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Bioinformatics is an emerging discipline where the interdisciplinary research holds great promise for the advancement of research and development in many complex areas. The research output generates a huge amount of data and information. Because of the heterogeneous nature of bioinformatics resources, difficulty in accessing pertinent information is the biggest challenge for the bioinformatics community. The integration of bioinformatics resources in a comprehensive manner is advocated by the bioinformatics user community as well as by information scientists serving this community. There are have already been some efforts made for integration of bioinformatics resources by the discrete bioinformatics community, but these are based on the requirement of their own area and arena. This paper aims to discuss the design and development of a tool for the integration of various heterogeneous bioinformatics information resources available over the internet.

The authors have developed a tool with the acronym “iBIRA” (Integrated Bioinformatics Information Resource Access) that associates the bioinformatics community with the bioinformatics “resourceome” (the term suggested for the “full set of bioinformatics resources” by Cannata et al.). Available over the internet. iBIRA (www.ibiranet.in) integrates bioinformatics resources in a way such that it is possible to locate, connect and communicate different categories of resources in a cohesive manner. A software engineering and database‐driven approach was used for the integration and organization of bioinformatics resources. Computational programming such as Hypertext Preprocessor (PHP), a server‐side dynamic web programming language, and MySQL as a database management system have been used. Dublin Core Metadata Standards have been used for the design of metadata for bioinformatics resources..

The term “resource” in the area of bioinformatics covers various entities such as journals, molecular biology databases, online annotation tools, patents, published documents (articles, books, etc), protocols, software tools, and web servers. It has been found that bioinformatics resources are heterogeneous in nature and available over the internet in different forms and formats. The fact that bioinformatics resources are scattered over the internet makes resource discovery difficult for the bioinformatics community, and there is need for a system that reorganizes these resources. The integration of all the resources of bioinformatics at a single platform (called “iBIRA”) provides significant “value added” to the bioinformatics community, those serving this population.

The iBIRA tool is a meta‐server developed to provide information service about the availability of various bioinformatics resources to the bioinformatics community. This will provide a value‐added benefit to the population in helping them to locate relevant resources for their education, research and training.

The purpose of this paper is to look at the sharp increase in academic patenting over the past 20 years and to raise important issues regarding the generation and diffusion of academic knowledge. Three key questions may be raised in this respect: What is behind the surge in academic patenting? Does patenting affect the quality and quantity of universities' scientific output? Does the patent system limit the freedom to perform academic research? The present paper seeks to summarize the existing literature on these issues.

The paper's approach is a review of the recent literature on academic patenting and research use of patented inventions, complemented with critical viewpoints and new data on academic patenting in Europe.

The evidence suggests that academic patenting has only limited effects on the direction, pace and quality of research. A virtuous cycle seems to characterise the patent‐publication relationship. Secondly, scientific anti‐commons show very little effects on academic researchers so far, limited to a few countries with weak or no research exemption regulations. In summary, the evidence leads the authors to conclude that the benefits of academic patenting on research exceed their potential negative effects.

The paper offers a critical overview of the available evidence on the links between patents and academic research, which may be useful both for individuals unfamiliar with this issue or for those experienced in the field who are looking for a state of the art discussion on recent debates.

This study aims to study the distribution characteristics of antibiotic resistance in direct-eating food and analysis of Citrobacter freundii genome and pathogenicity. Residual antibiotics and antibiotic resistance genes (ARGs) in the environment severely threaten human health and the ecological environment. The diseases caused by foodborne pathogenic bacteria are increasing daily, and the enhancement of antibiotic resistance of pathogenic bacteria poses many difficulties in the treatment of disease.

In this study, six fresh fruits and vegetable samples were selected for isolation and identification of culturable bacteria and analysis of antibiotic resistance. The whole genome of Citrobacter freundii isolated from cucumber was sequenced and analyzed by Oxford Nanopore sequencing.

The results show that 270 strains of bacteria were identified in 6 samples. From 12 samples of direct food, 2 kinds of probiotics and 10 kinds of opportunistic pathogens were screened. The proportion of Citrobacter freundii screened from cucumber was significantly higher than that from other samples, and it showed resistance to a variety of antibiotics. Whole genome sequencing showed that Citrobacter freundii was composed of a circular chromosome containing signal peptides, transmembrane proteins and transporters that could induce antibiotic efflux, indicating that Citrobacter freundii had strong adaptability to the environment. The detection of genes encoding carbohydrate active enzymes is more beneficial to the growth and reproduction of Citrobacter freundii in crops. A total of 29 kinds of ARGs were detected in Citrobacter freundii, mainly conferring resistance to fluoroquinolones, aminoglycosides, carbapenem, cephalosporins and macrolides. The main mechanisms are the change in antibiotic targets and efflux pumps, the change in cell permeability and the inactivation of antibiotics and the detection of virulence factors and ARGs, further indicating the serious risk to human health.

The detection of genomic islands and prophages increases the risk of horizontal transfer of virulence factors and ARGs, which spreads the drug resistance of bacteria and pathogenic bacteria more widely.

This chapter proposes an optimized innovative information technology as a means for achieving operational functionalities of real-time portable electronic health records, system interoperability, longitudinal health-risks research cohort and surveillance of adverse events infrastructure, and clinical, genome regions – disease and interventional prevention infrastructure. In application to the Dod-VA (Department of Defense and Veteran's Administration) health information systems, the proposed modernization can be carried out as an “add-on” expansion (estimated at $288 million in constant dollars) or as a “stand-alone” innovative information technology system (estimated at $489.7 million), and either solution will prototype an infrastructure for nation-wide health information systems interoperability, portable real-time electronic health records (EHRs), adverse events surveillance, and interventional prevention based on targeted single nucleotide polymorphisms (SNPs) discovery.

This study aims to treat the development and application of sequence characterised amplified region (SCAR) markers for the detection of plant based adulterants (dried red beet pulp and powdered Ziziphus nummularia fruits) in traded ground chilli.

Adulterant‐specific DNA fragments (red beet pulp specific – “Beet 01” and Z. nummularia specific – “Ziz 01”) identified by random amplified polymorphic DNA polymerase chain reaction (RAPD‐PCR) analysis were cloned and sequenced for SCAR marker development. Red beet pulp specific SCAR primer pair, B1, and Z. nummularia specific SCAR primer pair, Z1, were designed from the corresponding RAPD marker sequences to amplify SCAR markers of 320 bp and 389 bp, respectively. The utility of the SCAR markers for adulterant detection was verified in model blends of chilli powder with the adulterants. Six commercial samples of ground chilli powder were analysed using the SCAR markers.

SCAR markers could detect the adulterants at a concentration as low as 10 g adulterant kg⁻¹ of blended sample. The Z. nummularia SCAR marker could detect the presence of Z. nummularia fruit adulteration in one of the commercial samples. All the market samples tested were free from red beet pulp adulteration.

The PCR‐based method developed in the study is simple, rapid, and sensitive and has the potential to be developed into a quantitative analytical method and for commercial PCR kits for the large‐scale screening of ground chilli to detect and prevent plant‐based adulterants. The work has public health significance too, as ground chilli is one of the major spices consumed worldwide.

The study is the first report on the development of SCAR markers for adulterant detection in ground chilli. This work has relevance, as adulteration is a major concern of the sanitary and phytosanitary issues of the World Trade Organization (WTO) agreement.

This paper is the result of the research I undertook at Lancaster University with a Marie Curie Fellowship during the academic years 2000‐2002. The objective of this research was to study the limits and the challenges of the analogy between molecular geneticists’ work and hackers’ activities. By focusing on this analogy I aim to explore the different ethical and philosophical issues surrounding new genetics and its IPR regulations. The paper firstly will show the philosophical background lying behind the proposed analogy and analyses the sense in which we can talk of geneticists as “hackers.” It will provide grounds for the analogy by exploring some of the techniques used by geneticists; in particular it will focus on the so‐called Shotgun method for genomic sequencing. After having provided reasons for the proposed analogy I will claim that the open source philosophy used in the computer field would be a good way to regulate research in the genetics and in pharmaceutical field too. The open source philosophy would provide fair distribution of research opportunities around the globe with the shift from patenting to copyright in sensitive fields such as genetics.

Big Data analysis is one of the key challenges to the provision of health care to emerge in the last few years. This challenge has been spearheaded by the huge interest in the “4Ps” of health care (predictive, preventive, personalized, and participatory). Big Data offers striking development opportunities in health care and life sciences. Healthcare research is already using Big Data to analyze the spatial distribution of diseases such as diabetes mellitus at detailed geographic levels. Big Data is also being used to assess location-specific risk factors based on data of health insurance claims. Other studies in systems medicine utilize bioinformatics approaches to human biology which necessitate Big Data statistical analysis and medical informatics tools. Big Data is also being used to develop electronic algorithms to forecast clinical events in real time, with the intent to improve patient outcomes and thus reduce costs.

Yet, this Big Data era also poses critically difficult ethical challenges, since it is breaking down the traditional divisions between what belongs to public and private domains in health care and health research. Big Data in health care raises complex ethical concerns due to use of huge datasets obtained from different sources for varying reasons. The clinical translation of this Big Data is thus resulting in key ethical and epistemological challenges for those who use these data to generate new knowledge and the clinicians who eventually apply it to improve patient care.

Underlying this challenge is the fact that patient consent often cannot be collected for the use of individuals’ personal data which then forms part of this Big Data. There is also the added dichotomy of healthcare providers which use such Big Data in attempts to reduce healthcare costs, and the negative impact this may have on the individual with respect to privacy issues and potential discrimination.

Big Data thus challenges societal norms of privacy and consent. Many questions are being raised on how these huge masses of data can be managed into valuable information and meaningful knowledge, while still maintaining ethical norms. Maintaining ethical integrity may lack behind in such a fast-changing sphere of knowledge. There is also an urgent need for international cooperation and standards when considering the ethical implications of the use of Big Data-intensive information.

This chapter will consider some of the main ethical aspects of this fast-developing field in the provision of health care, health research, and public health. It will use examples to concretize the discussion, such as the ethical aspects of the applications of Big Data obtained from clinical trials, and the use of Big Data obtained from the increasing popularity of health mobile apps and social media sites.

Bioinformatics projects are currently under way at numerous universities and in industry. These projects typically involve processing large amounts of biological data and comparison of biological signals or sequences. Much of the existing work in bioinformatics software is based on such languages and platforms as Perl and Unix. This paper, proposes software architectures in Java to support biological applications allowing access of biological data using server‐side Java programs on the Internet. The architecture follows the standards of unified modeling language (UML). UML architecture diagrams are presented for the Java‐based bioinformatics applications. In addition, an overview of the Bio‐Soft project under way at The Biomedical Research Institute (BRI) of the University of Wisconsin‐Parkside is provided, which includes research and instructional software for bioinformatics applications.

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.

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

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.

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.

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

This research examines the association of physical development density, prevalence and types of microbes in colonized façade finishes of buildings in Enugu metropolis, Nigeria.

Survey and experimental research designs were adopted. A total of 383 buildings were investigated with samples collected from those with colonized façade finishes. The microbes were identified using the standard procedure for genomic sequencing with descriptive statistics, and the chi-square test used to analyse the data.

The results revealed a 64% prevalence of microbial colonization and a significant association between this and physical development density with 71.0% of the colonized buildings located in high-density neighbourhoods of the metropolis. The sequencing also showed 24 different microbes with Trichophyton tonsurans, Trichophyton mentagrophytes and Trichoderma harzianum species being the most common in the colonized façade finishes.

The research informs building professionals and owners of the specific microbes involved in the colonization of façade finishes of buildings in high-density urban areas. It also provides a clue about the nature of damages and defects associated with microbial colonization of building façades and the type of biocide additives required for the production of microbial-resistant façade finishes in the hot-humid tropical environment of Nigeria and beyond.

The study has shown that there is a significant relationship between the intensity of urban land use and microbial colonization of façade finishes of buildings. It also identified some new or less known microbes responsible for the biodeterioration of façade finishes and the effects this has on the buildings and public health in the hot-humid tropics of Enugu, Southeast Nigeria.