Biological data visualization is challenged by the growing complexity of datasets. Traditional single-data plots or simple juxtapositions often fail to fully capture dataset intricacies and interrelations. To address this, we introduce "cross-layout," a novel visualization paradigm that integrates multiple plot types in a cross-like structure, with a central main plot surrounded by secondary plots for enhanced contextualization and interrelation insights. We also introduce "Marsilea," a Python-based implementation of cross-layout visualizations, available in both programmatic and web-based interfaces to support users of all experience levels. This paradigm and its implementation offer a customizable, intuitive approach to advance biological data visualization.
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http://dx.doi.org/10.1186/s13059-024-03469-3 | DOI Listing |
Prog Lipid Res
January 2025
Lipids in Human Pathology, Institut d'Investigació Sanitària Illes Balears (IdISBa) - Health Research Institute of the Balearic Islands, Ctra. Valldemossa 79, Module G, Floor -1, E-07120 Palma, Balearic Islands, Spain; Research Unit, University Hospital Son Espases, Ctra Valldemossa 79, E-07120 Palma, Balearic Islands, Spain. Electronic address:
Lipid imaging mass spectrometry (LIMS) allows for establishing the bidimensional distribution of lipid species within a tissue section. One of the main advantages is the generation of spatial information on lipid species distribution at a spatial (lateral) resolution bordering on single-cell resolution with no need to isolate cells. Thus, LIMS images demonstrate, with a level of detail never described before, that lipid profiles are highly sensitive to cell type and pathophysiological state.
View Article and Find Full Text PDFCurr Biol
December 2024
Durrell Institute of Conservation and Ecology, University of Kent, Canterbury CT2 7NR, UK.
Conservation initiatives strive for reliable and cost-effective species monitoring. However, resource constraints mean management decisions are overly reliant on data derived from single methodologies, resulting in taxonomic or geographic biases. We introduce a data integration framework to optimize species monitoring in terms of spatial representation, the reliability of biodiversity metrics, and the cost of implementation, focusing on tigers and their principal prey (sambar deer and wild pigs).
View Article and Find Full Text PDFRes Vet Sci
December 2024
CIBERINFEC, ISCIII - CIBER Infectious Diseases, Health Institute Carlos III, Madrid, Spain; Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain.
Recent molecular and metagenomic studies have revealed that the obligate anaerobic protist Blastocystis is found more prevalently and with higher subtype diversities in herbivore species than in carnivore species. However, information on wild carnivore species is scarce. Here, we investigated the presence of Blastocystis by molecular methods in fecal DNA samples of free-ranging and captive Iberian lynxes from Spain (n = 243) and Portugal (n = 30).
View Article and Find Full Text PDFSci Total Environ
January 2025
Department of Biological and Agricultural Engineering, University of Arkansas, United States of America. Electronic address:
The increasing global demand for meat and dairy products, fueled by rapid industrialization, has led to the expansion of Animal Feeding Operations (AFOs) in the United States (US). These operations, often found in clusters, generate large amounts of manure, posing a considerable risk to water quality due to the concentrated waste streams they produce. Accurately mapping AFOs is essential for effective environmental and disease management, yet many facilities remain undocumented due to variations in federal and state regulations.
View Article and Find Full Text PDFEcotoxicol Environ Saf
January 2025
Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai 200032, China. Electronic address:
Surgery remains the primary treatment for solid malignant tumors, but controlling postoperative tumor recurrence and metastasis continues to be a major challenge. Understanding the factors that influence tumor recurrence and metastasis after surgery, as well as the underlying biological mechanisms, is critical. Previous studies suggest that anesthetic agents may increase the risk of tumor recurrence and metastasis in patients with cancer, but the mechanisms underlying these findings remain unclear.
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