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EcoliOverExpressionDB: a database of recombinant protein overexpression in E. coli

Habibi N, Samian MR, Hashim SZ, Norouzi A

Protein Expr. Purif., 2014 Mar;95:92-5.
PMID: 24333540 DOI: 10.1016/j.pep.2013.11.014

Recombinant protein production is a significant biotechnological process as it allows researchers to produce a specific protein in desired quantities. Escherichia coli (E. coli) is the most popular heterologous expression host for the production of recombinant proteins due to its advantages such as low cost, high-productivity, well-characterized genetics, simple growth requirements and rapid growth. There are a number of factors that influence the expression level of a recombinant protein in E. coli which are the gene to be expressed, the expression vector, the expression host, and the culture condition. The major motivation to develop our database, EcoliOverExpressionDB, is to provide a means for researchers to quickly locate key factors in the overexpression of certain proteins. Such information would be a useful guide for the overexpression of similar proteins in E. coli. To the best of the present researchers' knowledge, in general and specifically in E. coli, EcoliOverExpressionDB is the first database of recombinant protein expression experiments which gathers the influential parameters on protein overexpression and the results in one place.

Matched MeSH terms: Databases, Factual*
Fulltext A control chart based on cluster-regression adjustment for retrospective monitoring of individual characteristics

Ong HC, Alih E

PLoS One, 2015;10(4):e0125835.
PMID: 25923739 DOI: 10.1371/journal.pone.0125835

The tendency for experimental and industrial variables to include a certain proportion of outliers has become a rule rather than an exception. These clusters of outliers, if left undetected, have the capability to distort the mean and the covariance matrix of the Hotelling's T2 multivariate control charts constructed to monitor individual quality characteristics. The effect of this distortion is that the control chart constructed from it becomes unreliable as it exhibits masking and swamping, a phenomenon in which an out-of-control process is erroneously declared as an in-control process or an in-control process is erroneously declared as out-of-control process. To handle these problems, this article proposes a control chart that is based on cluster-regression adjustment for retrospective monitoring of individual quality characteristics in a multivariate setting. The performance of the proposed method is investigated through Monte Carlo simulation experiments and historical datasets. Results obtained indicate that the proposed method is an improvement over the state-of-art methods in terms of outlier detection as well as keeping masking and swamping rate under control.

Matched MeSH terms: Databases, Factual*
An Architecture of a Query Evaluation System For Deductive Databases

Ali Mamat

Sains Malaysiana, 1996;25.

The technology of deductive database is now mature enough due to the considerable research efforts that have been made on the field for the last ten years. This achievement is demonstrated by the emergence of efficient and easy to use systems with their capability of supporting a declarative, rule based style of expressing queries and applications on databases. This paper describes an overview of architecture of a query evaluation system for deductive databases that has been developed.
Teknologi pangkalan data deduktif sudah matang hasil daripada penyelidikan yang telah banyak dilakukan dalam tempoh 10 tahun yang lepas. Pencapaian ini dibuktikan melalui kemunculan sistem yang cekap dan mudah guna serta mempunyai keupayaan untuk mengungkap pertanyaan dan penggunaan ke atas pangkalan data secara deklaratif menerusi penggunaan petua. Dalam kertas ini diterangkan suatu ringkasan mengenai senibina sistem penilaian pertanyaan untuk pangkalan data deduktif yang sudah dibangunkan.

Matched MeSH terms: Databases, Factual
Association between cardiovascular diseases and apical periodontitis: an umbrella review

Jakovljevic A, Duncan HF, Nagendrababu V, Jacimovic J, Milasin J, Dummer PMH

Int Endod J, 2020 Oct;53(10):1374-1386.
PMID: 32648971 DOI: 10.1111/iej.13364

BACKGROUND: The existence of an association between cardiovascular diseases (CVDs) and apical periodontitis (AP) remains unclear because results obtained from previous clinical studies and reviews are inconsistent or inconclusive.
OBJECTIVE: To conduct an umbrella review to determine whether there is an association between CVDs and the prevalence of AP in adults.
METHODS: The protocol of the review was registered in the PROSPERO database (CRD42020185753). The literature search was conducted using the following electronic databases: Clarivate Analytics' Web of Science Scopus, PubMed and Cochrane Database of Systematic Reviews, from inception to May, 2020, with no language restrictions. Systematic reviews with or without meta-analysis that evaluated the association between CVDs and AP were included. Other types of studies, including narrative reviews, were excluded. Two reviewers independently performed a literature search, data extraction and quality assessment of included studies. Any disagreements or doubts were resolved by a third reviewer. The quality of the reviews was assessed using the AMSTAR 2 tool (A measurement tool to assess systematic reviews), with 16 items. A final categorization of the systematic reviews classified each as of 'high', 'moderate', 'low' or 'critically low' quality.
RESULTS: Four systematic reviews were included in the current review. Three reviews were graded by AMSTAR 2 as 'moderate' quality, whereas one review was graded as 'critically low' quality.
DISCUSSION: Only one systematic review included a meta-analysis. Substantial heterogeneity amongst the primary studies included within each systematic review was notable in preventing a pooled analysis.
CONCLUSIONS: From the limited 'moderate' to 'critically low' quality evidence available, the current umbrella review concluded that a weak association exists between CVDs and AP. In the future, well-designed, longitudinal clinical studies with long-term follow-up are required.

Matched MeSH terms: Databases, Factual
Fulltext Development and validation of a Database Forensic Metamodel (DBFM)

Al-Dhaqm A, Razak S, Othman SH, Ngadi A, Ahmed MN, Ali Mohammed A

PLoS One, 2017;12(2):e0170793.
PMID: 28146585 DOI: 10.1371/journal.pone.0170793

Database Forensics (DBF) is a widespread area of knowledge. It has many complex features and is well known amongst database investigators and practitioners. Several models and frameworks have been created specifically to allow knowledge-sharing and effective DBF activities. However, these are often narrow in focus and address specified database incident types. We have analysed 60 such models in an attempt to uncover how numerous DBF activities are really public even when the actions vary. We then generate a unified abstract view of DBF in the form of a metamodel. We identified, extracted, and proposed a common concept and reconciled concept definitions to propose a metamodel. We have applied a metamodelling process to guarantee that this metamodel is comprehensive and consistent.

Matched MeSH terms: Databases, Factual*
Fulltext A charismatic new species of green lacewing discovered in Malaysia (Neuroptera, Chrysopidae): the confluence of citizen scientist, online image database and cybertaxonomy

Winterton SL, Guek HP, Brooks SJ

Zookeys, 2012.
PMID: 22936863 DOI: 10.3897/zookeys.214.3220

An unusual new species of green lacewing (Neuroptera: Chrysopidae: Semachrysa jadesp. n.) is described from Selangor (Malaysia) as a joint discovery by citizen scientist and professional taxonomists. The incidental nature of this discovery is underscored by the fact that the species was initially photographed and then released, with images subsequently posted to an online image database. It was not until the images in the database were randomly examined by the professional taxonomists that it was determined that the species was in fact new. A subsequent specimen was collected at the same locality and is described herein along with another specimen identified from nearby Sabah.

Matched MeSH terms: Databases, Factual
Fulltext An elemental concentration open source database for hogdahl-convention and westcott-formalism based on ko-inaa method in malaysia

Yavar, A.R., S. Sarmani, Tan, C.Y., N.N. Rafie, Lim, S.W. Edwin, Khoo, K.S.

Journal of Nuclear and Related Technologies, 2012;2012(2):93-98.
MyJurnal

An electronic database has been developed and implemented for ko-INAA method in Malaysia. Databases are often developed according to national requirements. This database contains constant nuclear data for ko-INAA method; Hogdahl-convention and Westcott-formalism as 3 separate command user interfaces. It has been created using Microsoft Access 2007 under a Windows operating system. This database saves time and the quality of results can be assured when the calculation of neutron flux parameters and concentration of elements by ko-INAA method are utilised. An evaluation of the database was conducted by IAEA Soil7 where the results published which showed a high level of consistency.

Matched MeSH terms: Databases, Factual
Fulltext Ensemble learning method for the prediction of new bioactive molecules

Afolabi LT, Saeed F, Hashim H, Petinrin OO

PLoS One, 2018;13(1):e0189538.
PMID: 29329334 DOI: 10.1371/journal.pone.0189538

Pharmacologically active molecules can provide remedies for a range of different illnesses and infections. Therefore, the search for such bioactive molecules has been an enduring mission. As such, there is a need to employ a more suitable, reliable, and robust classification method for enhancing the prediction of the existence of new bioactive molecules. In this paper, we adopt a recently developed combination of different boosting methods (Adaboost) for the prediction of new bioactive molecules. We conducted the research experiments utilizing the widely used MDL Drug Data Report (MDDR) database. The proposed boosting method generated better results than other machine learning methods. This finding suggests that the method is suitable for inclusion among the in silico tools for use in cheminformatics, computational chemistry and molecular biology.

Matched MeSH terms: Databases, Factual
Construction of Protein Expression Network

Afiqah-Aleng N, Mohamed-Hussein ZA

Methods Mol Biol, 2021;2189:119-132.
PMID: 33180298 DOI: 10.1007/978-1-0716-0822-7_10

In this post-genomic era, protein network can be used as a complementary way to shed light on the growing amount of data generated from current high-throughput technologies. Protein network is a powerful approach to describe the molecular mechanisms of the biological events through protein-protein interactions. Here, we describe the computational methods used to construct the protein network using expression data. We provide a list of available tools and databases that can be used in constructing the network.

Matched MeSH terms: Databases, Factual
Fulltext Future trends and guidance for the triple bottom line and sustainability: a data driven bibliometric analysis

Tseng ML, Chang CH, Lin CR, Wu KJ, Chen Q, Xia L, et al.

Environ Sci Pollut Res Int, 2020 Sep;27(27):33543-33567.
PMID: 32572746 DOI: 10.1007/s11356-020-09284-0

This study conducts a comprehensive literature review of articles on the triple bottom line (TBL) published from January 1997 to September 2018 to provide significant insights and support to guide further discussion. There were three booms in TBL publications, occurring in 2003, 2011, and 2015, and many articles attempt to address the issue of sustainability by employing the TBL. This literature analysis includes 720, 132, and 58 articles from the Web of Science (WOS), Inspec, and Scopus databases, respectively, and reveals the gaps in existing research. To discover the barriers and points of overlap, these articles are categorized into six aspects of the TBL: economic, environmental, social, operations, technology, and engineering. Examining the top 3 journals in terms of published articles on each aspect reveals the research trends and gaps. The findings provide solid evidence confirming the argument that the TBL as currently defined is insufficient to cover the entire concept of sustainability. The social and engineering aspects still require more discussion to support the linkage of the TBL and to reinforce its theoretical basis. Additionally, to discover the gaps in the data sources, theories applied, methods adopted, and types of contributions, this article summarizes 82 highly cited articles covering each aspect. This article offers theoretical insights by identifying the top contributing countries, institutions, authors, keyword networks, and authorship networks to encourage scholars to push the current discussion further forward, and it provides practical insights to bridge the gap between theory and practice for enhancing the efficiency and effectiveness of improvements.

Matched MeSH terms: Databases, Factual
A dBASE III system for managing 35 mm slides in pathology

Wong KT, Chan KS

Malays J Pathol, 1990 Dec;12(2):101-6.
PMID: 2102964

We describe the design and management of a 35 mm slide database using a menu-driven dBASE III PLUS programme and a microcomputer in a large department of pathology that also caters for the individual pathologist. Existing systems described in the literature are geared towards slides of general medicine and do not address the needs of the individual pathologist. A total of 11,481 slides in the Department of Pathology, Faculty of Medicine, University of Malaya, were filed into a single database with each record representing one slide. Nine fields which comprised the slide accession number, reference number, slide category, SNOMED codes, and a description of the slide in natural language, seemed adequate for slide definition. The menu-driven programme had functions which included the abilities to add, delete, edit and back-up records, and to search for desired slides. Although slides may be searched for in various fields, we found that searches using natural language alone were both comprehensive and efficient, provided a standard format of description was adhered to and data entries scrutinized carefully for errors. We believe therefore, that for the pathologist working alone, coded language fields are not absolutely necessary, as manual coding and additional data entry can be time consuming. As expected, for databases larger than 10,000 slides, a 80286 microprocessor-based microcomputer was more efficient. We are of the opinion that a system such as ours is very useful for a large department of pathology or the individual pathologist to file and retrieve 35 mm slides.

Matched MeSH terms: Databases, Factual*
Fulltext Patient registries supplement. Foreword

Abdul Hamid M

Med J Malaysia, 2008 Sep;63 Suppl C:vii.
PMID: 19227668
Matched MeSH terms: Databases, Factual*
MPD3: a useful medicinal plants database for drug designing

Mumtaz A, Ashfaq UA, Ul Qamar MT, Anwar F, Gulzar F, Ali MA, et al.

Nat Prod Res, 2017 Jun;31(11):1228-1236.
PMID: 27681445 DOI: 10.1080/14786419.2016.1233409

Medicinal plants are the main natural pools for the discovery and development of new drugs. In the modern era of computer-aided drug designing (CADD), there is need of prompt efforts to design and construct useful database management system that allows proper data storage, retrieval and management with user-friendly interface. An inclusive database having information about classification, activity and ready-to-dock library of medicinal plant's phytochemicals is therefore required to assist the researchers in the field of CADD. The present work was designed to merge activities of phytochemicals from medicinal plants, their targets and literature references into a single comprehensive database named as Medicinal Plants Database for Drug Designing (MPD3). The newly designed online and downloadable MPD3 contains information about more than 5000 phytochemicals from around 1000 medicinal plants with 80 different activities, more than 900 literature references and 200 plus targets. The designed database is deemed to be very useful for the researchers who are engaged in medicinal plants research, CADD and drug discovery/development with ease of operation and increased efficiency. The designed MPD3 is a comprehensive database which provides most of the information related to the medicinal plants at a single platform. MPD3 is freely available at: http://bioinform.info .

Matched MeSH terms: Databases, Factual*
Fulltext Health Information Exchange (HIE): A literature review, assimilation pattern and a proposed classification for a new policy approach

Esmaeilzadeh P, Sambasivan M

J Biomed Inform, 2016 12;64:74-86.
PMID: 27645322 DOI: 10.1016/j.jbi.2016.09.011

OBJECTIVES: Literature shows existence of barriers to Healthcare Information Exchange (HIE) assimilation process. A number of studies have considered assimilation of HIE as a whole phenomenon without regard to its multifaceted nature. Thus, the pattern of HIE assimilation in healthcare providers has not been clearly studied due to the effects of contingency factors on different assimilation phases. This study is aimed at defining HIE assimilation phases, recognizing assimilation pattern, and proposing a classification to highlight unique issues associated with HIE assimilation.
METHODS: A literature review of existing studies related to HIE efforts from 2005 was undertaken. Four electronic research databases (PubMed, Web of Science, CINAHL, and Academic Search Premiere) were searched for articles addressing different phases of HIE assimilation process.
RESULTS: Two hundred and fifty-four articles were initially selected. Out of 254, 44 studies met the inclusion criteria and were reviewed. The assimilation of HIE is a complicated and a multi-staged process. Our findings indicated that HIE assimilation process consisted of four main phases: initiation, organizational adoption decision, implementation and institutionalization. The data helped us recognize the assimilation pattern of HIE in healthcare organizations.
CONCLUSIONS: The results provide useful theoretical implications for research by defining HIE assimilation pattern. The findings of the study also have practical implications for policy makers. The findings show the importance of raising national awareness of HIE potential benefits, financial incentive programs, use of standard guidelines, implementation of certified technology, technical assistance, training programs and trust between healthcare providers. The study highlights deficiencies in the current policy using the literature and identifies the "pattern" as an indication for a new policy approach.

Matched MeSH terms: Databases, Factual*
Fulltext Condorcet and borda count fusion method for ligand-based virtual screening

Ahmed A, Saeed F, Salim N, Abdo A

J Cheminform, 2014;6:19.
PMID: 24883114 DOI: 10.1186/1758-2946-6-19

BACKGROUND: It is known that any individual similarity measure will not always give the best recall of active molecule structure for all types of activity classes. Recently, the effectiveness of ligand-based virtual screening approaches can be enhanced by using data fusion. Data fusion can be implemented using two different approaches: group fusion and similarity fusion. Similarity fusion involves searching using multiple similarity measures. The similarity scores, or ranking, for each similarity measure are combined to obtain the final ranking of the compounds in the database.
RESULTS: The Condorcet fusion method was examined. This approach combines the outputs of similarity searches from eleven association and distance similarity coefficients, and then the winner measure for each class of molecules, based on Condorcet fusion, was chosen to be the best method of searching. The recall of retrieved active molecules at top 5% and significant test are used to evaluate our proposed method. The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints.
CONCLUSIONS: Simulated virtual screening experiments with the standard two data sets show that the use of Condorcet fusion provides a very simple way of improving the ligand-based virtual screening, especially when the active molecules being sought have a lowest degree of structural heterogeneity. However, the effectiveness of the Condorcet fusion was increased slightly when structural sets of high diversity activities were being sought.

Matched MeSH terms: Databases, Factual
Inverse frequency weighting of fragments for similarity-based virtual screening

Arif SM, Holliday JD, Willett P

J Chem Inf Model, 2010 Aug 23;50(8):1340-9.
PMID: 20672867 DOI: 10.1021/ci1001235

This paper discusses the weighting of two-dimensional fingerprints for similarity-based virtual screening, specifically the use of weights that assign greatest importance to the substructural fragments that occur least frequently in the database that is being screened. Virtual screening experiments using the MDL Drug Data Report and World of Molecular Bioactivity databases show that the use of such inverse frequency weighting schemes can result, in some circumstances, in marked increases in screening effectiveness when compared with the use of conventional, unweighted fingerprints. Analysis of the characteristics of the various schemes demonstrates that such weights are best used to weight the fingerprint of the reference structure in a similarity search, with the database structures' fingerprints unweighted. However, the increases in performance resulting from such weights are only observed with structurally homogeneous sets of active molecules; when the actives are diverse, the best results are obtained using conventional, unweighted fingerprints for both the reference structure and the database structures.

Matched MeSH terms: Databases, Factual
Fulltext On the integration and standardization of medication error data: taxonomies, terminologies, causes and contributing factors

Taib IA, McIntosh AS

Ther Adv Drug Saf, 2010 Dec;1(2):53-63.
PMID: 25083195 DOI: 10.1177/2042098610389850

A reliable database on the causes and contributing factors of medication errors can inform strategies for their prevention. To form a single database from multiple databases requires a process of integration that both maximizes the utility of the new data and minimizes the loss of information. Unfortunately, the terminologies used by different studies and databases may limit integration; therefore, terminologies must be standardized prior to integration.

Matched MeSH terms: Databases, Factual
Content-based image retrieval system for solid waste bin level detection and performance evaluation

Hannan MA, Arebey M, Begum RA, Basri H, Al Mamun MA

Waste Manag, 2016 Apr;50:10-9.
PMID: 26868844 DOI: 10.1016/j.wasman.2016.01.046

This paper presents a CBIR system to investigate the use of image retrieval with an extracted texture from the image of a bin to detect the bin level. Various similarity distances like Euclidean, Bhattacharyya, Chi-squared, Cosine, and EMD are used with the CBIR system for calculating and comparing the distance between a query image and the images in a database to obtain the highest performance. In this study, the performance metrics is based on two quantitative evaluation criteria. The first one is the average retrieval rate based on the precision-recall graph and the second is the use of F1 measure which is the weighted harmonic mean of precision and recall. In case of feature extraction, texture is used as an image feature for bin level detection system. Various experiments are conducted with different features extraction techniques like Gabor wavelet filter, gray level co-occurrence matrix (GLCM), and gray level aura matrix (GLAM) to identify the level of the bin and its surrounding area. Intensive tests are conducted among 250bin images to assess the accuracy of the proposed feature extraction techniques. The average retrieval rate is used to evaluate the performance of the retrieval system. The result shows that, the EMD distance achieved high accuracy and provides better performance than the other distances.

Matched MeSH terms: Databases, Factual
Fulltext World Checklist of Opiliones species (Arachnida). Part 2: Laniatores - Samooidea, Zalmoxoidea and Grassatoresincertae sedis

Kury AB, Souza DR, Pérez-González A

Biodivers Data J, 2015.
PMID: 26752965 DOI: 10.3897/BDJ.3.e6482

Including more than 6500 species, Opiliones is the third most diverse order of Arachnida, after the megadiverse Acari and Araneae. This database is part 2 of 12 of a project containing an intended worldwide checklist of species and subspecies of Opiliones, and it includes the members of the suborder Laniatores, infraorder Grassatores of the superfamilies Samooidea and Zalmoxoidea plus the genera currently not allocated to any family (i.e. Grassatores incertae sedis). In this Part 2, a total of 556 species and subspecies are listed.

Matched MeSH terms: Databases, Factual
Fulltext Content-based image retrieval using colour and shape fused features

Mas Rina Mustaffa, Fatimah Ahmad, Ramlan Mahmod, Shyamala Doraisamy

Pertanika Journal of Science & Technology, 2013;21(1):161-168.
MyJurnal

Multi-feature methods are able to contribute to a more effective method compared to single-feature
methods since feature fusion methods will be able to close the gap that exists in the single-feature
methods. This paper presents a feature fusion method, which focuses on extracting colour and shape features for content-based image retrieval (CBIR). The colour feature is extracted based on the proposed Multi-resolution Joint Auto Correlograms (MJAC), while the shape information is obtained through the proposed Extended Generalised Ridgelet-Fourier (EGRF). These features are fused together through a proposed integrated scheme. The feature fusion method has been tested on the SIMPLIcity image database, where several retrieval measurements are utilised to compare the effectiveness of the proposed method with few other comparable methods. The retrieval results show that the proposed Integrated Colour-shape (ICS) descriptor has successfully obtained the best overall retrieval performance in all the retrieval measurements as compared to the benchmark methods, which include precision (53.50%), precision at 11 standard recall levels (52.48%), and rank (17.40).

Matched MeSH terms: Databases, Factual

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