bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving the integration of AI into existing ecological inference workflows
Authors: Cowans Amber , Lambin Xavier , Hare Darragh , Sutherland Chris 
Published: December 2024

AbstractArtificial Intelligence (AI) has revolutionised the process of identifying species and individuals in audio recordings and camera trap images. However, despite developments in sensor technology, machine learning, and statistical methods, a general AI-assisted data-to-inference pipeline has yet to emerge.We argue that this is, in part, due to a lack of clarity around several decisions in existing workflows, including: the choice of classifier used (e.g., semi- vs. fully automated); how classifier confidence scores are used and interpreted; and the availability and selection of appropriate statistical methods for drawing ecological inferences.Here, we attempt to conceptualise a general workflow associated with automated tools in ecology. We motivate this perspective using our experiences with occupancy modelling using monitoring data collected through passive acoustic monitoring and camera trapping, identifying priority areas for future developments.We offer an accessible guide to support the ecological community in navigating and capitalising on rapid technological and methodological advances. We describe how different error types arise from both sensor-based monitoring and from classifiers themselves; how different error types are handled at each stage of the workflow; and finally, implications and opportunities associated with deciding on methods used at each step of the pipeline.We recommend that “black box” tools like neural network classification algorithms should be embraced in ecology, but widespread uptake requires more formal integration of AI into the existing ecological inference workflows. Like ecological AI more broadly, however, successful development of new data-to-inference pipelines is a multidisciplinary endeavour that requires input from everyone invested in collecting, processing, analysing, and using ecological monitoring data.
Feasibility of intravenous injections of pig plasma extracellular particles into rats — an acute study
Authors: Cherñavsky Nicolás , de Campos Zani Stepheny C. , Mori Marcelo A. , Zanvettor Nina T. 
Published: December 2024

AbstractBackgroundExtracellular particles (EPs), especially small extracellular vesicles (EVs), extracted from young animals are increasingly being studied in animal models as agents for regeneration and rejuvenation, with studies using EPs from one species injected into another showing no immune reaction. In this study, we aimed to investigate if the injection of Pig Plasma Extracellular Particles (PPEPs) into rats would produce an acute immune or toxic reaction.MethodsBlood from a young pig was collected, PPEPs were isolated by size exclusion chromatography and injected into young male Sprague-Dawley rats, while the control group received a sterile saline injection. After 9 days, the animals were euthanized and their organs were histologically analyzed for signs of cellular damage or immune infiltration.ResultsThe treated rats showed no signs of acute immunological reaction, behaving normally immediately after the injections and during the 9 days since the first injection. Throughout the trial period, the animals continued gaining weight normally and the histological analysis of their liver, kidney and spleen showed no signs of acute toxicity.ConclusionsPPEPs from young animals do not cause an acute immune or toxic response when injected intravenously into young male Sprague-Dawley rats.
Exploring the Impact of Apocarotenoids on PathogenicFusarium oxysporumf.sp.liniand Endophytic Fo47 strains
Authors: Kochneva Yelyzaveta , Burgberger-Stawarz Marta , Boba Aleksandra , Preisner Marta , Mierziak-Derecka Justyna , Kulma Anna 
Published: December 2024

AbstractTheFusarium oxysporum species complex(FOSC) contains highly specific plant pathogens and some nonpathogenic strains, such as Fo47. In our work we concentrated onFusarium oxysporumf.sp.lini(Foln), the specific flax pathogen and the endophytic strainFusarium oxysporum47 (Fo47), which is possibly protective for flax against pathogens. We investigated the influence of apocarotenoids like ionones and abscisic acid (ABA) on growth and development of these fungal strains considering possible fungicidal abilities of mentioned substances and comparing responses of fungi. The study shows inhibitory effect of ionones on mycelium growth of both Foln and Fo47. Our results also show the differences in apocarotenoid’s effect on studied strains in regards of sporulation,FUBgenes cluster activity and fusaric acid (FA) production.Author summaryIn this study, we investigated the interaction betweenFusarium oxysporum, a fungus that can either harm or potentially benefit plants, and natural plant-derived compounds known as apocarotenoids. We focused on two fungal strains: one that specifically infects flax plants, causing disease, and a nonpathogenic strain that may protect flax from pathogens. By examining the effects of apocarotenoids like ionones and abscisic acid, we aimed to understand how these compounds influence fungal growth, sporulation, toxin production, and gene activity related to pathogenicity. Our findings reveal that ionones inhibit the growth of both strains, suggesting their potential as antifungal agents. Interestingly, the two strains showed distinct responses to these compounds, particularly in their production of fusaric acid and activation of toxin-related genes. These results highlight the complexity of fungal interactions with plant-derived molecules and suggest that apocarotenoids could play a role in modulating fungal behavior. This work contributes to our understanding of plant-fungal interactions and may inform future strategies for managing crop diseases sustainably.
SS-31 protects against bleomycin-induced lung injury and fibrosis
Authors: Gu Quankuan , Wang Yunlong , Zhang Haichao , Yang Wei , Meng Xianglin , Zhao Mingyan 
Published: December 2024

AbstractObjectiveThe aim of this research was to investigate if the mitochondria-targeting peptide SS-31 could serve as a protective measure against bleomycin-induced pulmonary fibrosis in mice.MethodMice were split into four groups named CON group, SS-31 group, BLM group, and the BLM+ SS-31 group. SS-31 was administered daily from the day prior to the experiment for the control and model groups. Mice were euthanized after 28 days of the experiment, following which blood, bronchoalveolar lavage fluid, and lung tissue were collected for analysis.ResultsThe study demonstrated that SS-31 could potentially mitigate the reduction in mice. It was observed through HE and Masson staining, immunohistochemistry, hydroxyproline detection, and fibrosis index measurement via Western blot that SS-31 could alleviate pulmonary fibrosis caused by BLM. Electron microscopy and ATP detection further suggested that SS-31 might help protect mitochondrial structure and function. It was also found that SS-31 could reduce reactive oxygen species and myeloperoxidase, thereby alleviating the reduction of antioxidant factor MPO and SOD, as well as diminishing the inflammatory factors TNF-α, IL-1 β, and IL-6.ConclusionThe mitochondria-targeting drug SS-31 exhibited potential in mitigating bleomycin-induced pulmonary fibrosis, improving mitochondrial structural and functional damage, stabilizing the balance between oxidative and antioxidant systems, reducing inflammatory factor expression, and improving apoptosis in lung tissue.
CGMFinder Identifies Correlated Gene Modules from 3H scRNA-seq Data
Authors: Ma Wenping , Xie Xiaoliang Sunney 
Published: December 2024

AbstractCorrelated gene modules (CGMs) contain genes whose expression fluctuates together. Genes in CGMs are often functionally related and regulated by shared transcription factors. CGMs can be identified under steady-state conditions in populations of cells using single-cell RNA sequencing (scRNA-seq). Here, we introduce CGMFinder, a tool for CGM identification using “3H” scRNA-seq data (High mRNA capture efficiency, High cell numbers, and High sequencing depth). CGMFinder employs a graph-based filtering approach, first identifying CGM cores from highly-expressed genes and then linking noisy low-abundance genes to these cores. In lymphoblastoid cell line 3H datasets generated by in-lab and commercial protocols, CGMFinder accurately identifies CGMs enriched for gene ontologies or pathways. In cells grown under hypoxic conditions, CGMFinder successfully identified hypoxia-specific “glycolysis” and “response to oxygen levels” modules. Evaluations using ground truth correlation modules demonstrate that CGMFinder outperforms other CGM identification methods such as WGCNA and FastICA in scRNA-seq data.
PAG orchestrates T cell immune synapse function by binding to actin
Authors: Moore Emily K. , Strazza Marianne , Hu Xizi , Tymm Carly , Paiola Matthieu , Shannon Michael J. , Xie Xinping , Bukhari Shoiab , Lerrer Shalom , Mace Emily M. , Winchester Robert , Mor Adam 
Published: December 2024

AbstractMany immunotherapies impact T cell function by impacting the immune synapse. While immunotherapy is extremely successful in some patients, in many others, it fails to help or causes complications, including immune-related adverse events. Phosphoprotein Associated with Glycosphingolipid Rich Microdomains 1 (PAG) is a transmembrane scaffold protein with importance in T cell signaling. PAG has 10 tyrosine phosphorylation sites where many kinases and phosphatases bind. PAG is palmitoylated, so it localizes in lipid rafts of the membrane, and contains a C-terminal PDZ domain to link to the actin cytoskeleton. As a link between signaling-protein-rich membrane regions and the actin cytoskeleton, PAG is an exciting and novel target for manipulating immune function. Here, we sought to determine if PAG works with actin to control T cell synapse organization and function. We found that PAG and actin dynamics are tightly coordinated during synapse maturation. A PDZ domain mutation disrupts the PAG-actin interaction, significantly impairing synapse formation, stability, and function. To assess the impact of the PDZ mutation functionally in vivo, we employed a mouse model of type IV hypersensitivity and an OVA-tumor mouse model. In both systems, mice with T cells expressing PDZ-mutant PAG had diminished immune responses, including impaired cytotoxic function. These findings highlight the importance of the PAG-actin link for effective T cell immune synapse formation and function. The results of our study suggest that targeting PAG is a promising approach for modulating immune responses and treating immune-related diseases.One Sentence SummaryAdaptor protein PAG links to the actin cytoskeleton, and this link is essential for T cell synapse formation and cytotoxic function.
Semaglutide Analogues Enhancing GLP-1R Activation: A Dynamic Structural & Electrostatic Perspective
Authors: Li Wei 
Published: December 2024

AbstractOn December 5, 2017, the U.S. FDA approved Novo Nordisk A/S’s diabetes drug Ozempic, whose active ingredient, semaglutide, represents a major advancement in the class of glucagon-like peptide-1 (GLP-1) analogues. These analogues mimic the action of an intestinal hormone that promotes insulin secretion, thereby playing a pivotal role in metabolic regulation. Since then, semaglutide has profoundly transformed the treatment landscape for type 2 diabetes and obesity, demonstrating efficacy in glycemic control, weight management and cardiovascular risk mitigation. Yet, it remains an open question whether semaglutide is the best GLP-1 receptor (GLP-1R) agonist either as of now or in future. Given GLP-1R as the therapeutic target, a structural basis of the GLP-1-GLP-1R interaction is paramount for the design of GLP-1 analogues that fully harness the therapeutic potential of GLP-1R activation. Thus, this study employs a structural biophysical approach to enhance GLP-1R activation through the rational design of semaglutide analogues. By incorporating an electrostatic scaffold of interfacial salt bridges, site-specific missense mutations were engineered into the semaglutide backbone to establish additional stabilizing interactions with the extracellular domain (ECD) of GLP-1R, thereby enhancing ligand-receptor binding and activation. In addition to 564 semaglutide analogues, the structural biophysical analysis here also reveal the presence of an electrostatic scaffold comprising four salt bridges at the semaglutide-GLP-1R binding interface. Drawing parallels with the continued optimization of insulin analogues, this articles proposes that the electrostatic scaffold offers a robust framework for the continued development of next-generation GLP-1R agonists, enabling more precise and effective therapies for managing metabolic diseases.
Moving beyond the motor cortex: a brain-wide evaluation of target locations for intracranial speech neuroprostheses
Authors: Verwoert Maxime , Ottenhoff Maarten C. , Tousseyn Simon , van Dijk Johannes P. , Kubben Pieter L. , Herff Christian 
Published: December 2024

ABSTRACTSpeech is the fastest and most natural form of communication, which can be impaired in certain disorders. Speech brain- computer interfaces (BCIs) offer a solution by decoding brain activity into speech. Current neuroprosthetic devices focus on the motor cortex, which might not be usable in all patient populations. Fortunately, many other brain regions have been associated with the speech production process. Here, we investigate which regions are potential (alternative) targets for a speech BCI across a brain-wide distribution within a single study. The distribution includes sulci and subcortical areas, sampled with both a high temporal and a high spatial resolution. Thirty participants were recorded with intracranial electroencephalography during speech production, resulting in 3249 recorded contacts across the brain. We trained machine learning models to continuously predict speech from a brain-wide global to a single-channel local scale. Within each scale we examined a variation of selected electrode contacts based on anatomical features within participants. We found significant speech detection in both gray and white matter tissue, no significant difference between gyri and sulci at any of the analysis scales and limited contribution from subcortical areas. The best potential targets in terms of decoding accuracy and consistency are located within the depth of and surrounding the lateral fissure bilaterally, such as the (sub)central sulcus, transverse temporal gyrus (Heschls’ gyrus), the supramarginal cortex and parts of the insula. These results highlight the potential benefits of extending beyond the motor cortex and reaching the sulcal depth for speech neuroprostheses.
C. eleganshuntingtin,htt-1,promotes robust autophagy induction and survival under stress conditions
Authors: Chung Christine Hyein , Lee Hanee , Park Kyumin , Park Young Seo , Jung Roy , Seong Ihnsik , Lee Junho 
Published: December 2024

AbstractHuntingtin (HTT) is the gene responsible for Huntington’s disease (HD), a neurodegenerative disorder caused by a CAG trinucleotide repeat expansion mutation. While HD pathogenesis has traditionally been attributed to the toxic gain-of-function effects of mutant huntingtin (mHTT), increasing evidence underscores the critical role of wild-type HTT loss-of-function. Understanding the physiological roles of HTT is essential for elucidating HD mechanisms and developing effective therapeutic strategies. TheC. elegans htt-1gene, an ortholog of human HTT, remains largely uncharacterized. Here, we demonstrate thathtt-1promotes survival under stress conditions that requires autophagy as a defense mechanism. Specifically, we identify intestinalhtt-1as a key regulator ofC. eleganssurvival duringPseudomonas aeruginosaPA14 infection. Our findings reveal thathtt-1functions downstream of the MPK-1/ERK pathway to induce systemic autophagy and enhance host defense during immune challenges. Moreover, expression of wild-type human HTT inhtt-1mutant worms rescues the survival defect during PA14 infection. Expression of mutant human HTT, on the other hand, exacerbates survival deficits, underscoring the conserved function of HTT across species. Additionally, we found thathtt-1affects survival and autophagy under heat shock stress conditions. These results establishhtt-1as a critical regulator of survival and autophagy in response to both pathogenic bacterial infection and thermal stress.Author summaryHuntingtin plays essential roles in selective autophagy across various organisms, includingDrosophila,mice, and humans. Notably, theC. eleganshuntingtin ortholog,htt-1,remains largely uncharacterized. Here, we describe a novel pro-survival rolehtt-1in stress resistance. We show thathtt-1mutants exhibit significantly reduced survival duringPseudomonas aeruginosainfection. Expression of wild-type human HTT rescues the reduced survival ofhtt-1mutants, whereas mutant HTT further exacerbates the phenotype. These findings establishC. elegans htt-1as a valuable model for studying huntingtin biology and its roles in stress resistance. Downregulation of ERK inhtt-1mutants had no additional effect on survival, suggesting thathtt-1functions downstream of ERK. Interestingly,htt-1mutants display reduced autophagy, indicating thathtt-1functions in the ERK-autophagy signaling cascade during infection. Mechanistically, we propose thathtt-1regulates autophagy at the protein level. HTT-1 remains cytoplasmic, and autophagy-related gene transcripts remain stable, without downregulation, inhtt-1mutants following infection. Additionally,htt-1mutants exhibit reduced survival and impaired autophagy under heat stress. These results suggest thathtt-1may have a broader role in stress resilience extending beyond immune defense.
Striatal Astrocytes Influence Dopamine Dynamics and Behavioral State Transitions
Authors: Lazaridis Iakovos , Ahn Gun , Hirokane Kojiro , Choi Wonchang , Graybiel Ann M. 
Published: December 2024

AbstractWe demonstrate here that astrocytes in the striatum interact with striatal dopamine in bidirectional signaling with dopamine release actively driving surges in astrocytic Ca++, which in turn modulate and reduce subsequent dopamine release. These Ca++surges accurately predict behavioral state changes from task-engaged to task-disengaged states, but fail to predict detailed action parameters. We propose that interactions between striatal astrocytes and dopamine are strong candidates to modulate nigro-striato-nigral loop function underlying on-going behavioral state dynamics.
Invisible Spectrum: A model for minority community public engagement in cancer research
Authors: O’Grady Shane , Ralston Jessica C. , McKiernan Eadaoin , Lanigan Fiona , Salauddin Md , Sharmin Shayla , McVeigh Terri , Gallagher William M. , Guerin Suzanne , Rahman Arman , Kolch Walter 
Published: December 2024

AbstractBackgroundEthnic minority communities are often recognised as experiencing decreased accessibility to vital medical services as well as increased barriers to participation in research studies. These issues stem from a variety of social, cultural and economic factors, all of which must be taken into consideration when designing engagement initiatives for a particular community.Invisible Spectrumis an annual engagement initiative which seeks to promote effective communication and outreach to often-overlooked ethnic minority communities within Ireland, primarily those of Bangladeshi origin. The programme was developed in response to the traditionally low levels of engagement with healthcare services observed within these communities and seeks to empower communities in their own healthcare decision making.MethodsThis study reports a programme of community participation activity with an embedded empirical research component based on participatory action research. The team included researchers and leaders within the Bangladeshi and Arabic Muslim communities in Ireland. Over the course of four years, feedback polls, pre- and post-event surveys and in-depth interviews gathered the views and recommendations of attendees.ResultsFour annual events were held as part of theInvisible Spectrumprogramme, from 2019 to 2023. Feedback from participants consistently demonstrated high levels of satisfaction within the target communities while quantitative survey data also indicated improvements in key areas such as recognition of potential cancer symptoms and greater awareness of available screening services.ConclusionThere is a significant need to continually promote patient involvement and minority inclusion in healthcare and research initiatives. In line with this goal and after 4 successful years of running theInvisible Spectrumprogramme, we have developed a set of recommendations and guidelines for the successful development and organisation of minority community engagement initiatives. It is our hope that theInvisible Spectrumprogramme could be used as a model for future endeavours of a similar nature.
A foundation model for generalized brain MRI analysis
Authors: Tak Divyanshu , Garomsa Biniam A. , Chaunzwa Tafadzwa L. , Zapaishchykova Anna , Climent Pardo Juan Carlos , Ye Zezhong , Zielke John , Ravipati Yashwanth , Vajapeyam Sri , Mahootiha Maryam , Smith Ceilidh , Familiar Ariana M. , Liu Kevin X. , Prabhu Sanjay , Bandopadhayay Pratiti , Nabavizadeh Ali , Mueller Sabine , Aerts Hugo JWL , Huang Raymond Y. , Poussaint Tina Y. , Kann Benjamin H. 
Published: December 2024

ABSTRACTArtificial intelligence (AI) applied to brain magnetic resonance imaging (MRI) has the potential to improve disease diagnosis and management but requires algorithms with generalizable knowledge that can perform well in a variety of clinical scenarios. The field has been constrained, thus far, by limited training data and task-specific models that do not generalize well across patient populations and medical tasks. Foundation models, by leveraging self-supervised learning, pretraining, and targeted adaptation, present a promising paradigm to overcome these limitations. Here, we present Brain Imaging Adaptive Core (BrainIAC), a novel foundation model designed to learn generalized representations from unlabeled brain MRI data and serve as a core basis for diverse downstream application adaptation. Trained and validated on 48,519 brain MRIs across a broad spectrum of tasks, we demonstrate that BrainIAC outperforms localized supervised training and other pretrained models, particularly in low-data settings and high-difficulty tasks, allowing for application in scenarios otherwise infeasible. BrainIAC can be integrated into imaging pipelines and multimodal frameworks and may lead to improved biomarker discovery and AI clinical translation.