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Preprint

Preprint: explore 500 source-linked works published from 2026 to 2026, with original documents and citations.

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Includes records with this source-supplied label or an explicit phrase match in their metadata. Matches indicate a mention, not proof that a paper uses a method or tests a material. Source versions are consolidated by DOI.

Sources: biorxiv. Collection updated 2026-09-15. Counts describe this index, not the complete source archives.

bioRxiv2026

Readout-dependent time-of-flight weighting of absorption and flow in interferometric diffuse optics

Joint optical measurement of hemoglobin and blood-flow dynamics could provide a compact route to richer functional monitoring of tissue physiology. However, hybrid diffuse-optical systems commonly optimize photon time-of-flight (TOF) for individual readouts, even when absorption and flow are recovered from the same acquisition. Here, we asked whether a single TOF window can optimally preserve both signals. Dual-wavelength TOF-iSCOS recovered absorption, hemoglobin and relative blood-flow index (BFI) from the same interferometrically sensed optical field, while Early, Middle and Late photon windows provided progressively greater weighting of longer and deeper photon paths. During forearm cuff occlusion in 11 adults, absorption and flow showed markedly different TOF dependence: Late-gate BFI responses were retained, whereas absorption decreased to a median Late/Early ratio of 0.18. The resulting readout-by-TOF interaction was positive in all 11 participants (median 2.61 octaves, 95% bootstrap CI 2.44-3.22; exact sign-test P = 9.8 x 10-4). Readout-specific gate selection increased held-out response retention by 24.8% (95% CI 8.8-42.5%) relative to a single common gate. We then tested the approach during prefrontal working-memory activation in seven participants using a higher-load 2-back task relative to a low-load 0-back control. Late-gate BFI increased in all seven participants (+5.07%, 95% CI 1.46-8.68%; P = 0.014) and remained positive after adjustment using an Early-TOF signal, whereas hemoglobin responses were less consistent. Layered Monte Carlo modeling showed that the same detected photon histories acquire different absorption and dynamic-scattering sensitivity across TOF, linking the experimental effects to anatomy- and geometry-conditioned tissue weighting. Within the present geometry and photon budget, the central result is therefore not that one readout is intrinsically superior, but that absorption and flow recovered from the same optical field retain physiological information differently across photon time-of-flight.

bioengineering↗
bioRxiv2026

PhysiCelldFBA: Linking single-cell genome-scale metabolism to spatially explicit multicellular dynamics

Genome-scale metabolic models can predict how individual cells allocate resources and respond to their environment, yet few frameworks link single-cell metabolism to the spatial organisation of multicellular systems. Here we introduce PhysiCelldFBA, an extension of the PhysiCell agent-based framework that couples genome-scale dynamic flux balance analysis to off-lattice multicellular simulations. Each simulated cell carries its own metabolic model, allowing local environmental conditions to shape metabolism while metabolic activity feeds back on the surrounding environment, cellular behaviour, and spatial organisation. We first validate this coupling by showing that glucose consumption, CO2 production, and biomass accumulation remain mass-balanced in a closed E. coli system, with simulated biomass agreeing with analytical predictions to within 1%. We then demonstrate how metabolic phenotypes emerge from this coupling across microbial and mammalian systems. Spatial nutrient gradients generate metabolic stratification and acetate cross-feeding in growing E. coli colonies; diffusion-limited metabolism produces proliferative, hypoxic, and necrotic zones across a broad panel of metabolites in a tumour-like tissue; distinct, organism-specific metabolic networks give rise to syntrophic cross-feeding and spatial niche formation in a two-species consortium; and metabolic state couples energy availability to transitions between cellular motility and growth. Across these examples, metabolic stratification, cross-feeding, and phenotypic adaptation emerge from local metabolic optimisation and environmental feedback rather than being explicitly prescribed. PhysiCelldFBA therefore provides a general framework for simulating genome-scale metabolism at single-cell resolution and linking intracellular metabolic state to cellular behaviour and emergent organisation across scales.

systems biology↗
bioRxiv2026

Early establishment acts as a selective filter shaping climate-associated genomic variation in European beech

Climate change is increasing drought and heat stress in European forests, raising concerns about the capacity of long-lived tree species to respond to rapidly changing environmental conditions. While local adaptation has been documented in many forest trees, it remains unclear whether newly established seedlings, which form the forests of the future, are able to persist and adapt to these new climatic conditions. Here, we investigated genomic differences between naturally regenerated seedlings and trees of European beech (Fagus sylvatica) across the three regions of the German Biodiversity Exploratories using low-coverage whole-genome sequencing (5x) of 1,032 individuals. Population structure was primarily driven by geographic region, whereas genetic diversity was similar across life stages. Despite this genome-wide similarity, we detected allele frequency shifts between trees and seedlings, concentrated in narrow genomic windows. These shifts were strongest in surviving seedlings, suggesting that environmental filtering during early establishment may contribute to shaping the genetic composition of regenerating populations. The strongest signals were observed within the Swabian Alb, where sampled seedlings were 2-years old and had experienced a longer period of potential filtering prior to sampling. Genotype - environment association analyses identified loci associated with climatic variables, and subsequent GO enrichment analyses of genes linked to these loci revealed significantly more enriched GO terms in seedlings than in trees, suggesting stronger environmental filtering by the current climate in seedlings. In particular, we found associations with maximum air temperature, relative humidity, soil moisture, and precipitation, affecting genes involved in stress responses, growth, metabolism, and developmental processes. Together, our results demonstrate that young cohorts of European beech differ genetically from trees and reveal genomic patterns consistent with life-stage-dependent environmental filtering. These findings suggest that the genetic composition of early life-stages is already altered by current environmental conditions, possibly contributing to adaptation to new climatic conditions.

ecology↗
bioRxiv2026

Burning down the mouse: Effects of wildfire and post-fire reseeding on Sin Nombre virus prevalence in its reservoir host

Worldwide, physical habitats and biological communities are being reshaped by wildfire. Such changes have obvious potential to alter pathogen ecology, yet few studies, outside of those focused on ectoparasites, have tested the effects of wildfire on pathogen prevalence in wildlife. Even fewer have focused on the impacts of strategies for post-fire remediation on pathogen circulation. Here, we investigated the effect of wildfire and wildfire mitigation on the prevalence and viral load of Sin Nombre virus (SNV) infection in its reservoir host, the western deer mouse, using a study design of matched burned, unburned, and post-burn reseeded sites in northern New Mexico. In total, we screened 411 individual deer mice for SNV via RT-qPCR and analyzed the effect of wildfire and wildfire mitigation on relative mouse abundance, individual infection probability, site-level prevalence and viral load. Relative abundance was highest at reseeded sites, and model selection indicated that habitat structure, particularly the gradient from closed canopy to open-herbaceous habitat, was consistently associated with increased relative abundance. Similarly, SNV prevalence was significantly higher in reseeded sites than either burned or unburned sites but did not differ in burned versus unburned sites. Viral load did not differ between burn history types, and zero-inflated gamma hurdle models did not identify any strong predictors of viral load. Serendipitously, we were also able to investigate the impacts of an El Nino Southern Oscillation (ENSO) cycle on patterns of infection in a subsample of sites that were studied during and one year after an ENSO year and found that SNV prevalence increased significantly post-ENSO. Both reseeding and ENSO deliver resource pulses that can support increases in mouse density and thereby enhance SNV transmission. The impacts of post-fire management practices on SNV prevalence in its reservoir host that were revealed in this study should be considered when implementing such strategies and when utilizing treated areas.

ecology↗
bioRxiv2026

TheCellVision.org repository: expansion with high-content cell imaging projects on eukaryotic intracellular organization and DUB biology

High-content cell imaging approaches enable the systematic characterization of cellular function through the acquisition of multimodal information from large cohorts of live single cells. Yet, due to their scale and complexity, data acquired via such approaches are often challenging to meaningfully share across laboratories and effectively use for independent studies. Since its inception, the main purpose of TheCellVision.org repository has been to fill this gap, providing the research community with access to large-scale, multimodal single-cell datasets, in a structured, intuitive, and user-friendly way. Here, we report on the third major update of TheCellVision.org, which involves the expansion of the repository with the addition of data from two single-cell phenomics projects; the Intracellular Organization Dynamics project, which quantitatively maps changes in the morphology of 21 major subcellular structures in live yeast cells elicited by the systematic inhibition of essential genes, and the DUB Biology project, which describes changes in the concentration and localization of the budding yeast proteome in mutants of key deubiquitination enzymes (DUBs). With these additions, the repository now hosts six complementary high-content imaging projects which collectively explore the dynamics of intracellular organization and the proteome during changes in cell state and in response to environmental and genetic perturbations.

cell biology↗
bioRxiv2026

The emerging medium-scale: Prioritising fisheries management for elasmobranch conservation.

Fishing pressure has substantially increased over time and elasmobranchs are among the most vulnerable marine taxa impacted. 'Small-scale' and 'large-scale' are terms frequently used to describe fisheries, yet definitions used across the globe are inconsistent. The global impact of small-scale fisheries on elasmobranch decline is increasingly evident. However, ambiguous vessel-capacity classifications undermine effective conservation management. Technological advancements have led to the emergence of medium-capacity vessels that sit between small and large-scale classifications, creating regulatory gaps that increase bycatch impacts on vulnerable elasmobranchs. Beyond vessel size, the gear specificities and practices also affect interaction with species caught incidentally, and can alter bycatch risk for vulnerable elasmobranchs. Manta and devil rays (collectively, mobulids) represent a pelagic ray group that includes species listed as Critically Endangered with high risk of extinction, largely due to bycatch threats. To prioritise fisheries management for conservation, we assess the contribution of fishing gear specifications and practices to mobulid bycatch as a case study in their largest fishery globally. We use a Huber-robust extension to a Hurdle negative binomial model to assess the impact of fishery characteristics and operational specificities on mobulid bycatch risk. We find that within the Food and Agriculture Organization (FAO) of the United Nations' broad international fleet classification of small-scale vessels based on overall length ([≤]24 m), the 'medium-capacity vessels' in India are twice as likely to catch mobulids than small-scale vessels. Further, increased fishing intensity, measured in five-day increments, doubles mobulid bycatch risk. Our results indicate the emergence of a distinct medium-capacity fishery class in rapidly developing blue-economy nations, shaped by rising technological capacity and exemptions from large-scale management measures. We propose a comprehensive re-conceptualisation of small-scale fisheries to ensure that advanced medium-capacity vessels are subject to management measures commensurate with their bycatch impact. Our recommended re-conceptualisation is complementary to FAO's SSF characterisation matrix and would promote fishery-level sustainability and enable bycatch risk mitigation for elasmobranchs, including manta and devil rays. Further, for congruence between elasmobranch demography and regulations, we recommend that fisheries management measures distinguish vessel capacities for elasmobranch bycatch risk and apply biologically relevant regulations to the associated fisheries scale.

ecology↗
bioRxiv2026

Convergent stochastic assembly governs reef biofilm microbiomes across ecologically distinct benthic substrates

Understanding the processes that shape microbial biodiversity and community structure is a key objective of the field of microbial ecology. The processes driving assembly of benthic biofilm bacteria on functionally important reef substrates, such as crustose coralline algae (CCA) and calcium carbonate, are not well understood, despite their critical contributions to the maintenance of biodiversity and ecosystem function on reefs. To characterize the patterns of community assembly and biogeography on these substrates, climax biofilm bacterial communities from 11 reef sites were collected, and full 16S small subunit rRNA genes were sequenced. Though CCA- and carbonate-associated communities demonstrated different diversity, composition, and correlations with environmental conditions, communities on both substrates were assembled according to similar processes. Stochastic processes dominated assembly on both substrates, primarily drift with moderate influence from dispersal limitation and selection. Sub-communities of habitat generalists and specialists, as well as rare and abundant taxa, experienced disparate patterns of assembly that remained consistent between substrates, highlighting the importance of individual taxa traits in shaping community assembly. These results provide insight into the factors shaping benthic biofilm bacterial assembly and biogeography in a tropical reef ecosystem and contribute to understanding of reef resilience in the face of environmental change.

ecology↗
bioRxiv2026

A Nanoheater-Integrated Fluorescence Lifetime Thermometer for Investigating Subcellular Heat Shock Factor 1 Responses

Subcellular thermal engineering provides a powerful approach for investigating and manipulating biological processes. However, existing subcellular heating platforms capable of combining spatially confined heating, quantitative thermometry and simultaneous imaging of cellular responses remain limited. We developed a quantitative nanoheater-thermometer (qNanoHT), a polymeric nanoparticle integrating a temperature-sensitive fluorescent, dye and a photothermal dye. qNanoHT determines local temperature from fluorescence lifetime using fluorescence lifetime imaging microscopy (FLIM), thereby reducing susceptibility to photobleaching, focal drift and variations in probe concentration compared with intensity-based methods. The platform enabled real-time measurement at a subcellular heat spot while the dynamics of heat shock factor 1 (HSF1) were monitored in living cells. Heating at a single intracellular site was sufficient to induce HSF1 foci. Foci induced by mild heating at approximately 38 {degrees}C dissolved after heating ceased, whereas those induced by stronger heating at approximately 41 {degrees}C persisted and were associated with caspase-3/7 activation and apoptosis. Notably, qNanoHT-mediated subcellular heating induced HSF1 foci at a lower measured temperature than uniform whole-cell heating approximately 38 {degrees}C versus 39 {degrees}C indicating that the spatial extent of heating influences the HSF1 activation threshold. qNanoHT therefore provides a quantitative platform for relating local intracellular temperature to cellular stress responses and subsequent cell fate.

bioengineering↗
bioRxiv2026

A direct, MFRN-independent Fe(II) transfer pathway at mitochondria-lysosome contacts

Mitochondrial iron homeostasis is fundamental to respiration and redox balance, and its dysregulation is implicated in neurodegeneration, cardiomyopathy, and metabolic diseases. Although lysosomes harbor the major cellular iron reservoir, the prevailing model holds that mitochondria acquire Fe(II) directly from the cytosolic labile iron pool (LIP) via MFRN transporters. Here, we challenge the canonical view by identifying a direct, MFRN-independent Fe(II) transfer pathway at mitochondria-lysosome contacts (MLCs). This VPS39/TOMM22/SFXN1-coordinated pathway enables lysosome-to-mitochondria Fe(II) flux bypassing the cytosolic LIP. Using live-cell structured illumination microscopy (SIM), we visualize direct Fe(II) transfer specifically occurring at MLCs. Multiple lines of evidence confirm that VPS39 and TOMM22 stabilize MLCs, while SFXN1 serves as the core effector protein for this MLC-dependent Fe(II) transport. Notably, SFXN1 knockdown markedly reduces mitochondrial Fe(II) levels independent of its established serine transport function. This pathway reveals a major route for mitochondrial Fe(II) acquisition to support redox homeostasis.

cell biology↗
bioRxiv2026

Dynamic microtubules drive yolk-cytoplasm segregation in the syncytial Drosophila embryo

Yolk-cytoplasm segregation is among the earliest spatial organization events in the developing embryo of many oviparous animals. The segregation process is intimately linked to early embryonic cleavage and pattern formation, and exhibits a wide range of spatial and temporal diversity. However, the underlying cytoskeletal mechanism remains largely unknown, except for a small number of species. Using quantitative live imaging, we investigated yolk segregation in the Drosophila embryo during the syncytial nuclear cycles 11-14. We find that the yolk vesicles move progressively inward in spatial and temporal coordination with the inward expanding microtubule networks that are nucleated from centrosomes positioned at the cortex, whereas cortical actin meshwork remains spatially restricted. Using the gnu RNAi embryo to decouple nuclear migration and division from cytoskeletal dynamics, we establish causality with targeted pharmacological disruption and find that microtubule dynamics is required for yolk segregation, while depolymerization of actin has no discernible effect. In support of a mechanism of growth-propelled passive displacement, microtubule plus end comets come in apparent contact with yolk vesicles, and injected, inert microbeads are displaced towards the embryo center presumably by the same pushing force. These findings identify microtubule polymerization as a predominant driver of yolk-cytoplasm segregation in Drosophila and suggest that diverse cytoskeletal mechanisms evolved to accomplish this crucial reorganization process

developmental biology↗
bioRxiv2026

Motile bacteria collectively transport soil water during host colonisation

Nutrient availability in soil is temporally and spatially heterogeneous, and, as a result, microbial migration is critical for many species. The nature of microbial movement in soil, however, is unknown due to a lack of observations and experimental data. We developed live-imaging and image-analysis techniques to track the movement of single cells through soil to elucidate how Bacillus subtilis utilises pore space during the early root colonisation. The study reveals that the bacterium can modify fluid pathways to create streams, even at low bulk cell density. The phenomenon was influenced by pore structure, distance from the root and the viscosity of the soil solution. By generating macroscopic fluid motion, bacteria may also be able to travel faster and farther than individually, while limiting energy expenditure.

microbiology↗
bioRxiv2026

TALE-independent transcriptional activation of the rice executor gene Xa23 is regulated via histone acetylation during zygote development

Transcription activator-like effectors (TALEs) from Xanthomonas activate transcription of executor (E) genes in host plants, leading to cell death and thereby restricting proliferation of biotrophic pathogens. Because E gene transcripts had only been detected upon activation by cognate Xanthomonas TALEs, E genes were thought to function exclusively in plant immunity. Here, we detect TALE-independent transcription of the rice E gene Xa23 in zygotes 4-6 hours after gamete fusion. Histone deacetylase inhibition induces Xa23 transcription in unfertilized egg cells, implicating histone acetylation in Xa23 regulation. We identified potential cis-regulatory elements and transcription start sites associated with native Xa23 transcription during zygote development. Together, our findings suggest that Xa23 is a developmentally regulated gene with a native role during early zygote development. This supports a previously proposed model in which E genes have native functions in development, while fortuitous upstream polymorphisms can create TALE-binding sites that convert them into immune executors.

plant biology↗
bioRxiv2026

Attenuated Salmonella-Mediated Delivery of GSDMD Potentiates PD-1 Blockade Therapy against Melanoma

Immunotherapy has emerged as a core therapeutic strategy for melanoma. Programmed death protein 1 (PD-1) is a critical immune checkpoint molecule that restrains host anti-tumor immunity, and therapeutic agents blocking the PD-1 signaling pathway have been widely deployed in clinical practice. Nevertheless, single-agent PD-1 blockade fails to elicit robust clinical responses in the majority of patients. Therefore, there is an urgent unmet need to develop combinatorial regimens capable of augmenting the anti-tumor efficacy of PD-1 inhibition. Gasdermin D (GSDMD), a pore-forming effector protein that orchestrates pyroptosis, exerts inherent anti-tumor activities upon overexpression. However, whether GSDMD can synergize with PD-1 blockade to enhance therapeutic outcomes against melanoma remains poorly defined. To address this question, we established an attenuated Salmonella engineered strain for targeted delivery of GSDMD, and further investigated the anti-melanoma therapeutic efficacy of combining this engineered bacterium with anti-PD-1 antibody via immunofluorescence staining, flow cytometry and other analytical approaches. Our in vivo results demonstrated that combinatorial treatment markedly suppressed melanoma progression in tumor-bearing mice relative to monotherapy with either GSDMD-expressing bacteria or anti-PD-1 antibody alone. Mechanistically, co-treatment upregulated intratumoral expression of GSDMD and the pro-apoptotic protein BAX, while simultaneously downregulating PD-1 expression. In addition, the GSDMD/anti-PD-1 combination significantly elevated the proportions of CD4 and CD8 T lymphocytes in both peripheral blood and splenic tissues, and facilitated robust tumor infiltration by these two T cell subsets. Compared with phosphate-buffered saline (PBS) and scramble control groups, combinatorial therapy promoted tumor infiltration of M1-type tumor-associated macrophages (TAMs) and repolarized TAMs away from the immunosuppressive M2 phenotype. Consistently, serum levels of the pro-inflammatory cytokines TNF- and IFN-{gamma} were markedly elevated following combined intervention. Collectively, this study verifies that attenuated Salmonella carrying GSDMD synergizes with anti-PD-1 antibody to elicit potent anti-tumor effects in melanoma-bearing mice by amplifying systemic and intratumoral anti-tumor immune responses, which provides a preclinical rationale for novel combinatorial therapeutic strategies against melanoma.

cancer biology↗
bioRxiv2026

Feasibility of adopting water displacement and 3D scanning methods to quantify lung volume reduction in ex vivo models

Lung volume reduction is a treatment for chronic obstructive pulmonary disease (COPD) patients with severe emphysema. Currently, in vivo animal models are used as a first step to quantify the efficiency of novel lung volume reduction treatments. By quantifying lung volume reduction in ex vivo samples, animal testing may be reduced. This study proposes two new methods for quantifying lung volume reduction in ex vivo tissue: water displacement and three-dimensional (3D) scanning. Porcine lung lobes were inflated and treated with cyanoacrylate glue to simulate lung volume reduction. Volume changes were measured using a custom water displacement setup and in a ventilated setting using a handheld Artec Space Spider 3D surface scanner. Both techniques detected post-treatment volume reductions. Water displacement offers a simple, cost-effective approach for isolated lung lobes, while 3D scanning enables volumetric analysis of intact lungs under ventilated conditions. These methods provide a reliable intermediate step between in vitro and in vivo testing, reducing animal use and improving preclinical assessment of novel lung volume altering interventions.

bioengineering↗
bioRxiv2026

The enlightened entomologist: fast, non-destructive whole-arthropod clearing for three-dimensional imaging

Arthropods are a strikingly diverse phylum of invertebrates with segmented bodies, chitinous exoskeletons, and jointed limbs, many of which are colloquially referred to as insects. Their pigmented and optically dense bodies pose a considerable challenge for microscopy. While early naturalists focused on external features, modern approaches combining tissue clearing and fluorescence microscopy seek to explore internal anatomy in three dimensions. However, both chemical clearing and three-dimensional (3-D) microscopy are specialized techniques and often require considerable adaptation and optimization across species. Here, we introduce a versatile, fast, effective and non-toxic clearing method that renders diverse arthropods transparent within hours to days. Existing upright microscopes or macroscopes can be upgraded with a modular and affordable light-sheet microscope, allowing rapid volumetric imaging of arthropods. Our pipeline is fully compatible with dye staining and immunofluorescence labeling, while endogenous autofluorescence provides valuable anatomical context and facilitates 3-D reconstruction.

zoology↗
bioRxiv2026

Modelling and measuring effects of shear stress in extrusion bioprinting of endothelial- epithelial cell co-cultures

Extrusion-based bioprinting enables the development of tissue-like constructs; however, the impact of printing-associated shear stress on cell viability and function remains a critical consideration. To address this, we developed a comprehensive workflow combining rheological characterization, computational fluid dynamics (CFD) modelling, and experimental validation to predict and assess shear stress effects during bioprinting. The rheological properties of gelatin methacryloyl (GelMA) at 5 % (w/v, 20 {degrees}C) and 10 % (30 {degrees}C) concentrations were modelled, comparing various non-Newtonian regression models. CFD simulations were validated using micro-particle image velocimetry, showing agreement between predicted and measured velocities. The impact of bioprinting-associated shear stress on cell viability was assessed using a co-culture of human umbilical vein endothelial cells and breast epithelial cells. Immediate post-printing analysis revealed increased apoptosis in GelMA 5 % (w/v, 20 {degrees}C), although 10 % (w/v) GelMA demonstrated higher shear stress levels compared to 5 % GelMA. After 1 day of culture in crosslinked hydrogels, apoptosis increased in extrusion pressure, demonstrating the impact of low levels of acute shear stress. This workflow provides a robust methodology for predicting acute shear stress impacts during bioprinting, laying the foundation for future optimization studies.

bioengineering↗
bioRxiv2026

Herpes simplex virus 1 subverts the mitochondrial network to support the infection: A lesson on mitochondrial versatility

Herpes simplex virus 1 (HSV-1) infects approximately 67% of the population worldwide. It establishes lifelong reservoirs in sensory neurons and has been linked to several diseases including neuronal dysfunction. Disruption of mitochondrial homeostasis is a hallmark of HSV-1 infection, however a molecular understanding of these changes and their significance is not yet well defined. HSV-1 infection causes a UL12.5-dependent inhibition of mitochondrial biogenesis through the loss of mitochondrial DNA and mitochondrial transcription factors, PGC-1 (peroxisome proliferator-activated receptor-gamma co-activator) and TFAM (mitochondrial transcription factor). Conversely, UL12.5-independent mechanisms inhibit mitochondrial fusion by activating the OMA1 metallopeptidase that cleaves the inner mitochondrial membrane fusion protein OPA1 (optic atrophy protein 1) and by down-modulating the outer mitochondrial membrane fusion protein MFN2 (mitofusin 2). This inhibition of fusion results in a smaller mitochondrial network that clusters to perinuclear regions, likely supplying energy for viral replication and envelopment. The inner mitochondrial membrane protein TIM23 is also down-modulated during infection in a UL12.5-independent mechanism. Failure of the virus to promote these changes negatively impacts the infection. Despite these changes, mitochondria are protected from mitophagy due to the viral-induced degradation of several mitophagy adaptor proteins, whereby damaged mitochondrial components, including mitochondrial DNA, are extruded via extracellular vesicles. These mitochondrial changes still support functions necessary for HSV-1 infection. Basal cell respiration is preserved, while spare respiratory capacity and extracellular acidification rates increase, indicating glycolytic activity. Mitochondrial membrane potential is also preserved. Overall, our studies provide mechanistic insight into how HSV-1 impacts mitochondria, which could contribute to viral pathogenesis.

microbiology↗
bioRxiv2026

Evaluating Large Language Models as Tools to Navigate Researchers in Rapidly Evolving Research Landscapes: A Case Study in Cancer Drug Response Prediction

Large Language Models (LLMs) have emerged as promising tools for assisting researchers in automating and accelerating the synthesis of literature reviews. However, their reliability is a significant concern due to issues like factual inaccuracies and hallucinations. The key question is whether LLMs can reliably provide comprehensive, up-to-date overviews and analyses. This study evaluates the performance of three leading LLMs (OpenAI's ChatGPT, Google's Gemini, and DeepSeek) on the complex task of generating a comprehensive survey paper on deep learning for cancer Drug Response Prediction (DRP). By testing both standard and Deep Research (DR) / Deep Think (DT) modes of LLMs with prompts of varying detail, this paper assesses key academic dimensions, including reference management, content quality, and analytical depth. Key findings reveal that while DR modes of LLMs significantly improve reliability by eliminating hallucinations, performance variations exist across models and prompts. A trade-off between reference quantity and integration quality was observed, and even the best-performing models lacked the analytical depth of human experts, often requiring extensive human supervision. The study concludes that LLMs currently serve as powerful assistive tools but still cannot replace the critical validation and synthesis provided by human researchers. Choosing the best LLM to use depends on the task in hand, while several strategies can be implemented to improve the produced output.

scientific communication and education↗
Compare source metadata on this page
WorkPublishedSource identifierSource
Readout-dependent time-of-flight weighting of absorption and flow in interferometric diffuse optics2026-09-0310.64898/2026.09.02.748230v1biorxiv
PhysiCelldFBA: Linking single-cell genome-scale metabolism to spatially explicit multicellular dynamics2026-09-0310.64898/2026.09.02.748294v1biorxiv
Early establishment acts as a selective filter shaping climate-associated genomic variation in European beech2026-09-0310.64898/2026.09.02.748467v1biorxiv
Burning down the mouse: Effects of wildfire and post-fire reseeding on Sin Nombre virus prevalence in its reservoir host2026-09-0310.64898/2026.09.02.748549v1biorxiv
TheCellVision.org repository: expansion with high-content cell imaging projects on eukaryotic intracellular organization and DUB biology2026-09-0310.64898/2026.09.02.748561v1biorxiv
The emerging medium-scale: Prioritising fisheries management for elasmobranch conservation.2026-09-0310.64898/2026.09.02.748653v1biorxiv
Convergent stochastic assembly governs reef biofilm microbiomes across ecologically distinct benthic substrates2026-09-0310.64898/2026.09.02.748686v1biorxiv
A Nanoheater-Integrated Fluorescence Lifetime Thermometer for Investigating Subcellular Heat Shock Factor 1 Responses2026-09-0310.64898/2026.09.02.748709v1biorxiv
A direct, MFRN-independent Fe(II) transfer pathway at mitochondria-lysosome contacts2026-09-0310.64898/2026.09.02.748755v1biorxiv
Dynamic microtubules drive yolk-cytoplasm segregation in the syncytial Drosophila embryo2026-09-0310.64898/2026.09.02.748760v1biorxiv
Motile bacteria collectively transport soil water during host colonisation2026-09-0310.64898/2026.09.02.748768v1biorxiv
TALE-independent transcriptional activation of the rice executor gene Xa23 is regulated via histone acetylation during zygote development2026-09-0310.64898/2026.09.02.748781v1biorxiv
Attenuated Salmonella-Mediated Delivery of GSDMD Potentiates PD-1 Blockade Therapy against Melanoma2026-09-0310.64898/2026.09.02.748795v1biorxiv
Feasibility of adopting water displacement and 3D scanning methods to quantify lung volume reduction in ex vivo models2026-09-0310.64898/2026.09.02.748797v1biorxiv
The enlightened entomologist: fast, non-destructive whole-arthropod clearing for three-dimensional imaging2026-09-0310.64898/2026.09.02.748800v1biorxiv
Modelling and measuring effects of shear stress in extrusion bioprinting of endothelial- epithelial cell co-cultures2026-09-0310.64898/2026.09.02.748801v1biorxiv
Herpes simplex virus 1 subverts the mitochondrial network to support the infection: A lesson on mitochondrial versatility2026-09-0310.64898/2026.09.02.748825v1biorxiv
Evaluating Large Language Models as Tools to Navigate Researchers in Rapidly Evolving Research Landscapes: A Case Study in Cancer Drug Response Prediction2026-09-0310.64898/2026.09.02.748827v1biorxiv

These are bibliographic comparisons, not experimental rankings. Follow the original document for methods and conditions.