Using xslt:
example:
$ curl -s "ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/comm_use.A-B.xml.tar.gz" | tar xvz 3_Biotech/PMC4624140.nxml --to-command 'xsltproc --novalid transform.xsl 3_Biotech/PMC4624140.nxml'
3_Biotech/PMC4624140.nxml
Microorganisms are one of the tools used to detoxify toxic compounds present in the environment. Free suspended or immobilized microbial cells can be used for this purpose. However, the immobilized microbial cells have many advantages over free suspended cells under different conditions. For instance, the immobilization of whole cells increases degradation rate owing to increased cell population density, cell wall permeability, and extracellular microbial enzymes stability are improved, cells can be easily removed from the reaction mixture, higher operational stability and storage stability, reuse of immobilized cells in continuous reactors, and allows the bioreactors to operate at flow rates different from the growth rate of the microorganisms (Bettmann and Rehm 1984; Hall and Rao 1989; Cassidy et al. 1996; Ha et al. 2009; Zheng et al. 2009). In addition, the immobilized cell systems act as a protective cover in the presence of toxic compounds and are more resistant to pH or temperature changes. However, free suspended cells have better mass transfer aspects compared to immobilized bacterial or fungal cells (Trevors et al. 1992; Zheng et al. 2009).In the last two decades, there have been intensive researches on the use of immobilized microbial cells as biocatalysts, using numerous reactors like fed batch, semi-continuous fed batch, and continuous packed bed reactor. Each reactor type possesses its disadvantages and advantages, and the choice of a particular type of a reactor may depend on the operational conditions, and inexpensive and non-toxic support inert material for microbial cell immobilization, etc., (Zheng et al. 2009). Bacterial cells immobilized on various matrices have been used extensively for biodegradation of various toxic nitroaromatics such as trinitrotoluene (TNT) (Rho et al. 2001; Ullah et al. 2010), nitrobenzene (Zheng et al. 2009; Qi et al. 2012), 2-nitrotoluene (Mulla et al. 2013), and 3-nitrobenzoate (Mulla et al. 2012).Pendimethalin [N-(1-ethyl propyl) 2,6-dinitro-3,4-xylidine], a common water and soil contaminant, herbicide of dinitroaniline group, is used to control weeds in various crop plants. The use of pendimethalin may adversely affect endangered species of terrestrial and semi-aquatic plants and invertebrates (Kole et al. 1994). One of the best strategies to degrade the hazardous compounds (including pendimethalin) is to use microorganisms. There are few reports on the degradation of pendimethalin by free cells of Fusarium oxysporum and Paecilomyces variotii (Singh and Kulshrestha 1991), Azotobacter chroococcum (Kole et al. 1994), Bacillus circulans (Megadi et al. 2010), and fungus Lecanicillium saksenae (Pinto et al. 2012). However, there is no report on the degradation of pendimethalin by immobilized bacterial or fungal cells. The aim of the present investigation was therefore to compare the pendimethalin degradation by freely suspended and immobilized cells of Bacillus lehensis XJU on various matrices in batch and semi-continuous degradation, and to evaluate the effect of pH, temperature, and storage stability of pendimethalin degradation rate by polyurethane foam (PUF)-immobilized bacterial cells.
see Pmc Xml Parsing