Search results for: shotgun metagenomic sequence analysis

Authors: Rajkumar Ghosh

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The Out-of-Sequence Thrust (OOST) is a common phenomenon in collisional tectonic settings like the Himalayas. These OOSTs are activated in different locations at different time frames. These OOST are linked with the multiple Himalayan Thrusts. Apart from minimal documentation in geological mapping for OOST, there exists a lack of field data to establish OOST in the field. This work has considered three thrusts from NW Himalaya in Himachal Pradesh with published data from other sources, allowing a re-examination for correlation of OOST. For the Sutlej section, the approach has been to do fieldwork and microstructural studies. The information related to the cross-cut signature of S/C- and relative time relation could help to predict the nature of OOST. The activation timing, along with the basis of identification of OOST in Higher Himalayan, was documented in various literature. Compilation of the Grain Boundary Migration (GBM) associated temperature range (400–750 °C) was documented from microstructural studies along the Jhakri-Chaura section. No such significant temperature variation across thrusts was observed. Strain variation paths using S Ʌ C angle measurement were carried out along the Jeori-Wangtu transect to distinguish overprinting structures for OOSTs. Near the Chaura Thrust (CT), angular variation of S Ʌ C was documented, and it varies within a range of 15° - 28 °. Along the NH22 (National Highway, 22), all tectonic units of the orogen are exposed in NW Himalaya, INDIA. But there are inherent difficulties in finding field evidence of OOST, largely due to the lack of adequate surface morphology, including topography and drainage pattern.

Keywords: out-of-sequence thrust (OOST), main central thrust (MCT), south tibetan detachment system (STDS), jhakri thrust (JT), sarahan thrust (ST), chaura thrust (CT), higher himalaya (HH), greater himalayan crystalline (GHC)

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Authors: S. M. Kulkarni, D. S. Bormane, S. L. Nalbalwar

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The rapid development in the technology have dramatic impact on the medical health care field. Medical data base obtained with latest machines like CT Machine, MRI scanner requires large amount of memory storage and also it requires large bandwidth for transmission of data in telemedicine applications. Thus, there is need for video compression. As the database of medical images contain number of frames (slices), hence while coding of these images there is need of motion estimation. Motion estimation finds out movement of objects in an image sequence and gets motion vectors which represents estimated motion of object in the frame. In order to reduce temporal redundancy between successive frames of video sequence, motion compensation is preformed. In this paper three step search (TSS) block matching algorithm is implemented on different types of video sequences. It is shown that three step search algorithm produces better quality performance and less computational time compared with exhaustive full search algorithm.

Keywords: block matching, exhaustive search motion estimation, three step search, video compression

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Authors: Alexis John de Britto

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Studies were performed to select the superior genotypes based on intra-specific variations, caused by phytogeographical, climatic and edaphic parameters of three anti cancer drug yielding mangrove plants such as Acanthus ilicifolius L., Calophyllum inophyllum L. and Excoecaria agallocha L. using ISSR (Inter Simple Sequence Repeats) markers and phytochemical analysis such as preliminary phytochemical tests, TLC, HPTLC, HPLC and antioxidant tests. The plants were collected from five different geographical locations of the East Coast of south India. Genetic heterozygosity, Nei’s gene diversity, Shannon’s information index and Percentage of polymorphism between the populations were calculated using POPGENE software. Cluster analysis was performed using UPGMA algorithm. AMOVA and correlations between genetic diversity and soil factors were analyzed. Combining the molecular and phytochemical variations superior genotypes were selected. Conservation constraints and methods of efficient exploitation of the species are discussed.

Keywords: anti-cancer drug yielding plants, DNA fingerprinting, phytochemical analysis, selection of superior genotypes

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Authors: Khaled Igbaria

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Laila Al-Othman is a well-known feminist writer in Kuwait and the entire Arab world. She was born in 1943 in Kuwait to a large and wealthy family. The author has written several short stories, as well as novels, such as The Woman and the Cat (1985) and Wasumayya Comes out of the Sea (1986), which was chosen as one of the best 100 Arab novels of the 21st century. Another prominent novel of hers is Ṣamt al-Farāshāt [Silence of the Butterflies] (2007), which was highly controversial in her native Kuwait upon publication. For this study, her engagement in feminism was achieved by exploring the different ways in which her novel, Ṣamt al-Farāshāt [Silence of the Butterflies], addresses several feminist issues, mainly forced marriage, rape and sexual abuse, gender-based physical, sexual violence, and enforced silence. This paper focuses on demonstrating social obstacles and continuous trauma caused by a sequence of pain experienced by Arab females in their patriarchal society. This study argues that the novel reveals a sustained effort to raise the banner of feminism and a strong desire to liberate Arab women from patriarchal domination. Al-Othman successfully and uniquely represents women as gender-based traumatic victims of sexual and physical violence, forced silence, and general oppression in the patriarchal Arab society, as those needing help, support, protection, and liberation. They are not represented as independent or free. Methodologically, the study employs a qualitative literary analysis method in addition to trauma theory psychoanalysis, concentrating on feminist issues highlighted in the novel.

Keywords: Al-Othman, Arab women pain, trauma within narration., Silence of the Butterflies

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Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

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A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: bacteria chromosome, bacterial identification, sequence, primer generation

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Authors: G. Sava, I. Popa, T. Sava, A. Ion, M. Ilie, C. Manailescu, A. Robu

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At the RoAMS laboratory in Bucharest we have looked for a head-to-head meeting between AMS radiocarbon dating and dendrochronology dating, aiming to point out and explain any differences or similarities that might appear between their output results. As a subject of this investigation, we have fixed our attention on a sequence of tree rings spanning on a period of 700 years, starting with 1000 AD. The samples were collected from the northern Romanian territory within Moldavia region, and were provided by the ‘Marin Dracea - National Institute for Research and Development in Forestry’. All the 23 single ring wood samples were radiocarbon dated using alpha-cellulose extraction, followed by graphitization in an AGE3 installation. A wiggle matching procedure was applied to reduce the radiocarbon uncertainties for the calibrated ages. The results showed a good agreement on 3 out of 4 wood cores, the age-shifting of one of the wood cores being interpreted as an uncertain dendrochronology matching, which was further corrected.

Keywords: wiggle matching, tree-ring radiocarbon dating, dendrochronology, AMS radiocarbon dating, radiocarbon dating in Romania

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Authors: Salman Akrokayan

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Synthetic cDNA (ScDNA) of granulocyte colony-stimulating factor (G-CSF) was constructed using a DNA synthesizer with the aim to increase its expression level. 5' end of the ScDNA of G-CSF coding region was modified by decreasing the GC content without altering the predicted amino acids sequence. The identity of the resulting protein from ScDNA was confirmed by the highly specific enzyme-linked immunosorbent assay. In conclusion, a synthetic G-CSF cDNA in combination with the recombinant DNA protocol offers a rapid and reliable strategy for synthesizing the target protein. However, the commercial utilization of this methodology requires rigorous validation and quality control.

Keywords: synthetic cDNA, recombinant G-CSF, cloning, gene expression

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Authors: Elena Pozdnyakova

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“Government Relations” is a field of knowledge presently taught at the majority of universities around the globe. English as the default language can become the language of teaching since the issues discussed are both global and national in character. However for this field of knowledge key concepts and their word representations in English don’t often coincide with those in other languages. International master’s degree students abroad as well as students, taught the course in English at their national universities, are exposed to difficulties, connected with correct conceptualizing of terminology of GR in British and American academic traditions. The study was carried out during the GR English language course elaboration (pilot research: 2013 -2015) at Moscow State Institute of Foreign Relations (University), Russian Federation. Within this period, English language instructors designed and elaborated the three-semester course of GR. Methodologically the course design was based on elaboration model with the special focus on conceptual elaboration sequence and theoretical elaboration sequence. The course designers faced difficulties in concept selection and theoretical elaboration sequence. To improve the results and eliminate the problems with concept selection, a new, corpus-based approach was worked out. The computer-based tool WordSmith 6.0 was used with the aim to build a model of key concept selection. The corpus of GR English texts consisted of 1 million words (the study corpus). The approach was based on measuring effect size, i.e. the percent difference of the frequency of a word in the study corpus when compared to that in the reference corpus. The results obtained proved significant improvement in the process of concept selection. The corpus-based model also facilitated theoretical elaboration of teaching materials.

Keywords: corpus-based study, English as the default language, key concepts, measuring effect size, model of key concept selection

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Authors: Peng Wang, Tigang Jiang

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The computer based lip reading method of different languages cannot be universal. At present, for the research of Chinese lip reading, whether the work on data sets or recognition algorithms, is far from mature. In this paper, we study the Chinese lipreading method based on machine learning, and propose a Chinese Sentence-level lip-reading network (CNLipNet) model which consists of spatio-temporal convolutional neural network(CNN), recurrent neural network(RNN) and Connectionist Temporal Classification (CTC) loss function. This model can map variable-length sequence of video frames to Chinese Pinyin sequence and is trained end-to-end. More over, We create CNLRS, a Chinese Lipreading Dataset, which contains 5948 samples and can be shared through github. The evaluation of CNLipNet on this dataset yielded a 41% word correct rate and a 70.6% character correct rate. This evaluation result is far superior to the professional human lip readers, indicating that CNLipNet performs well in lipreading.

Keywords: lipreading, machine learning, spatio-temporal, convolutional neural network, recurrent neural network

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Authors: Noshaba Dilbar, Aisha Tahir, Amer Jamil

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During the last decade, DNA barcoding proved to be an authentic tool for discovery and identification of plants. In the present study, DNA barcoding of two species, Fagonia arabica and Fagonia indica was done for differentiation by using matK region. matK gene is considered as a universal barcode because of its easy alignment and high discrimination ability. In this study, matK yielded 100% sequencing results. The sequences from both plants were aligned at clustal W and observed that there is no nucleotide variation and polymorphism among both sequences. This was further analysed by BLAST which showed the similar sequences from different plants belonging to same family but didn’t find sequence of both species. Considering this, the resulted sequence was submitted by the name of Fagonia arabica with accession number KM276890. In the end, we analysed the results from BOLD which gave us the final conclusion that both plants are same as their matK sequences are 100% identical. In literature, both Fagonia indica and Fagonia arabica names are used for this plant but there is no clear differentiation has been observed in these plants. Results evaluate that Fagonia indica and Fagonia arabica are the alternative names of same plant.

Keywords: DNA barcoding, Fagonia arabica, Fagonia indica, matK

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Authors: Aviv Yaniv, Ron Ben Arosh, Nadav Gasner, Michael Konviser, Arbel Yaniv

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This paper introduces two methods for the evaluation of Question Decomposition Meaning Representation (QDMR) as predicted by sequence-to-sequence model and COPYNET parser for natural language questions processing, motivated by the fact that previous evaluation metrics used for this task do not take into account some characteristics of the representation, such as partial ordering structure. To this end, several heuristics to extract such partial dependencies are formulated, followed by the hereby proposed evaluation methods denoted as Proportional Graph Matcher (PGM) and Conversion to Normal String Representation (Nor-Str), designed to better capture the accuracy level of QDMR predictions. Experiments are conducted to demonstrate the efficacy of the proposed evaluation methods and show the added value suggested by one of them- the Nor-Str, for better distinguishing between high and low-quality QDMR when predicted by models such as COPYNET. This work represents an important step forward in the development of better evaluation methods for QDMR predictions, which will be critical for improving the accuracy and reliability of natural language question-answering systems.

Keywords: NLP, question answering, question decomposition meaning representation, QDMR evaluation metrics

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Authors: Watcharapan Sukkerd, Teeradej Wuttipornpun

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This paper aims to present non-population search algorithms called tabu search (TS), simulated annealing (SA) and variable neighborhood search (VNS) to minimize the total cost of capacitated MRP problem in multi-stage assembly flow shop with two alternative machines. There are three main steps for the algorithm. Firstly, an initial sequence of orders is constructed by a simple due date-based dispatching rule. Secondly, the sequence of orders is repeatedly improved to reduce the total cost by applying TS, SA and VNS separately. Finally, the total cost is further reduced by optimizing the start time of each operation using the linear programming (LP) model. Parameters of the algorithm are tuned by using real data from automotive companies. The result shows that VNS significantly outperforms TS, SA and the existing algorithm.

Keywords: capacitated MRP, tabu search, simulated annealing, variable neighborhood search, linear programming, assembly flow shop, application in industry

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Authors: Thobela Conco, Sheena Kumari, Chika Nnadozie, Mahmoud Nasr, Thor A. Stenström, Mushal Ali, Arshad Ismail, Faizal Bux

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The discharge of antibiotics and its residues into the wastewater treatment plants (WWTP’s) create a conducive environment for the development of antibiotic resistant pathogens. This presents a risk of potential dissemination of antibiotic resistant pathogens and antibiotic resistance genes into the environment. It is, therefore, necessary to study the level of antibiotic resistance genes (ARG’s) among bacterial pathogens that proliferate in biological wastewater treatment systems. In the current study, metagenomic and meta-transcriptomic sequences of samples collected from the influents, secondary effluents and post chlorinated effluents of three wastewater treatment plants treating domestic and hospital effluents in Durban, South Africa, were analyzed for profiling of ARG’s among bacterial pathogens. Results show that a variety of ARG’s, mostly, aminoglycoside, β-lactamases, tetracycline and sulfonamide resistance genes were harbored by diverse bacterial genera found at different stages of treatment. A significant variation in diversity of pathogen and ARGs between the treatment plant was observed; however, treated final effluent samples from all three plants showed a significant reduction in bacterial pathogens and detected ARG’s. Both pre- and post-chlorinated samples showed the presence of mobile genetic elements (MGE’s), indicating the inefficiency of chlorination to remove of ARG’s integrated with MGE’s. In conclusion, the study showed the wastewater treatment plant efficiently caused the reduction and removal of certain ARG’s, even though the initial focus was the removal of biological nutrients.

Keywords: antibiotic resistance, mobile genetic elements, wastewater, wastewater treatment plants

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Authors: Rajkumar Ghosh

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Out-of-sequence thrusts (OOST) are reported at different geographic locations with various local names along Siwalik Himalaya (SH), Lesser Himalaya (LH), Higher Himalaya (HH) from Bhutan, India, Nepal, and Pakistan Himalayan range. Most of OOSTs have been identified within the upper LH, and the lower HH based on geochronological age jump across. These thrusts activated from Late Miocene to recent. The Chaura Thrust (CT) was deciphered from age jump of Apatite Fission Track (AFT) and considered as blind thrust base on variable exhumation rates in Chaura region, Satluj river valley, Himachal Pradesh. CT is located north of Jhakri Thrust (JhT) and is also differently identified as Sarahan thrust (ST). Structural documentation from the rocks near the OOST in Chaura was not so far done. Detail structural study of the Jeori Group of rocks was carried out in this study to understand the manifestation of the Chaura thrust and associated structures in meso- to micro-scale. Box fold, scar fold, kink fold, crenulation cleavages, and boudins are developed in the Chaura region. These structures usually do not indicate shear sense. When studied under an optical microscope, the Chaura samples reveal that the mica fish are usually lenticular with aspect ratio (R) varying from 6–11 and inclination angle (α) from 15–40°. According to ‘R’ and ‘α’, elongated sigmoid shaped mica fish and parallelogram shaped mica fish were also documented. Asymmetric mica fish demonstrate top-to-S/SW ductile shear, which is similar as that of Chaura thrust. Grain boundary migration (GBM) structures in quartzo-feldspathic grains from Jeori Group of rocks indicate deformation temperature ranging from 400 to 650°C. This can indicate that the OOST at Chaura, i.e., the Chaura Thrust, underwent thrusting in the ductile regime.

Keywords: out-of-sequence thrust, chaura thrust, sarahan thrust, jakhri thrust, higher himalaya, s/c- fabric

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Authors: Shibo Wei, Ting Jiang

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Convolutional-recurrent neural networks (CRN) have achieved much success recently in the speech enhancement field. The common processing method is to use the convolution layer to compress the feature space by multiple upsampling and then model the compressed features with the LSTM layer. At last, the enhanced speech is obtained by deconvolution operation to integrate the global information of the speech sequence. However, the feature space compression process may cause the loss of information, so we propose to model the upsampling result of each step with the residual LSTM layer, then join it with the output of the deconvolution layer and input them to the next deconvolution layer, by this way, we want to integrate the global information of speech sequence better. The experimental results show the network model (RES-CRN) we introduce can achieve better performance than LSTM without residual and overlaying LSTM simply in the original CRN in terms of scale-invariant signal-to-distortion ratio (SI-SNR), speech quality (PESQ), and intelligibility (STOI).

Keywords: convolutional-recurrent neural networks, speech enhancement, residual LSTM, SI-SNR

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Authors: C. Shalini Devi

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This work describes the stress concentration in a rectangular specimen with a circular hole made up of hybrid composite material with the combination of glass/carbon with epoxy. The arrangements of cross ply lamina in the sequence of alternative carbon and glass, using carbon fiber in panel, gives more strength to the structure as the carbon properties are higher when compared to glass. Typical aircraft and automobile components are with cut-outs, and such cut-outs reduce the weight of the aircraft according to the weight reduction law and also they reduce the bulking load carrying capacity. Experimental investigations were carried out using three specimens as per ASTM D5766 and three specimens as per ASTM D3039 in the Universal Testing Machine. Stress concentration in the rectangular specimen with a hole is also analysed using FEA and comparing the results.

Keywords: composite, stress concentration, finite element analysis, tensile strength

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Authors: Martina I. Reinhold, Theresa Bacon-Baguley

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Background: Medical knowledge continuously evolves and to help health care providers to stay up-to-date, evidence-based medicine (EBM) has emerged as a model. The practice of EBM requires new skills of the health care provider, including directed literature searches, the critical evaluation of research studies, and the direct application of the findings to patient care. This paper describes the integration and evaluation of an evidence-based medicine course sequence into a Physician Assistant curriculum. This course sequence teaches students to manage and use the best clinical research evidence to competently practice medicine. A survey was developed to assess the outcomes of the EBM course sequence. Methodology: The cornerstone of the three-semester sequence of EBM are interactive small group discussions that are designed to introduce students to the most clinically applicable skills to identify, manage and use the best clinical research evidence to improve the health of their patients. During the three-semester sequence, the students are assigned each semester to participate in small group discussions that are facilitated by faculty with varying background and expertise. Prior to the start of the first EBM course in the winter semester, PA students complete a knowledge-based survey that was developed by the authors to assess the effectiveness of the course series. The survey consists of 53 Likert scale questions that address the nine objectives for the course series. At the end of the three semester course series, the same survey was given to all students in the program and the results from before, and after the sequence of EBM courses are compared. Specific attention is paid to overall performance of students in the nine course objectives. Results: We find that students from the Class of 2016 and 2017 consistently improve (as measured by percent correct responses on the survey tool) after the EBM course series (Class of 2016: Pre- 62% Post- 75%; Class of 2017: Pre- 61 % Post-70%). The biggest increase in knowledge was observed in the areas of finding and evaluating the evidence, with asking concise clinical questions (Class of 2016: Pre- 61% Post- 81%; Class of 2017: Pre- 61 % Post-75%) and searching the medical database (Class of 2016: Pre- 24% Post- 65%; Class of 2017: Pre- 35 % Post-66 %). Questions requiring students to analyze, evaluate and report on the available clinical evidence regarding diagnosis showed improvement, but to a lesser extend (Class of 2016: Pre- 56% Post- 77%; Class of 2017: Pre- 56 % Post-61%). Conclusions: Outcomes identified that students did gain skills which will allow them to apply EBM principles. In addition, the outcomes of the knowledge-based survey allowed the faculty to focus on areas needing improvement, specifically the translation of best evidence into patient care. To address this area, the clinical faculty developed case scenarios that were incorporated into the lecture and discussion sessions, allowing students to better connect the research studies with patient care. Students commented that ‘class discussion and case examples’ contributed most to their learning and that ‘it was helpful to learn how to develop research questions and how to analyze studies and their significance to a potential client’. As evident by the outcomes, the EBM courses achieved the goals of the course and were well received by the students. 

Keywords: evidence-based medicine, clinical education, assessment tool, physician assistant

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

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

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

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Authors: J. Suneetha, Vijayalaxmi

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Sequential Pattern Mining involves applying data mining methods to large data repositories to extract usage patterns. Sequential pattern mining methodologies used to analyze the data and identify patterns. The patterns have been used to implement efficient systems can recommend on previously observed patterns, in making predictions, improve usability of systems, detecting events, and in general help in making strategic product decisions. In this paper, identified performance of approximate sequential pattern mining defines as identifying patterns approximately shared with many sequences. Approximate sequential patterns can effectively summarize and represent the databases by identifying the underlying trends in the data. Conducting an extensive and systematic performance over synthetic and real data. The results demonstrate that ApproxMAP effective and scalable in mining large sequences databases with long patterns.

Keywords: multiple data, performance analysis, sequential pattern, sequence database scalability

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Authors: Nikolaos Mamalis

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The work of the eminent architect and composer has undoubtedly been influenced both by his architecture and collaboration with Le Corbusier and by the conquests of the musical avant-garde of the 20th century (Schoenberg, Messian, Bartock, electroacoustic music). It is known that the golden mean and the Fibonacci sequence played a momentous role in the Architectural Avant-garde (Modulor) and expanded on musical pursuits. Especially in the 50s (serialism), it was a structural tool for composition. Xenakis' architectural and musical work (Sacrifice, Metastasis, Rebonds, etc.) received the influence of the Golden Section, as has been repeatedly demonstrated. However, the idea of this retrospective sequence and the reflection raised by the search for new proportions, both in the architectural and the musical work of Xenakis, was not limited to constituting a step, a workable formula that acted unifyingly with regard to the other parameters of the musical work, or as an aesthetic model that makes sense - philosophically and poetically - an anthropocentric dimension as in other composers (see Luigi Nono) ̇ triggered a qualitative leap, an opening of the composer to the assimilation of mathematical concepts and scientific types in music and the consolidation of new sound horizons of stochastic music.

Keywords: golden ratio, music, space, stochastic music

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Authors: Parul Johri, Mala Trivedi

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

Keywords: aquaporins, carbon, dynamic prgramming, MIPs

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Authors: E. L. Albuquerque, U. L. Fulco, G. S. Ourique

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The focus of this work is on the numerical investigation of the charge transport properties of the de novo-designed alpha3 polypeptide, as well as in its variants, all of them probed by gene engineering. The theoretical framework makes use of a tight-binding model Hamiltonian, together with ab-initio calculations within quantum chemistry simulation. The alpha3 polypeptide is a 21-residue with three repeats of the seven-residue amino acid sequence Leu-Glu-Thr-Leu-Ala-Lys-Ala, forming an alpha–helical bundle structure. Its variants are obtained by Ala→Gln substitution at the e (5th) and g (7th) position, respectively, of the alpha3 polypeptide amino acid sequence. Using transmission electron microscopy and atomic force microscopy, it was observed that the alpha3 polypeptide and one of its variant do have the ability to form fibrous assemblies, while the other does not. Our main aim is to investigate whether or not the biased alpha3 polypeptide and its variants can be also identified by quantum charge transport measurements through current-voltage (IxV) curves as a pattern to characterize their fibrous assemblies. It was observed that each peptide has a characteristic current pattern, which may be distinguished by charge transport measurements, suggesting that it might be a useful tool for the development of biosensors.

Keywords: charge transport properties, electronic transmittance, current-voltage characteristics, biological sensor

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Authors: Aishik Deb, Rituparna Sinha

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We have developed an algorithm to detect the abnormal segment/"structural variation in the genome across a number of samples. We have worked on simulated as well as real data from the BAM Files and have designed a segmentation algorithm where abnormal segments are detected. This algorithm aims to improve the accuracy and performance of the existing CNV-CH algorithm. The next-generation sequencing (NGS) approach is very fast and can generate large sequences in a reasonable time. So the huge volume of sequence information gives rise to the need for Big Data and parallel approaches of segmentation. Therefore, we have designed a map-reduce approach for the existing CNV-CH algorithm where a large amount of sequence data can be segmented and structural variations in the human genome can be detected. We have compared the efficiency of the traditional and map-reduce algorithms with respect to precision, sensitivity, and F-Score. The advantages of using our algorithm are that it is fast and has better accuracy. This algorithm can be applied to detect structural variations within a genome, which in turn can be used to detect various genetic disorders such as cancer, etc. The defects may be caused by new mutations or changes to the DNA and generally result in abnormally high or low base coverage and quantification values.

Keywords: cancer detection, convex hull segmentation, map reduce, next generation sequencing

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Authors: Mahdi Fakoor, Seyed Mohammad Navid Ghoreishi

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Composite patching is a common way for reinforcing the cracked pipes and cylinders. The effects of composite patch reinforcement on fracture parameters of a cracked pipe depend on a variety of parameters such as number of layers, angle, thickness, and material of each layer. Therefore, stacking sequence optimization of composite patch becomes crucial for the applications of cracked pipes. In this study, in order to obtain the optimal stacking sequence for a composite patch that has minimum weight and maximum resistance in propagation of cracks, a coupled Multi-Objective Genetic Algorithm (MOGA) and Finite Element Method (FEM) process is proposed. This optimization process has done for longitudinal and transverse semi-elliptical cracks and optimal stacking sequences and Pareto’s front for each kind of cracks are presented. The proposed algorithm is validated against collected results from the existing literature.

Keywords: multi objective optimization, pareto front, composite patch, cracked pipe

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Authors: Isabelle Snyder, Travis Smith

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Microgrid protection presents challenges to conventional protection techniques due to the low-induced fault current. Protection relays present in microgrid applications require a combination of settings groups to adjust based on the architecture of the microgrid in islanded and grid-connected modes. In a radial system where the microgrid is at the other end of the feeder, directional elements can be used to identify the direction of the fault current and switch settings groups accordingly (grid-connected or microgrid-connected). However, with multiple microgrid connections, this concept becomes more challenging, and the direction of the current alone is not sufficient to identify the source of the fault current contribution. ORNL has previously developed adaptive relaying schemes through other DOE-funded research projects that will be evaluated and used as a baseline for this research. The four protection techniques in this study are labeled as follows: (1) Adaptive Current only Protection System (ACPS), Intentional (2) Unbalanced Control for Protection Control (IUCPC), (3) Adaptive Protection System with Communication Controller (APSCC) (4) Adaptive Model-Driven Protective Relay (AMDPR).

Keywords: adaptive relaying, microgrid protection, sequence components, islanding detection

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Authors: Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Y. Rafii

Abstract:

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system can facilitate targeted genome editing in organisms. Dual or single guide RNA (gRNA) can program the Cas9 nuclease to cut target DNA in particular areas; thus, introducing concise mutations either via error-prone non-homologous end-joining repairing or via incorporating foreign DNAs by homologous recombination between donor DNA and target area. In spite of high demand of such promising technology, developing a well-organized procedure in order for reliable mining of potential target sites for gRNAs in large genomic data is still challenging. Hence, we aimed to perform high-throughput detection of target sites by specific PAMs for not only common Streptococcus pyogenes (SpCas9) but also for Neisseria meningitides (NmCas9) CRISPR-Cas systems. Previous research confirmed the successful application of such RNA-guided Cas9 orthologs for effective gene targeting and subsequently genome manipulation. However, Cas9 orthologs need their particular PAM sequence for DNA cleavage activity. Activity levels are based on the sequence of the protospacer and specific combinations of favorable PAM bases. Therefore, based on the specific length and sequence of PAM followed by a constant length of the target site for the two orthogonals of Cas9 protein, we created a reliable procedure to explore possible gRNA sequences. To mine CRISPR target sites, four different searching modes of sgRNA binding to target DNA strand were applied. These searching modes are as follows i) coding strand searching, ii) anti-coding strand searching, iii) both strand searching, and iv) paired-gRNA searching. Finally, a complete list of all potential gRNAs along with their locations, strands, and PAMs sequence orientation can be provided for both SpCas9 as well as another potential Cas9 ortholog (NmCas9). The artificial design of potential gRNAs in a genome of interest can accelerate functional genomic studies. Consequently, the application of such novel genome editing tool (CRISPR/Cas technology) will enhance by presenting increased versatility and efficiency.

Keywords: CRISPR/Cas9 genome editing, gRNA mining, SpCas9, NmCas9

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Authors: M. Michael Gromiha, A. Mary Thangakani, Sandeep Kumar, D. Velmurugan

Abstract:

The main cause of several neurodegenerative diseases such as Alzhemier, Parkinson, and spongiform encephalopathies is formation of amyloid fibrils and plaques in proteins. We have analyzed different sets of proteins and peptides to understand the influence of sequence-based features on protein aggregation process. The comparison of 373 pairs of homologous mesophilic and thermophilic proteins showed that aggregation-prone regions (APRs) are present in both. But, the thermophilic protein monomers show greater ability to ‘stow away’ the APRs in their hydrophobic cores and protect them from solvent exposure. The comparison of amyloid forming and amorphous b-aggregating hexapeptides suggested distinct preferences for specific residues at the six positions as well as all possible combinations of nine residue pairs. The compositions of residues at different positions and residue pairs have been converted into energy potentials and utilized for distinguishing between amyloid forming and amorphous b-aggregating peptides. Our method could correctly identify the amyloid forming peptides at an accuracy of 95-100% in different datasets of peptides.

Keywords: aggregation, amyloids, thermophilic proteins, amino acid residues, machine learning techniques

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Authors: Nkwanyang L. Takem, Christopher M. Agyingi

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

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

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Authors: Juan Manuel Martinez Alvarez, Michele Chiumenti

Abstract:

This work explores the benefit of the thermo-metallurgical simulation to tackle the Wire Laser Additive Manufacturing (WLAM) of low-carbon steel components. The Finite Element Analysis is calibrated by process monitoring via thermal imaging and thermocouples measurements, to study the complex thermo-metallurgical behavior inherent to the WLAM process of low carbon steel parts.A critical aspect is the analysis of the heterogeneity in the resulting microstructure. This heterogeneity depends on both the thermal history and the residual stresses experienced during the WLAM process. Because of low carbon grades are highly sensitive to quenching, a high-gradient microstructure often arises due to the layer-by-layer metal deposition in WLAM. The different phases have been identified by scanning electron microscope. A clear influence of the heterogeneities on the final mechanical performance has been established by the subsequent mechanical characterization. The thermo-metallurgical analysis has been used to determine the actual thermal history and the corresponding thermal gradients during the printing process. The correlation between the thermos-mechanical evolution, the printing parameters and scanning sequence has been established. Therefore, an enhanced printing strategy, including optimized process window has been used to minimize the microstructure heterogeneity at ArcelorMittal.

Keywords: additive manufacturing, numerical simulation, metallurgy, steel

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Authors: Salah R. Al Zaidee, Ali S. Mahdi

Abstract:

Except for simple problems of statically determinate structures, optimum design problems in structural engineering have implicit objective functions where structural analysis and design are essential within each searching loop. With these implicit functions, the structural engineer is usually enforced to write his/her own computer code for analysis, design, and searching for optimum design among many feasible candidates and cannot take advantage of available software for structural analysis, design, and searching for the optimum solution. The meta-model is a regression model used to transform an implicit objective function into objective one and leads in turn to decouple the structural analysis and design processes from the optimum searching process. With the meta-model, well-known software for structural analysis and design can be used in sequence with optimum searching software. In this paper, the meta-model has been used to develop an explicit objective function for plane steel frames subjected to dead, live, and seismic forces. Frame topology is assumed as predefined based on architectural and functional requirements. Columns and beams sections and different connections details are the main design variables in this study. Columns and beams are grouped to reduce the number of design variables and to make the problem similar to that adopted in engineering practice. Data for the implicit objective function have been generated based on analysis and assessment for many design proposals with CSI SAP software. These data have been used later in SPSS software to develop a pure quadratic nonlinear regression model for the explicit objective function. Good correlations with a coefficient, R², in the range from 0.88 to 0.99 have been noted between the original implicit functions and the corresponding explicit functions generated with meta-model.

Keywords: meta-modal, objective function, steel frames, seismic analysis, design

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