This work introduces minimum accumulative degeneracy, a variant of the degenerate primer design problem, which is particularly useful when a large number of sequences are to be covered by a set of restricted number of primers. A primer set, which is designed on a minimum accumulative degeneracy basis, especially helps to reduce nonspecific PCR amplification of undesired DNA fragments, as fewer primer species are present in PCR. A Boltzmann machine is designed to solve the minimum accumulative degeneracy degenerate primer design problem, called the MAD-DPD Boltzmann machine. This algorithm shows great flexibility, as it can be determined either to solve the problem with strict fidelity to covering all input sequences or to exclude some input sequences if it results in less degenerate primers. This Boltzmann machine is successfully implemented in designing a new set of primers for amplification of antibody variable fragments from mouse spleen cells, which theoretically covers more diverse antibody sequences than currently available primers. The MAD-DPD Boltzmann machine is available online at bioinf.cs.ipm.ir/download/MAD_DPD08172007.zip.
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http://dx.doi.org/10.2144/000112694 | DOI Listing |
JMIR Mhealth Uhealth
January 2025
Ludwig Boltzmann Institute for Digital Health and Prevention, Salzburg, Austria.
Background: There has been a surge in the development of apps that aim to improve health, physical activity (PA), and well-being through behavior change. These apps often focus on creating a long-term and sustainable impact on the user. Just-in-time adaptive interventions (JITAIs) that are based on passive sensing of the user's current context (eg, via smartphones and wearables) have been devised to enhance the effectiveness of these apps and foster PA.
View Article and Find Full Text PDFSensors (Basel)
January 2025
Department of Electrical Engineering, American University of Sharjah, Sharjah 26666, United Arab Emirates.
Accurately identifying and discriminating between different brain states is a major emphasis of functional brain imaging research. Various machine learning techniques play an important role in this regard. However, when working with a small number of study participants, the lack of sufficient data and achieving meaningful classification results remain a challenge.
View Article and Find Full Text PDFJ Clin Med
January 2025
Department of Trauma Surgery, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
: Tactile gnosis derives from the interplay between the hand's tactile input and the memory systems of the brain. It is the prerequisite for complex hand functions. Impaired sensation leads to profound disability.
View Article and Find Full Text PDFJ R Soc Interface
January 2025
Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.
Can a micron-sized sack of interacting molecules autonomously learn an internal model of a complex and fluctuating environment? We draw insights from control theory, machine learning theory, chemical reaction network theory and statistical physics to develop a general architecture whereby a broad class of chemical systems can autonomously learn complex distributions. Our construction takes the form of a chemical implementation of machine learning's optimization workhorse: gradient descent on the relative entropy cost function, which we demonstrate can be viewed as a form of integral feedback control. We show how this method can be applied to optimize any detailed balanced chemical reaction network and that the construction is capable of using hidden units to learn complex distributions.
View Article and Find Full Text PDFCells
December 2024
Department of Herbal Pharmacology, College of Korean Medicine, Gachon University, 1342 Seongnamdae-ro, Sujeong-gu, Seongnam-si 13120, Republic of Korea.
The NLRP3 inflammasome, plays a critical role in the pathogenesis of rheumatoid arthritis (RA) by activating inflammatory cytokines such as IL1β and IL18. Targeting NLRP3 has emerged as a promising therapeutic strategy for RA. In this study, a multidisciplinary approach combining machine learning, quantitative structure-activity relationship (QSAR) modeling, structure-activity landscape index (SALI), docking, molecular dynamics (MD), and molecular mechanics Poisson-Boltzmann surface area MM/PBSA assays was employed to identify novel NLRP3 inhibitors.
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