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

number of machine learning algorithms available in the bioinformatic toolbox to predict cleavage sites of viral proteases. Choosing the correct method is essential for accurate predictions. Previously, this information has been useful for the design of antivirals. This study aims to apply and compare several machine learning algorithms to an HCV NS3P dataset and to see whether differences in sequence-data transformation and model selection improves prediction accuracies based on three performance metrics. Methods Datasets The dataset obtained by Narayanan et al

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

be affected by a greater or lesser extent of error. The preanalytical phase comprises test selection and specimen collection, processing, handling, and delivery to the testing site; the analytic phase includes selection of test methods, performance of test procedures, monitoring and verification of the accuracy and reliability of test results, and documentation of test findings; The postanalytical phase includes reporting test results and archiving records, reports, and tested specimens ( 7 ). Errors are very likely to emerge during the pre-analytical phase and

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

´s interior since eons. After the use of biopolymers, they undergo biodegradation and composting by the metabolism of living organisms, which generates biomass and CO 2 ; CO 2 , in turn, gets fixed again by the photosynthetic performance of green plants to rebuild the renewable feedstocks originally used for biopolymer synthesis, which closes the cycle of anabolism and catabolism of biopolymer feedstocks. This differs drastically from the life-cycle processes of petrochemical plastics, the thermal degradation of which results in a misbalance of CO 2 through combustion

Open access
Artificial intelligence used in genome analysis studies

supplied without correspondence with the outputs (y) ( 10 ). In this case, the goal is to find hidden patterns or intrinsic structures that have been provided in the data. Through this process, it is possible to make inferences regarding data without having an exact answer and a supervisor to correct possible errors ( 11 ). Reinforcement learning : Reinforcement learning differs from the supervised method in that there is no supervisor; hence, the model is based on the reward (measured as the evaluation of the achievied performance) ( 12 ). Based on this signal, the

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

extracts using high performance liquid chromatography (HPLC). Materials and Methods Isolation of endophytic fungus, fermentation and extraction of metabolites Fresh leaves of Newbouldia laevis, Ocimum gratissimum , and Carica papaya were collected from Agulu, Anambra State, Nigeria. Isolation of endophytic fungi from the plant leaves was carried out as described by Eze et al . ( 40 ). The plant leaves were washed thoroughly in running tap water and then cut into small fragments (about 1 cm 2 ). The leaf fragments were surface-sterilized by immersion in 2

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Electrochemical impedimetric detection of stroke biomarker NT-proBNP using disposable screen-printed gold electrodes


Stroke is the second top leading cause of death globally. It is caused by an abrupt interruption of blood flow to the brain. In that course, brain natriuretic peptide (BNP) and its derivative N-terminal pro b-type natriuretic peptide (NT-proBNP), neurohormones produced mainly by the heart ventricles in response to excessive stretching of cardiomyocytes (heart muscle cells), are proven to be good biomarkers for heart failure diagnosis. Moreover, there is growing clinical interest of the use of NT-proBNP for stroke diagnosis and prognosis because it is significantly associated with cardioembolic stroke and secondary stroke reoccurrence, with sensitivity >90% and specificity >80%. However, in diagnostic settings, there is still a need to address the encountered analytical problems, particularly assay specificity and set up. In this study, a novel approach for NT-proBNP detection is demonstrated using an electrochemical immunoassay method. A label-free impedimetry immunosensor for stroke biomarker was developed using modified disposable screen-printed gold electrodes (SPGE) hosting specific anti-NT-proBNP capture antibody. The performance of our immunosensor was studied in the presence of NT-proBNP in both buffered and mock (porcine) plasma samples. A linear relation between the relative total resistance (ΔRtot) responses and the NT-proBNP concentrations in buffer was observed in a range from 0.1 to 5 ng mL-1 with a correlation coefficient (R2) of 0.94656. Overall, the biosensor has demonstrated the capability to quantitate NT-proBNP and differentiate such concentrations in a low concentration range, especially among 0, 0.1, 0.5, 1, and 3 ng mL-1 in plasma samples within 25 min. This range is valuable not only for classifying cardioembolic stroke (higher or equal to 0.5 ng mL-1), but also predicting the risk of secondary stroke reoccurrence (higher than 0.255 ng mL-1). Our biosensor has the potential to be used as an easy-to-use point-of-care test that is both accurate and affordable.

Open access
Motion artifact detection in colonoscopy images

images with no artifact (clear) was tried automatically. Experts have to select among all the videos and images that are clear and after this process is completed they have to decide on the disease type. Deciding clear images visually has two main drawbacks: Firstly, this process is time-consuming for the experts in a highly busy daily schedule, and secondly, since the decisions are subjective and dependent on the experts’ performance, human factors such as fatigue, sleepiness or lack of experience may negatively affect the accuracy of clear images and disease

Open access
Contributions of biotechnology to meeting future food and environmental security needs

, Ranger Russet and Atlantic varieties, which contain only wild and cultivated potato genes, have received US Dept. of Agriculture, Food and Drug Administration and Environmental Protection Agency clearance, for growth and sale in the United States, as well as from Health Canada and the Canadian Food Inspection Agency ( 23 ). Marketing consents for import of Innate potatoes are currently being pursued in at least a further eight different countries. 20 years on since the first biotechnology potato, the future use of biotechnology to enhance potato performance and provide

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MAB2.0 project: Integrating algae production into wastewater treatment

mechanically remove solid materials, followed by the secondary treatment to reduce organic matter and nutrients. Tertiary treatment may be also applied to polish the effluent. These steps are referred as the water line, while the usual aerated activated sludge mechanism as secondary treatment results in sludge to be managed in the sludge line. WWTPs are focusing on the water line as that delivers clean water which is the main performance and legal indicator; improvement of the sludge line by means of energy and cost efficiency, as well as its environmental performance is

Open access
Application of whey retentate as complex nitrogen source for growth of the polyhydroxyalkanoate producer Hydrogenophaga pseudoflava strain DSM1023

silage. Whey retentate was particularly selected for this study to complement the excellent performance of the strain in producing PHAs from whey permeate as carbon source ( 16 , 17 ); using both the permeate and the retentate fraction in a PHA production process would pave the way towards a complete utilization of the surplus material whey, which, due to its high (bio)chemical oxygen demand, currently poses environmental threats when disposed as waste into aquatic environments ( 29 ). In addition, this new application of whey retentate for PHA biosynthesis can be

Open access