctuation marks (PM) in school texts of Brazilian and French students and the comments on these PM made spontaneously by the students during the ongoing text. Assuming textual genetics as an investigative field within a dialogical and enunciative approach, we defined a common methodological design in two 1st year classrooms (7 years old) of the primary school, one classroom in Brazil (Maceio) and the other one in France (Paris). Through a multimodal capture system of writing processes in real time and space (Ramos System), we recorded the collaborative writing proposal in dyads in each of the classrooms. This system preserves the classroom’s ecological characteristics and provides a video recording synchronized with dialogues, gestures and facial expressions of the students, the stroke of the pen’s ink on the sheet of paper and the movement of the teacher and students in the classroom. The multimodal register of the writing process allowed access to the text in progress and the comments made by the students on what was being written. In each proposed text production, teachers organized their students in dyads and requested that they should talk, combine and write a fictional narrative. We selected a Dyad of Brazilian students (BD) and another Dyad of French students (FD) and we have filmed 6 proposals for each of the dyads. The proposals were collected during the 2nd Term of 2013 (Brazil) and 2014 (France). In 6 texts written by the BD there were identified 39 PMs and 825 written words (on average, a PM every 23 words): Of these 39 PMs, 27 were highlighted orally and commented by either student. In the texts written by the FD there were identified 48 PMs and 258 written words (on average, 1 PM every 5 words): Of these 48 PM, 39 were commented by the French students. Unlike what the studies on punctuation acquisition point out, the PM that occurred the most were hyphens (BD) and commas (FD). Despite the significant difference between the types and quantities of PM in the written texts, the recognition of the need for writing PM in the text in progress and the comments have some common characteristics: i) the writing of the PM was not anticipated in relation to the text in progress, then they were added after the end of a sentence or after the finished text itself; ii) the need to add punctuation marks in the text came after one of the students had ‘remembered’ that a particular sign was needed; iii) most of the PM inscribed were not related to their linguistic functions, but the graphic-visual feature of the text; iv) the comments justify or explain the PM, indicating metalinguistic reflections made by the students. Our results indicate how the comments of the BD and FD express the dialogic and subjective nature of knowledge acquisition. Our study suggests that the initial learning of PM depends more on its graphic features and interactional conditions than on its linguistic functions.

Keywords: collaborative writing, erasure, graphic marks, learning, metalinguistic awareness, textual genesis

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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: Ayse Ozge Demir, Nihat Mert

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In this research, Kilis and Honamli goats are used, which are specific local genetic resources of Turkey. The herds were independent, but they had similar care and nutrition circumstances. From each breed 30 samples were taken, in all 120 samples were collected. Erytrocyte, all blood and serum samples were used for hemoglobine (Hb), glutathione (GSH) and Tf with Cp analysis, respectively. In the analysis of this samples, Hb and Tf bands were determined by electrophoresis. However, Cp and GSH levels were analyzed by the spectrophotometer. Three Hb phenotypes (AA, BB, AB) and Six Tf phenotypes (AA, AB, AC, BB, BC, CC) were determined in this study. In addition, both the observed and the expected values of polymorphic characteristic for 2 characters were presented according to the Hardy-Weinberg Equilibrium (HWE). Cp levels were detected as 0.822 ± 0.055 mg/dl and 1.793 ± 0.109 mg/dl in Kilis and Honamli herds, respectively. GSH levels were detected as, 42,486 ± 1,034 mg/dl and 33.515 ± 0.345 mg/dl in these breeds, respectively,. On the other hand, the high and low GSH levels (GSHH and GSHh) of herds were presented.

Keywords: electrophoresis, gene resource, goat, spectrophotometer

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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: 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: 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: 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

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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: Amna Abdalla Mohammed Khalid, Pietro Parisse, Silvia Onesti, Loredana Casalis

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Basic cellular processes as DNA replication are crucial to cell life. Understanding at the molecular level the mechanisms that govern DNA replication in proliferating cells is fundamental to understand disease connected to genomic instabilities, as a genetic disease and cancer. A key step for DNA replication to take place, is unwinding the DNA double helix and this carried out by proteins called helicases. The archaeal MCM (minichromosome maintenance) complex from Methanothermobacter thermautotrophicus have being studied using Atomic Force Microscopy (AFM), imaging in air and liquid (Physiological environment). The accurate analysis of AFM topographic images allowed to understand the static conformations as well the interaction dynamic of MCM and DNA double helix in the present of ATP.

Keywords: DNA, protein-DNA interaction, MCM (mini chromosome manteinance) complex, atomic force microscopy (AFM)

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

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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: Yan Torres, Fernanda Simoes, Francisco Petrucci-Fonseca, Freddie-Jeanne Richard

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The non-invasive samples are an alternative of collecting genetic samples directly. Non-invasive samples are collected without the manipulation of the animal (e.g., scats, feathers and hairs). Nevertheless, the use of non-invasive samples has some limitations. The main issue is degraded DNA, leading to poorer extraction efficiency and genotyping. Those errors delayed for some years a widespread use of non-invasive genetic information. Possibilities to limit genotyping errors can be done using analysis methods that can assimilate the errors and singularities of non-invasive samples. Genotype matching and population estimation algorithms can be highlighted as important analysis tools that have been adapted to deal with those errors. Although, this recent development of analysis methods there is still a lack of empirical performance comparison of them. A comparison of methods with dataset different in size and structure can be useful for future studies since non-invasive samples are a powerful tool for getting information specially for endangered and rare populations. To compare the analysis methods, four different datasets used were obtained from the Dryad digital repository were used. Three different matching algorithms (Cervus, Colony and Error Tolerant Likelihood Matching - ETLM) are used for matching genotypes and two different ones for population estimation (Capwire and BayesN). The three matching algorithms showed different patterns of results. The ETLM produced less number of unique individuals and recaptures. A similarity in the matched genotypes between Colony and Cervus was observed. That is not a surprise since the similarity between those methods on the likelihood pairwise and clustering algorithms. The matching of ETLM showed almost no similarity with the genotypes that were matched with the other methods. The different cluster algorithm system and error model of ETLM seems to lead to a more criterious selection, although the processing time and interface friendly of ETLM were the worst between the compared methods. The population estimators performed differently regarding the datasets. There was a consensus between the different estimators only for the one dataset. The BayesN showed higher and lower estimations when compared with Capwire. The BayesN does not consider the total number of recaptures like Capwire only the recapture events. So, this makes the estimator sensitive to data heterogeneity. Heterogeneity in the sense means different capture rates between individuals. In those examples, the tolerance for homogeneity seems to be crucial for BayesN work properly. Both methods are user-friendly and have reasonable processing time. An amplified analysis with simulated genotype data can clarify the sensibility of the algorithms. The present comparison of the matching methods indicates that Colony seems to be more appropriated for general use considering a time/interface/robustness balance. The heterogeneity of the recaptures affected strongly the BayesN estimations, leading to over and underestimations population numbers. Capwire is then advisable to general use since it performs better in a wide range of situations.

Keywords: algorithms, genetics, matching, population

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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

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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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Authors: Wen-Chung Wang, Xue-Lan Qiu

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Ipsative tests have been widely used in vocational and career counseling (e.g., the Jackson Vocational Interest Survey). Pairwise-comparison items are a typical item format of ipsative tests. When the two statements in a pairwise-comparison item measure two different constructs, the item is referred to as a multidimensional pairwise-comparison (MPC) item. A typical MPC item would be: Which activity do you prefer? (A) playing with young children, or (B) working with tools and machines. These two statements aim at the constructs of social interest and investigative interest, respectively. Recently, new item response theory (IRT) models for ipsative tests with MPC items have been developed. Among them, the Rasch ipsative model (RIM) deserves special attention because it has good measurement properties, in which the log-odds of preferring statement A to statement B are defined as a competition between two parts: the sum of a person’s latent trait to which statement A is measuring and statement A’s utility, and the sum of a person’s latent trait to which statement B is measuring and statement B’s utility. The RIM has been extended to polytomous responses, such as preferring statement A strongly, preferring statement A, preferring statement B, and preferring statement B strongly. To promote the new initiatives, in this study we developed computerized adaptive testing algorithms for MFC items and evaluated their performance using simulations and two real tests. Both the RIM and its polytomous extension are multidimensional, which calls for multidimensional computerized adaptive testing (MCAT). A particular issue in MCAT for MPC items is the within-person statement exposure (WPSE); that is, a respondent may keep seeing the same statement (e.g., my life is empty) for many times, which is certainly annoying. In this study, we implemented two methods to control the WPSE rate. In the first control method, items would be frozen when their statements had been administered more than a prespecified times. In the second control method, a random component was added to control the contribution of the information at different stages of MCAT. The second control method was found to outperform the first control method in our simulation studies. In addition, we investigated four item selection methods: (a) random selection (as a baseline), (b) maximum Fisher information method without WPSE control, (c) maximum Fisher information method with the first control method, and (d) maximum Fisher information method with the second control method. These four methods were applied to two real tests: one was a work survey with dichotomous MPC items and the other is a career interests survey with polytomous MPC items. There were three dependent variables: the bias and root mean square error across person measures, and measurement efficiency which was defined as the number of items needed to achieve the same degree of test reliability. Both applications indicated that the proposed MCAT algorithms were successful and there was no loss in measurement proficiency when the control methods were implemented, and among the four methods, the last method performed the best.

Keywords: computerized adaptive testing, ipsative tests, item response theory, pairwise comparison

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Authors: Paula I. Buonfiglio, Carlos David Bruque, Lucia Salatino, Vanesa Lotersztein, Sebastián Menazzi, Paola Plazas, Ana Belén Elgoyhen, Viviana Dalamón

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Hearing loss (HL) is the most prevalent sensorineural disorder affecting about 10% of the global population, with more than half due to genetic causes. About 1 in 500-1000 newborns present congenital HL. Most of the patients are non-syndromic with an autosomal recessive mode of inheritance. To date, more than 100 genes are related to HL. Therefore, the Whole-exome sequencing (WES) technique has become a cost-effective alternative approach for molecular diagnosis. Nevertheless, new challenges arise from the detection of novel variants, in particular missense changes, which can lead to a spectrum of genotype-to-phenotype correlations, which is not always straightforward. In this work, we aimed to identify the genetic causes of HL in isolated and familial cases by designing a multistep approach to analyze target genes related to hearing impairment. Moreover, we performed in silico and in vivo analyses in order to further study the effect of some of the novel variants identified in the hair cell function using the zebrafish model. A total of 650 patients were studied by Sanger Sequencing and Gap-PCR in GJB2 and GJB6 genes, respectively, diagnosing 15.5% of sporadic cases and 36% of familial ones. Overall, 50 different sequence variants were detected. Fifty of the undiagnosed patients with moderate HL were tested for deletions in STRC gene by Multiplex ligation-dependent probe amplification technique (MLPA), leading to 6% of diagnosis. After this initial screening, 50 families were selected to be analyzed by WES, achieving diagnosis in 44% of them. Half of the identified variants were novel. A missense variant in MYO6 gene detected in a family with postlingual HL was selected to be further analyzed. A protein modeling with AlphaFold2 software was performed, proving its pathogenic effect. In order to functionally validate this novel variant, a knockdown phenotype rescue assay in zebrafish was carried out. Injection of wild-type MYO6 mRNA in embryos rescued the phenotype, whereas using the mutant MYO6 mRNA (carrying c.2782C>A variant) had no effect. These results strongly suggest the deleterious effect of this variant on the mobility of stereocilia in zebrafish neuromasts, and hence on the auditory system. In the present work, we demonstrated that our algorithm is suitable for the sequential multigenic approach to HL in our cohort. These results highlight the importance of a combined strategy in order to identify candidate variants as well as the in silico and in vivo studies to analyze and prove their pathogenicity and accomplish a better understanding of the mechanisms underlying the physiopathology of the hearing impairment.

Keywords: diagnosis, genetics, hearing loss, in silico analysis, in vivo analysis, WES, zebrafish

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Authors: Thibaud Berthomier, Ali Mansour, Luc Bressollette, Frédéric Le Roy, Dominique Mottier, Léo Fréchier, Barthélémy Hermenault

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Deep Venous Thrombosis (DVT) occurs when a thrombus is formed within a deep vein (most often in the legs). This disease can be deadly if a part or the whole thrombus reaches the lung and causes a Pulmonary Embolism (PE). This disorder, often asymptomatic, has multifactorial causes: immobilization, surgery, pregnancy, age, cancers, and genetic variations. Our project aims to relate the thrombus epidemiology (origins, patient predispositions, PE) to its structure using ultrasound images. Ultrasonography and elastography were collected using Toshiba Aplio 500 at Brest Hospital. This manuscript compares two classification approaches: spectral clustering and scattering operator. The former is based on the graph and matrix theories while the latter cascades wavelet convolutions with nonlinear modulus and averaging operators.

Keywords: deep venous thrombosis, ultrasonography, elastography, scattering operator, wavelet, spectral clustering

Procedia PDF Downloads 462

Authors: Svetlana Zhikrivetskaya, Nataliya Shirokova, Roman Bikanov, Elizaveta Musatova, Yana Kovaleva, Nataliya Vetrova, Ekaterina Pomerantseva

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Nowadays there is a growing number of couples with conceiving problems due to male or female infertility. Genetic abnormalities are responsible for about 31% of all cases of male infertility. These abnormalities include both chromosomal aberrations or aneuploidies and mutations in certain genes. Chromosomal abnormalities can be easily identified, thus the development of screening panels able to reveal genetic reasons of male infertility on gene level is of current interest. There are approximately 2,000 genes involved in male fertility that is the reason why it is very important to determine the most clinically relevant in certain population and ethnic conditions. An infertility screening panel containing 48 mutations in genes AMHR2, CFTR, DNAI1, HFE, KAL1, TSSK2 and AZF locus which are the most clinically relevant for the European population according to databases NCBI and ClinVar was designed. The aim of this research was to confirm clinic relevance of these mutations in the Russian population. Genotyping was performed in 220 patients with different types of male infertility and in 57 healthy males with normozoospermia. Mutations were identified by end-point PCR with TaqMan probes in microfluidic plates. The frequency of 5 mutations in healthy males and 13 mutations in patients with infertility was revealed and estimated. The frequency of mutation c.187C>G in HFE gene was significantly lower for healthy males (8.8%) compared with patients (17.7%) and the values for the European population according to ExAc database (13.7%) and dbSNP (17.2%). Analysis of c.3454G>C, and c.1545_1546delTA mutations in the CFTR gene revealed increased frequency (0.9 and 0.2%, respectively) in patients with infertility compared with data for the European population (0.04%, respectively (ExAc, European (Non-Finnish) and for the Aggregated Populations (0.002% (ExAc), because there is no data for European population for c.1545_1546delTA mutation. The frequency of del508 mutation (CFTR) in patients (1.59%) were lower comparing with male infertility Europeans (3.34-6.25% depending on nationality) and at the same level with healthy Europeans (1.06%, ExAc, European (Non-Finnish). Analysis of c.845G>A (HFE) mutation resulted in decreased frequency in patients (1.8%) in contrast with the European population data (5.1%, respectively, ExAc, European (Non-Finnish). Moreover, obtained data revealed no statistically significant frequency difference for c.845G>A mutation (HFE) between healthy males in the Russian and the European populations. Allele frequencies of mutations c.350G>A (CFTR), c.193A>T (HFE), c.774C>T, and c.80A>G (gene TSSK2) showed no significantly difference among patients with infertility, healthy males and Europeans. Analysis of AZF locus revealed increased frequency for AZFc microdeletion in patients with male infertility. Thereby, the new data of the allele frequencies in infertility patients in the Russian population was obtained. As well as the frequency differences of mutations associated with male infertility among patients, healthy males in the Russian population and the European one were estimated. The revealed differences showed that for high effectiveness of screening panel detecting genetically caused male infertility it is very important to consider ethnic and population characteristics of patients which will be screened.

Keywords: allele frequency, azoospermia, male infertility, mutation, population

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Authors: Wuthichai Wongthatsanekorn, Nuntana Matheekrieangkrai

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This research proposes Bee Algorithm (BA) to optimize Ready Mixed Concrete (RMC) truck scheduling problem from single batch plant to multiple construction sites. This problem is considered as an NP-hard constrained combinatorial optimization problem. This paper provides the details of the RMC dispatching process and its related constraints. BA was then developed to minimize total waiting time of RMC trucks while satisfying all constraints. The performance of BA is then evaluated on two benchmark problems (3 and 5construction sites) according to previous researchers. The simulation results of BA are compared in term of efficiency and accuracy with Genetic Algorithm (GA) and all problems show that BA approach outperforms GA in term of efficiency and accuracy to obtain optimal solution. Hence, BA approach could be practically implemented to obtain the best schedule.

Keywords: bee colony optimization, ready mixed concrete problem, ruck scheduling, multiple construction sites

Procedia PDF Downloads 366

Authors: Nasreen Abdulmannan

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Fetal abnormalities are categorized as a structural abnormality, non-structural abnormality, or a combination of both. Fetal structural abnormalities (FSA) include, but are not limited, to Down syndrome, congenital diaphragmatic hernia, and cleft lip and palate. These abnormalities can be detected in the first weeks of pregnancy, which is almost around 9 - 20 weeks gestational. Etiological factors for FSA are unknown; however, transmitted genetic risk can be one of these factors. Consanguineous marriage often referred to as inbreeding, represents a significant risk factor for FSA due to the increased likelihood of deleterious genetic traits shared by both biological parents. In a country such as the Kingdom of Saudi Arabia (KSA), consanguineous marriage is high, which creates a significant risk of children being born with congenital abnormalities. Historically, the practice of consanguinity occurred commonly among European royalty. For example, Great Britain’s Queen Victoria married her German first cousin, Prince Albert of Coburg. Although a distant blood relationship, the United Kingdom’s Queen Elizabeth II married her cousin, Prince Philip of Greece and Denmark—both of them direct descendants of Queen Victoria. In Middle Eastern countries, a high incidence of consanguineous unions still exists, including in the KSA. Previous studies indicated that a significant gap exists in understanding the lived experiences of Saudi women dealing with an FSA-complicated pregnancy. Eleven participants were interviewed using a semi-structured interview format for this qualitative phenomenological study investigating the lived experiences of pregnant Saudi women carrying a child with FSA. This study explored the gaps in current literature regarding the lived experiences of pregnant Saudi women whose pregnancies were complicated by FSA. In addition, the researcher acquired knowledge about the available support and resources as well as the Saudi cultural perspective on FSA. This research explored the lived experiences of pregnant Saudi women utilizing Giorgi’s (2009) approach to data collection and data management. Findings for this study cover five major themes: (1) initial maternal reaction to the FSA diagnosis per ultrasound screening; (2) strengthening of the maternal relationship with God; (3) maternal concern for their child’s future; (4) feeling supported by their loved ones; and (5) lack of healthcare provider support and guidance. Future research in the KSA is needed to explore the network support for these mothers. This study recommended further clinical nursing research, nursing education, clinical practice, and healthcare policy/procedures to provide opportunities for improvement in nursing care and increase awareness in KSA society.

Keywords: fetal structural abnormalities, psychological distress, health provider, health care

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Authors: Mariam Bibi, Rubab Mehboob, Mehreen Sirshar

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Satisfying the customer requirements is the ultimate goal of producing or developing any product. The quality of the product is decided on the bases of the level of customer satisfaction. There are different techniques which have been reported during the survey which enhance the quality of the product through software defect prediction and by locating the missing software requirements. Some mining techniques were proposed to assess the individual performance indicators in collaborative environment to reduce errors at individual level. The basic intention is to produce a product with zero or few defects thereby producing a best product quality wise. In the analysis of survey the techniques like Genetic algorithm, artificial neural network, classification and clustering techniques and decision tree are studied. After analysis it has been discovered that these techniques contributed much to the improvement and enhancement of the quality of the product.

Keywords: data mining, defect prediction, missing requirements, software quality

Procedia PDF Downloads 444

Authors: Mikhail S. Zastrozhin, Valery V. Smirnov, Dmitry A. Sychev, Ludmila M. Savchenko, Evgeny A. Bryun, Mark O. Nechaev

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Cytochrome P-450 isoenzyme 3A4 takes part in the biotransformation of medical drugs. The activity of CYP isoenzymes depends on genetic (polymorphisms of genes which encoded it) and phenotypic factors (a kind of food, a concomitant drug therapy). The aim of the study was to evaluate a carbamazepine effect on the CYP3A4 activity in patients with alcohol addiction. The study included 25 men with alcohol dependence, who received haloperidol during the exacerbation of the addiction. CYP3A4 activity was assessed by urinary 6-beta-hydroxycortisol/cortisol ratios measured by high performance liquid chromatography with mass spectrometry. The study modeled a graph and an equation of the logarithmic regression, that reflects the dependence of CYP3A4 activity on a dose of carbamazepine: y = 5,5 * 9,1 * 10-5 * x2. The study statistically significant demonstrates the effect of carbamazepine on CYP2D6 isozyme activity in patients with alcohol addiction.

Keywords: CYP3A4, biotransformation, carbamazepine, alcohol abuse

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Authors: Santhosh Srinivasan, Vipul Garhiya, Shahul Hamid Khan

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Environmental performance along with social performance is becoming vital factors for industries to achieve global standards. With a good environmental policy global industries are differentiating them from their competitors. This paper concentrates on multi stage, multi product and multi period manufacturing network. Single objective mathematical models for a total cost for the entire forward supply chain and reverse chain are considered. Here five different problems are considered by varying the number of facilities for illustration. M-MOGA, Shuffle Frog Leaping algorithm (SFLA) and CPLEX are used for finding the optimal solution for the mathematical model.

Keywords: closed loop supply chain, genetic algorithm, random search, multi period, green supply chain

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Authors: Oya Bulut, Oguzhan Avci, Zafer Bulut, Atilla Simsek

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Livestock breeders have focused on the improvement of production traits with little or no attention for improvement of disease resistance traits. In order to determine the association between the genetic structure of the individual gene loci with possibility of the occurrence and the development of diseases, MHC (major histocompatibility complex) are frequently used. Because of their importance in the immune system, MHC locus is considered as candidate genes for resistance/susceptibility against to different diseases. Major histocompatibility complex (MHC) molecules play a critical role in both innate and adaptive immunity and have been considered candidate molecular markers of an association between polymorphisms and resistance/susceptibility to diseases. The purpose of this study is to give some information about MHC genes become an important area of study in recent years in terms of animal husbandry and determine the relation between MHC genes and resistance/susceptibility to disease.

Keywords: MHC, polymorphism, disease, resistance

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Authors: B. Merdas

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The Guelma region constitutes a vast geothermal field whose local geothermal gradient is very high. Indeed, various thermal and thermo sources emerging in the region, including some at relatively high temperatures. In the mio Pliocene Hammam N'bails, basin emerges a hot spring that leaves develop a thick series of thermal travertine linked to it. Near the thermal emergences has settled a very special mineralization antimony and zinc and lead. The results of analyses of the thermal waters of the source of Hammam N'bails and the associated travertine, show abnormal values in Pb, Sb, Zn, As, and other metals, demonstrating the genetic link between those waters and mineralization. Hammam N'bails mineralizations by their mineral assembling represented and their association with the hot springs, are very similar to epithermal deposits with precious metals (gold and silver) like Senator mine in Turkey or ‘Carlin-type’ in Nevada (USA).

Keywords: hot springs, mineralization; basement faults, Guelma, NE Algeria

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