Publications by authors named "Steven Andrews"

Turbulence and sound are important cues for oyster reef larval recruitment. Numerous studies have found a relationship between turbulence intensity and swimming behaviors of marine larvae, while others have documented the importance of sounds in enhancing larval recruitment to oyster reefs. However, the relationship between turbulence and the reef soundscape is not well understood.

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Biochemical reaction networks perform a variety of signal processing functions, one of which is computing the integrals of signal values. This is often used in integral feedback control, where it enables a system's output to respond to changing inputs, but to then return exactly back to some pre-determined setpoint value afterward. To gain a deeper understanding of how biochemical networks are able to both integrate signals and perform integral feedback control, we investigated these abilities for several simple reaction networks.

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Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks.

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Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology in order to lend a new perspective on the evolved designs of cells' underlying reaction networks.

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Clinical decision support systems (CDSS) for the ongoing decision making required to support health behavior change for chronic disease management should incorporate behavioral science (e.g., a collaborative goal setting workflow) with more common CDSS components (i.

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Purpose Of Review: Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently associated with cancer and can result in cells acquiring an ability to divide and grow uncontrollably. Because signaling pathways play such a significant role in cancer initiation and advancement, their constituent proteins are attractive therapeutic targets.

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Article Synopsis
  • Somatic mutations play a crucial role in cancer development, with many known driver mutations found in protein coding regions, but the impact of mutations in miRNAs and their binding sites is poorly understood.
  • This study created cancer-specific miRNA regulatory networks for 30 cancer types, analyzing over 3.5 million mutations and revealing that mutations in miRNAs often occur alongside mutations in their target genes, influencing gene expression.
  • The findings highlight 148 potential driver mutations that disrupt miRNA networks, suggesting that downregulated targets in 3' UTRs may act as tumor suppressors, and they introduce a web portal (mGI-map) to help researchers explore this data for future biomarker and drug development.
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We conducted a range-wide investigation of the dynamics of site-level reproductive rate of northern spotted owls using survey data from 11 study areas across the subspecies geographic range collected during 1993-2018. Our analytical approach accounted for imperfect detection of owl pairs and misclassification of successful reproduction (i.e.

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Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface.

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Motivation: Smoldyn is a particle-based biochemical simulator that is frequently used for systems biology and biophysics research. Previously, users could only define models using text-based input or a C/C++ application programming interface (API), which were convenient, but limited extensibility.

Results: We added a Python API to Smoldyn to improve integration with other software tools, such as Jupyter notebooks, other Python code libraries and other simulators.

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Breeding dispersal, the movement from one breeding territory to another, is rare for philopatric species that evolved within relatively stable environments, such as the old-growth coniferous forests of the Pacific Northwest. Although dispersal is not inherently maladaptive, the consequences of increased dispersal on population dynamics in populations whose historical dispersal rates are low could be significant, particularly for a declining species. We examined rates and possible causes of breeding dispersal based on a sample of 4,118 northern spotted owls (Strix occidentalis caurina) monitored in seven study areas over 28 yr, 1990-2017, in Oregon and Washington, USA.

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We describe an implementation of a pilot integration to embed SDoH-based data visualizations into the EHR in real time for clinical staff treating children with asthma.

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Background: In the homeless population, barriers to housing and supportive services include a lack of control or access to data. Disparate data formats and storage across multiple organizations hinder up-to-date intersystem access to records and a unified view of an individual's health and documentation history. The utility of blockchain to solve interoperability in health care is supported in recent literature, but the technology has yet to be tested in real-life conditions encompassing the complex regulatory standards in the health sector.

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Biological cells are complex environments that are densely packed with macromolecules and subdivided by membranes, both of which affect the rates of chemical reactions. It is well known that crowding reduces the volume available to reactants, which increases reaction rates, and also inhibits reactant diffusion, which decreases reaction rates. This work investigates these effects quantitatively using analytical theory and particle-based simulations.

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Many biological molecules exist in multiple variants, such as proteins with different posttranslational modifications, DNAs with different sequences, and phospholipids with different chain lengths. Representing these variants as distinct species, as most biochemical simulators do, leads to the problem that the number of species, and chemical reactions that interconvert them, typically increase combinatorially with the number of ways that the molecules can vary. This can be alleviated by "rule-based modeling methods," in which software generates the chemical reaction network from relatively simple "rules.

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Despite employing diverse molecular mechanisms, many different cell signaling systems avoid losing information by transmitting it in a linear manner.

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Motivation: Smoldyn is a spatial and stochastic biochemical simulator. It treats each molecule of interest as an individual particle in continuous space, simulating molecular diffusion, molecule-membrane interactions and chemical reactions, all with good accuracy. This article presents several new features.

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Many cell signaling systems, including the yeast pheromone response system, exhibit "dose-response alignment" (DoRA), in which output of one or more downstream steps closely matches the fraction of occupied receptors. DoRA can improve the fidelity of transmitted dose information. Here, we searched systematically for biochemical network topologies that produced DoRA.

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Background: Inflammation is an essential component of arthritis pain. Nerve growth factor (NGF) plays a key role in acute and chronic pain states especially those associated with inflammation. NGF acts through tropomyosin-receptor-kinase A (TrkA).

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The outer membrane of gram-negative bacteria is composed of phospholipids in the inner leaflet and lipopolysaccharides (LPS) in the outer leaflet. LPS is an endotoxin that elicits a strong immune response from humans, and its biosynthesis is in part regulated via degradation of LpxC (EC 3.5.

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Experimental measurements require calibration to transform measured signals into physically meaningful values. The conventional approach has two steps: the experimenter deduces a conversion function using measurements on standards and then calibrates (or normalizes) measurements on unknown samples with this function. The deduction of the conversion function from only the standard measurements causes the results to be quite sensitive to experimental noise.

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Trace metal data for Proterozoic marine euxinic sediments imply that the expansion of nitrogen-fixing cyanobacteria and diversification of eukaryotes were delayed while the availability of bioessential metals such as molybdenum in the ocean was limited. However, there is increasing recognition that the Mesoproterozoic evolution of nitrogen fixation and eukaryotic life may have been promoted in marginal marine and terrestrial environments, including lakes, rather than in the deep ocean. Molybdenum availability is critical to life in lakes, just as it is in the oceans.

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Lipid A is a highly conserved component of lipopolysaccharide (LPS), itself a major component of the outer membrane of Gram-negative bacteria. Lipid A is essential to cells and elicits a strong immune response from humans and other animals. We developed a quantitative model of the nine enzyme-catalyzed steps of Escherichia coli lipid A biosynthesis, drawing parameters from the experimental literature.

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We report generation and characterization of pain-related behavior in a minimally invasive facet joint degeneration (FJD) animal model in rats. FJD was produced by a non-open percutaneous puncture-induced injury on the right lumbar FJs at three consecutive levels. Pressure hyperalgesia in the lower back was assessed by measuring the vocalization response to pressure from a force transducer.

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