Search results for: fixation sequence

Authors: Bin Liu

Abstract:

Prokaryotic promoter, consisted of two short DNA sequences located at in -35 and -10 positions, is responsible for controlling the initiation and expression of gene expression. Different types of promoters have different functions, and their consensus sequences are similar. In addition, their consensus sequences may be different for the same type of promoter, which poses difficulties for promoter identification. Unfortunately, all existing computational methods treat promoter identification as a binary classification task and can only identify whether a query sequence belongs to a specific promoter type. It is desired to develop computational methods for effectively identifying promoters and their types. Here, a two-layer predictor is proposed to try to deal with the problem. The first layer is designed to predict whether a given sequence is a promoter and the second layer predicts the type of promoter that is judged as a promoter. Meanwhile, we also analyze the importance of feature and sequence conversation in two aspects: promoter identification and promoter type identification. To the best knowledge of ours, it is the first computational predictor to detect promoters and their types.

Keywords: promoter, promoter type, random forest, sequence information

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Authors: C. Baidada, M. H. Abidi, A. Jakimi, E. H. El Kinani

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Reverse engineering has become a viable method to measure an existing system and reconstruct the necessary model from tis original. The reverse engineering of behavioral models consists in extracting high-level models that help understand the behavior of existing software systems. In this paper, we propose an approach for the reverse engineering of sequence diagrams from the analysis of execution traces produced dynamically by an object-oriented application using petri nets. Our methods show that this approach can produce state diagrams in reasonable time and suggest that these diagrams are helpful in understanding the behavior of the underlying application. Finally we will discuss approachs and tools that are needed in the process of reverse engineering UML behavior. This work is a substantial step towards providing high-quality methodology for effectiveand efficient reverse engineering of sequence diagram.

Keywords: reverse engineering, UML behavior, sequence diagram, execution traces, petri nets

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Authors: Marian Dragomir, Alin Dragomir

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In the paper, two fault location algorithms are presented for transmission lines which use the line parameters to estimate the distance to the fault. The first algorithm uses only the measurements from one end of the line and the positive and zero sequence parameters of the line, while the second one uses the measurements from both ends of the line and only the positive sequence parameters of the line. The algorithms were tested using a transmission grid transposed in MATLAB. In a first stage it was established a fault location base line, where the algorithms mentioned above estimate the fault locations using the exact line parameters. After that, the positive and zero sequence resistance and reactance of the line were calculated again for different ground resistivity values and then the fault locations were estimated again in order to compare the results with the base line results. The results show that the algorithm which uses the zero sequence impedance of the line is the most sensitive to the line parameters modifications. The other algorithm is less sensitive to the line parameters modification.

Keywords: estimation algorithms, fault location, line parameters, simulation tool

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Authors: Muhammad Tarmidzi, Reza M. G. Gani, Andri Luthfi

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The purpose of this study is to identify rock zone containing hydrocarbons with calculating rock property includes volume shale, total porosity, effective porosity and water saturation. Identification method rock property based on GR log, resistivity log, neutron log and density rock. Zoning is based on sequence stratigraphic markers that are sequence boundary (SB), transgressive surface (TS) and flooding surface (FS) which correlating ten well log in blok “M”. The results of sequence stratigraphic correlation consist of eight zone that are two LST zone, three TST zone and three HST zone. The result of rock property calculation in each zone is showing two LST zone containing hydrocarbons. LST-1 zone has average volume shale (Vsh) 25%, average total porosity (PHIT) 14%, average effective porosity (PHIE) 11% and average water saturation 0,83. LST-2 zone has average volume shale (Vsh) 19%, average total porosity (PHIT) 21%, average effective porosity (PHIE) 17% and average water saturation 0,82.

Keywords: hydrocarbons zone, petrophysic, rock property, sequence stratigraphic

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Authors: Lamiche Chaabane

Abstract:

In this study, a new method for solving sequence alignment problem is proposed, which is named ITS (Improved Tabu Search). This algorithm is based on the classical Tabu Search (TS). ITS is implemented in order to obtain results of multiple sequence alignment. Several ideas concerning neighbourhood generation, move selection mechanisms and intensification/diversification strategies for our proposed ITS is investigated. ITS have generated high-quality results in terms of measure of scores in comparison with the classical TS and simple iterative search algorithm.

Keywords: multiple sequence alignment, tabu search, improved tabu search, neighbourhood generation, selection mechanisms

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Authors: Ernesto Linan, Linda Cruz, Lucero Becerra

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In this paper, a new hybridized algorithm based on Chemical Reaction Optimization and Simulated Annealing is proposed to solve the alignment sequence Problem. The Chemical Reaction Optimization is a population-based meta-heuristic algorithm based on the principles of a chemical reaction. Simulated Annealing is applied to solve a large number of combinatorial optimization problems of general-purpose. In this paper, we propose hybridization between Chemical Reaction Optimization algorithm and Simulated Annealing in order to solve the Sequence Alignment Problem. An initial population of molecules is defined at beginning of the proposed algorithm, where each molecule represents a sequence alignment problem. In order to simulate inter-molecule collisions, the process of Chemical Reaction is placed inside the Metropolis Cycle at certain values of temperature. Inside this cycle, change of molecules is done due to collisions; some molecules are accepted by applying Boltzmann probability. The results with the hybrid scheme are better than the results obtained separately.

Keywords: chemical reaction optimization, sequence alignment problem, simulated annealing algorithm, metaheuristics

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Authors: Abdelfatah Elsenosy, Mahmoud Ebrahim

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Background: Distal radius fractures are commonly encountered in orthopedic practice, especially in elderly patients. A number of clinical papers have supported the idea that anatomic restoration of the distal end of the radius is essential to gain superior results. Aim and objectives: The aim of the study is to systematically review the literature for the management of distal end radius in elderly persons (conservative treatment versus percutaneous wire fixation) as regards radiological and functional outcomes. Subjects and methods: Studies were identified from the Medline, Cochrane, EMBASE, and Google Scholar databases were searched until 2019 using combinations of the following search terms: distal radius fracture, conservative treatment, non-operative treatment, and nonsurgical treatment, surgical treatment, operative, elderly, and older. Reference lists of relevant studies were manually searched. Results: There was no statistical significance difference between CI and PKF groups’ frequency of complication in all of the selected studies. Based on the results, we recommend more analysis regarding every parameter of the radiographic and functional results and specific complications related to each fixation need to be accomplished, which requires more Randomized controlled trials (RCTs) with high quality. Conclusion: Surgical treatment seems to be more effective distal radius fracture compared with conservative treatment when the radiographic outcomes were analyzed, and no significant differences were detected in the functional outcomes and complication rate.

Keywords: radius, fracture, surgical, RCTs, conservative, radiographic, outcomes, orthopedic

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Authors: Jisoo Kim, Min Su Lee, Sunmook Lee

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Durability assessment of nanocomposite-based bone fixation device was performed by flexural fatigue tests, for which the changes in the life cycles of nanocomposite samples synthesized by blending bioabsorbable polymer (PLGA) and ceramic nanoparticles (β-TCP) with different ratios were monitored. The nanocomposite samples were kept in a constant temperature/humidity chamber at 37°C/50%RH for varied incubation periods for the degradation of nanocomposite samples under the temperature/humidity stress. It was found that the life cycles were increasing as the incubation time in the chamber were increasing in the initial stage irrespective of sample compositions, which was due to the annealing effect of the polymer. However, the life cycle was getting shorter as the incubation time increased afterward, which was due to the overall degradation of nanocomposites. It was found that the life cycle of the nanocomposite sample with high ceramic content was shorter than the one with low ceramic content, which was attributed to the increased brittleness of the composite with high ceramic content. The changes in chemical properties were also monitored by FT-IR, which indicated that the degradation of the biodegradable polymer could be confirmed by the increased intensities of carboxyl groups and hydroxyl groups since the hydrolysis of ester bonds connecting two successive monomers yielded carboxyl end groups and hydroxyl groups.

Keywords: bioabsorbable polymer, bone fixation device, ceramic nanoparticles, durability assessment, fatigue test

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Authors: Nishal Parbhoo, John B. Dewar, Samantha Gildenhuys

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Rotavirus is the major cause of severe gastroenteritis worldwide in children aged 5 and younger. Death rates are high particularly in developing countries. The mature rotavirus is a non-enveloped triple-layered nucleocapsid containing 11 double-stranded RNA segments. Here a global view on the sequence and structure of the three main capsid proteins, VP7, VP6, and VP2 is taken by generating a consensus sequence for each of these rotavirus proteins, for each species obtained from published data of representative rotavirus genotypes from across the world and across species. The degree of conservation between species was represented on homology models for each of the proteins. VP7 shows the highest level of variation with 14 - 45 amino acids showing conservation of less than 60%. These changes are localized to the outer surface which is exposed to antibodies alluding to a possible mechanism in evading the immune system. The middle layer, VP6 shows lower variability with only 14-32 sites having lower than 70% conservation. The inner structural layer made up of VP2 showed the lowest variability with only 1-16 sites having less than 70% conservation across species. The results correlate with proteins’ multiple structural roles. Although the nucleotide sequences vary due to an error-prone replication and lack of proofreading, the corresponding amino acid sequence of VP2, 6 and 7 remains conserved. Sequence conservation maintained for the virus results in stable protein structures, fit for function. This can be exploited in drug design, molecular studies and biotechnological applications.

Keywords: amino acid sequence conservation, capsid protein, protein structure, vaccine candidate

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Authors: Adam Rosiński

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This paper discusses an experiment conducted with two groups of participants, composed of musicians and non-musicians, in order to investigate the impact of the speed of a sound sequence and the order of sounds on the grouping of sounds into sequences of six tones. Significant differences were observed between musicians and non-musicians with respect to the threshold sequence speed at which the sequence was split into two streams. The differences in the results for the two groups suggest that the musical education of the participating listeners may be a vital factor. The criterion of musical education should be taken into account during experiments so that the results obtained are reliable, uniform, and free from interpretive errors.

Keywords: auditory scene analysis, education, hearing, psychoacoustics

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Authors: T. Padma, Jayashree S. Pillai

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Random entities are an essential component in any cryptographic application. The suitability of a number theory based novel pseudorandom sequence called Pseudorandom Partial Quotient Sequence (PPQS) generated from the continued fraction expansion of irrational numbers, in cryptographic applications, is analyzed in this paper. An approach to build the algorithm around a hard mathematical problem has been considered. The PQ sequence is tested for randomness and its suitability as a cryptographic key by performing randomness analysis, key sensitivity and key space analysis, precision analysis and evaluating the correlation properties is established.

Keywords: pseudorandom sequences, key sensitivity, correlation, security analysis, randomness analysis, sensitivity analysis

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Authors: Hongmin Deng, Qionghua Wang

Abstract:

A modified two dimensional (2D) logistic map based on cross feedback control is proposed. This 2D map exhibits more random chaotic dynamical properties than the classic one dimensional (1D) logistic map in the statistical characteristics analysis. So it is utilized as the pseudo-random (PN) sequence generator, where the obtained real-valued PN sequence is quantized at first, then applied to radio frequency identification (RFID) communication system in this paper. This system is experimentally validated on a cortex-M₀ development board, which shows the effectiveness in key generation, the size of key space and security. At last, further cryptanalysis is studied through the test suite in the National Institute of Standards and Technology (NIST).

Keywords: chaos encryption, logistic map, pseudo-random sequence, RFID

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Authors: Jung Ho Yang, Yong Soo Kim

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Electrical units are operated by electrical and electronic components. An environmental test sequence is useful for testing electrical units to reduce reliability issues. This study introduces test sequence guidelines based on relevant principles and considerations for electronic testing according to international standard IEC-60068-1 and the United States military standard MIL-STD-810G. Then, test sequences were proposed based on the descriptions for each test. Finally, General Motors (GM) specification GMW3172 was interpreted and compared to IEC-60068-1 and MIL-STD-810G.

Keywords: reliability, environmental test sequence, electrical units, IEC 60068-1, MIL-STD-810G

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Authors: G. Tamilpavai, C. Vishnuppriya

Abstract:

Bioinformatics is an active research area which combines biological matter as well as computer science research. The longest common subsequence (LCSS) is one of the major challenges in various bioinformatics applications. The computation of the LCSS plays a vital role in biomedicine and also it is an essential task in DNA sequence analysis in genetics. It includes wide range of disease diagnosing steps. The objective of this proposed system is to find the longest common subsequence which presents in a normal and various disease affected human DNA sequence using Self Organizing Map (SOM) and LCSS. The human DNA sequence is collected from National Center for Biotechnology Information (NCBI) database. Initially, the human DNA sequence is separated as k-mer using k-mer separation rule. Mean and median values are calculated from each separated k-mer. These calculated values are fed as input to the Self Organizing Map for the purpose of clustering. Then obtained clusters are given to the Longest Common Sub Sequence (LCSS) algorithm for finding common subsequence which presents in every clusters. It returns nx(n-1)/2 subsequence for each cluster where n is number of k-mer in a specific cluster. Experimental outcomes of this proposed system produce the possible number of longest common subsequence of normal and disease affected DNA data. Thus the proposed system will be a good initiative aid for finding disease causing sequence. Finally, performance analysis is carried out for different DNA sequences. The obtained values show that the retrieval of LCSS is done in a shorter time than the existing system.

Keywords: clustering, k-mers, longest common subsequence, SOM

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Authors: Kyung Jin Kim, Jiwon Kwak, Jae-Hoon Lee, Soo Suk Lee

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We describe an innovative method for highly specific detection of miRNAs using a specially modified method of poly(A) adaptor RT-qPCR. We use uniquely designed specific extension sequence, which plays important role in providing an opportunity to affect high specificity of miRNA detection. This method involves two steps of reactions as like previously reported and which are poly(A) tailing and reverse-transcription followed by real-time PCR. Firstly, miRNAs are extended by a poly(A) tailing reaction and then converted into cDNA. Here, we remarkably reduced the reaction time by the application of short length of poly(T) adaptor. Next, cDNA is hybridized to the 3’-end of a specific extension sequence which contains miRNA sequence and results in producing a novel PCR template. Thereafter, the SYBR Green-based RT-qPCR progresses with a universal poly(T) adaptor forward primer and a universal reverse primer. The target miRNA, miR-106b in human brain total RNA, could be detected quantitatively in the range of seven orders of magnitude, which demonstrate that the assay displays a dynamic range of at least 7 logs. In addition, the better specificity of this novel extension-based assay against well known poly(A) tailing method for miRNA detection was confirmed by melt curve analysis of real-time PCR product, clear gel electrophoresis and sequence chromatogram images of amplified DNAs.

Keywords: microRNA(miRNA), specific extension sequence, RT-qPCR, poly(A) tailing assay, reverse transcription

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Authors: Vidhu Mitha Goutham, Ruma Mukherjee

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The low availability of well-trained, unlimited, dynamic-access models for specific languages makes it hard for corporate users to adopt quick translation techniques and incorporate them into product solutions. As translation tasks increasingly require a dynamic sequence learning curve; stable, cost-free opensource models are scarce. We survey and compare current translation techniques and propose a modified sequence to sequence model repurposed with attention techniques. Sequence learning using an encoder-decoder model is now paving the path for higher precision levels in translation. Using a Convolutional Neural Network (CNN) encoder and a Recurrent Neural Network (RNN) decoder background, we use Fairseq tools to produce an end-to-end bilingually trained Spanish-English machine translation model including source language detection. We acquire competitive results using a duo-lingo-corpus trained model to provide for prospective, ready-made plug-in use for compound sentences and document translations. Our model serves a decent system for large, organizational data translation needs. While acknowledging its shortcomings and future scope, it also identifies itself as a well-optimized deep neural network model and solution.

Keywords: attention, encoder-decoder, Fairseq, Seq2Seq, Spanish, translation

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Authors: Nahed Al-Hajeri

Abstract:

There are several reasons which lead to a delay in project completion, out of all, one main reason is the delay in deliverable processing, i.e. submission and review of documents. Most of the project cycles start with a list of deliverables but without a sequence of submission of the same, means without a direction to move, leading to overlapping of activities and more interdependencies. Hence Project Design Deliverables (PDD) is developed as a solution to Organize Transmittals (Documents/Drawings) received from contractors/consultants during different phases of an EPC (Engineering, Procurement, and Construction) projects, which gives proper direction to the stakeholders from the beginning, to reduce inter-discipline dependency, avoid overlapping of activities, provide a list of deliverables, sequence of activities, etc. PDD attempts to provide a list and sequencing of the engineering documents/drawings required during different phases of a Project which will benefit both client and Contractor in performing planned activities through timely submission and review of deliverables. This helps in ensuring improved quality and completion of Project in time. The successful implementation begins with a detailed understanding the specific challenges and requirements of the project. PDD will help to learn about vendor document submissions including general workflow, sequence and monitor the submission and review of the deliverables from the early stages of Project. This will provide an overview for the Submission of deliverables by the concerned during the projects in proper sequence. The goal of PDD is also to hold responsible and accountability of all stakeholders during complete project cycle. We believe that successful implementation of PDD with a detailed list of documents and their sequence will help organizations to achieve the project target.

Keywords: EPC (Engineering, Procurement, and Construction), project design deliverables (PDD), econometrics sciences, management sciences

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Authors: Anthony John Walker, Glen Bright

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The challenge faced by manufactures, when producing custom products, is that each product needs exact components. This can cause work-in-process instability due to component matching constraints imposed on assembly cells. Clearing type flow control policies have been used extensively in mediating server access between multiple arrival processes. Although the stability and performance of clearing policies has been well formulated and studied in the literature, the growth in arrival to departure sequence disorder for each arriving job, across a serving resource, is still an area for further analysis. In this paper, a closed form industrial model has been formulated that characterizes arrival-to-departure sequence disorder through stable manufacturing systems under clearing type flow control policy. Specifically addressed are the effects of sequence disorder imposed on a downstream assembly cell in terms of work-in-process instability induced through component matching constraints. Results from a simulated manufacturing system show that steady state average sequence disorder in parallel upstream processing cells can be balanced in order to decrease downstream assembly system instability. Simulation results also show that the closed form model accurately describes the growth and limiting behavior of average sequence disorder between parts arriving and departing from a manufacturing system flow controlled via clearing policy.

Keywords: assembly system constraint, custom products, discrete sequence disorder, flow control

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Authors: Himanshu Kumar Gupta

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The Jaisalmer Basin is one of the parts of the Rajasthan basin in northwestern India. The presence of five major unconformities/hiatuses of varying span i.e. at the top of Archean basement, Cambrian, Jurassic, Cretaceous, and Eocene have created the foundation for constructing a sequence stratigraphic framework. Based on basin formative tectonic events and their impact on sedimentation processes three first-order sequences have been identified in Rajasthan Basin. These are Proterozoic-Early Cambrian rift sequence, Permian to Middle-Late Eocene shelf sequence and Pleistocene - Recent sequence related to Himalayan Orogeny. The Permian to Middle Eocene I order sequence is further subdivided into three-second order sequences i.e. Permian to Late Jurassic II order sequence, Early to Late Cretaceous II order sequence and Paleocene to Middle-Late Eocene II order sequence. In this study, Late Jurassic to Early Cretaceous sequence was identified and log-based interpretation of smaller order T-R cycles have been carried out. A log profile from eastern margin to western margin (up to Shahgarh depression) has been taken. The depositional environment penetrated by the wells interpreted from log signatures gave three major facies association. The blocky and coarsening upward (funnel shape), the blocky and fining upward (bell shape) and the erratic (zig-zag) facies representing distributary mouth bar, distributary channel and marine mud facies respectively. Late Jurassic Formation (Baisakhi-Bhadasar) and Early Cretaceous Formation (Pariwar) shows a lesser number of T-R cycles in shallower and higher number of T-R cycles in deeper bathymetry. Shallowest well has 3 T-R cycles in Baisakhi-Bhadasar and 2 T-R cycles in Pariwar, whereas deeper well has 4 T-R cycles in Baisakhi-Bhadasar and 8 T-R cycles in Pariwar Formation. The Maximum Flooding surfaces observed from the stratigraphy analysis indicate major shale break (high shale content). The study area is dominated by the alternation of shale and sand lithologies, which occurs in an approximate ratio of 70:30. A seismo-geological cross section has been prepared to understand the stratigraphic thickness variation and structural disposition of the strata. The formations are quite thick to the west, the thickness of which reduces as we traverse towards the east. The folded and the faulted strata indicated the compressional tectonics followed by the extensional tectonics. Our interpretation is supported with seismic up to second order sequence indicates - Late Jurassic sequence is a Highstand Systems Tract (Baisakhi - Bhadasar formations), and the Early Cretaceous sequence is Regressive to Lowstand System Tract (Pariwar Formation).

Keywords: Jaisalmer Basin, sequence stratigraphy, system tract, T-R cycle

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Authors: Michele Sinico

Abstract:

The psychological present has an actual extension. When a sequence of instantaneous stimuli falls in this short interval of time, observers perceive a compresence of events in succession and the temporal order depends on the qualitative relationships between the perceptual properties of the events. Two experiments were carried out to study the influence of perceptual grouping, with and without temporal displacement, on the duration of auditory sequences. The psychophysical method of adjustment was adopted. The first experiment investigated the effect of temporal displacement of a white noise on sequence duration. The second experiment investigated the effect of temporal displacement, along the pitch dimension, on temporal shortening of sequence. The results suggest that the temporal order of sounds, in the case of temporal displacement, is organized along the pitch dimension.

Keywords: time perception, perceptual present, temporal displacement, Gestalt laws of perceptual organization

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Authors: Mmatladi D. Mnguni, Mustapha Mohammed, George Y. Mahama, Alhassan L. Abdulai, Felix D. Dakora

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Industrial-based nitrogen (N) fertilizers are justifiably credited for the current state of food production across the globe, but their continued use is not sustainable and has an adverse effect on the environment. The search for greener and sustainable technologies has led to an increase in exploiting biological systems such as legumes and organic amendments for plant growth promotion in cropping systems. Although the benefits of legume rotation with cereal crops have been documented, the full benefits of soybean-sorghum rotation systems have not been properly evaluated in Africa. This study explored the benefits of soybean-sorghum rotation through assessing N₂ fixation and water-use efficiency of soybean in rotation with sorghum with and without organic and inorganic amendments. The field trials were conducted from 2017 to 2020. Sorghum was grown on plots previously cultivated to soybean and vice versa. The succeeding sorghum crop received fertilizer amendments [organic fertilizer (5 tons/ha as poultry litter, OF); inorganic fertilizer (80N-60P-60K) IF; organic + inorganic fertilizer (OF+IF); half organic + inorganic fertilizer (HIF+OF); organic + half inorganic fertilizer (OF+HIF); half organic + half inorganic (HOF+HIF) and control] and was arranged in a randomized complete block design. The soybean crop succeeding fertilized sorghum received a blanket application of triple superphosphate at 26 kg P ha⁻¹. Nitrogen fixation and water-use efficiency were respectively assessed at the flowering stage using the ¹⁵N and ¹³C natural abundance techniques. The results showed that the shoot dry matter of soybean plants supplied with HOF+HIF was much higher (43.20 g plant-1), followed by OF+HIF (36.45 g plant⁻¹), and HOF+IF (33.50 g plant⁻¹). Shoot N concentration ranged from 1.60 to 1.66%, and total N content from 339 to 691 mg N plant⁻¹. The δ¹⁵N values of soybean shoots ranged from -1.17‰ to -0.64‰, with plants growing on plots previously treated to HOF+HIF exhibiting much higher δ¹⁵N values, and hence lower percent N derived from N₂ fixation (%Ndfa). Shoot %Ndfa values varied from 70 to 82%. The high %Ndfa values obtained in this study suggest that the previous year’s organic and inorganic fertilizer amendments to sorghum did not inhibit N₂ fixation in the following soybean crop. The amount of N-fixed by soybean ranged from 106 to 197 kg N ha⁻¹. The treatments showed marked variations in carbon (C) content, with HOF+HIF treatment recording the highest C content. Although water-use efficiency varied from -29.32‰ to -27.85‰, shoot water-use efficiency, C concentration, and C:N ratio were not altered by previous fertilizer application to sorghum. This study provides strong evidence that previous HOF+HIF sorghum residues can enhance N nutrition and water-use efficiency in nodulated soybean.

Keywords: ¹³C and ¹⁵N natural abundance, N-fixed, organic and inorganic fertilizer amendments, shoot %Ndfa

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Authors: Sireesha Tamada, Debraj Bhattacharjee, Pranab K. Dan, Prabha Bhola

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The most important component in an automotive transmission system is the gearbox which controls the speed of the vehicle. In an automatic transmission, the right positioning of actuators ensures efficient transmission mechanism embodiment, wherein the challenge lies in formulating the number of actuators associated with modelling a gearbox. Data with respect to actuation and gear shifting sequence has been retrieved from the available literature, including patent documents, and has been used in this proposed heuristics based methodology for modelling actuation sequence in a gear box. This paper presents a methodological approach in designing a gearbox for the purpose of obtaining an optimal shifting sequence. The computational model considers factors namely, the number of stages and gear teeth as input parameters since these two are the determinants of the gear ratios in an epicyclic gear train. The proposed transmission schematic or stick diagram aids in developing the gearbox layout design. The number of iterations and development time required to design a gearbox layout is reduced by using this approach.

Keywords: automatic transmission, gear-shifting, multi-stage planetary gearbox, rank ordered clustering

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Authors: S. Haider, B. Bhushan

Abstract:

Eye Gaze behaviour of individuals with and without intellectual disability are investigated in an eye tracking study in terms of sensitivity to Nonaccidental (NAPs) and Metric (MPs) shape properties. Total fixation time is used as an indirect measure of attention allocation. Studies have found Mean reaction times for non accidental properties (NAPs) to be shorter than for metric (MPs) when the MP and NAP differences were equalized. METHODS: Twenty-five individuals with intellectual disability (mild and moderate level of Mental Retardation) and twenty-seven normal individuals were compared on mean total fixation duration, accuracy level and mean reaction time for mild NAPs, extreme NAPs and metric properties of images. 2D images of cylinders were adapted and made into forced choice match-to-sample tasks. Tobii TX300 Eye Tracker was used to record total fixation duration and data obtained from the Areas of Interest (AOI). Variable trial duration (total reaction time of each participant) and fixed trail duration (data taken at each second from one to fifteen seconds) data were used for analyses. Both groups did not differ in terms of fixation times (fixed as well as variable) across any of the three image manipulations but differed in terms of reaction time and accuracy. Normal individuals had longer reaction time compared to individuals with intellectual disability across all types of images. Both the groups differed significantly on accuracy measure across all image types. Normal individuals performed better across all three types of images. Mild NAPs vs. Metric differences: There was significant difference between mild NAPs and metric properties of images in terms of reaction times. Mild NAPs images had significantly longer reaction time compared to metric for normal individuals but this difference was not found for individuals with intellectual disability. Mild NAPs images had significantly better accuracy level compared to metric for both the groups. In conclusion, type of image manipulations did not result in differences in attention allocation for individuals with and without intellectual disability. Mild Nonaccidental properties facilitate better accuracy level compared to metric in both the groups but this advantage is seen only for normal group in terms of mean reaction time.

Keywords: eye gaze fixations, eye movements, intellectual disability, stimulus properties

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Authors: Raphael C. Zero, Thiago A. S. S. Rocha, Marita V. Cardozo, Caio C. C. Santos, Alisson D. S. Fechis, Antonio C. Shimano, FabríCio S. Oliveira

Abstract:

Biomechanical analysis is an important factor in tissue studies. The objective of this study was to determine the feasibility of a new anatomical technique and quantify the changes in skin and the jejunum resistance of cats’ corpses throughout the process. Eight adult cat cadavers were used. For every kilogram of weight, 120ml of fixative solution (95% 96GL ethyl alcohol and 5% pure glycerin) was applied via the external common carotid artery. Next, the carcasses were placed in a container with 96 GL ethyl alcohol for 60 days. After fixing, all carcasses were preserved in a 30% sodium chloride solution for 60 days. Before fixation, control samples were collected from fresh cadavers and after fixation, three skin and jejunum fragments from each cadaver were tested monthly for strength and displacement until complete rupture in a universal testing machine. All results were analyzed by F-test (P <0.05). In the jejunum, the force required to rupture the fresh samples and the samples fixed in alcohol for 60 days was 31.27±19.14N and 29.25±11.69N, respectively. For the samples preserved in the sodium chloride solution for 30 and 60 days, the strength was 26.17±16.18N and 30.57±13.77N, respectively. In relation to the displacement required for the rupture of the samples, the values of fresh specimens and those fixed in alcohol for 60 days was 2.79±0.73mm and 2.80±1.13mm, respectively. For the samples preserved for 30 and 60 days with sodium chloride solution, the displacement was 2.53±1.03mm and 2.83±1.27mm, respectively. There was no statistical difference between the samples (P=0.68 with respect to strength, and P=0.75 with respect to displacement). In the skin, the force needed to rupture the fresh samples and the samples fixed for 60 days in alcohol was 223.86±131.5N and 211.86±137.53N respectively. For the samples preserved in sodium chloride solution for 30 and 60 days, the force was 227.73±129.06 and 224.78±143.83N, respectively. In relation to the displacement required for the rupture of the samples, the values of fresh specimens and those fixed in alcohol for 60 days were 3.67±1.03mm and 4.11±0.87mm, respectively. For the samples preserved for 30 and 60 days with sodium chloride solution, the displacement was 4.21±0.93mm and 3.93±0.71mm, respectively. There was no statistical difference between the samples (P=0.65 with respect to strength, and P=0.98 with respect to displacement). The resistance of the skin and intestines of the cat carcasses suffered little change when subjected to alcohol fixation and preservation in sodium chloride solution, each for 60 days, which is promising for use in surgery training. All experimental procedures were approved by the Municipal Legal Department (protocol 02.2014.000027-1). The project was funded by FAPESP (protocol 2015-08259-9).

Keywords: anatomy, conservation, fixation, small animal

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Authors: Muhammad Umair, Tanveer Hussain, Khubab Shaker, Yasir Nawab, Muhammad Maqsood, Madeha Jabbar

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The term comfort is defined as 'the absence of unpleasantness or discomfort' or 'a neutral state compared to the more active state'. Comfort mainly is of three types: sensorial (tactile) comfort, psychological comfort and thermo-physiological comfort. Thermophysiological comfort is determined by the air permeability and moisture management properties of the garment. The aim of this study was to investigate the effect of weave structure and picking sequence on the comfort properties of woven fabrics. Six woven fabrics with two different weave structures i.e. 1/1 plain and 3/1 twill and three different picking sequences: (SPI, DPI, 3PI) were taken as input variables whereas air permeability, wetting time, wicking behavior and overall moisture management capability (OMMC) of fabrics were taken as response variables and a comparison is made of the effect of weave structure and picking sequence on the response variables. It was found that fabrics woven in twill weave design and with simultaneous triple pick insertion (3PI) give significantly better air permeability, shorter wetting time and better water spreading rate, as compared to plain woven fabrics and those with double pick insertion (DPI) or single pick insertion (SPI). It could be concluded that the thermophysiological comfort of woven fabrics may be significantly improved simply by selecting a suitable weave design and picking sequence.

Keywords: air permeability, picking sequence, thermophysiological comfort, weave design

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Authors: Sameer Gupta, Prant Gupta

Abstract:

Context: Fractures in the distal humerus are complex and challenging injuries for orthopaedic surgeons that can be effectively treated with open reduction and internal fixation. Aims: The study analyses clinical outcomes in patients with intra-articular distal humerus fractures (AO type 13 C3 excluded) treated using a different method of fixation ( LCPMS). Subject and Methods: A study was performed, and the author's personal experiences were reported. Thirty patients were treated using an intercondylar screw with lateral column plating and percutaneous medial column screw fixation. Detailed analysis was done for functional outcomes (average arc of motion, union rate, and complications). Statistical Analysis Used: SPSS software version 22.0 was used for statistical analysis. Results: In our study, at the end of 6 months, Overall good to excellent results were achieved in 28 patients out of 30 after analysis on the basis of MEP score. The majority of patients regained full arc of motion, achieved fracture union without any major complications, and were able to perform almost all activities of daily living (which required good elbow joint movements and functions). Conclusion: We concluded that this novel method provides adequate stability and anatomical reconstruction with an early union rate observed at the end of 6 months. Excellent functional outcome was observed in almost all the patients because of less operating time and initiation of early physiotherapy, as most of the patients experienced mild nature of pain post-surgery.

Keywords: intra arricular distal humerus fracture, percutaneous medial screw, lateral column plate, arc of motion

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Authors: Mudawamah Mudawamah, Muhammad Z. Fadli, Gatot Ciptadi, Aulanni’am

Abstract:

Canary breeders have spread throughout Indonesian regions for the low-middle society and become an income source for them. The interesting phenomenon of the canary market is the feather colours become one of determining factor for the price. The advantages of this research were contributed to the molecular database as a base of selection and mating for the Indonesia canary breeder. The research method was experiment with the genome obtained from canary blood isolation. The genome did the PCR amplification with PMEL marker followed by sequencing. Canaries were used 24 heads of light and dark colour feathers. Research data analyses used BioEdit and Network 4.6.0.0 software. The results showed that all samples were amplification with PMEL gene with 500 bp fragment length. In base sequence of 40 was found Cytosine(C) in the light colour canaries, while the dark colour canaries was obtained Thymine (T) in same base sequence. Sequence results had 286-415 bp fragment and 10 haplotypes. The conclusions were the PMEL gene (gene of white pigment) was likely to be used PMEL gene to detect molecular genetic variation of dark and light colour feather.

Keywords: canary, haplotype, PMEL, sequence

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Authors: Imana Shahrin Tania, Mohammad Ali

Abstract:

The present study reports the synthesis, characterization and application of nano-sized zinc-oxide (ZnO) particles on a cotton fabric surface. The aim of the investigations is to impart the antimicrobial activity on textile cloth. Nanoparticle is synthesized by wet chemical method from zinc sulphate and sodium hydroxide. SEM (scanning electron micrograph) images are taken to demonstrate the surface morphology of nanoparticles. XRD analysis is done to determine the crystal size of the nanoparticle. With the conformation of nanoformation, the cotton woven fabric is treated with ZnO nanoparticle by mechanical thermo-fixation (pad-dry-cure) technique. To increase the wash durability of nano treated fabric, an acrylic binder is used as a fixing agent. The treated fabric shows up to 90% bacterial reduction for S. aureus (Staphylococcus aureus) and 87% for E. coli (Escherichia coli) which is appreciable for bacteria protective clothing.

Keywords: nanoparticle, zinc oxide, cotton fabric, antibacterial activity, binder

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

Procedia PDF Downloads 133

Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

Procedia PDF Downloads 122