Artif Intell Med
AnacletoLab, Computer Science Department, Università degli Studi di Milano, Milan, Italy; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; CINI, Infolife National Laboratory, Roma, Italy; Department of Computer Science, Aalto University, Espoo, Finland. Electronic address:
Published: December 2024
Multi-omics data have revolutionized biomedical research by providing a comprehensive understanding of biological systems and the molecular mechanisms of disease development. However, analyzing multi-omics data is challenging due to high dimensionality and limited sample sizes, necessitating proper data-reduction pipelines to ensure reliable analyses. Additionally, its multimodal nature requires effective data-integration pipelines. While several dimensionality reduction and data fusion algorithms have been proposed, crucial aspects are often overlooked. Specifically, the choice of projection space dimension is typically heuristic and uniformly applied across all omics, neglecting the unique high dimension small sample size challenges faced by individual omics. This paper introduces a novel multi-modal dimensionality reduction pipeline tailored to individual views. By leveraging intrinsic dimensionality estimators, we assess the curse-of-dimensionality impact on each view and propose a two-step reduction strategy for significantly affected views, combining feature selection with feature extraction. Compared to traditional uniform reduction pipelines in a crucial and supervised multi-omics analysis setting, our approach shows significant improvement. Additionally, we explore three effective unsupervised multi-omics data fusion methods rooted in the main data fusion strategies to gain insights into their performance under crucial, yet overlooked, settings.
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http://dx.doi.org/10.1016/j.artmed.2024.103049 | DOI Listing |
Proc Natl Acad Sci U S A
January 2025
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390.
Neurotransmitter release is triggered in microseconds by Ca-binding to the Synaptotagmin-1 C-domains and by SNARE complexes that form four-helix bundles between synaptic vesicles and plasma membranes, but the coupling mechanism between Ca-sensing and membrane fusion is unknown. Release requires extension of SNARE helices into juxtamembrane linkers that precede transmembrane regions (linker zippering) and binding of the Synaptotagmin-1 CB domain to SNARE complexes through a "primary interface" comprising two regions (I and II). The Synaptotagmin-1 Ca-binding loops were believed to accelerate membrane fusion by inducing membrane curvature, perturbing lipid bilayers, or helping bridge the membranes, but SNARE complex binding through the primary interface orients the Ca-binding loops away from the fusion site, hindering these putative activities.
View Article and Find Full Text PDFMedicine (Baltimore)
January 2025
Department of Spinal Surgery, Shenzhen Third People's Hospital, Shenzhen, China.
This study analyzes the risk factors related to the complications of anterior thoracolumbar tuberculosis in adults and to provide clinical reference. A total of 98 adult patients with thoracolumbar tuberculosis undergoing anterior surgery in our hospital from February 2020 to December 2023 were selected, and the clinical data and postoperative complications were collected. The clinical characteristics were analyzed, and the risk factors related to surgical complications were analyzed by univariate analysis and multi-factor logistic regression model.
View Article and Find Full Text PDFJ Physiol
January 2025
Department of Biomedical Sciences, University of Padova, Padova, Italy.
Short-term unloading experienced following injury or hospitalisation induces muscle atrophy and weakness. The effects of exercise following unloading have been scarcely investigated. We investigated the functional and molecular adaptations to a resistance training (RT) programme following short-term unloading.
View Article and Find Full Text PDFMol Biol Rep
January 2025
Department of Pathology and Laboratory Medicine, Baylor Scott and White Medical Center, Baylor College of Medicine, Temple, TX, USA.
Background: Brain intraparenchymal schwannoma is a rare clinical entity, generally curable with adequate resection.
Methods And Results: We describe a case in a male patient first presenting at 19 months of age, the youngest reported age for this lesion. It also appears to be the first case connected to a germline TSC2 p.
Sci Rep
January 2025
Department of Laboratory Medicine, Clinical Pathology and Genetics, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
Vulvar cancer is a rare gynaecological disease that can be caused by infection with human papillomavirus (HPV). The mutational frequencies and landscape for HPV-associated and HPV-independent vulvar tumor development are supposedly two distinctly different pathways and more detailed knowledge on target biological mechanisms for individualized future treatments is needed. The study included formalin-fixed paraffin-embedded (FFPE) samples from 32 cancer patients (16 HPV-negative and 16 HPV-associated), treated in Örebro, Sweden from 1988 to 2008.
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