Biology subjects

Nelson, S.

Publications and source records attributed to Nelson, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Development of low cost, robust and reproducible biofilm static and pharmacodynamic assays

SynopsisO_ST_ABSBackgroundC_ST_ABSThe complexity of diagnosing and treating biofilm-associated infections necessitates a comprehensive strategy to mitigate the rising rates of antimicrobial resistance (AMR). Microtiter plate methods are used globally for determination of biofilm eradication concentrations (MBEC) but few have been adapted to observe pharmacodynamic observations. Here, we describe a method which allows for both static and pharmacodynamic assays of biofilm evaluation. MethodsA total of 150 clinical isolates from Southmead Hospital were assessed, representing five bacterial species (N=30 per bacterial species): Pseudomonas aeruginosa, Escherichia coli, Streptococcus pneumoniae, Staphylococcus aureus and Klebsiella pneumoniae. MBECs were determined using a developed method using 96 well plates and glass beads. MBECs of seven different antibiotics were compared to those determined using the established Calgary biofilm device (CBD). Dynamic pharmacodynamic evaluations to produce Biofilm Time Kill curve (BTKC) based on published planktonic time kill curve (TKC) data and ISO recommendations were carried out using the glass bead model for K. pneumoniae and ciprofloxacin, S. aureus and levofloxacin and S. pneumoniae and vancomycin. Quantification of biofilm biomass was assessed at 0, 2, 4, 8 and 24 hours and compared to planktonic culture survival under comparable challenge conditions. ResultsComparing MBEC results for all bacterial strains and antibiotic challenges showed no statistical difference between the glass bead and CBD methods (P <0.05). Biofilm BTKC AUBKC were inferior to planktonic equivalents but demonstrated specific pharmacodynamic patterns of biofilm reduction efficacy. MBEC correlated with biofilm BTKC penetration in line with clinical observations for S. aureus vs vancomycin and S. pneumoniae vs levofloxacin. ConclusionsThe glass bead biofilm models provide robust, reproducible alternatives to the traditional methods of determining MBEC and bridge the gap with biofilm pharmacodynamic evaluations. These methods also provide a low-cost option to current methods as only standard laboratory equipment is required, allowing for the generation of comprehensive data sets. This ensures greater translatability to complex in vitro models and clinical scenarios.

microbiology↗

bioRxiv2026

Cortical Thickness and Curvature in Autism and ADHD: A Mega-Analysis

BackgroundExisting evidence suggests cortical morphometric alterations occur in people with autism and ADHD. However, these findings remain tentative due to small sample sizes, heterogeneous imaging pipelines, varied statistical approaches, and limited harmonization across acquisition sites. Few studies have applied standardized processing to large, clinically enriched datasets or addressed site-related batch effects. MethodsWe leveraged six large-scale brain imaging datasets (n = 9,647; male=5,835; female=3,812; ages 5-64 years), including 1,533 individuals with ADHD, 1,080 with autism spectrum disorder, and 7,034 matched controls. All imaging data were processed using the validated ABCD-HCP pipeline, with cortical parcellation into 360 regions based on the Human Connectome Project (HCP) atlas, and ComBat harmonization was applied to account for variability across 67 acquisition sites. Group-level differences in cortical thickness and sulcal curvature were examined with ANCOVAs, controlling for covariates and using Bonferroni correction for multiple comparisons. ResultsOur analyses revealed distinct neuroanatomical signatures for both autism and ADHD. Individuals with autism exhibited regionally thinner cortex and curvature alterations particularly in the Cingulo-Opercular network. In contrast, individuals with ADHD displayed regionally thicker cortex, particularly in the default mode and somatomotor networks, alongside curvature differences. Control participants showed intermediate patterns, suggesting that autism and ADHD may represent diverging extremes of cortical maturation. ConclusionsCortical thickness and curvature emerge as potential biomarkers that can advance understanding of neurodevelopmental conditions and disentangle heterogeneity across diagnostic groups. These findings highlight the value of harmonized, large-scale, standardized analyses for resolving inconsistencies in the literature.

neuroscience↗

bioRxiv2025

Dedicated nanoparticle flow cytometry for single extracellular vesicle phenotyping: Performance of the CytoFLEX Nano

Accurate discrimination of extracellular vesicles (EVs) from non-vesicular nanoparticles and robust phenotyping of individual EVs directly within complex biofluids are essential to advance understanding of EV biology and to realize their potential as biomarkers and therapeutic agents. Conventional flow cytometers, originally designed for cellular analysis, lack the scatter and fluorescence sensitivity, dynamic range, and event-rate control required for quantitative characterization of nanoscale vesicles and are particularly susceptible to coincident (swarm) detection. Dedicated nanoparticle flow cytometers have been developed to address these limitations, and here we systematically evaluate the suitability of the CytoFLEX Nano (Beckman Coulter) for EV analysis. Using a series of calibration beads of different materials, fluorescent liposomes, and EVs isolated from peritoneal fluid and cell culture medium, we assess size-detection thresholds, scatter and fluorescence sensitivity, dynamic range, and volumetric counting accuracy. These data provide practical guidance for implementing nanoscale flow cytometry in EV research and support the informed adoption of dedicated nanoparticle cytometers in studies adhering to current EV reporting standards.

cell biology↗

bioRxiv2025

Examining the heritability of functional brain networks in adolescence

Discovering mechanisms underlying mental illness requires disentangling genetic and environmental factors influencing mental health. Researchers have started investigating the brains role as a potential intermediate biomarker linking genes and environment to mental health; however, understanding how much genetics shapes adolescent brain function remains elusive. Using data from the ABCD study (5,247 unrelated, 330 dizygotic, 248 monozygotic twin subjects), we estimated the heritability of functional connectivity and topography using both SNP and twin data. SNP-based heritability was calculated using genetic correlation and the recently developed AdjHE-RE estimator. We found low SNP heritability for brain functional connectivity (median = 2e-10% Gordon, 5.8e-7% probabilistic) and topography (max = 2%). Twin estimates using ACE models replicated prior findings from the literature (median = 8.9e-6% Gordon, 6% probabilistic, 27% topography). This suggest that additive genetic effects are minimally associated with functional brain features in adolescents highlighting the importance of considering both genetic and environmental factors when studying the development of functional brain networks and their relevance to mental health.

genomics↗

bioRxiv2025

PERRC: Protease Engineering with Reactant Residence Time Control

Proteases with engineered specificity hold great potential for targeted therapeutics, protein circuit construction, and biotechnology applications. However, many proteases exhibit broad substrate specificity, limiting their applications. Engineering protease specificity remains challenging because evolving a protease to recognize a new substrate, without counterselecting against its native substrate, often results in high residual activity on the original substrate. To address this, we developed Protease Engineering with Reactant Residence Time Control (PERRC), a platform that exploits the correlation between endoplasmic reticulum (ER) retention sequence strength and ER residence time. PERRC allows precise control over the stringency of protease evolution by adjusting counterselection to selection substrate ratios. Using PERRC, we evolved an orthogonal tobacco etch virus protease variant, TEVESNp, that selectively cleaves a substrate (ENLYFES) that differs by only one amino acid from its parent sequence (ENLYFQS). TEVESNp exhibits a remarkable 65-fold preference for the evolved substrate, marking the first example of an engineered orthogonal protease driven by such a slight difference in substrate recognition. Furthermore, TEVESNp functions as a competent protease for constructing orthogonal protein circuits in bacteria, and molecular dynamic simulations analysis reveals subtle yet functionally significant active site rearrangements. PERRC is a modular dual-substrate display system that facilitates precise engineering of protease specificity.

synthetic biology↗

bioRxiv2024

Discovery of cyclic peptide natural product inhibitors of Balamuthia mandrillaris

Balamuthia mandrillaris is a pathogenic free-living amoeba that causes infection of central nervous system, called Balamuthia amoebic encephalitis (BAE), as well as cutaneous and systemic diseases. Patients infected with B. mandrillaris have a high mortality rate due to the lack of effective treatments. A combination of non-optimized antimicrobial drug regimen is typically recommended; however, they have poor parasite activity and can cause various severe side effects. Cyclic peptides exhibit a broad spectrum of antimicrobial activities and lower cytotoxicity. In this study, we evaluated the anti-B. mandrillaris effect of cyclic peptides. The predicted natural product-43 (pNP-43), identified from the SNaPP (Synthetic Natural Product Inspired Cyclic Peptides) library, and its derivates displayed a significant inhibition for B. mandrillaris trophozoites. Eight pNPs had IC50s <5 M. Furthermore, all hit pNPs demonstrated minimal hemolytic and cytotoxic effects on human cells. Our study first indicates the anti-B. mandrillaris effect of cyclic peptides, which provides a new direction for drug development. Further studies of the mechanism of action and in vivo effects will be elucidated to confirm the potency as a treatment for B. mandrillaris infection in the future.

pharmacology and toxicology↗

bioRxiv2024

Detection of clade 2.3.4.4b highly pathogenic H5N1 influenza virus in New York City

Highly pathogenic avian influenza viruses of the H5N1 clade 2.3.4.4b arrived in North America in the winter of 2021/2022. These viruses have spread across the Americas causing morbidity and mortality in both wild and domestic birds as well as some mammalian species, including cattle. Many surveillance programs in wildlife as well as commercial poultry operations have detected these viruses. Here we conducted surveillance of avian species in the urban environment in New York City. We detected highly pathogenic H5N1 viruses in six samples from four different bird species and performed full genome sequencing. Sequence analysis showed the presence of multiple different genotypes. Our work highlights that the interface between animals and humans that may give rise to zoonotic infections or even pandemics is not limited to rural environments and commercial poultry operations but extends into the heart of our urban centers. ImportanceWhile surveillance for avian influenza viruses is often focused on migratory routes and their associated stop-over locations, or commercial poultry operations, many bird species - including migratory birds - frequent or live in urban green spaces and wetlands. This brings them into contact with a highly dense population of humans and pets providing an extensive urban animal-human interface in which the general public may have little awareness of circulating infectious diseases. This study focuses on virus surveillance at this interface, combined with culturally responsive science education and community outreach.

microbiology↗

bioRxiv2024

Dynamic fibroblast-immune interactions shape wound healing after brain injury

Fibroblasts coordinate the response to tissue injury, directing organ regeneration versus scarring. In the central nervous system (CNS), fibroblasts are uncommon cells enriched at tissue borders, and their molecular, cellular, and functional interactions after brain injury are poorly understood. Here we define the fibroblast response to sterile brain damage across time and space. Early pro-fibrotic myofibroblasts infiltrated CNS lesions and were functionally and spatially organized by fibroblast TGF{beta} signaling, pro-fibrotic macrophages and microglia, and perilesional brain glia that activated TGF{beta} via integrin v{beta}8. Early myofibroblasts subsequently transitioned into a variety of late states, including meningeal and lymphocyte-interactive fibroblasts that persisted long term. Interruption of this dynamic fibroblast-macrophage-glial coordination impaired brain wound healing and the resolution of neuroinflammation, disrupted generation of late de novo CNS lymphocyte niches, and increased mortality in a stroke model. This work highlights an unexpected role of fibroblasts as coordinate regulators of CNS healing and neuroinflammation after brain injury.

immunology↗

bioRxiv2024

Loss of function in RBBP5 results in a syndromic neurodevelopmental disorder associated with microcephaly

PurposeEpigenetic dysregulation has been associated with many inherited disorders. RBBP5 encodes a core member of the protein complex that methylates histone 3 lysine-4 (H3K4) and has not been implicated in human disease. MethodsWe identify five unrelated individuals with de novo heterozygous pathogenic variants in RBBP5. Three truncating and two missense variants were identified in probands with neurodevelopmental symptoms including global developmental delay, intellectual disability, microcephaly, and short stature. Here, we investigate the pathogenicity of the variants through protein structural analysis and transgenic Drosophila models. ResultsBoth missense p.T232I and p.E296D variants affect evolutionarily conserved amino acids and are expected to interfere with the interface between RBBP5 and the histones. In Drosophila, ubiquitous overexpression of human RBBP5 is lethal in the larval developmental stage. Loss of Rbbp5 leads to a reduction in brain size, and the human reference, p.T232I, or p.E296D variant transgenes fail to rescue loss of Rbbp5. Expression of either missense variant in an Rbbp5 null background results in a less severe microcephaly phenotype than the human reference, indicating both p.T232I and p.E296D variants are loss-of-function alleles. ConclusionDe novo heterozygous variants in RBBP5 are associated with a syndromic neurodevelopmental disorder. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/578086v1_ufig1.gif" ALT="Figure 1"> O_LINKSMALLFIG WIDTH=200 HEIGHT=24 SRC="FIGDIR/small/578086v1_ufig1a.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@11337daorg.highwire.dtl.DTLVardef@b7f4d8org.highwire.dtl.DTLVardef@12bc283org.highwire.dtl.DTLVardef@1ef4e09_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2024

AAV-based delivery of RNAi targeting Ataxin-2 improves survival, strength, and pathology in mouse models of rapidly and slowly progressive sporadic ALS

Amyotrophic lateral sclerosis (ALS) is characterized by motor neuron death due to nuclear loss and cytoplasmic aggregation of the splice factor TDP-43. Pathologic TDP-43 associates with stress granules (SGs) and downregulating the SG-associated protein Ataxin-2 (Atxn2) using antisense oligonucleotides (ASO) prolongs survival in the TAR4/4 sporadic ALS mouse model, a strategy now in clinical trials. Here, we used AAV-mediated RNAi delivery to achieve lasting and targeted Atxn2 knockdown after a single injection. To achieve this, a novel AAV with improved transduction potency of our target cells was used to deliver Atxn2-targeting miRNAs. Mouse dosing studies demonstrated 55% Atxn2 knockdown in frontal cortex and 25% knockdown throughout brainstem and spinal cord after intracerebroventricular injection at a dose 40x lower than used in other recent studies. In TAR4/4 mice, miAtxn2 treatment increased mean and median survival by 54% and 45% respectively (p<0.0003). Mice showed robust improvement across strength-related measures ranging from 24-75%. Interestingly, treated mice showed increased vertical activity above wildtype, suggesting unmasking of an FTD phenotype with improved strength. Histologically, lower motor neuron survival improved with a concomitant reduction in CNS inflammatory markers. Additionally, phosphorylated TDP-43 was reduced to wildtype levels. Bulk RNA sequencing revealed correction of 153 genes in the markedly dysregulated transcriptome of mutant mice, several of which are described in the human ALS literature. In slow progressing hemizygous mice, treatment rescued weight loss and improved gait at late time points. Cumulatively the data support the utility of AAV-mediated RNAi against Atxn2 as a robust and translatable treatment strategy for sporadic ALS.

neuroscience↗

bioRxiv2023

Distinct latitudinal patterns of shifting spring phenology across the Appalachian Trail Corridor

Warming associated with climate change will likely continue to advance the onset of spring phenology for many forest plants across the eastern United States. Understory forbs and spring ephemerals which fix a disproportionate amount of carbon during spring may be negatively affected by earlier canopy closure (i.e., phenological windows), however, information on the spatial patterns of phenological change for these communities is still lacking. To assess the potential for changes in spring phenological windows we synthesized observations from the Appalachian Mountain Clubs (AMC) Mountain Watch (MW) project, the National Phenology Network (NPN), and AMCs iNaturalist projects between 2004 and 2022 (n = 118,250) across the length of the Appalachian Trail (AT) Corridor (34{degrees}N-46{degrees}N latitude). We used hierarchical Bayesian modeling to examine the sensitivity of day of year of flowering and leaf-out for 11 understory species and 14 canopy tree species to mean spring temperature (April-June). We conducted analyses across the AT Corridor, partitioned by regions of 4{degrees} latitude (South, Mid-Atlantic, and North). Spring phenologies for both understory plants and canopy trees advanced with warming ([~]6 days/{degrees}C and [~]3 days/{degrees}C, respectively). However, sensitivity of each group varied by latitude, with phenology of trees and understory plants advancing to a greater degree in the mid-Atlantic region ([~]10 days/{degrees}C) than the southern or northern regions ([~]5 days/{degrees}C). While we find evidence that phenological windows remain stable in southern and mid-Atlantic portions of the AT, we observed an expansion of the spring phenological window in the north where there was greater understory temperature sensitivity compared to trees ([~]1.6 days/{degrees}C). Our analyses indicate differential sensitivity of forest plant phenology to potential warming across a large latitudinal gradient in the eastern United States. Further, evidence for a temperature-driven expansion of the spring phenological window suggests a potential beneficial effect for understory plants, although phenological mismatch with potential pollinators is possible. Using various extensive citizen-science derived datasets allows us to synthesize regional- and continental-scale data to explore spatial and temporal trends in spring phenology related to warming. Such data can help to standardize approaches in phenological research and its application to forest climate resiliency.

ecology↗

bioRxiv2023

XCP-D: A Robust Pipeline for the post-processing of fMRI data

Functional neuroimaging is an essential tool for neuroscience research. Pre-processing pipelines produce standardized, minimally pre-processed data to support a range of potential analyses. However, post-processing is not similarly standardized. While several options for post-processing exist, they tend not to support output from disparate pre-processing pipelines, may have limited documentation, and may not follow BIDS best practices. Here we present XCP-D, which presents a solution to these issues. XCP-D is a collaborative effort between PennLINC at the University of Pennsylvania and the DCAN lab at the University at Minnesota. XCP-D uses an open development model on GitHub and incorporates continuous integration testing; it is distributed as a Docker container or Singularity image. XCP-D generates denoised BOLD images and functional derivatives from resting-state data in either NifTI or CIFTI files, following pre-processing with fMRIPrep, HCP, and ABCD-BIDS pipelines. Even prior to its official release, XCP-D has been downloaded >3,000 times from DockerHub. Together, XCP-D facilitates robust, scalable, and reproducible post-processing of fMRI data.

neuroscience↗

bioRxiv2023

Rapid nongenomic estrogen signaling controls alcohol drinking behavior

Ovarian-derived estrogen is a key modulator of numerous physiological processes via genomic and nongenomic mechanisms, including signaling non-canonically at membrane-associated estrogen receptors in the brain to rapidly regulate neuronal function. However, the mechanisms mediating estrogen regulation of behaviors such as alcohol consumption remain unclear. Early alcohol drinking confers greater risk for alcohol use disorder in women than men, and binge alcohol drinking is correlated with high circulating estrogen levels, but a causal role for estrogen signaling in driving alcohol drinking in gonadally-intact animals has not been established. We found that female mice displayed greater binge alcohol drinking and reduced avoidance behavior when circulating estrogen was high during the proestrus phase of the estrous cycle than when it was low, contributing to sex differences in these behaviors. The pro-drinking, but not anxiolytic, effect of high endogenous estrogen state occurred via rapid estrogen signaling at membrane-associated estrogen receptor alpha in the bed nucleus of the stria terminalis, which promoted synaptic excitation of corticotropin-releasing factor neurons and facilitated their activity during alcohol drinking behavior. This study is the first to demonstrate a rapid, nongenomic signaling mechanism for ovarian-derived estrogen signaling in the brain controlling behavior in gonadally intact females, and it establishes a causal role for estrogen in an intact hormonal context for driving alcohol consumption that contributes to known sex differences in this behavior.

neuroscience↗

bioRxiv2023

Perturbations of glutathione and sphingosine metabolites in Port Wine Birthmark patient-derived induced pluripotent stem cells

Port Wine Birthmark (PWB) is a congenital vascular malformation in the skin, occurring in 1-3 per 1,000 live births. We recently generated PWB-derived induced pluripotent stem cells (iPSCs) as clinically relevant disease models. The metabolites associated with the pathological phenotypes of PWB-derived iPSCs are unknown, which we aimed to explore in this study. Metabolites were separated by ultra-performance liquid chromatography and were screened with electrospray ionization mass spectrometry. Orthogonal partial least-squares discriminant analysis, multivariate and univariate analysis were used to identify differential metabolites (DMs). KEGG analysis was used for the enrichment of metabolic pathways. A total of 339 metabolites were identified. There were 22 DMs confirmed with 9 downregulated DMs including sphingosine and 13 upregulated DMs including glutathione in PWB iPSCs as compared to controls. Pathway enrichment analysis confirmed the upregulation of glutathione and downregulation of sphingolipid metabolism in PWB-derived iPSCs as compared to normal ones. We next examined the expression patterns of the key factors associated with glutathione metabolism in PWB lesions. We found that hypoxia-inducible factor 1 (HIF1), glutathione S-transferase Pi 1 (GSTP1), {gamma}-glutamyl transferase 7 (GGT7), and glutamate cysteine ligase modulatory subunit (GCLM) were upregulated in PWB vasculatures as compared to blood vessels in normal skins. Our data demonstrate that there are perturbations in sphingolipid and cellular redox homeostasis in the PWB vasculature, which may facilitate cell survival and pathological progression. Our data imply that upregulation of glutathione may contribute to laser-resistant phenotypes in the PWB vasculature.

cell biology↗

bioRxiv2023

Butyrate enhances Clostridioides difficile sporulation in vitro

Short chain fatty acids (SCFAs) are products of bacterial fermentation that help maintain important gut functions such as the intestinal barrier, signaling, and immune homeostasis. The main SCFAs acetate, propionate, and butyrate have demonstrated beneficial effects for the host, including importance in combatting infections caused by pathogens such as Clostridioides difficile. Despite the potential role of SCFAs in mitigating C. difficile infection, their direct effect on C. difficile remains unclear. Through a set of in vitro experiments, we investigated how SCFAs influence C. difficile growth, sporulation, and toxin production. Similar to previous studies, we observed that butyrate decreased growth of C. difficile strain 630 in a dose-dependent manner. The presence of butyrate also increased C. difficile sporulation, with minimal increases in toxin production. RNA-Seq analysis validated our experimental results, demonstrating increased expression of sporulation-related genes in conjunction with alternative metabolic and related C. difficile regulatory pathways, such as the carbon catabolite repressor, CcpA. Collectively, these data suggest that butyrate may signal alternative C. difficile metabolic pathways, thus modifying its growth and virulence to persist in the gut environment. IMPORTANCESeveral studies suggest that butyrate may be important in alleviating gut infections, such as reducing inflammation caused by the healthcare-associated Clostridioides difficile. While studies in both animal models and human studies correlate high levels of butyrate with reduced C. difficile burden, the direct impact of butyrate on C. difficile remains unclear. Our study demonstrates that butyrate directly influences C. difficile by increasing its sporulation and modifying its metabolism, potentially using butyrate as a biomarker to shift survival strategies in a changing gut environment. These data point to additional therapeutic approaches to combat C. difficile in a butyrate-directed manner.

microbiology↗

bioRxiv2023

The Genome of the Soybean Gall Midge (Resseliella maxima)

The cecidomyiid fly, soybean gall midge, Resseliella maxima Gagne, is a recently discovered insect that feeds on soybean plants in the Midwest US. Resseliella maxima larvae feed on soybean stems which may induce plant death and can cause considerable yield losses, making it an important agricultural pest. From three pools of 50 adults each, we used long-read nanopore sequencing to assemble a R. maxima reference genome. The final genome assembly is 206 Mb with 64.88X coverage, consisting of 1009 contigs with an N50 size of 714 kb. The assembly is high quality with a BUSCO score of 87.8%. Genome-wide GC level is 31.60% and DNA methylation was measured at 1.07%. The R. maxima genome is comprised of 21.73% repetitive DNA, which is in line with other cecidomyiids. Protein prediction annotated 14,798 coding genes with 89.9% protein BUSCO score. Mitogenome analysis indicated that R. maxima assembly is a single circular contig of 15,301 bp and shares highest identity to the mitogenome of the Asian rice gall midge, Orseolia oryzae (Wood-Mason). The R. maxima genome has one of the highest completeness levels for a cecidomyiid and will provide a resource for research focused on the biology, genetics, and evolution of cecidomyiids, as well as plant-insect interactions in this important agricultural pest.

genomics↗

bioRxiv2023

Analysis of donor pancreata defines the transcriptomic signature and microenvironment of early pre-neoplastic pancreatic lesions

The adult healthy human pancreas has been poorly studied given lack of indication to obtain tissue from the pancreas in the absence of disease and rapid postmortem degradation. We obtained pancreata from brain dead donors thus avoiding any warm ischemia time. The 30 donors were diverse in age and race and had no known pancreas disease. Histopathological analysis of the samples revealed PanIN lesions in most individuals irrespective of age. Using a combination of multiplex immunohistochemistry, single cell RNA sequencing, and spatial transcriptomics, we provide the first ever characterization of the unique microenvironment of the adult human pancreas and of sporadic PanIN lesions. We compared healthy pancreata to pancreatic cancer and peritumoral tissue and observed distinct transcriptomic signatures in fibroblasts, and, to a lesser extent, macrophages. PanIN epithelial cells from healthy pancreata were remarkably transcriptionally similar to cancer cells, suggesting that neoplastic pathways are initiated early in tumorigenesis. Statement of significanceThe causes underlying the onset of pancreatic cancer remain largely unknown, hampering early detection and prevention strategies. Here, we show that PanIN are abundant in healthy individuals and present at a much higher rate than the incidence of pancreatic cancer, setting the stage for efforts to elucidate the microenvironmental and cell intrinsic factors that restrain, or, conversely, promote, malignant progression.

cancer biology↗

bioRxiv2022

Demystifying image-based machine learning: A practical guide to automated analysis of field imagery using modern machine learning tools

Image-based machine learning methods are quickly becoming among the most widely-used forms of data analysis across science, technology, and engineering. These methods are powerful because they can rapidly and automatically extract rich contextual and spatial information from images, a process that has historically required a large amount of manual labor. The potential of image-based machine learning methods to change how researchers study the ocean has been demonstrated through a diverse range of recent applications. However, despite their promise, machine learning tools are still under-exploited in many domains including species and environmental monitoring, biodiversity surveys, fisheries abundance and size estimation, rare event and species detection, the study of wild animal behavior, and citizen science. Our objective in this article is to provide an approachable, application-oriented guide to help researchers apply image-based machine learning methods effectively to their own research problems. Using a case study, we describe how to prepare data, train and deploy models, and avoid common pitfalls that can cause models to underperform. Importantly, we discuss how to diagnose problems that can cause poor model performance on new imagery to build robust tools that can vastly accelerate data acquisition in the marine realm. Code to perform our analyses is provided at https://github.com/heinsense2/AIO_CaseStudy

ecology↗