Biology subjects

Hoffman, B.

Publications and source records attributed to Hoffman, B..

12 recordsLinked to original sources

bioRxiv2026

BirdCODE: Detecting bird communication at scale

Deep learning-based animal sound identification is regularly applied to large audio datasets for ecological monitoring and citizen science, but existing methods lack the fine temporal resolution required to extract insights into animal communication from these same datasets. Here we introduce Bird Communication Detector (BirdCODE), a deep learning model that detects and classifies the vocalizations of over 9000 bird species with precise temporal boundaries, a several hundredfold increase the number of species over previous bioacoustic sound event detection models. In extensive benchmarking, BirdCODE achieves state-of-the-art performance in detection and classification of bird sounds. Applying BirdCODE to 1.3M citizen-science recordings, we present four case studies of how BirdCODE-computed sound event boundaries can be used to carry out phylogenetic analyses, to describe geographic and temporal variation in acoustic communication, and to characterize cross-species interactions. Together, these demonstrate how BirdCODE can enable large-scale, data-driven studies of bird communication. Model code, weights, and predictions are publicly available.

bioinformatics↗

bioRxiv2026

Repertoire-wide contextual mapping reveals signal functions in cooperatively breeding crows

Communication structures society, and is likewise shaped by relationships and shared tasks; yet, for most socially complex species, we know little of their full vocal repertoire and its functions. We investigated how communication structures the who, what, and when of social interactions in cooperative carrion crows - group-living birds who rely on coordinated behaviors, as in chick care. Leveraging machine learning to integrate large-scale data from crow-borne audio-loggers and nest cameras, we charted the vocal repertoire across 24 cooperative groups and mapped all discovered call types to behaviors and social context. We found that crows used a rich repertoire across three domains of joint behavior - flocking, chick care, and territorial display. Relatively quiet call types were abundant and included close-range calls that may coordinate chick care by announcing nest visits. Our study demonstrates how combining continuous-capture data and machine learning can reveal a holistic understanding of how vocalizations function across contexts.

animal behavior and cognition↗

bioRxiv2026

BioDCASE: Using data challenges to make community advances in computational bioacoustics

Computational bioacoustics has seen significant advances in recent decades. However, the rate of insights from automated analysis of bioacoustic audio lags behind our rate of collecting the data - due to key capacity constraints in data annotation and bioacoustic algorithm development. Gaps in analysis methodology persist: not because they are intractable, but because of resource limitations in the bioacoustics community. To bridge these gaps, we advocate the open science method of data challenges, structured as public contests. We conducted a bioacoustics data challenge named BioDCASE, within the format of an existing event (DCASE). In this work we report on the procedures needed to select and then conduct useful bioacoustics data challenges. We consider aspects of task design such as dataset curation, annotation, and evaluation metrics. We report the three tasks included in BioDCASE 2025 and the resulting progress made. Based on this we make recommendations for open community initiatives in computational bioacoustics.

animal behavior and cognition↗

bioRxiv2026

Zebra finch females flexibly communicate with each other and with AI-driven acoustic interaction models

Vocal interactions are fundamental for social functioning across animals, including humans. The diverse rules underlying these exchanges remain largely unknown, and emerging AI technologies offer promising avenues for investigation. We used computational tools to collect and analyze >1,000 hours of vocal interactions between female zebra finches and discovered that their interactions were characterized by correlated call production and structure, rapid acoustic modulation, and response selectivity. To test these interaction rules, we developed a generative audio large language model (ZF-AIM Acoustic Interaction Model) that engaged in real-time vocal exchanges with birds. When birds interacted with ZF-AIM, their vocal production and flexibility recapitulated key naturalistic features, which did not happen with non-interactive playbacks. Targeted ablations of ZF-AIM revealed that call timing and structure differentially contribute to natural vocal interactions. Using these AI-animal interactions, we demonstrate how AI can be leveraged to reveal fundamental rules underlying animal communication.

animal behavior and cognition↗

bioRxiv2024

WRAD core perturbation impairs DNA replication fidelity promoting immunoediting in pancreatic cancer

It is unclear how cells counteract the potentially harmful effects of uncoordinated DNA replication in the context of oncogenic stress. Here, we identify the WRAD (WDR5/RBBP5/ASH2L/DPY30) core as a modulator of DNA replication in pancreatic ductal adenocarcinoma (PDAC) models. Molecular analyses demonstrated that the WRAD core interacts with the replisome complex, with disruption of DPY30 resulting in DNA re-replication, DNA damage, and chromosomal instability (CIN) without affecting cancer cell proliferation. Consequently, in immunocompetent models, DPY30 loss induced T cell infiltration and immune-mediated clearance of highly proliferating cancer cells with complex karyotypes, thus improving anti-tumor efficacy upon anti-PD-1 treatment. In PDAC patients, DPY30 expression was associated with high tumor grade, worse prognosis, and limited response to immune checkpoint blockade. Together, our findings indicate that the WRAD core sustains genome stability and suggest that low intratumor DPY30 levels may identify PDAC patients who will benefit from immune checkpoint inhibitors.

cancer biology↗

bioRxiv2024

Evaluating Paraspinal Muscle Response and Compensation via Musculoskeletal Modeling in Spinal Stenosis Surgeries

IntroductionLumbar spinal stenosis is a common cause of lower back pain and weakness in elderly patients. The gold standard treatment for this is lumbar laminectomy which involves widespread muscle damage to the multifidus, a complete loss of the posterior tension band which contains the supraspinous and interspinous ligaments. However, in recent years minimally invasive techniques such as bilateral and unilateral laminotomy have become more popular and are showing efficacy in the decompression of spinal stenosis. Due to its minimally invasive approach, the muscle retraction required for laminotomy is less intensive than that required for laminectomy. The overall body of literature on the surgical treatment of spinal stenosis is sparse in its interrogation of the biomechanical outcomes of these techniques and to our knowledge, there are no current publications that incorporate muscle forces. MethodsA previously validated thoracolumbar ribcage finite element (FE) model was used for this study. Three different surgeries, traditional laminectomy, unilateral and bilateral midline sparing approaches at L4-L5 segment were simulated by removing the spinous process, supraspinous, and interspinous ligaments. The segmental range of motion (ROM) for all models were acquired and input into a musculoskeletal modelling software to calculate muscle forces. ResultsUnilateral and bilateral laminotomy showed similar muscle forces for every muscle group in both flexion and extension motion. While comparing the muscle forces in laminotomy to the laminectomy in extension motion displayed an increase in Iliocostalis lumborum (IL) by 12 % and multifidus (MF) by 16% and decrease in transverse abdominus (TA) by 138% and erector spine (ES) by 12%. For flexion, there was an increase in IL by 35%, and MF by 12%. ConclusionOur results highlight that laminectomy, which involves the removal of paraspinal muscles and posterior ligamentous structures to relieve stenosis, can lead to increased instability and necessitate muscle compensation, particularly in adjacent and thoracic spine segments. Conversely, midline sparing approaches such as laminotomies, are associated with decreased muscle compensation across spinal segments and enhanced stability.

bioengineering↗

bioRxiv2024

Biomechanical Implications of Spinopelvic Alignment on Femoral Head Cartilage and the Proximal Femoral Physis in Slipped Capital Femoral Epiphysis: A Theoretical Finite Element Analysis

BackgroundSlipped capital femoral epiphysis (SCFE) is a prevalent pediatric hip disorder. Recent studies suggest the spines sagittal profile may influence the proximal femoral growth plates slippage, an aspect not extensively explored. This study utilizes finite element analysis to investigate how different spinopelvic alignments affect shear stress and potential slippage at the growth plate. MethodsA finite element model was developed from CT scans of a healthy adult male lumbar spine, pelvis, and femurs. The model was subjected to various sagittal alignments through rotational boundary conditions. Simulations of two-leg stance, one-leg stance, walking heel strike, ascending stairs heel strike, and descending stairs heel strike were conducted. Parameters measured included hip joint contact area, stress, and maximum Tresca (shear) stress on the growth plate. FindingsPosterior pelvic tilt cases indicated larger shear stresses compared to the anterior pelvic tilt variants except in two leg stance. Two leg stance resulted in decreases in the posterior tilted pelvi variants compared to anterior tilted pelvi, however a combination of posterior pelvic tilt and high pelvic incidence indicated larger shear stresses on the growth plate. One leg stance and heal strike resulted in higher shear stress on the growth plate in posterior pelvic tilt variants compared to anterior pelvic tilt, with a combination of posterior pelvic tilt and high pelvic incidence resulting in the largest shear stress. InterpretationOur findings suggest that posterior pelvic tilt and high pelvic incidence can lead to increased shear stress at the growth plate. Activities performed in patients with these alignments may predispose to biomechanical loading that shears the growth plate, potentially causing slippage.

bioengineering↗

bioRxiv2021

Bcl-xL restricts transcriptional, morphological and functional decompensation of β-cell mitochondria under chronic glucose excess

In the progression of diabetes, pancreatic islet {beta}-cells respond to increased metabolic demand with functional compensation, followed by pathogenic decompensation of mitochondria-dependent insulin secretion. It is not clear what mechanisms drive, or control, mitochondrial decompensation. Here, we report that anti-apoptotic Bcl-xL maintains mitochondrial integrity in {beta}-cells under non-apoptotic levels of glucose stress. Prolonged glucose excess causes transcriptional reprogramming of glycolysis and {beta}-cell identity genes, while sensitizing glucose-stimulated Ca2+ signaling and insulin secretion. Deletion of Bcl-xL amplifies this insulin hypersecretion and increases mitochondrial fusion, mitochondrial volume, and oxygen consumption, whereas ATP-coupled respiration and mitochondrial hyperpolarization become impaired. Of note, Bcl-xL-deficient {beta}-cells have impaired Pgc-1 expression, and develop specific defects in the expression of Tfam, mitochondrial ribosomal genes, and OXPHOS components under glucose stress. Bcl-xL limits high glucose-induced mitochondrial ROS (mitoROS) levels and pharmacological normalization of mitoROS in Bcl-xL KO cells rescues glucose-induced defects in mitochondrial gene expression and changes to {beta}-cell identity. Our data identify mitoROS as a primary retrograde driver of transcriptional re-wiring in {beta}-cells exposed to excess glucose, and reveal Bcl-xL as an important safeguard against transcriptional and functional decompensation of {beta}-cell mitochondria. Bcl-xL and mitoROS may thus be viable targets to prevent early {beta}-cell dysfunction and the progression of diabetes.

cell biology↗

bioRxiv2021

H3K4 Methylation in β-cells Prevents Transcriptional Downregulation and Variance Associated with Type 2 Diabetes

Pancreatic {beta}-cells control glucose homeostasis via regulated production and secretion of insulin. This function arises from a highly specialized gene expression program which is established during development and then sustained, with limited flexibility, in terminally differentiated {beta}-cells. Dysregulation of this program is seen in type 2 diabetes (T2D) but mechanisms that preserve gene expression or underlie its dysregulation in mature {beta}-cells are not well resolved. Here we show that trithorax group-dependent histone H3 lysine 4 trimethylation (H3K4me3) maintains expression of genes important for insulin biosynthesis and glucose-responsiveness in {beta}-cells. Transcriptional changes in H3K4me3-deficient {beta}-cells lead to severe hyperglycemia in adult mice. We show that H3K4me3 deficiency leads to a less active and more repressed epigenome profile, which locally correlates with gene expression deficits but does not globally reduce gene expression. Instead, developmentally regulated genes and genes in weakly active or suppressed states particularly rely on H3K4 methylation. We then show that H3K4me3 is re-organized in diabetic Leprdb/db mouse islets in favour of weakly active and disallowed genes at the expense of terminal {beta}-cell markers with broad H3K4me3 peaks. Our results point to key roles of H3K4me3 in maintaining mature {beta}-cell function and establishing a dysfunctional transcriptome in diabetic islets.

cell biology↗

bioRxiv2019

A Modification of the Bielschowsky Silver Stain for Alzheimer Neuritic Plaques: Suppression of Artifactual Staining by Pretreatment with Oxidizing Agents

The Bielschowsky silver method has been the most commonly-used histological stain for demonstrating the neuritic plaques and neurofibrillary tangles that define Alzheimers disease (AD). The stain has been critical to providing a common measure allowing large clinicopathological correlation studies that have demonstrated statistically significant and independent contributions of both lesion types to cognitive impairment and dementia. The continuing relevance of neuritic plaques, and the Bielschowsky stain as the method of choice for their demonstration, is also indicated by its use as the US Food and Drug Administration (FDA) \"standard of truth\" for autopsy confirmation of the validity of PET amyloid imaging agents. Many modifications of the Bielschowsky stain have been published but it is still known to frequently generate artifactual staining that at times mimics the appearance of amyloid plaques. In this study we found that pretreatment with oxidizing agents prior to the initial incubation in silver nitrate eliminates these artifacts and reduces the commonly observed high background staining. This new method may be valuable for Alzheimers disease (AD) researchers and neuropathologists.

neuroscience↗

bioRxiv2019

A Molecular Tension Sensor for N-Cadherin Reveals Distinct Forms of Mechanosensitive Adhesion Assembly in Adherens and Synaptic Junctions

N-cadherin mediates physical linkages in a variety of force-generating and load-bearing tissues. To enable visualization and quantification of mechanical loads experienced by N-Cadherin, we developed a genetically-encoded FRET-based tension sensor for this protein. We observe that N-Cadherin supports non-muscle myosin II (NMII) activity-dependent loads within the adherens junctions (AJs) of VSMCs and the synaptic junctions (SJs) of neurons. To probe the relationship between mechanical loads and AJ/SJ formation, we evaluated the relationships between N-cadherin tension and the size of these adhesion structures. In VSMCs, no relationship between N-cadherin tension and AJ size was observed, consistent with previously observed homeostatic regulation of mechanical loading. In neurons, a strong correlation between SJ size and N-cadherin load was observed, demonstrating an absence of homeostatic regulation. Treatment with glycine, a known initiator of synapse maturation, lead to increased SJ size and N-cadherin load, suggesting a role for mechanosensitive signaling in this process. Correspondingly, we observe that NMII activity is required for the Src-mediated phosphorylation of NMDAR subunit GluN2B at Tyr 1252, which is a key event in synaptic potentiation. Together these data demonstrate N-cadherin tension is subject to cell type specific regulation and that mechanosensitive signaling occurs within SJs.

bioengineering↗

bioRxiv2017

The signaling lipid sphingosine 1-phosphate regulates mechanical pain

Somatosensory neurons mediate responses to diverse mechanical stimuli, from innocuous touch to noxious pain. While recent studies have identified distinct populations of A mechanonociceptors (AMs) that are required for mechanical pain, the molecular underpinnings of mechanonociception remain unknown. Here, we show that the bioactive lipid sphingosine 1-phosphate (S1P) and S1P Receptor 3 (S1PR3) are critical regulators of acute mechanonociception. Genetic or pharmacological ablation of S1PR3, or blockade of S1P production, significantly impaired the behavioral response to noxious mechanical stimuli, with no effect on responses to innocuous touch or thermal stimuli. These effects are mediated by fast-conducting A mechanonociceptors, which displayed a significant decrease in mechanosensitivity in S1PR3 mutant mice. We show that S1PR3 signaling tunes mechanonociceptor excitability via modulation of KCNQ2/3 channels. Our findings define a new role for S1PR3 in regulating neuronal excitability and establish the importance of S1P/S1PR3 signaling in the setting of mechanical pain thresholds.

neuroscience↗