The momentum gained by research on biologics has not been met yet with equal thrust on the informatics side. There is a noticeable lack of software for data management that empowers the bench scientists working on the development of biologic therapeutics. SARvision|Biologics is a tool to analyze data associated with biopolymers, including peptides, antibodies, and protein therapeutics programs. The program brings under a single user interface tools to filter, mine, and visualize data as well as those algorithms needed to organize sequences. As part of the data-analysis tools, we introduce two new concepts: mutation cliffs and invariant maps. Invariant maps show the variability of properties when a monomer is maintained constant in a position of the biopolymer. Mutation cliff maps draw attention to pairs of sequences where a single or limited number of point mutations elicit a large change in a property of interest. We illustrate the program and its applications using a peptide data set collected from the literature.
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http://dx.doi.org/10.1021/ci400333x | DOI Listing |
J Vis
January 2025
Department of Cognitive Sciences and Neurobiology and Behavior, University of California, Irvine, California, USA.
A salience map is a topographic map that has inputs at each x,y location from many different feature maps and summarizes the combined salience of all those inputs as a real number, salience, which is represented in the map. Of the more than 1 million Google references to salience maps, nearly all use the map for computing the relative priority of visual image components for subsequent processing. We observe that salience processing is an instance of substance-invariant processing, analogous to household measuring cups, weight scales, and measuring tapes, all of which make single-number substance-invariant measurements.
View Article and Find Full Text PDFIntegrating spatial and temporal information is essential for our sensory experience. While psychophysical evidence suggests spatial dependencies in duration perception, few studies have directly tested the neural link between temporal and spatial processing. Using ultra-high-field functional MRI and neuronal-based modeling, we investigated how and where the processing and the representation of a visual stimulus duration is linked to that of its spatial location.
View Article and Find Full Text PDFPhys Rev Lett
December 2024
GISC, Departamento de Matemáticas, Universidad Carlos III de Madrid, 28911 Leganés, Madrid, Spain.
Recent studies of wetting in a two-component square-gradient model of interfaces in a fluid mixture, showing three-phase bulk coexistence, have revealed some highly surprising features. Numerical results show that the density profile paths, which form a tricuspid shape in the density plane, have curious geometric properties, while conjectures for the analytical form of the surface tensions imply that nonwetting may persist up to the critical end points, contrary to the usual expectation of critical point wetting. Here, we solve the model exactly and show that the profile paths are conformally invariant quartic algebraic curves that change genus at the wetting transition.
View Article and Find Full Text PDFMed Image Anal
December 2024
School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
Continual test-time adaptation (CTTA) aims to continuously adapt a source-trained model to a target domain with minimal performance loss while assuming no access to the source data. Typically, source models are trained with empirical risk minimization (ERM) and assumed to perform reasonably on the target domain to allow for further adaptation. However, ERM-trained models often fail to perform adequately on a severely drifted target domain, resulting in unsatisfactory adaptation results.
View Article and Find Full Text PDFJ Cell Mol Med
December 2024
The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China.
To uncover the complex immune mechanisms driving inflammation in ankylosing spondylitis and lay the groundwork for identifying new therapeutic targets and innovative approaches, we conducted 10× single-cell sequencing on bone marrow cell samples collected from the vertebrae of three AS patients and three non-AS patients. Using single-cell sequencing data, we analysed the expression of differentially expressed genes (DEGs) by comparing AS patients with non-AS patients. Key genes among the related DEGs were identified through protein-protein interaction networks and hub gene screening and further validated using immunohistochemistry.
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