bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiological and injury-induced microglial dynamics across the lifespan
Authors: Tieu Taryn , Cruz Anne-Jolene N. , Weinstein Jonathan R. , Shih Andy Y. , Coelho-Santos Vanessa 
Published: October 2024

ABSTRACTMicroglia are brain’s resident immune cells known for their dynamic responses to tissue and vascular injury. Little is known about how microglial activity differs across the life-stages of early development, adulthood, and aging. Using two-photon live imaging, we show that microglia in the adult cerebral cortex exhibit highly ramified processes and relatively immobile somata under basal conditions. Their responses to injury occur over minutes and are highly coordinated neighboring microglia. In neonates, microglia are denser and more mobile but less morphologically complex. Their responses to focal laser-induced injuries of capillaries or parenchymal tissue are uncoordinated, delayed and persistent over days. In the aged brain, microglia somata remain immobile under basal conditions but their processes become less ramified. Their responses to focal injuries remain coordinated but are slower and less sensitive. These studies confirm that microglia undergo significant changes in their morphology, distribution, dynamics and response to injury across the lifespan.HIGHLIGHTSMicroglia undergo significant morphological and dynamic changes between life-stages.Neonatal microglia are highly dynamic, less morphologically complex and mount delayed responses to focal injury compared to adult microglia.Aged microglia are slightly less ramified and their responses to focal injury are slow and less sensitive than adult microglial.Maturation of microglial morphology in the developing cortex is disrupted by focal laser injury.Abstract Figure
Microplate micromilling: A customizable platform to support the prototyping, development and testing of microphysiological culture models
Authors: Reynolds Jacob I. , Adams Meredith , Jimenez Jose , Johnson Brian P. 
Published: October 2024

AbstractThe development of microphysiological cell culture models (MPMs) that align with the throughput demands of drug and chemical testing are needed to help reduce animal testing, aide in the discovery of new drugs, and identify harmful chemical exposures. To address this need, we have developed a process for rapid prototyping MPM devices using computer numerical control (CNC) micromilling of commercially available microplates. Microchannels are cut out of the existing microplate structure and ports are drilled into the bottom of the wells to interface the wells. To test versatility and benchmark to another rapid-prototyping approach, we manufactured common microfluidic features into microplates using four different CNC mills as well as a 3D printer. Cell viability was assessed for polystyrene (PS) well plates and two 3D printed resins (MED610 and VeroClear) with the PS showing >2.5-fold increase in cell growth after three days. Machines were tested on their ability to create common device features including a traditional microfluidic device as well as a custom design incorporating complex geometries. Features were measured by confocal microscopy. We found that features including 1000µm ports, 800µm microchannels, 200µm phase-guides, and 500µm post arrays were machined and the range of CVs for features were 1.02-4.42, 1.32-3.50, 2.34-16.58, 6.25-16.40 respectively, while the 3D printed features exhibited maximal CVs of 20.98, 11.68, 23.60, and 10.01 for the same features. Predictably, more expensive machines generally showed higher accuracy and lower variation, but many features could be created accurately and precisely by inexpensive (<$3000) machines facilitating the broader use of this technology to create a user customizable platform to support the prototyping, development, and testing of human relevant models with broad applications across the life sciences.Graphical abstractMultiple CNC mills are assessed on accuracy and precision of microfluidic features of interest for microphysiological model development creation.
Heterogeneity and plasticity of the naïve CD4+T cell compartment
Authors: Sajani Alia , Schaafsma Evelien , Croteau Walburga , ElTanbouly Mohamed , Nowak Elizabeth C. , Cheng Chao , Burns Christopher M. , Turk Mary Jo , Noelle Randolph J. , Lines J. Louise 
Published: October 2024

AbstractWhile naïve CD4+T cells have historically been considered a homogenous population, recent studies have provided evidence that functional heterogeneity exists within this population. Using single cell RNA sequencing (scRNAseq), we identify five transcriptionally distinct naïve CD4+T cell subsets that emerge within the single positive stage in the thymus: a quiescence cluster (TQ), a memory-like cluster (TMEM), a TCR reactive cluster (TTCR), an IFN responsive cluster (TIFN), and an undifferentiated cluster (TUND). Elevated expression of transcription factors KLF2, Mx1, and Nur77 within the TQ, TIFN, and TMEMclusters, respectively, allowed enrichment of these subsets for further analyses. Functional studies using sorted cells revealed that naïve T cell subsets have distinctive functional biases upon stimulation. Furthermore, treatment of mice with inflammatory stimuli imparted a state of reduced responsiveness on naïve T cells, evidenced by a reduction in cytokine productionex vivo. In human lupus patients, naïve CD4+T cell cluster frequencies were distorted, with the TIFNcluster expanding proportionately with disease score. Our data show that naïve T cells are influenced by host environment, with functional consequences manifesting upon activation. These findings highlight a need to explore how naïve T cells can become distorted in cancer, autoimmunity, and infectious diseases.SummaryThis study describes the transcriptional heterogeneity of murine and human naïve CD4+T cells as comprising of multiple discrete clusters that impact CD4+T cell fate and trajectories. Naïve CD4+T cells experiencing inflammatory environments exhibit an altered transcriptional state that influences their functional trajectory.
Hierarchical Organization of Visual Feature Attention Control
Authors: Meyyappan Sreenivasan , Ding Mingzhou , Mangun George R 
Published: October 2024

AbstractAttention can be deployed in anticipation of visual stimuli based on features such as their color or direction of motion. This anticipatory feature-based attention involves top-down neural control signals from the frontoparietal network that bias visual cortex to enhance the processing of attended information and suppress distraction. So, for example, anticipatory attention control can enable effective selection based on stimulus color while ignoring distracting information about stimulus motion. But as well, anticipatory attention can be focused more narrowly, for example, to select specific colors or motion directions that define task-relevant events and objects. One important question that remains open is whether anticipatory attention control first biases broad feature dimensions such as color versus motion before biasing the specific feature attributes (e.g., blue vs. green). To investigate this, we recorded EEG activity during a task where participants were cued to either attend to a color (blue or green) or a motion direction (up or down) on a trial-by-trial basis. Applying multivariate decoding approaches to the EEG alpha band (8-12 Hz) activity during the attention control period (cue-target interval), we observed significant decoding for both the attended dimensions (color vs. motion)andspecific feature attributes (blue vs. green; up vs. down). Importantly, the temporal onset of the dimension-level biasing (color vs. motion) preceded that of the attribute-level biasing (e.g., blue vs. green). These findings demonstrate that the top-down control of feature-based attention proceeds in a hierarchical fashion, first biasing the broad feature dimension, and then narrowing to the specific feature attribute.Significance StatementDuring voluntary feature-based attention, electrophysiological and neuroimaging studies have highlighted the role of anticipatory (top-down) biasing of the sensory cortex in enhancing the selection of attended stimulus attributes, but little is known about how this is achieved. In particular, it is not clear whether attending to an attribute such as a color (blue vs. green) or motion direction (up vs. down)firstbiases all neural structures coding that dimension (color/motion) before biasing the specific attribute, or if the top-down signals directly bias only the attended attribute. Using EEG and multivariate decoding, we report that top-down attention control follows a hierarchical organization: first, the broader attended feature dimension is biased, which is followed by the biasing of the specific feature attribute.
In-gel refolding allows fluorescence detection of fully denatured GFPs after SDS-PAGE
Authors: Shiratori Misa , Tsuyuki Rio , Asanuma Miwako , Kawabata Saki , Yoshioka Hiromasa , Ohgane Kenji 
Published: October 2024

AbstractGreen fluorescent proteins (GFPs) have been widely used as fusion tags, especially to visualize subcellular localization and dynamics of the fused partner proteins. Also, GFPs serve as fluorescent tags in size-exclusion chromatography and native-PAGE, facilitating the evaluation of expression levels and quality of the expressed fusion proteins. However, the fluorescent detection of GFPs is generally incompatible with denaturing SDS-polyacrylamide gel electrophoresis (PAGE), where the samples are heat-denatured before loading. Accordingly, detecting GFP-fused proteins after SDS-PAGE usually relies on western blotting with anti-GFP antibodies. To enable in-gel fluorescence detection of SDS-PAGE-separated GFPs, some protocols employ mild denaturing conditions to keep the GFPs intact. However, such mild denaturation sometimes results in partial denaturation of the proteins and irregular electrophoretic mobility that is not proportional to their molecular weights. Here, we demonstrate that the fully denatured GFPs can be refolded within the gel by cyclodextrin-mediated removal of SDS in the presence of 20% methanol, enabling the in-gel fluorescence detection of the GFP-fused proteins. The protocol is compatible with subsequent total protein staining and western blotting. Although future studies are needed to clarify the scope and generality, the technique developed here would provide a simple, time- and cost-effective alternative to the immunodetection of GFPs.HighlightsFully denatured GFPs could be in-gel refolded to enable fluorescence detection.? cyclodextrin effectively removed SDS to assist in the in-gel refolding of GFPs.GFPs amenable for in-gel refolding include GFPuv, EGFP, turboGFP, and sfGFP.Compatible with total protein staining and western blotting.The in-gel refolding procedure was successfully applied to two turboGFP-fusion proteins.Graphical abstract
BioLLMNet: Enhancing RNA-Interaction Prediction with a Specialized Cross-LLM Transformation Network
Authors: Tahmid Md Toki , Abir Abrar Rahman , Bayzid Md. Shamsuzzoha 
Published: October 2024

AbstractExisting computational methods for the prediction of RNA related interactions often rely heavily on manually crafted features. Language model features for bio-sequences has gain significant popularity in proteomics and genomics. However, during interaction prediction, how language model features from different modalities should be combined to extract the most representative features is yet to be explored. We introduce BioLLMNet, a novel framework that introduces an effective combination approach for multi-modal bio-sequences. BioLLMNet provides a way to transform feature space of different molecule’s language model features and uses learnable gating mechanism to effectively fuse features. Rigorous evaluations show that BioLLMNet achieves state-of-the-art performance in RNA-protein, RNA-small molecule, and RNA-RNA interactions, outperforming existing methods in RNA-associated interaction prediction.
Regeneration of Sensory Hair Cells and Restoration of Vestibular Function by Notch Inhibition
Authors: Lahlou Hanae , Zhu Hong , Zhou Wu , Edge Albert S.B. 
Published: October 2024

AbstractSensory hair cell loss in the vestibular organs of the inner ear causes balance disorders which are essentially irreversible due to the lack of significant hair cell regeneration. Here, we administered a γ-secretase inhibitor to an adult mouse model of vestibular hair cell loss. The treatment resulted in complete regeneration of type II and partial restoration of type I hair cells after one month and restored vestibuloocular reflexes across all frequencies of rotational and linear acceleration. Further recovery was apparent at 8 months. Genetic deletion ofNotch1in supporting cells identified Notch1 as the target of the drug. The results demonstrate that a single injection of a γ-secretase inhibitor is a viable therapy for functional restoration of the vestibular system in patients with balance disorders.
Spectral estimation at the edge
Authors: Patel Shivangi , Psarou Eleni , Mönke Gregor , Fries Pascal 
Published: October 2024

AbstractCognitive functions depend on neuronal communication, which is subserved by the synchronization of neuronal rhythms. Rhythms are characterized by their frequency, power and phase. If the phase of a rhythm just preceding an input is predictive of the neuronal or behavioral response to the input, this provides strong evidence for a functional role of the rhythm. Yet, this requires estimating the phase of a rhythm at the edge of the epoch. This is challenging, because any phase estimation that is spectrally specific requires a finite window length often combined with tapers that de-emphasize the signal close to the edge. To overcome this, we propose a method that builds on previously described approaches based on autoregressive modeling of the data and corresponding extrapolation beyond the edge. In contrast to related previous approaches, the modeling is based on the broadband signals, avoiding filtering-related group delays, and the extrapolation is performed multiple times, allowing averaging and thereby the reduction of extrapolation noise. The new method provided more accurate phase estimation at the edge for most simulated datasets, and for an empirical dataset from awake macaque area V4. We propose that the enhanced phase estimation accuracy at the edge might help to investigate the functional roles of brain rhythms and potentially also to improve phase-specific stimulation for clinical applications.
Combined Nanodrops Imaging and Ultrasound Localization Microscopy for Detecting Intracerebral Hemorrhage
Authors: Lin Bing-Ze , Fan Alexander Changyu , Wang Yike , Lowerison Matthew R. , Dong Zhijie , You Qi , Sekaran Nathiya Vaithiyalingam Chandra , Llano Daniel , Borden Mark , Song Pengfei 
Published: October 2024

AbstractObjectiveAdvanced imaging methods are crucial for understanding stroke mechanisms and discovering effective treatments to reduce bleeding and enhance recovery. In preclinicalin vivostroke imaging, MRI, CT, and optical imaging are commonly used to evaluate stroke outcomes in rodent models. However, MRI and CT have limited spatial resolution for rodent brains, and optical imaging is hindered by limited imaging depth of penetration. Here we introduce a novel contrast-enhanced ultrasound imaging method to overcome these challenges and characterize intracerebral hemorrhage with unique insights.MethodsWe combined microbubble (MB)-based ultrasound localization microscopy (ULM) and nanodrop (ND)- based vessel leakage imaging to achieve simultaneous microvascular imaging and hemorrhage detection. ULM maps brain-wide cerebral vasculature with high spatial resolution and identifies microvascular impairments around hemorrhagic areas. NDs are sub-micron liquid-core particles which can extravasate due to blood-brain barrier (BBB) breakdown, serving as positive contrast agents to detect hemorrhage sites.ResultsOur findings demonstrate that NDs could effectively accumulate in the hemorrhagic site and reveal the location of the bleeding areas upon activation by focused ultrasound beams. ULM further reveals the microvascular damage manifested in the form of reduced vascularity and decreased blood flow velocity across areas affected by the hemorrhagic stroke.ConclusionThe results demonstrate that sequential ULM combined with ND imaging is a useful imaging tool for basicin vivoresearch in stroke with rodent models where brain-wide detection of active bleeding and microvascular impairment are essential.
Mitigation of multi-scale biases in cell-type deconvolution for spatially resolved transcriptomics using HarmoDecon
Authors: Wang Zirui , Xu Ke , Liu Yang , Xu Yu , Zhang Lu 
Published: October 2024

AbstractThe advent of spatially resolved transcriptomics (SRT) has revolutionized our understanding of tissue molecular microenvironments by enabling the study of gene expression in its spatial context. However, many SRT platforms lack single-cell resolution, necessitating cell-type deconvolution methods to estimate cell-type proportions in SRT spots. Despite advancements in existing tools, these methods have not addressed biases occurring at three scales: individual spots, entire tissue samples, and discrepancies between SRT and reference scRNA-seq datasets. These biases result in overbalanced cell-type proportions for each spot, mismatched cell-type fractions at the sample level, and data distribution shifts across platforms. To mitigate these biases, we introduce HarmoDecon, a novel semi-supervised deep learning model for spatial cell-type deconvolution. HarmoDecon leverages pseudo-spots derived from scRNA-seq data and employs Gaussian Mixture Graph Convolutional Networks to address the aforementioned issues. Through extensive simulations on multi-cell spots from STARmap and osmFISH, HarmoDecon outperformed 11 state-of-the-art methods. Additionally, when applied to legacy SRT platforms and 10x Visium datasets, HarmoDecon achieved the highest accuracy in spatial domain clustering and maintained strong correlations between cancer marker genes and cancer cells in human breast cancer samples. These results highlight the utility of HarmoDecon in advancing spatial transcriptomics analysis.
Cross-catalytic enhancement of peptides and RNA from a common prebiotic activated intermediate
Authors: Roy Raya , Sawant Anupam A. , Rajamani Sudha 
Published: October 2024

AbstractPrevious origin of life studies have demonstrated the presence of amino acids and nucleotides in the same prebiotic milieu. In this study, we set out to understand the interplay of amino acids with linear or cyclic nucleotides under prebiotically pertinent reaction conditions, especially for its implications for biomolecular evolution. We characterized the cross-catalytic effect of oligomerization, potentially stemming from the simultaneous presence of these two biochemically important monomers. Qualitative and quantitative analysis indicated the formation of longer AMP oligomers and peptides, with 8-10 fold increase in specific reaction scenarios, when compared to reactions that evaluated the monomer oligomerization in isolation. The reason behind such an increase in yield and length, in case of both the oligomers, was the formation of a reactive intermediate. This aminoacylated-AMP (AMP-aa) resulted from a condensation reaction between the nucleotide and the amino acid. We extended this to other amino acids with different R chain characteristics, to comprehend the properties required for the formation of AMP-aa under our reaction conditions. The nonenzymatic formation of these aminoacylated AMP, which in turn resulted in longer oligomers, indicates the plausibility of the emergence of initial steps involved in a primordial translation system.
Symptom-modulating satRNAs of cucumoviruses affect the orientation and feeding behaviour ofMyzus persicae
Authors: Wrzesińska-Krupa Barbara , Strażyński Przemysław , Frąckowiak Patryk , Obrępalska-Stęplowska Aleksandra 
Published: October 2024

ABSTRACTPlant viruses evolved mechanisms to manipulate host plants to replicate and be efficiently transmitted by insect vectors. In the context of non-persistently transmitted viruses, an important strategy is to change the plant’s metabolism to attract the vectors, and subsequently repel viruliferous insects from the infected plants to facilitate the virus transmission to neighbouring plants. The presence of satellite RNAs (satRNAs), which accompany certain plant RNA virus species and strains, leads to changes in the host plants, such as alterations in the virus-induced infection symptoms, either exacerbating or attenuating them. This study aimed to analyse the influence of satRNAs on the orientation and feeding behaviour of the cucumovirus insect vector –Myzus persicae, which might consequently contribute to the virus transmission efficiency. The hypothesis behind this study was that satRNAs of cucumoviruses alter these insect activities toward virus-infected plants, and strongly symptom-deteriorating satRNAs might negatively affect the attractiveness of the infected plants for aphids. Using two cucumoviruses, peanut stunt virus (PSV) and cucumber mosaic virus (CMV), and their satRNAs, which induce divergent infection symptoms, olfactometry and electrical penetration graph (EPG) monitoring analyses were performed. The results showed that satRNAs which presence leads to disease symptom exacerbation might alter the orientation behaviour of aphids by reducing the attractiveness of the plants and discouraging aphids from feeding. This phenomenon may contribute to the better persistence in the environment of satRNAs alleviating disease symptoms compared to the worsening ones, benefiting the virus by not destroying the plant and prolonging the virus’ exposure to insect vectors.
IL-1β Signalling Modulates T Follicular Helper and Regulatory Cells in Human Lymphoid Tissues
Authors: Vaineau Romain , Jeger-Madiot Raphaël , Ali-Moussa Samir , Prudhomme Laura , Debarnot Hippolyte , Coatnoan Nicolas , Dubois Johanna , Binvignat Marie , Vantomme Hélène , Gouritin Bruno , Fourcade Gwladys , Engeroff Paul , Belbézier Aude , Luscan Romain , Denoyelle Françoise , Lorenzon Roberta , Ribet Claire , Rosenzwajg Michelle , Bellier Bertrand , Klatzmann David , Tchitchek Nicolas , Graff-Dubois Stéphanie 
Published: October 2024

AbstractBackgroundDysregulation of the T follicular helper (Tfh) and T follicular regulatory (Tfr) homeostasis in the germinal center (GC) can result in antibody-mediated autoimmunity. While interleukin-1β (IL-1β) has been shown to be an important modulator of the GC response in animal models via the expression of IL-1 agonist (IL-1R1) and antagonist (IL-1R2) receptors on follicular T cells, such regulation has not yet been studied in humans.MethodsWe investigated Tfh and Tfr phenotypes in human secondary lymphoid organs — namely tonsils, spleens, and mesenteric lymph nodes — using flow cytometry, single-cell transcriptomics, andin vitrocell culture. We also benchmarked our findings with a cohort of patients with autoimmune and inflammatory diseases.ResultsWe found that Tfh and Tfr cells exhibit organ-specific phenotypes related to their activation status and IL-1 receptor expression. An excess of IL-1R1 over IL-1R2 was linked to the emergence of a unique activated Tfr subset that combines features of both Treg and GC-Tfh cells. Single-cell transcriptomics andin vitrostudies showed that IL-1β signaling through IL-1R1 promotes follicular T-cell activation. Inhibiting IL-1β resulted in upregulation of IL-1R1 expression, showing a fine-tuned regulation. In autoimmune patients, high IL-1β and circulating Tfr levels correlated with higher autoantibody levels, linking inflammation, IL-1β signaling, and the Tfr/Tfh balance.ConclusionsOur study underscores the pivotal role of IL-1β in follicular T-cell activation, contributing to pathological antibody production in humans. Targeting IL-1β signaling in Tfh and Tfr cells could offer new treatment strategies for antibody-mediated autoimmune diseases.