Keith A.

Open Access Article by Madelyn J. Hill Madelyn J. Hill SciProfiles Scilit Preprints.org

Sequence data, such as nucleotides or amino acids, are crucial in advancing our understanding of biology. However, investigating and analyzing sequencing data and genotype–phenotype associations present several challenges, including noise components that arise from the sequencing, nonlinear genotype–phenotype associations, collinearity between input features, and high dimensionality of the input data. Machine learning (ML) algorithms have proven to be effective in detecting intricate and nonstructural patterns, making them a valuable tool for studies focused on genotype–phenotype associations. Yet, there needs to be more user-friendly ML implementations that leverage the unique features of high-volume DNA sequence data. Here, we introduce deepBreaks, a generic approach that detects important positions (genotypes) in sequence data that are associated with phenotypic traits. deepBreaks compares the performance of multiple ML algorithms and prioritizes positions based on the best-fit models. It is open-source software with online documentation and examples available at https://github/omicsEye/deepBreaks .

Silica-based glasses have found numerous applications in every field of human endeavor. Understanding their mechanical behavior under high strain r...

Here the authors show that tissue-resident memory and exhausted T cells in tumors are distinct populations that are shaped by relative presence or absence of TCR signals, suggesting that a tailored therapeutic strategy is needed to target each subset.

Men undergoing cancer therapy are at risk of treatment-related infertility, which can negatively affect quality of life. Although fertility preservation (FP) is routinely recommended for men of reproductive age who are diagnosed with cancer, less is known about how they navigate these decisions or what informational and emotional supports they require across the diagnosis–treatment–survivorship trajectory. We conducted a qualitative secondary analysis of a subset of data from a broader study of cancer and FP decision-making. In-depth interviews with 12 men who had undergone fertility-threatening cancer treatments and had experienced FP were analyzed using a thematic analysis approach. Participants reported gaps in clear, timely and practical information, including costs, clinic access, sperm storage and future use. Men and their partners described feelings of fear, uncertainty and diminished control, especially when decisions had to be made quickly, before treatment began. Their choices were influenced not only by clinical advice but also by social expectations related to masculinity. Structural/logistical barriers such as diagnostic uncertainty, illness severity and poorly coordinated care pathways further undermined their agency and contributed to distress. These findings indicate that men’s experience of FP is not a straightforward medical procedure but a complex and ongoing process with logistical, informational and psychosocial challenges. Integrating organized counselling and continuous emotional support into oncology care may reduce distress and enhance decision-making processes.

Background and ObjectivesLow circulating vitamin D in later life has been associated with increased risk of cognitive impairment and clinical dementia. However, whether serum vitamin D in early midlife is associated with neuroimaging markers of ...

Despite considerable interest in using stable-hydrogen isotope ratio (δD) measurements in ecological research, it was previously unknown whether hy...

Background and ObjectivesDespite a well-established amyloid-tau neurodegeneration cascade in Alzheimer disease (AD), the extent and mechanistic relevance of tau pathology in cerebral amyloid angiopathy (CAA), a disease of vascular amyloid deposition, ...

Embedding a small fraction of force-sensitive mechanophores as cross-links into common polymers enhances ballistic energy dissipation.