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Article
Publication date: 28 March 2008

Chengpeng Bi

Multiple sequence alignment (MSA) is one of essential bioinformatics methods for decoding cis‐regulatory elements in gene regulation, predicting structure and function of…

Abstract

Purpose

Multiple sequence alignment (MSA) is one of essential bioinformatics methods for decoding cis‐regulatory elements in gene regulation, predicting structure and function of proteins and RNAs, reconstructing phylogenetic tree, and other common tasks in biomolecular sequence analysis. The purpose of this paper is to describe briefly the basic concepts and formulations of gapped MSA and un‐gapped motif discovery approaches, and then review computational intelligence (CI) applications in MSA and motif‐finding problems.

Design/methodology/approach

This paper performs exhaustive literature review on the MSA and motif discovery using CI techniques.

Findings

Although CI‐based MSA algorithms were developed nearly a decade ago, most recent CI effort seems attempted to tackle the NP‐complete motif discovery problem. Applications of various CI techniques to solve motif discovery problem, including neural networks, self‐organizing map, genetic algorithms, swarm intelligence and combinations thereof, are surveyed. Finally, the paper concludes with discussion and perspective.

Practical implications

The algorithms and software discussed in this paper can be used to align DNA, RNA and protein sequences, discover motifs, predict functions and structures of protein and RNA sequences, and estimate phylogenetic tree.

Originality/value

The paper contributes to the first comprehensive survey of CI techniques that are applied to MSA and motif discovery.

Details

International Journal of Intelligent Computing and Cybernetics, vol. 1 no. 1
Type: Research Article
ISSN: 1756-378X

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Article
Publication date: 17 June 2019

Wan Abd Al Qadr Imad Wan-Mohtar, Anita Klaus, Acga Cheng, Shardana Aiga Salis and Sarina Abdul Halim-Lim

The purpose of this paper is to identify the strain of oyster mushroom (OM) Pleurotus sapidus cultivated in a local (commercial) farm, and to generate a total quality…

Abstract

Purpose

The purpose of this paper is to identify the strain of oyster mushroom (OM) Pleurotus sapidus cultivated in a local (commercial) farm, and to generate a total quality index (TQI) on the strain using different modified atmosphere packaging (MAP) gas mixtures.

Design/methodology/approach

A phylogenetic tree was constructed using the MEGA software to identify the specific strain of P. sapidus grown in a local farm. The effects of MAP on fresh fruiting bodies of the identified strain were determined under three conditions: high carbon dioxide packaging (HCP: 20 per cent CO2, 15 per cent O2), low carbon dioxide packaging (LCP: 2 per cent CO2, 30 per cent O2) and high nitrogen packaging (HNP: 85 per cent N2, 15 per cent O2). All samples were stored at 4 oC for up to ten days, and subjected to total phenolic content (TPC), colour retention (CR) and sensory analysis. Quality parameters such as chewiness and odour were used to obtain the TQI.

Findings

From the phylogenetic analysis, a new strain (P. sapidus strain QDR) with 99 per cent similarity to P. sapidus was identified. Among the three MAP treatments, HCP recorded the highest TPC (2.85 mg GAE/g) and CR (60.36) after ten days, although only its CR was significantly different (p<0.05) from the control. Feedback from 30 sensory panellists indicated that both HCP and LCP were generally more effective in retaining the colour–odour of OM. The optimum TQI for HCP was obtained based on the observed parameters, which is useful for the large-scale packaging of OM.

Originality/value

Scientific evidence has revealed that packaging trend for commercially grown OM affects consumer’s acceptance.

Details

British Food Journal, vol. 121 no. 8
Type: Research Article
ISSN: 0007-070X

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Management for Scientists
Type: Book
ISBN: 978-1-78769-203-9

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Book part
Publication date: 19 March 2019

Abstract

Details

Management for Scientists
Type: Book
ISBN: 978-1-78769-203-9

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Article
Publication date: 22 October 2018

Xu Jiang and Liu Yanbin

Based on the significance of ectomycorrhizae (ECM) and increased publication activity on this subject, it was decided to carry out a bibliometric analysis of scientific…

Abstract

Purpose

Based on the significance of ectomycorrhizae (ECM) and increased publication activity on this subject, it was decided to carry out a bibliometric analysis of scientific outputs in this area. The purpose of this study is to reveal the research trends of scientific outputs on ECM for the past 30 years and provide a potential guide for future research.

Design/methodology/approach

A method of bibliometric analysis was performed, based on the online version of the Science Citation Index Expanded, Web of Science, from 1986 to 2017. The authors evaluated the publication types, languages, source countries, journals, the patterns of publication outputs, most-cited articles, most-productive authors, institutional distributions, subject categories, high-frequency keywords and keywords plus and high-frequency terms in the title and abstract of ectomycorrhizal research. Keywords, keywords plus and high-frequency terms in the title and abstract were analyzed via VOSviewer to illustrate the extent of co-occurrence. This study further describes the recent research priority or hotspots and reveals the research trends.

Findings

From 1986 to 2017, the publication output on ECM showed a rising trend; the number of articles has rapidly increased after 2003. Based on co-occurrence analysis for keywords, keywords plus and terms in the title and abstract, “ectomycorrhizal fungi” is the most popular keyword and keywords plus; “concentration” is the most high-frequency terms in the title and abstracts. Plant biology, mycology and ecology are the hotspots in the ectomycorrhizal research. Ectomycorrhizal taxonomy, the molecular mechanisms of ectomycorrhizal symbioses and the common mycorrhizal networks are the future direction.

Originality/value

A bibliometric analysis has been carried out to analyze the trends of ECM research with 30 years. This study provides a potential guide for future research related to ectomycorrhizae.

Details

The Electronic Library, vol. 36 no. 4
Type: Research Article
ISSN: 0264-0473

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Article
Publication date: 14 October 2020

Haiyan Ge, Xintian Liu, Yu Fang, Haijie Wang, Xu Wang and Minghui Zhang

The purpose of this paper is to introduce error ellipse into the bootstrap method to improve the reliability of small samples and the credibility of the S-N curve.

Abstract

Purpose

The purpose of this paper is to introduce error ellipse into the bootstrap method to improve the reliability of small samples and the credibility of the S-N curve.

Design/methodology/approach

Based on the bootstrap method and the reliability of the original samples, two error ellipse models are proposed. The error ellipse model reasonably predicts that the discrete law of expanded virtual samples obeys two-dimensional normal distribution.

Findings

By comparing parameters obtained by the bootstrap method, improved bootstrap method (normal distribution) and error ellipse methods, it is found that the error ellipse method achieves the expansion of sampling range and shortens the confidence interval, which improves the accuracy of the estimation of parameters with small samples. Through case analysis, it is proved that the tangent error ellipse method is feasible, and the series of S-N curves is reasonable by the tangent error ellipse method.

Originality/value

The error ellipse methods can lay a technical foundation for life prediction of products and have a progressive significance for the quality evaluation of products.

Details

Engineering Computations, vol. 38 no. 1
Type: Research Article
ISSN: 0264-4401

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Article
Publication date: 7 April 2020

Sourav Kumar Bhoi, Sanjaya Kumar Panda, Kalyan Kumar Jena, Chittaranjan Mallick and Akhtar Khan

Fish are considered as one of the important aquatic animals in the planet. They play a vital role in the nutrient cycle. They can be considered as one of the healthy food…

Abstract

Purpose

Fish are considered as one of the important aquatic animals in the planet. They play a vital role in the nutrient cycle. They can be considered as one of the healthy food for human beings. They can also act as a solution for some of the human health problems. If fish are affected by several diseases, they in turn provide an adverse effect on human health. Therefore, it is very much essential to protect fish from being affected by any diseases.

Design/methodology/approach

This paper is mainly focused on the identification of the red spot diseased area in fish. In this work, a fuzzy rule based method (FRBAM) and triangular membership function (TMFN) is used to identify the red spot disease (RSD) in the fish by analyzing several red spot diseased fish (RSDF) images. The canny edge detector is used for intermediate processing of RSDF images.

Findings

The proposed method is able to identify the red pixels over the fish by marking the affected area with red color by using a standard RGB model.

Originality/value

The proposed method follows FRBAM and TMFN in order to detect the RSD and canny edge detector for processing of RSDF images. Finally, it is tested using ten different image sizes and the results show its better performance in terms of detection of RSD affected regions of fish and execution time.

Details

Grey Systems: Theory and Application, vol. 10 no. 3
Type: Research Article
ISSN: 2043-9377

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Article
Publication date: 6 November 2017

Arezoo Pedramfar, Keivan Beheshti Maal and Sayed Hossein Mirdamadian

Corrosion-producing microorganisms have different physiology and include sulfate-reducing bacteria, iron oxidizers and magnesium oxidizers. Biocorrosion has been seen in…

Abstract

Purpose

Corrosion-producing microorganisms have different physiology and include sulfate-reducing bacteria, iron oxidizers and magnesium oxidizers. Biocorrosion has been seen in various industries, especially the petrochemicals and oil industries. One proposal to solve this problem is the use of bacteriophages to treat the bacteria-caused corrosion. The aims of this study were isolation and identification of corrosion-producing bacteria from petroleum pipeline corrosion as well as finding their specific bacteriophages for phage therapy purposes.

Design/methodology/approach

The sample pipes with the corrosion were obtained from the Gandomkar petroleum pipeline station, Chaharmahal and Bakhtiari, Iran. For screening the corrosion-producing bacteria, the rusted pipe samples were cultured in a selective culture medium, manganese agar. The purified individual colonies were subjected to molecular examinations. For isolating bacteriophages from silversmithing workshops wastewater in Isfahan, whole plate titration methods and transmission electron microscopy were used to isolate and detect phages.

Findings

The cultivation of corrosion-based material on manganese agar after 18 hours incubation at 30°C resulted in the isolation of cream-colored colonies. The microscopic examinations showed Gram-negative coccobacilli. Based on molecular examinations, the isolated bacteria were identified as Stenotrophomonas maltophilia strain PBM-IAUF-2 with Genebank accession number of KU145278.1. The found bacteriophage was related to the Siphoviridae family of phages.

Originality/value

This paper is the first report of isolation and identification of corrosion-producing bacteria and its specific lytic phages from Gandomkar petroleum pipeline station, Chaharmahal and Bakhtiari, Iran. The biological procedures for preventing the microbial corrosion could be an asset and considered as a potential in the petroleum and industrial microbiology. Phage therapy is considered as one of the economical methods for reducing the biocorrosion.

Details

Anti-Corrosion Methods and Materials, vol. 64 no. 6
Type: Research Article
ISSN: 0003-5599

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Abstract

Details

The Purpose-Driven University
Type: Book
ISBN: 978-1-83867-283-6

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Article
Publication date: 7 August 2009

Danielle Mihram and G. Arthur Mihram

The aim is to report on the 175th Annual Meeting of the American Association for the Advancement of Science (AAAS), held in February 2009 in Chicago.

Abstract

Purpose

The aim is to report on the 175th Annual Meeting of the American Association for the Advancement of Science (AAAS), held in February 2009 in Chicago.

Design/methodology/approach

Provides a concise review of the conference, whose theme was Our Planet and Its Life: Origins and Futures.

Findings

Not surprisingly, because of the primary focus on Darwin and the ecology of the earth, there were few symposia that concentrated on the application of technology outside of the Life Sciences and of the Earth Sciences. However, in view of the current evolution of “cloud computing” and the formation of “mega grids,” there were two symposia devoted to these topics.

Originality/value

The paper is a useful summary of a conference of interest to library and information management professionals.

Details

Library Hi Tech News, vol. 26 no. 7
Type: Research Article
ISSN: 0741-9058

Keywords

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