For two-class problems, we introduce and construct mappings of high-dimensional instances into dissimilarity (distance)-based Class-Proximity Planes. The Class Proximity Projections are extensions of our earlier relative distance plane mapping, and thus provide a more general and unified approach to the simultaneous classification and visualization of many-feature datasets. The mappings display all L-dimensional instances in two-dimensional coordinate systems, whose two axes represent the two distances of the instances to various pre-defined proximity measures of the two classes. The Class Proximity mappings provide a variety of different perspectives of the dataset to be classified and visualized. We report and compare the classification and visualization results obtained with various Class Proximity Projections and their combinations on four datasets from the UCI data base, as well as on a particular high-dimensional biomedical dataset.
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http://dx.doi.org/10.1016/j.jbi.2011.04.004 | DOI Listing |
Chem Sci
January 2025
Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Netherlands
Disordered proteins and domains are ubiquitous throughout the proteome of human cell types, yet the biomolecular sciences lack effective tool compounds and chemical strategies to study this class of proteins. In this context, we introduce a novel covalent tool compound approach that combines proximity-enhanced crosslinking with histidine trapping. Utilizing a maleimide-cyclohexenone crosslinker for efficient cysteine-histidine crosslinking, we elucidated the mechanism of this dual-reactive tool compound class.
View Article and Find Full Text PDFAmyotroph Lateral Scler Frontotemporal Degener
January 2025
Stan Cassidy Centre for Rehabilitation, Fredericton, New Brunswick, Canada.
Objective: Previous studies have hinted at an association between water exposure and the development of ALS. However, proximity measures to these water sources have been limited to questionnaires or large buffers due to a lack of fine geospatial measures. They also do not distinguish the various classes of hydrographic features.
View Article and Find Full Text PDFProteins that selectively bind to a target of interest are foundational components of research pipelines , diagnostics , and therapeutics . Current immunization-based , display- based , and computational approaches for discovering binders are laborious and time- consuming - taking months or more, suffer from high false positives - necessitating extensive secondary screening, and have a high failure rate, especially for disordered proteins and other challenging target classes. Here we establish Phage-Assisted Non-Continuous Selection of Protein Binders (PANCS-binders), an selection platform that links the life cycle of M13 phage to target protein binding though customized proximity-dependent split RNA polymerase biosensors, allowing for complete and comprehensive high-throughput screening of billion-plus member protein variant libraries with high signal-to-noise.
View Article and Find Full Text PDFAdv Sci (Weinh)
January 2025
School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China.
Sulfur-fluoride exchange (SuFEx) reaction is an emerging class of click chemistry reaction. Owing to its efficient reactivity under physiological conditions, SuFEx reaction is used to construct covalent protein drugs. Herein, a covalent affibody-molecular glue drug conjugate nanoagent is reported, which can irreversibly bind with its target protein through proximity-enabled SuFEx reaction.
View Article and Find Full Text PDFLinear digital filters are at the core of image reconstruction and processing for many coherent optical imaging techniques, such as digital holography (DH) or optical coherence tomography (OCT). They can also be efficiently implemented using fast Fourier transform (FFT) with appropriate transfer/filter functions that operate in the frequency domain. However, even with optimal filter design, they suffer from side effects such as sidelobe generation or resolution limitations, e.
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