bluuebunny/crossref_metadata_2025_split huggingface dataset:
High Dimensional Proteomic Multiplex Imaging of the Central Nervous System Using the COMET™ System
Authors: Najem Hinda , Pacheco Sebastian , Turunen Jillyn , Tripathi Shashwat , Steffens Alicia , McCortney Kathleen , Walshon Jordain , Chandler James , Stupp Roger , Lesniak Maciej S. , Horbinski Craig M. , Winkowski Dan , Kowal Joanna , Burks Jared K. , Heimberger Amy B. 
Published: February 2025

AbstractSequential multiplex methodologies such as Akoya CODEX, Miltenyi MACSima, Rarecyte Orion, and others require modification of the antibodies by conjugation to an oligo or a specific fluorophore which means the use of off-the-shelf reagents is not possible. Modifications of these antibodies are typically performed via reduction chemistry and thus require verification and validation post-modification. Fixed panels are therefore developed due to various limitations including spectral overlap that creates spectral unmixing issues, steric hindrance, harsh antibody removal, and tissue degradation throughout the labeling. As such, a complex interrogation evaluating multiple study hypotheses and/or endpoints requires the development of sequential panels, reconstruction, and realignment of the tissue that necessitate a z-stack strategy. Standardized antibody panels are typically fixed and require substantial validation efforts to modify a single target and thus do not evolve with the pace of research interests. To increase the throughput of profiling cells within the human central nervous system (CNS), we developed and validated a CNS-specific library with an associated analysis platform using the newly developed Lunaphore COMETTMplatform. The COMETTMis an automated staining/imaging instrument integrating a reagent deck for staining buffers and off-the-shelf label-free primary antibodies and fluorophore-labeled secondary antibodies, which feed into a circular plate holding up to 4 slides that are automatically imaged in microscope-operated control software. For this study, standard formalin fixed paraffin embedded histology slides are used. However, the COMET is capable of imaging fresh-frozen samples using specialized settings. Our methodologies address an unmet need in the neuroscience field while leveraging prior developmental efforts in the domain of immunology spatial profiling. Cataloging and validating a large series of antibodies on the COMET™ along with developing CNS autofluorescence management strategies while optimizing standard operating procedures have allowed for the visualization at the subcellular level. Forty analytes can be used to analyze one specimen which has clinical utility in cases in which the CNS can only be sampled by biopsy. CNS biopsies, depending on the anatomical location, can have limited available volume to a degree that requires prioritization and restriction to select analysis. In-depth bioinformatic imaging analysis can be done using standard bioinformatic tools and software such as Visiopharm®. These results establish a general framework for imaging and quantifying cell populations and networks within the CNS while providing the scientific community with standard operating procedures.
Polymer-assisted assembly of giant vesicles in physiological solutions
Authors: Cooper Alexis , Vijayananda Vignesha , Pazzi Joseph , Subramaniam Anand Bala 
Published: February 2025

AbstractObtaining high yields of giant unilamellar vesicles (GUVs) in solutions of physiological ionic strengths is one of the major challenges in the use of GUVs in cell-mimicking applications. This is because the free energy cost for forming GUVs increases in solutions of high ionic strengths due increased adhesion between membranes. Gel coated glass slides used in gel-assisted assembly shows promise in assembling GUVs in salty solutions. However, only limited types of gel forming polymers are known to be effective. Extensive localized micrometer-scale dewetting of the polymer film from the substrate upon hydration results in low yields of GUVs from commonly used polymers such as agarose and polyvinyl alcohol. Furthermore, for polymers that show limited dewetting, increased temperatures, required for assembling GUVs composed of lipids with high transition temperatures, results in significant dewetting which limits the temperature at which assembly can occur. Here, we show that nanocellulose paper provides a facile means of suppressing dewetting of water-soluble polymers in the gel-assisted hydration method. With dewetting is suppressed, only low amounts of polymers are necessary to obtain high yields of GUVs. We show the significant extension of the temperature range of GUV assembly using paper supported gel-assisted hydration by assembling GUVs at high yield with raft forming mixtures that require assembly at 45 °C. Moreover, we demonstrate that using nanocellulose paper as a substrate allows the assembly of GUVs from novel polymer classes such as biocompatible hyaluronic acid and dextran. We show the usage of scaled-down nanocellulose paper for the encapsulation of complex reactions in GUVs and the large scale assembly of GUVs for prototissue applications. Using nanocellulose paper as a substrate for polymer-assisted assembly of giant vesicles opens new avenues for using GUVs for biomedical and biophysical applications.
Proteome analysis of daily urine samples of pregnant rats unveils developmental processes of fetus as well as physiological changes of mother rats
Authors: Wang Haitong , Ge Linna , Chen Sijie , Sun Longqin , Sun Wei , Gao Youhe 
Published: February 2025

AbstractSignificant physiological changes occur in both fetus and mother during pregnancy. Urine proteins have been shown to reflect a wide range of physiological and pathological changes in the body. To comprehensively explore the daily changes in urine proteins during pregnancy, this study employed low-abundance protein-enriched magnetic nanobeads to conduct an in-depth analysis of the daily changes in urine proteins throughout the entire pregnancy of rats. Based on the 3,455 identified urine proteins, fetal and maternal dynamic changes were observed in the pregnancy group compared to the control group, including blastocyst formation and cell division in the early stage of pregnancy, embryonic development and organ morphogenesis in the intermediate and mid-to-late stages of pregnancy, and maternal-specific change such as lactation in the late stage of pregnancy. These results indicate that urine protein can reflect the fetal and maternal dynamic physiological alterations during pregnancy, which suggests the potential value of urine protein analysis in pregnancy health monitoring. It is emphasized that the analysis focuses on the daily variations in the urine proteins, as these daily changes are expected to reveal more dynamic and detailed information about the physiological processes during pregnancy.
The Current Landscape of Plasma Proteomics: Technical Advances, Biological Insights, and Biomarker Discovery
Authors: Kirsher Douglas Y. , Chand Shreya , Phong Aron , Nguyen Bich , Szoke Balazs G. , Ahadi Sara 
Published: February 2025

AbstractPlasma is a rich source of biomolecules, including proteins, that reflect both health and disease. Due to their key roles in biological processes, proteins hold significant potential as biomarkers, fueling the rise of plasma proteome profiling in recent years. Despite widespread adoption, few studies have directly compared different plasma proteomics platforms, particularly those using mass spectrometry. Our study provides a comprehensive comparison of seven platforms across three leading technologies - SomaLogic, Olink, and Mass Spectrometry (MS) - including affinity-based approaches and various MS techniques, covering over 13,000 proteins. By applying these methods to the same cohort, we assess their performance, revealing key differences and complementary strengths. Our findings offer valuable insights for researchers, highlighting trade-offs in coverage and their implications for biomarker discovery and clinical applications. This study serves as an essential resource, offering both technical evaluation and biological insights to support the development of novel diagnostics and therapeutics through plasma proteomics.
Development of iPSC-Derived T Cells Targeting EGFR Neoantigens in Non-Small Cell Lung Cancer
Authors: Niizuma Kouta , Nishimura Toshinobu , Villanueva Jonathan , Amaya Laura , Fowler Jonas L. , Isobe Taichi , Nakauchi Yusuke , Saavedra Brandon , Xu Haojun , Nakanishi Mahito , Wilkinson Adam C. , Loh Kyle M. , Shrager Joseph B. , Nakauchi Hiromitsu 
Published: February 2025

ABSTRACTA long-sought goal of cancer immunotherapy is to mass-produce T cells that specifically target tumor neoantigens. One decisive challenge is the identification of neoantigens derived from cancer driver genes. Here, we identify T cells that recognize the NSCLC-associated EGFR C797S mutation, which confers resistance to current inhibitors and is linked to poor prognosis. To overcome limitations in T cell availability, we reprogrammed EGFR C797S-specific T cells into induced pluripotent stem cells (iPSCs) and re-differentiated them into CD8 T cells. These iPSC-derived T cells specifically recognized the EGFR C797S mutation and effectively killed cancer cells expressing this mutation. Our findings underscore the potential of targeting driver mutation-derived neoantigens for immunotherapy and demonstrate that iPSC-derived T cells can mediate antitumor effects. Collectively, this approach combining neoantigen identification with T cell reprogramming may offer a promising strategy for targeting drug-resistant tumors.
CellScope: High-Performance Cell Atlas Workflow with Tree-Structured Representation
Authors: Li Bingjie , Lin Runyu , Ni Tianhao , Yan Guanao , Burns Mannix , Li Jingyi Jessica , Yao Zhigang 
Published: February 2025

ABSTRACTSingle-cell sequencing enables comprehensive profiling of individual cells, revealing cellular heterogeneity and function with unprecedented resolution. However, current analysis frameworks lack the ability to simultaneously explore and visualize cellular hierarchies at multiple biological levels. To address these limitations, we present CellScope, an innovative framework for constructing high-resolution cell atlases at multiple clustering levels. CellScope employs a two-step manifold fitting process for gene selection and noise reduction, followed by agglomerative clustering, and uniquely integrates UMAP visualization with hierarchical clustering to intuitively represent cellular relationships simultaneously at multiple levels—such as cell lineage, cell type, and cell subtype levels. Compared to established pipelines such as Seurat and Scanpy, CellScope comprehensively improves clustering performance, visualization clarity, computational efficiency, and algorithm interpretability, while reducing dependence on hyperparameters across a multitude of single-cell datasets. Most importantly, it can reveal new biological insights that other contemporary methods are unable to detect, thereby deepening our understanding of cellular heterogeneity and function, and potentially informing disease research.
Spatial and single-cell expression analyses reveal complex expression domains in early wheat spike development
Authors: Xu Xiaosa , Lin Huiqiong , Zhang Junli , Burguener German , Paraiso Francine , Tumelty Connor , Li Chengxia , Liu Yuchen , Dubcovsky Jorge 
Published: February 2025

ABSTRACTWheat is an important crop for global food security and a better understanding of the molecular mechanisms driving spike and spikelet development can inform the engineering of more productive varieties. In this study, we integrated single-molecule fluorescencein situhybridization (smFISH) and single-cell RNA sequencing (scRNA-seq) to generate an atlas of cell types and expression domains during the early stages of wheat spike development. We characterized spatiotemporal expression of 99 genes by smFISH in 48,225 cells at the early transition (W1.5), late double ridge (W2.5) and lemma primordia (W3.25) stages. These cells were clustered into 21 different expression domains, including four beneath the developing spikelets and three different meristematic regions, which were consistent across spikelets and sections. We also identified genes differentially expressed during the transition of the inflorescence meristem into a terminal spikelet. The smFISH study was complemented by the scRNA-seq profiling of 26,009 cells from W2.5 and W3.25 that were clustered into 23 distinct cell types. We annotated the single-cell clusters as meristem, boundary domains, cortex, central spike, epidermis, and vasculature by using known markers, co-expression analysis of genes selected from the smFISH study, and correlation matrices of clusters identified in both studies. The scRNA-seq data uncovered genes associated with boundary genesTCP24andFZP, as well as the meristematic genesAGL6andULT1.The smFISH and scRNA-seq studies provided complementary tools for characterizing the gene networks that regulate spike development, supporting the functional characterization of key regulatory genes, and informing the engineering of more productive wheat spikes.
Towards population genetic assessments and species abundance from environmental DNA: A case study with zebrafish in controlled aquaria
Authors: Meenakshisundaram Abinaya , Jarman Simon , Power Haylea , Kennington Jason W. , Thomas Luke 
Published: February 2025

AbstractDeveloping robust methods for amplifying and analysing highly-polymorphic nuclear genetic markers from environmental samples could assist in the reliable and scalable long-term monitoring of elusive, threatened or invasive species that are otherwise challenging to observe. In this study, we used zebrafish in controlled aquaria to apply forensic science approaches and demonstrate that microhaplotypes, which are short segments of nuclear DNA (100–300bp) containing two or more single nucleotide polymorphisms (SNPs), can be amplified from trace DNA in water samples to accurately estimate population genetic diversity and species abundance. We successfully amplified a panel of 17 microhaplotypes that comprised 69 SNPs which could reliably estimate population-level allele frequencies and genetic diversity estimates from water DNA. The panel of microhaplotypes amplified from water samples from replicate tanks strongly matched allele frequency estimates from corresponding tissue samples, and could also be used for estimating number of contributors from multi-individual samples. Our research demonstrates the effectiveness and potential of amplifying microhaplotype panels from eDNA as a non-invasive and scalable tool for population genetic studies of aquatic species.
Modulations of thalamo-cortical coupling during voluntary movement in patients with essential tremor
Authors: Steina Alexandra , Sure Sarah , Butz Markus , Vesper Jan , Schnitzler Alfons , Hirschmann Jan 
Published: February 2025

AbstractThe ventral intermediate nucleus of the thalamus (VIM) is the main thalamic hub for processing cerebellar inputs and the main deep brain stimulation target for the treatment of essential tremor (ET). As such, it presumably plays a critical role in motor control. So far, however, this structure has been rarely investigated in humans, and almost all of the existing studies focus on tremor. Here, we set out to study neural oscillations in the VIM and their coupling to cortical oscillations during voluntary movement.We investigated thalamo-cortical coupling by means of simultaneous recordings of thalamic local field potentials and magnetoencephalography in 10 ET patients with externalized deep brain stimulation electrodes. Brain activity was measured while patients were pressing a button repeatedly in response to a visual cue. In a whole-brain analysis of coherence between VIM and cortex, we contrasted activity around a pre-movement baseline and button pressing.Button pressing was associated with a bilateral decrease of thalamic power in the alpha (8– 12 Hz) and beta (13–21 Hz) band and a contralateral power increase in the gamma (35– 90 Hz) band. Moreover, changes in VIM-cortex coherence were observed. Alpha/low beta (8– 20 Hz) coherence decreased before and during movement, and the effect localized to the supplementary motor area and premotor cortex. A rebound of high beta (21–35 Hz) coherence occurred in the same region, but was more focal than the suppression. Pre-movement levels of thalamo-cortex low-beta coherence correlated with reaction time.Our results demonstrate that voluntary movement is associated with modulations of behaviourally relevant thalamic coupling, primarily to premotor areas. We observed a clear distinction between low- and high-beta frequencies and our results suggest that the concept of “antikinetic” beta oscillations, originating from research on Parkinson’s disease, is transferable to ET.
Transcriptomic insights into the role of miR394 in the regulation of flowering time inArabidopsis thaliana
Authors: Belen Federico , Bernardi Yanel , Reutemann Andrea , Vegetti Abelardo , Dotto Marcela 
Published: February 2025

AbstractThe initiation of flowering is a highly coordinated process that requires synchronization of endogenous plant developmental program with environmental signals through a complex interplay of genetic regulatory networks. The developmental shift from vegetative to reproductive stage is controlled by multiple flowering pathways, which together with other signals participate in the orchestration of flowering time regulation. Collectively, the different pathways converge to modulate the expression of key floral integrator genes, which subsequently trigger the expression of genes related to the differentiation of the vegetative shoot apical meristem into a flower meristem with the subsequent development of floral organs. We had previously demonstrated a role for miR394 in the regulation of flowering time, sincemir394a mir394bdouble mutant plants harboring T-DNA insertions in the twoMIR394 Arabidopsisgenes exhibited an early flowering phenotype correlated with modified expression of flowering genes. In the present study we provide transcriptomic data and histological staining of reporter lines to give further insight into the role of miR394 in the regulation of flowering time inArabidopsis thalianaand present an initial bioinformatic characterization of a newly identified lncRNA, which is found partially overlapping theMIR394Blocus, and therefore we namedMIR394B-ASSOCIATEDTRANSCRIPT(MIRAST). We identified differential domains of expression during flower development, which together with the transcriptomic analysis allows us to propose a role for miR394 in the fine tuning ofArabidopsisflower development through the regulation of transcription factors and chromatin remodeling factors.Key messageDifferential domains of activity ofMIR394AandMIR394Bgene promoters together with transcriptomic analysis of mutant plants, indicate that miR394 participates in the fine tuning ofArabidopsisflower development through regulation of transcription factors and chromatin remodeling factors.
Clade-specific multiplex digital PCR assay for monkeypox virus detection in wastewater
Authors: Pitton Melissa , Gan Charles , Schmidhalter Patrick , Ort Christoph , Julian Timothy R. 
Published: February 2025

AbstractMonkeypox virus (MPXV) is a zoonotic pathogen that has recently caused outbreaks in non-endemic areas. Wastewater-based surveillance (WBS) offers substantial potential for monitoring MPVX clades, and it can inform population-level disease dynamics. Here, we report a four-plex digital PCR assay to detect and quantify different clades and subclades of MPXV. The assay demonstrated specificity in distinguishing and quantifying MPXV by clade, which is advantageous for application in both clinical and wastewater settings.
Depression and Anxiety Symptom Networks Across the Lifespan
Authors: Harlev Daniel , Vituri Aya , Shahar Moni , Wolpe Noham 
Published: February 2025

ABSTRACTBackgroundThe relationship between anxiety and depressive symptoms is complex and may vary across the lifespan. Symptom network analyses offer a powerful tool to examine these interactions, but few studies have directly compared symptom networks in younger and older adults.MethodsWe analysed data from the Cambridge Centre for Ageing and Neuroscience (Cam-CAN) study, including 786 participants aged 18 to 88, who reported at least subclinical levels of symptoms on the Hospital Anxiety and Depression Scale (HADS). Network analysis was employed to examine symptom communities, within- and between-community connectivity, and centrality measures across age groups.ResultsThe overall network structure, largely separating anxiety and depressive symptoms into two communities, remained stable across age groups. However, in older adults, there was a reduction in connectivity within the depression community, and a reduction in between-community connectivity for both the depression and anxiety communities. Moreover, while “panic” emerged as a consistently central symptom across both age groups, “rumination” and “restlessness” were the key bridge symptoms in young and older adults, respectively.DiscussionOur findings reveal both stable and dynamic aspects of depression and anxiety symptoms across the lifespan. Reduced within-community connectivity for depressive symptoms suggests greater heterogeneity in how depression manifests in older populations. The shift in bridging symptoms, from cognitive (rumination) in young adults to somatic (restlessness) in older adults, suggests subtle yet clinically important differences in how depression and anxiety are linked across the lifespan. Our results underscore the need for tailored, age-dependent treatment in depression and anxiety.
Reporting of pre-analytical Processes in Biobanked Biomaterials: A Missed Opportunity to Address the Replicability Crisis in Clinical Biomarker Research
Authors: Jansen Jannes A.W. , van den Brand Mariël A. , de Vegt Femmie , Swinkels Dorine W. 
Published: February 2025

AbstractBiobanks are crucial for clinical biomarker research, but pre-analytical processing can impact sample suitability. Insufficient reporting of pre-analytical methods can lead to invalid conclusions. This study evaluated the pre-analytical reporting quality in 294 clinical biomarker studies using biobank plasma and serum samples published from 2018 to 2023, based on the SPREC and BRISQ guidelines. The analysis revealed frequent incomplete reporting. Key underreported elements included fasting time (reported in 31% of articles), freeze-thaw cycles (22.8%), internal transport (8.5%), and centrifugation settings (20-35%). Demographic data (96.9%), storage temperatures (81%), and blood tube additives (82.7%) were more consistently reported. No significant correlation was found between reporting quality and journal impact factor. This highlights the need for standardized pre-analytical reporting to improve research replicability and biomarker study quality.