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A comparison of machine learning algorithms for the prediction of Hepatitis C NS3 protease cleavage sites

Sci Mob Comput. 2015;4(5):358–64. 36. McLachlan Geoffrey J., Do K-A, Ambroise C. Analyzing microarray gene expression data / Geoffrey J. McLachlan, Kim-Anh Do, Christopher Ambroise. Wiley-Interscience Hoboken, N.J; 2004. 213–214 p. 37. Metz CE. Basic principles of ROC analysis. Semin Nucl Med. 1978;8(4):283–98. 38. Raghavan V, Bollmann P, S. Jung G. A critical investigation of recall and precision as measures of retrieval system performance. ACM Trans Inf Syst. 1989;7(3):205–29. 39. Matthews BW. Comparison of the predicted and observed

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Switching from petro-plastics to microbial polyhydroxyalkanoates (PHA): the biotechnological escape route of choice out of the plastic predicament?

) production. J Clean Prod 2018; 181: 72–87. 20. Koller M, Braunegg G. Advanced approaches to produce polyhydroxyalkanoate (PHA) biopolyesters in a sustainable and economic fashion. The EuroBiotech Journal 2018; 2(2): 89-103. 21. Carvalho G, Oehmen A, Albuquerque MG, Reis MAM. The relationship between mixed microbial culture composition and PHA production performance from fermented molasses. New Biotechnol 2014; 31(4): 257-263. 22. Akaraonye E, Moreno C, Knowles JC, Keshavarz T, Roy I. Poly(3-hydroxybutyrate) production by Bacillus cereus SPV using

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Quality assurance of genetic laboratories and the EBTNA practice certification, a simple standardization assurance system for a laboratory network

Abstract

Analytical laboratory results greatly influence medical diagnosis, about 70% of medical decisions are based on laboratory results. Quality assurance and quality control are designed to detect and correct errors in a laboratory’s analytical process to ensure both the reliability and accuracy of test results. Unreliable performance can result in misdiagnosis and delayed treatment. Furthermore, improved quality guarantees increased productivity at a lower cost. Quality assurance programmes include internal quality control, external quality assessment, proficiency surveillance and standardization. It is necessary to try to ensure compliance with the requirements of the standards at all levels of the process. The sources of these standards are the International Standards Organization (ISO), national standards bodies, guidelines from professional organisations, accreditation bodies and governmental regulations. Laboratory networks increase the performance of laboratories in support of diagnostic screening programme. It is essential that genetic laboratories of a network have procedures underpinned by a robust quality assurance system to minimize errors and to reassure the clinicians and the patients that international standards are being met. This article provides an overview of the bases of quality assurance and its importance in genetic tests and it reports the EBTNA quality assurance system which is a clear and simple system available for access to adequate standardization of a genetic laboratory’s network.

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Screening of metabolites from endophytic fungi of some Nigerian medicinal plants for antimicrobial activities

Abstract

Endophytic fungi associated with Nigerian plants have recently generated significant interest in drug discovery programmes due to their immense potential to contribute to the discovery of new bioactive compounds. This study was carried out to investigate the secondary metabolites of endophytic fungi isolated from leaves of Newbouldia laevis, Ocimum gratissimum, and Carica papaya. The plants were collected from Agulu, Anambra State, South-East Nigeria. Endophytic fungal isolation, fungal fermentation; and extraction of secondary metabolites were carried out using standard methods. The crude extracts were screened for antimicrobial activities using the agar well diffusion method, and were also subjected to high performance liquid chromatography (HPLC) analysis to identify their constituents. A total of five endophytic fungi was isolated, two from N. laevis (NL-L1 and NL-L2), one from O. gratissimum (SL-L1), and two from C. papaya (PPL-LAC and PPL-LE2). In the antimicrobial assay, the extracts of NL-L2, SL-L1, and PPL-LE2 displayed mild antibacterial activity against both Gram negative and Gram positive test bacteria. PPL-LAC extract showed mild activity only against S. aureus, while no antimicrobial activity was recorded for NL-L1 extract. All the endophytic fungal extracts showed no activity against the test fungi C. albicans and A. fumigatus. HPLC analysis of the fungal extracts revealed the presence of ethyl 4-hydroxyphenyl acetate and ferulic acid in NL-L1; ruspolinone in NL-L2; protocatechuic acid, scytalone, and cladosporin in SL-L1; indole-3-acetic acid and indole-3-carbaldehyde in PPL-LE2; and indole-3-acetic acid in PPL-LAC. The findings of this study revealed the potentials possessed by these plants as source of endophytes that express biological active compounds. These endophytes hold key of possibilities to the discovery of novel molecules for pharmaceutical, agricultural and industrial applications.

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Optical properties of translucent zirconia: A review of the literature

-stabilized zirconium dioxide compared to porcelain-veneered crowns and lithium disilicate crowns. Acta Odontol Scand 2014;72:145-153. 60. Beuer F, Stimmelmayr M, Gueth JF, et al. In vitro performance of full-contour zirconia single crowns. Dent Mater 2012;28:449-456. 61. Holand W, Schweiger M, Watzke R, et al. Ceramics as biomaterials for dental restoration. Expert Rev Med Devices 2008;5:729-745. 62. Fischer J, Stawarczyk B and Hammerle CH. Flexural strength of veneering ceramics for zirconia. J Dent 2008; 36: 316-321. 63. Glidewell Laboratories. About Us

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Indoor air pollution and the contribution of biosensors

homes in Edmonton, Canada. Building and Environment, 2015; 90: p. 114-124. 6. Bako-Biro Z, Wargocki P, Weschler CJ,Fanger PO, Effects of pollution from personal computers on perceived air quality, SBS symptoms and productivity in offices. Indoor Air, 2004; 14(3): p. 178-187. 7. Lee SC, Chan LY,Chiu MY, Indoor and outdoor air quality investigation at 14 public places in Hong Kong. Environment International, 1999; 25(4): p. 443-450. 8. Hong T, Kim J,Lee M, Integrated task performance score for the building occupants based on the CO2 concentration and

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Classification of coronary artery disease data sets by using a deep neural network

Abstract

In this study, a deep neural network classifier is proposed for the classification of coronary artery disease medical data sets. The proposed classifier is tested on reference CAD data sets from the literature and also compared with popular representative classification methods regarding its classification performance. Experimental results show that the deep neural network classifier offers much better accuracy, sensitivity and specificity rates when compared with other methods. The proposed method presents itself as an easily accessible and cost-effective alternative to currently existing methods used for the diagnosis of CAD and it can be applied for easily checking whether a given subject under examination has at least one occluded coronary artery or not.

Open access
Artificial intelligence used in genome analysis studies

Abstract

Next Generation Sequencing (NGS) or deep sequencing technology enables parallel reading of multiple individual DNA fragments, thereby enabling the identification of millions of base pairs in several hours. Recent research has clearly shown that machine learning technologies can efficiently analyse large sets of genomic data and help to identify novel gene functions and regulation regions. A deep artificial neural network consists of a group of artificial neurons that mimic the properties of living neurons. These mathematical models, termed Artificial Neural Networks (ANN), can be used to solve artificial intelligence engineering problems in several different technological fields (e.g., biology, genomics, proteomics, and metabolomics). In practical terms, neural networks are non-linear statistical structures that are organized as modelling tools and are used to simulate complex genomic relationships between inputs and outputs. To date, Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNN) have been demonstrated to be the best tools for improving performance in problem solving tasks within the genomic field.

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Formal- and high-structured kinetic process modelling and footprint area analysis of binary imaged cells: Tools to understand and optimize multistage-continuous PHA biosynthesis

Abstract

Competitive polyhydroxyalkanoate (PHAs) production requires progress in microbial strain performance, feedstock selection, downstream processing, and more importantly according to the process design with process kinetics of the microbial growth phase and the phase of product formation. The multistage continuous production in a bioreactor cascade was described for the first time in a continuously operated, flexible five-stage bioreactor cascade that mimics the characteristics involved in the engineering process of tubular plug flow reactors. This process was developed and used for Cupriavidus necator-mediated PHA production at high volumetric and specific PHA productivity (up to 2.31 g/(Lh) and 0.105 g/(gh), respectively). Based on the experimental data, formal kinetic and high structured kinetic models were established, accompanied by footprint area analysis of binary imaged cells. As a result of the study, there has been an enhanced understanding of the long-term continuous PHA production under balanced, transient, and nutrient-deficient conditions that was achieved on both the micro and the macro kinetic level. It can also be concluded that there were novel insights into the complex metabolic occurrences that developed during the multistage- continuous production of PHA as a secondary metabolite. This development was essential in paving the way for further process improvement. At the same time, a new method of specific growth rate and specific production rate based on footprint area analysis was established by using the electron microscope.

Open access
Lower limb phantom design and production for blood flow and pressure tests

Abstract

Phantoms are specifically designed objects that are utilized or imaged to evaluate, analyze and tune the performance of experimental devices. In this project, it is aimed to design a phantom that responds in a similar manner with how human blood circulation would act in specific flow and pressure tests such as pulse measurement. Ballistic gelatin is a member of hydrogel family with 250 Bloom value which resembles human muscle tissue in terms of mechanical features. That’s why we carried out a uniaxial compression test on our gelatin sample to analyze its similarity of human muscle tissue in terms of elastic modulus, stiffness and rupture strength. Test results indicated that our gelatin sample has approximate values with organic human muscle tissue. Designed model was X-rayed and the similarities of the model to human texture were compared. After producing of lower limb phantoms, we carried out a circulation test through them by the aid of a peristaltic pump to simulate the actual blood circulation of human body limbs. This designed phantom is made ready for available flow and pressure tests.

Open access