Biology subjects

Moore, W.

Publications and source records attributed to Moore, W..

7 recordsLinked to original sources

bioRxiv2026

Factors Affecting Germination of a Dominant Salt Marsh Species are Context-Dependent: Implications for Coastal Seed-Based Restoration

Restoration of coastal salt marshes is often limited by their capability to revegetate, either through natural recruitment or active planting methods. Despite the critical need for efficient revegetation methods, direct seeding remains an underrepresented approach in coastal wetland restoration. Additionally, tidal inundation poses special challenges for coastal Seed-Based Restoration (SBR) relative to terrestrial habitats, with tides displacing seeds from the marsh platform. To determine factors potentially influencing successful establishment in coastal wetlands, we conducted a series of greenhouse and lab experiments with Salicornia pacifica (pickleweed), the dominant plant in California marshes. We determined pickleweed seed viability using standardized germination tests. Additionally, we tested factors that influence pickleweed seed viability and germination rates, such as soil moisture, soil type, and sowing depth. We found that pickleweed seeds had an average viability of 22.5%, which increased with larger-sized seeds. We also determined that the most effective dormancy-breaking pretreatments varied by soil type: a one-day cold stratification in freshwater maximized germination in benign soils, whereas a seven-day cold stratification in saltwater maximized germination in stressful soils. Finally, we determined that the optimal conditions for sowing seeds are surface sowing under moderate moisture. Creating conditions to maximize viability and germination is crucial to ensure the greatest chance of successful revegetation post restoration. Our study, which sequentially tested factors affecting different phases of the early life history of a dominant foundation species, can inform SBR for other coastal plants. This approach can help coastal land managers successfully implement SBR for habitat restoration.

plant biology↗

bioRxiv2025

IDR searcher: a search engine solution for public image resource

We introduce the IDR searcher, an open-source search engine designed to ease the exploration of datasets hosted in public bioimaging resources. The application offers a fast, efficient, cost-effective solution for datasets discovery and has the potential to address current disparities in finding quality datasets for exploratory research and to provide the foundation for cross-resource search.

bioinformatics↗

bioRxiv2025

MUDflow: Combining Neural Networks, UMAP and DBM Clustering to Identify Cell Populations Accurately, Quickly and Easily in Mass and Fluorescence Cytometry

Identifying cell populations in flow cytometry data is mostly done via a "manual gating" method that often lacks verifiability and reproducibility, even in the hands of experienced investigators. Recently developed automatic gating methods have been shown to have good performance in cell population identification, but may require fine-tuned setup from experts or struggle to identify small populations. Here, we introduce an easily trainable multilayer perceptron neural network for automatic gating (MLPgater). Compared to the three popular automatic gating methods LDA, FlowSOM and PhenoGraph on three mass and six fluorescence cytometry datasets, MLPgater is most accurate by a substantial margin, tied with LDA as the fastest and uniquely able to replace manual gating except for training purposes. Furthermore, we show that combining MLPgater with UMAPs guided dimensionality reduction feature and DBMs clustering (MUDflow) effectively detects new populations that did not exist or were not identified in the training set.

bioinformatics↗

bioRxiv2023

PIEZO2-dependent rapid pain system in humans and mice.

The PIEZO2 ion channel is critical for transducing light touch into neural signals but is not considered necessary for transducing acute pain in humans. Here, we discovered an exception - a form of mechanical pain evoked by hair pulling. Based on observations in a rare group of individuals with PIEZO2 deficiency syndrome, we demonstrated that hair-pull pain is dependent on PIEZO2 transduction. Studies in control participants showed that hair-pull pain triggered a distinct nocifensive response, including a nociceptive reflex. Observations in rare A{beta} deafferented individuals and nerve conduction block studies in control participants revealed that hair-pull pain perception is dependent on A{beta} input. Single-unit axonal recordings revealed that a class of cooling-responsive myelinated nociceptors in human skin is selectively tuned to painful hair-pull stimuli. Further, we pharmacologically mapped these nociceptors to a specific transcriptomic class. Finally, using functional imaging in mice, we demonstrated that in a homologous nociceptor, Piezo2 is necessary for high-sensitivity, robust activation by hair-pull stimuli. Together, we have demonstrated that hair-pulling evokes a distinct type of pain with conserved behavioral, neural, and molecular features across humans and mice.

neuroscience↗

bioRxiv2023

OME-Zarr: a cloud-optimized bioimaging file format with international community support

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself - OME-Zarr - along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.

bioinformatics↗

bioRxiv2021

Virtual Touch: Sensing and Feeling with Ultrasound.

The sense of touch codes the detection and properties of physical objects on the body via mechanoreceptors within the skin. Technological advancements, such as ultrasonic haptic devices, are now able to touch without touching, claiming this is virtual touch. An initial aim of the study was to investigate subjective intensity and pleasantness ratings of ultrasound stimulation and the influence of top-down factors using the Touch Experience and Attitudes Questionnaire (TEAQ). Self-reported intensity and pleasantness ratings were measured in response to ultrasound stimuli. A second aim was to record from individual low threshold mechanoreceptors using the technique of microneurography in an attempt to determine which mechanoreceptors are activated by ultrasound stimulation of the skin. The major findings here were that microneurography found SAI and SAII units did not respond to ultrasound stimuli; intensity and pleasantness ratings were significantly different between age groups. Ultrasound can produce a variety of sensations with varying intensity and pleasantness ratings. A limitation of the study was the unexpected force difference generated between modulations. These findings have implications for mid-air haptics, somatosensory affective research, and virtual reality. Future research should focus on microneurography investigation of FA fibre responses to ultrasound.

neuroscience↗

bioRxiv2021

OME-NGFF: scalable format strategies for interoperable bioimaging data

Biological imaging is one of the most innovative fields in the modern biological sciences. New imaging modalities, probes, and analysis tools appear every few months and often prove decisive for enabling new directions in scientific discovery. One feature of this dynamic field is the need to capture new types of data and data structures. While there is a strong drive to make scientific data Findable, Accessible, Interoperable and Reproducible (FAIR 1), the rapid rate of innovation in imaging impedes the unification and adoption of standardized data formats. Despite this, the opportunities for sharing and integrating bioimaging data and, in particular, linking these data to other "omics" datasets have never been greater. Therefore, to every extent possible, increasing "FAIRness" of bioimaging data is critical for maximizing scientific value, as well as for promoting openness and integrity. In the absence of a common, FAIR format, two approaches have emerged to provide access to bioimaging data: translation and conversion. On-the-fly translation produces a transient representation of bioimage metadata and binary data but must be repeated on each use. In contrast, conversion produces a permanent copy of the data, ideally in an open format that makes the data more accessible and improves performance and parallelization in reads and writes. Both approaches have been implemented successfully in the bioimaging community but both have limitations. At cloud-scale, those shortcomings limit scientific analysis and the sharing of results. We introduce here next-generation file formats (NGFF) as a solution to these challenges.

bioinformatics↗