Search results for: writing DNA code from scratch.

Authors: L. K. Davis

Abstract:

The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time based DNA codes, writing DNA code from scratch.

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Authors: Robersy Sánchez, Ricardo Grau

Abstract:

A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represent one or more hypothetical bases with unspecific pairing. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvements of a primitive DNA repair system could make possible the transition from the ancient to the modern genetic code. Our results suggest that the Watson-Crick base pairing and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as the transition from the former to the later. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences.

Keywords: Genetic code vector space, primeval genetic code, power spectrum.

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Authors: Abdelkader Magdy, Magdy Saeb, A. Baith Mohamed, Ahmed Khadragi

Abstract:

The Deoxyribonucleic Acid (DNA) which is a doublestranded helix of nucleotides consists of: Adenine (A), Cytosine (C), Guanine (G) and Thymine (T). In this work, we convert this genetic code into an equivalent digital signal representation. Applying a wavelet transform, such as Haar wavelet, we will be able to extract details that are not so clear in the original genetic code. We compare between different organisms using the results of the Haar wavelet Transform. This is achieved by using the trend part of the signal since the trend part bears the most energy of the digital signal representation. Consequently, we will be able to quantitatively reconstruct different biological families.

Keywords: Digital Signal, DNA, Fluctuation part, Haar wavelet, Nucleotides, Trend part.

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Authors: Eman Alzahrani, Hala M. Abo-Dief, Ashraf T. Mohamed

Abstract:

The present work is aimed at examining carbon steel oil pipelines corrosion using three natural extracts (Eruca Sativa, Rosell and Mango peels) that are used as inhibitors of different concentrations ranging from 0.05-0.1wt. %. Two sulphur compounds are used as corrosion mediums. Weight loss method was used for measuring the corrosion rate of the carbon steel specimens immersed in technical white oil at 100ºC at various time intervals in absence and presence of the two sulphur compounds. The corroded specimens are examined using the chemical wear test, scratch test and hardness test. The scratch test is carried out using scratch loads from 0.5 Kg to 2.0 Kg. The scratch width is obtained at various scratch load and test conditions. The Brinell hardness test is carried out and investigated for both corroded and inhibited specimens. The results showed that three natural extracts can be used as environmentally friendly corrosion inhibitors.

Keywords: Inhibition, natural extract, pipelines corrosion, sulphur compounds.

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Authors: Said Hadjerrouit

Abstract:

Wikis are promoted as collaborative writing tools that allow students to transform a text into a collective document by information sharing and group reflection. However, despite the promising collaborative capabilities of wikis, their pedagogical value regarding collaborative writing is still questionable. Wiki alone cannot make collaborative writing happen, and students do not automatically become more active, participate, and collaborate with others when they use wikis. To foster collaborative writing and active involvement in wiki development there is a need for a systematic approach to wikis. Themain goal of this paper is to propose and evaluate a co-writing approach to the development of wikis, along with the study of three wiki applications to report on pedagogical implications of collaborative writing in higher education.

Keywords: Co-writing development approach, MediaWiki, socio-constructivist epistemology, wiki.

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Authors: S. Mawlood, L. Dennany, N. Watson, B. Pickard

Abstract:

DNA analysis has been widely accepted as providing valuable evidence concerning the identity of the source of biological traces. Our work has showed that DNA samples can survive on cartridges even after firing. The study also raised the possibility of determining other information such as the age of the donor. Such information may be invaluable in certain cases where spent cartridges from automatic weapons are left behind at the scene of a crime. In spite of the nature of touch evidence and exposure to high chamber temperatures during shooting, we were still capable to retrieve enough DNA for profile typing. In order to estimate age of contributor, DNA methylation levels were analyzed using EpiTect system for retrieved DNA. However, results were not conclusive, due to low amount of input DNA.

Keywords: Age prediction, Fired cartridge, Trace DNA sample.

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Authors: Keunhong Chae, Seokho Yoon

Abstract:

We propose a code acquisition scheme called improved multiple-shift (IMS) for optical code division multiple access systems, where the optical orthogonal code is used instead of the pseudo noise code. Although the IMS algorithm has a similar process to that of the conventional MS algorithm, it has a better code acquisition performance than the conventional MS algorithm. We analyze the code acquisition performance of the IMS algorithm and compare the code acquisition performances of the MS and the IMS algorithms in single-user and multi-user environments.

Keywords: Code acquisition, optical CDMA, optical orthogonal code, serial algorithm.

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Authors: G. Tamilpavai, C. Vishnuppriya

Abstract:

Studying DNA (deoxyribonucleic acid) sequence is useful in biological processes and it is applied in the fields such as diagnostic and forensic research. DNA is the hereditary information in human and almost all other organisms. It is passed to their generations. Earlier stage detection of defective DNA sequence may lead to many developments in the field of Bioinformatics. Nowadays various tedious techniques are used to identify defective DNA. The proposed work is to analyze and identify the cancer-causing DNA motif in a given sequence. Initially the human DNA sequence is separated as k-mers using k-mer separation rule. The separated k-mers are clustered using Self Organizing Map (SOM). Using Levenshtein distance measure, cancer associated DNA motif is identified from the k-mer clusters. Experimental results of this work indicate the presence or absence of cancer causing DNA motif. If the cancer associated DNA motif is found in DNA, it is declared as the cancer disease causing DNA sequence. Otherwise the input human DNA is declared as normal sequence. Finally, elapsed time is calculated for finding the presence of cancer causing DNA motif using clustering formation. It is compared with normal process of finding cancer causing DNA motif. Locating cancer associated motif is easier in cluster formation process than the other one. The proposed work will be an initiative aid for finding genetic disease related research.

Keywords: Bioinformatics, cancer motif, DNA, k-mers, Levenshtein distance, SOM.

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Authors: R. K. Tuli

Abstract:

In present communication, we have developed the suitable constraints for the given the mean codeword length and the measures of entropy. This development has proved that Renyi-s entropy gives the minimum value of the log of the harmonic mean and the log of power mean. We have also developed an important relation between best 1:1 code and the uniquely decipherable code by using different measures of entropy.

Keywords: Codeword, Instantaneous code, Prefix code, Uniquely decipherable code, Best one-one code, Mean codewordlength

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Authors: Seung Pil Pack

Abstract:

Deaminated lesions were produced via nitrosative oxidation of natural nucleobases; uracul (Ura, U) from cytosine (Cyt, C), hypoxanthine (Hyp, H) from adenine (Ade, A), and xanthine (Xan, X) and oxanine (Oxa, O) from guanine (Gua, G). Such damaged nucleobases may induce mutagenic problems, so that much attentions and efforts have been poured on the revealing of their mechanisms in vivo or in vitro. In this study, we employed these deaminated lesions as useful probes for analysis of DNA-binding/recognizing proteins or enzymes. Since the pyrimidine lesions such as Hyp, Oxa and Xan are employed as analogues of guanine, their comparative uses are informative for analyzing the role of Gua in DNA sequence in DNA-protein interaction. Several DNA oligomers containing such Hyp, Oxa or Xan substituted for Gua were designed to reveal the molecular interaction between DNA and protein. From this approach, we have got useful information to understand the molecular mechanisms of the DNA-recognizing enzymes, which have not ever been observed using conventional DNA oligomer composed of just natural nucleobases.

Keywords: Deaminated lesion, DNA-protein interaction, DNA-recognizing enzymes

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Authors: Manpreet Singh, Parvinder Singh Sandhu, Manjinder Singh Kahlon

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There are many classical algorithms for finding routing in FPGA. But Using DNA computing we can solve the routes efficiently and fast. The run time complexity of DNA algorithms is much less than other classical algorithms which are used for solving routing in FPGA. The research in DNA computing is in a primary level. High information density of DNA molecules and massive parallelism involved in the DNA reactions make DNA computing a powerful tool. It has been proved by many research accomplishments that any procedure that can be programmed in a silicon computer can be realized as a DNA computing procedure. In this paper we have proposed two tier approaches for the FPGA routing solution. First, geometric FPGA detailed routing task is solved by transforming it into a Boolean satisfiability equation with the property that any assignment of input variables that satisfies the equation specifies a valid routing. Satisfying assignment for particular route will result in a valid routing and absence of a satisfying assignment implies that the layout is un-routable. In second step, DNA search algorithm is applied on this Boolean equation for solving routing alternatives utilizing the properties of DNA computation. The simulated results are satisfactory and give the indication of applicability of DNA computing for solving the FPGA Routing problem.

Keywords: FPGA, Routing, DNA Computing.

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Authors: Alexandra Oliveros, Miguel Sotaquirá

Abstract:

DNA microarray technology is widely used by geneticists to diagnose or treat diseases through gene expression. This technology is based on the hybridization of a tissue-s DNA sequence into a substrate and the further analysis of the image formed by the thousands of genes in the DNA as green, red or yellow spots. The process of DNA microarray image analysis involves finding the location of the spots and the quantification of the expression level of these. In this paper, a tool to perform DNA microarray image analysis is presented, including a spot addressing method based on the image projections, the spot segmentation through contour based segmentation and the extraction of relevant information due to gene expression.

Keywords: Contour segmentation, DNA microarrays, edge detection, image processing, segmentation, spot addressing.

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Authors: Zuwairie Ibrahim, Yusei Tsuboi, Osamu Ono, Marzuki Khalid

Abstract:

Deoxyribonucleic Acid or DNA computing has emerged as an interdisciplinary field that draws together chemistry, molecular biology, computer science and mathematics. Thus, in this paper, the possibility of DNA-based computing to solve an absolute 1-center problem by molecular manipulations is presented. This is truly the first attempt to solve such a problem by DNA-based computing approach. Since, part of the procedures involve with shortest path computation, research works on DNA computing for shortest path Traveling Salesman Problem, in short, TSP are reviewed. These approaches are studied and only the appropriate one is adapted in designing the computation procedures. This DNA-based computation is designed in such a way that every path is encoded by oligonucleotides and the path-s length is directly proportional to the length of oligonucleotides. Using these properties, gel electrophoresis is performed in order to separate the respective DNA molecules according to their length. One expectation arise from this paper is that it is possible to verify the instance absolute 1-center problem using DNA computing by laboratory experiments.

Keywords: DNA computing, operation research, 1-center problem.

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Authors: Kazuaki Maeda

Abstract:

This paper proposes a new technique to detect code clones from the lexical and syntactic point of view, which is based on PALEX source code representation. The PALEX code contains the recorded parsing actions and also lexical formatting information including white spaces and comments. We can record a list of parsing actions (shift, reduce, and reading a token) during a compiling process after a compiler finishes analyzing the source code. The proposed technique has advantages for syntax sensitive approach and language independency.

Keywords: Code Clones, Source Code Representation, XML, Parser, Parser Generator

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Authors: Chaiwat Tantarangsee

Abstract:

The purposes of this study are 1) to study the frequent English writing errors of students registering the course: Reading and Writing English for Academic Purposes II, and 2) to find out the results of writing error correction by using coded indirect corrective feedback and writing error treatments. Samples include 28 2nd year English Major students, Faculty of Education, Suan Sunandha Rajabhat University. Tool for experimental study includes the lesson plan of the course; Reading and Writing English for Academic Purposes II, and tool for data collection includes 4 writing tests of short texts. The research findings disclose that frequent English writing errors found in this course comprise 7 types of grammatical errors, namely Fragment sentence, Subject-verb agreement, Wrong form of verb tense, Singular or plural noun endings, Run-ons sentence, Wrong form of verb pattern and Lack of parallel structure. Moreover, it is found that the results of writing error correction by using coded indirect corrective feedback and error treatment reveal the overall reduction of the frequent English writing errors and the increase of students’ achievement in the writing of short texts with the significance at .05.

Keywords: Coded indirect corrective feedback, error correction, error treatment, frequent English writing errors.

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Authors: Mohammed S. Assiri

Abstract:

In EFL programs, rating scales used in writing assessment are often constructed by intuition. Intuition-based scales tend to provide inaccurate and divisive ratings of learners’ writing performance. Hence, following an empirical approach, this study attempted to develop a rating scale for elementary-level writing at an EFL program in Saudi Arabia. Towards this goal, 98 students’ essays were scored and then coded using comprehensive taxonomy of writing constructs and their measures. An automatic linear modeling was run to find out which measures would best predict essay scores. A nonparametric ANOVA, the Kruskal-Wallis test, was then used to determine which measures could best differentiate among scoring levels. Findings indicated that there were certain measures that could serve as either good predictors of essay scores or differentiators among scoring levels, or both. The main conclusion was that a rating scale can be empirically developed using predictive and discriminative statistical tests.

Keywords: Analytic scoring, rating scales, writing assessment, writing performance.

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Authors: Chaiwat Tantarangsee

Abstract:

The purposes of this study are 1) to study the frequent English writing errors of students registering the course: Reading and Writing English for Academic Purposes II, and 2) to find out the results of writing error correction by using coded indirect corrective feedback and writing error treatments. Samples include 28 2nd year English Major students, Faculty of Education, Suan Sunandha Rajabhat University. Tool for experimental study includes the lesson plan of the course; Reading and Writing English for Academic Purposes II, and tool for data collection includes 4 writing tests of short texts. The research findings disclose that frequent English writing errors found in this course comprise 7 types of grammatical errors, namely Fragment sentence, Subject-verb agreement, Wrong form of verb tense, Singular or plural noun endings, Run-ons sentence, Wrong form of verb pattern and Lack of parallel structure. Moreover, it is found that the results of writing error correction by using coded indirect corrective feedback and error treatment reveal the overall reduction of the frequent English writing errors and the increase of students’ achievement in the writing of short texts with the significance at .05.

Keywords: Coded indirect corrective feedback, error correction, and error treatment.

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Authors: Esmaeil Hassannejad

Abstract:

Some of the students' problems in writing skill stem from inadequate preparation for the writing assignment. Students should be taught how to write well when they arrive in language classes. Having selected a topic, the students examine and explore the theme from as large a variety of viewpoints as their background and imagination make possible. Another strategy is that the students prepare an Outline before writing the paper. The comparison between the two mentioned thought provoking techniques was carried out between the two class groups –students of Islamic Azad University of Dezful who were studying “Writing 2" as their main course. Each class group was assigned to write five compositions separately in different periods of time. Then a t-test for each pair of exams between the two class groups showed that the t-observed in each pair was more than the t-critical. Consequently, the first hypothesis which states those who utilize Brainstorming as a thought provoking technique in prewriting phase are more successful than those who outline the papers before writing was verified.

Keywords: Brainstorming, Outlining, Prewriting, Thought provoking techniques

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Authors: R. Manaffar, R. Maleki, S. Zare, N. Agh, S. Soltanian, B. Sehatnia, P. Sorgeloos, P. Bossier, G. Van Stappen

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Artemia is one of the most conspicuous invertebrates associated with aquaculture. It can be considered as a model organism, offering numerous advantages for comprehensive and multidisciplinary studies using morphologic or molecular methods. Since DNA extraction is an important step of any molecular experiment, a new and a rapid method of DNA extraction from adult Artemia was described in this study. Besides, the efficiency of this technique was compared with two widely used alternative techniques, namely Chelex® 100 resin and SDS-chloroform methods. Data analysis revealed that the new method is the easiest and the most cost effective method among the other methods which allows a quick and efficient extraction of DNA from the adult animal.

Keywords: APD, Artemia, DNA extraction, Molecularexperiments

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Authors: Sadaf Khalid, Jahanzaib Sarwar, Rabia Tauseef

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No matter how much perfect we become in our practical skills regarding the implementation of learned ideas, the need of technical writing capability cannot be neglected being a professional. Technical writing is a way of communicating the ideas in written which otherwise need to be presented orally. Technical writing skills have always been the need of the time, as they are required for internal as well as external official communication in both formal and informal manner. Moreover, they are the best way to capture the attention of your customers by presenting information in effective manner. This paper aims to analyze the importance of technical writing skills in professional industries of Pakistan by conducting a survey. Survey results presented in this paper clearly depicts the importance of formal and informal written communication media used in different professional industries in Pakistan. Analysis and discussion of the extent to which the alternative ways of communication besides technical writing have got importance in Pakistan is also an important aspect of this survey.

Keywords: Technical writing, Survey, Oral communication, Globalization, Communication trends, Formal Communication Media, Informal Communication, Audience

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Authors: M. S. Muhammad, S. M. W. Masra, K. Kipli, N. Zamhari

Abstract:

The capturing of gel electrophoresis image represents the output of a DNA computing algorithm. Before this image is being captured, DNA computing involves parallel overlap assembly (POA) and polymerase chain reaction (PCR) that is the main of this computing algorithm. However, the design of the DNA oligonucleotides to represent a problem is quite complicated and is prone to errors. In order to reduce these errors during the design stage before the actual in-vitro experiment is carried out; a simulation software capable of simulating the POA and PCR processes is developed. This simulation software capability is unlimited where problem of any size and complexity can be simulated, thus saving cost due to possible errors during the design process. Information regarding the DNA sequence during the computing process as well as the computing output can be extracted at the same time using the simulation software.

Keywords: DNA computing, PCR, POA, simulation software

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Authors: Luciana Montera

Abstract:

DNA shuffling is a powerful method used for in vitro evolute molecules with specific functions and has application in areas such as, for example, pharmaceutical, medical and agricultural research. The success of such experiments is dependent on a variety of parameters and conditions that, sometimes, can not be properly pre-established. Here, two computational models predicting DNA shuffling results is presented and their use and results are evaluated against an empirical experiment. The in silico and in vitro results show agreement indicating the importance of these two models and motivating the study and development of new models.

Keywords: Computer simulation, DNA shuffling, in silico andin vitro comparison.

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Authors: S. Behnia, S. Fathizadeh

Abstract:

Conductivity properties of DNA molecule is investigated in a simple, but chemically specific approach that is intimately related to the Su-Schrieffer-Heeger (SSH) model. This model is a tight-binding linear nanoscale chain. We have tried to study the electrical current flowing in DNA and investigated the characteristic I-V diagram. As a result, It is shown that there are the (quasi-) ohmic areas in I-V diagram. On the other hand, the regions with a negative differential resistance (NDR) are detectable in diagram.

Keywords: Charge transfer in DNA, Chaos theory, Molecular electronics, Negative Differential resistance.

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Authors: Aaidha Hammad

Abstract:

This study examines the phenomenon of code switching among teenagers in the Maldives while they carry out conversations through Facebook in the form of “Facebook Chatting”. The current study aims at evaluating the frequency of code-switching and it investigates between what languages code-switching occurs. Besides the study identifies the types of words that are often codeswitched and the triggers for code switching. The methodology used in this study is mixed method of qualitative and quantitative approach. In this regard, the chat log of a group conversation between 10 teenagers was collected and analyzed. A questionnaire was also administered through online to 24 different teenagers from different corners of the Maldives. The age of teenagers ranged between 16 and 19 years. The findings of the current study revealed that while Maldivian teenagers chat in Facebook they very often code switch and these switches are most commonly between Dhivehi and English, but some other languages are also used to some extent. It also identified the different types of words that are being often code switched among the teenagers. Most importantly it explored different reasons behind code switching among the Maldivian teenagers in Facebook chatting.

Keywords: Code-switching, Facebook, Facebook chatting Maldivian teenagers.

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Authors: Hilal A. Fadhil, Syed A. Aljunid, R. Badlishah Ahmed

Abstract:

In this paper we study the use of a new code called Random Diagonal (RD) code for Spectral Amplitude Coding (SAC) optical Code Division Multiple Access (CDMA) networks, using Fiber Bragg-Grating (FBG), FBG consists of a fiber segment whose index of reflection varies periodically along its length. RD code is constructed using code level and data level, one of the important properties of this code is that the cross correlation at data level is always zero, which means that Phase intensity Induced Phase (PIIN) is reduced. We find that the performance of the RD code will be better than Modified Frequency Hopping (MFH) and Hadamard code It has been observed through experimental and theoretical simulation that BER for RD code perform significantly better than other codes. Proof –of-principle simulations of encoding with 3 channels, and 10 Gbps data transmission have been successfully demonstrated together with FBG decoding scheme for canceling the code level from SAC-signal.

Keywords: FBG, MFH, OCDMA, PIIN, BER.

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Authors: Hairuzila Idrus, Zullina Hussain Shaari, Razol Mahari Mohd Ali

Abstract:

Peer review is an activity where students review their classmates- writing and then evaluate the content, development, unity and organization. Studies have shown that peer review activities benefit both the reviewer and the writer in developing their reading and writing skills. Furthermore, peer review activities may also enhance students- soft skills. This study was conducted to find out the benefits of peer review activity in a technical writing class based on engineering students- perceptions. The study also highlights how these benefits could improve the students- soft skills. A set of questionnaire was given to 200 undergraduate students of a technical writing course. The results of the study indicate that the activity could help improve their critical thinking skills, written and oral communication skills, as well as team work. This paper further discusses how the implications of these benefits could help enhance students- soft skills.

Keywords: Peer review, soft skills, technical writing.

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Authors: Qiu Chen, Feifei Lee, Koji Kotani, Tadahiro Ohmi

Abstract:

In this paper, we propose an efficient hierarchical DNA sequence search method to improve the search speed while the accuracy is being kept constant. For a given query DNA sequence, firstly, a fast local search method using histogram features is used as a filtering mechanism before scanning the sequences in the database. An overlapping processing is newly added to improve the robustness of the algorithm. A large number of DNA sequences with low similarity will be excluded for latter searching. The Smith-Waterman algorithm is then applied to each remainder sequences. Experimental results using GenBank sequence data show the proposed method combining histogram information and Smith-Waterman algorithm is more efficient for DNA sequence search.

Keywords: Fast search, DNA sequence, Histogram feature, Smith-Waterman algorithm, Local search

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Authors: Kazuaki Maeda

Abstract:

This paper describes a code clone visualization method, called FC graph, and the implementation issues. Code clone detection tools usually show the results in a textual representation. If the results are large, it makes a problem to software maintainers with understanding them. One of the approaches to overcome the situation is visualization of code clone detection results. A scatter plot is a popular approach to the visualization. However, it represents only one-to-one correspondence and it is difficult to find correspondence of code clones over multiple files. FC graph represents correspondence among files, code clones and packages in Java. All nodes in FC graph are positioned using force-directed graph layout, which is dynami- cally calculated to adjust the distances of nodes until stabilizing them. We applied FC graph to some open source programs and visualized the results. In the author’s experience, FC graph is helpful to grasp correspondence of code clones over multiple files and also code clones with in a file.

Keywords: code clone detection, program comprehension, software maintenance, visualization

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Authors: H. Elsawy, A. Jeltsch

Abstract:

EcoDam is an adenine-N6 DNA methyltransferase that methylates the GATC sites in the Escherichia coli genome. DNA-adenine methylation is not present in higher eukaryotes including humans. These observations raise the possibility that dam inhibitors may be used as anti-microbial agents. Polyphosphate (Poly(P)) is an important metabolite and signaling molecule in prokaryotes and eukaryotes. Here, by using gel retardation experiments to investigate the competition of DNA binding by EcoDam in the presence of polyphosphate, we found that Poly (P) strongly interferes with DNA binding by EcoDam, while same concentration of monophosphate does not. In addition, we demonstrated that Poly (P) binding inhibits the activity of EcoDam and our results suggest that Poly (P) led to strong inhibition of the EcoDam catalytic activity, while monophosphate had only moderate effect.

Keywords: Antibacterial drugs, EcoDam inhibitors, Polyphosphate.

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Authors: Mohamed S. Sasi, Adel M. Mlitan, Abdulfattah M. Alkherraz

Abstract:

This research project aims to investigate difference in relative rates concerning phosphoryl transfer relevant to biological catalysis of DNA and RNA in the pH-independent reactions. Activated Models of DNA and RNA for alkyl-aryl phosphate diesters (with 4-nitrophenyl as a good leaving group) have successfully been prepared to gather kinetic parameters. Eyring plots for the pH– independent hydrolysis of 1 and 2 were established at different temperatures in the range 100–160 °C. These measurements have been used to provide a better estimate for the difference in relative rates between the reactivity of DNA and RNA cleavage. Eyring plot gave an extrapolated rate of kH2O = 1 × 10-10 s -1 for 1 (RNA model) and 2 (DNA model) at 25°C. Comparing the reactivity of RNA model and DNA model shows that the difference in relative rates in the pH-independent reactions is surprisingly very similar at 25°. This allows us to obtain chemical insights into how biological catalysts such as enzymes may have evolved to perform their current functions.

Keywords: DNA & RNA Models, Relative Rates, Reactivity.

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