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Motivation: Progress in systems biology depends on developing scalable informatics tools to predictively model, visualize, and flexibly store information about complex biological systems. Scalability of these tools, as well as their ability to integrate within larger frameworks of evolving tools, is critical to address the multi-scale and size complexity of biological systems.
Results: Using current software technology, such as self-generation of database and object code from UML schemas, facilitates rapid updating of a scalable expert assistance system for modeling biological pathways. Distribution of key components along with connectivity to external data sources and analysis tools is achieved via a web service interface.
Availability: All sigmoid modeling software components and supplementary information are available through: http://www.igb.uci.edu/servers/sb.html.
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http://dx.doi.org/10.1007/978-1-4419-5913-3_58 | DOI Listing |
Mol Ecol
September 2025
State Key Laboratory of Soil and Water Conservation and Desertification Control, College of Soil and Water Conservation Science and Engineering, Northwest A&F University, Shaanxi, People's Republic of China.
Increasing evidence indicates that the loss of soil microbial α-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial α-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal α- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal α-diversity declined under high environmental stress across three soil layers (0-20 cm, 20-40 cm and 40-60 cm).
View Article and Find Full Text PDFNeurotrauma Rep
August 2025
Department of Radiology, Weill Cornell Medicine; New York, New York, USA.
Traumatic brain injury (TBI) impairs attention and executive function, often through disrupted coordination between cognitive and autonomic systems. While electroencephalography (EEG) and pupillometry are widely used to assess neural and autonomic responses independently, little is known about how these systems interact in TBI. Understanding their coordination is essential to identify compensatory mechanisms that may support attention under conditions of neural inefficiency.
View Article and Find Full Text PDFiScience
September 2025
Max Planck Institute of Psychiatry, 80804 Munich, Germany.
Isoform-specific expression patterns have been linked to stress-related psychiatric disorders such as major depressive disorder (MDD). To further explore their involvement, we constructed co-expression networks using total gene expression (TE) and isoform ratio (IR) data from affected ( = 210, 81% with depressive symptoms) and unaffected ( = 95) individuals. Networks were validated using advanced graph generation methods.
View Article and Find Full Text PDFMater Today Bio
October 2025
University of Maribor, Faculty of Medicine, Institute of Biomedical Sciences, Taborska Ulica 8, SI-2000, Maribor, Slovenia.
Catheter associated urinary tract infection (CAUTI) is the most frequent healthcare associated infection, arising from microbial adhesion to catheter surfaces, biofilm development, and the growing problem of antimicrobial resistance. Many publications have addressed CAUTI epidemiology, biofilm biology, or biomaterials for catheters in isolation, yet there is little literature that connects these areas into a coherent translational perspective. This review seeks to fill that gap by combining an overview of biofilm pathophysiology with recent advances in material based innovations for catheter design, including nanostructured and responsive coatings, sensor enabled systems, additive manufacturing, and three dimensional printing.
View Article and Find Full Text PDFFront Genet
August 2025
Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States.
This study introduces a Drought Adaptation Index (DAI), derived from Best Linear Unbiased Prediction (BLUP), as a method to assess drought resilience in switchgrass ( L.). A panel of 404 genotypes was evaluated under drought-stressed (CV) and well-watered (UC) conditions over four consecutive years (2019-2022).
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