bluuebunny/crossref_metadata_2025 huggingface dataset:
3D Reconstruction of Dinoflagellate Chromosomes from Hi-C Data Refutes the Cholesteric Liquid Crystal Hypothesis
Authors: Philipp Lucas , Marinov Georgi K. , Todd Stephen , Weber Stephanie C.
Published: January 2025

Dinoflagellates contain permanently condensed chromosomes that are often described as liquid crystalline. Specifically, a Cholesteric Liquid Crystal (CLC) model was proposed in which DNA is organized into parallel fibers within stacked discs, such that the fiber orientation rotates by a constant angle between adjacent discs. Extrachromosomal loops extending from the discs were hypothesized to be more accessible and thus to contain transcriptionally active genes. Although the CLC model captures some features of dinoflagellate chromosome structure, its validity has not been rigorously tested against modern genomic data. Here, we use chromatin conformation capture (Hi-C) data to simulate 3D conformations of chromosome scaffolds for two dinoflagellate species,Symbiodinium kawagutiiandSymbiodinium microadriaticum. These polymer conformations are compact helices with significant orientational and nematic order. However, we find no evidence of cholesteric discs. Moreover, simulated Hi-C contact maps of CLC structures lack topologically associating domains (TADs), which are observed in experimental Hi-C contact maps for these species. Finally, by mapping RNA-seq data onto our simulated conformations, we show that actively transcribed genes are present throughout the entire chromosome, and not exclusively on extrachromosomal loops or at the surface. Our results refute the long-standing CLC model and suggest that dinoflagellate chromosomes are organized into condensed but non-crystalline structures that do not impede transcription.

Significance Statement

Dinoflagellates have permanently condensed chromosomes that are structurally unique among eukaryotes. These chromosomes are often described as cholesteric liquid crystals (CLCs). In this article, we generate three-dimensional polymer conformations from chromatin conformation capture (Hi-C) data. Our results indicate that, while dinoflagellate chromosomes are organized into compact helical structures, they do not contain parallel stacks of flat discs and are therefore not CLCs. Mapping RNA-seq data onto our simulated conformations reveals actively transcribed genes throughout the entire chromosome, contradicting CLC model predictions and raising questions as to the role of condensation and extrachromosomal loops in regulating gene expression.
Tunneling CARs: Increasing CAR T tumor infiltration through the overexpression of MMP7 and SPP1
Authors: Van Pelt Stacey N , White Mark , Tat Candise , Hooper Devyn , Talbot Lindsay , Fernandes Rohan , Rooney Cliona , Omer Bilal
Published: January 2025

Chimeric antigen receptor T cell (CAR T) therapy has demonstrated remarkable efficacy in hematologic malignancies but has struggled to achieve comparable success in solid tumors. A key obstacle is the extracellular matrix (ECM) in solid tumors, which significantly impedes CAR T cell infiltration. In clinical trials, neuroblastoma (NB) has shown responsiveness to GD2-directed CAR T therapy, however, the failure of GD2.CAR Ts to effectively clear bulky disease - characterized by dense ECM - highlights the critical challenge of infiltration. In this study, we demonstrate that GD2.CAR Ts exhibit a unique infiltration-restriction compared to other CAR Ts and endogenous T cells. A separate analysis of clinical datasets identified MMP7 and SPP1 (OPN) as candidate genes to improve the infiltration of GD2.CAR Ts as these were upregulated in tumor-infiltrating leukocytes. MMP-7 and OPN overexpression enhanced CAR T extravasation (p < .001) and interstitial movement (p < .05) in ECM-dense environments in vitro. Overexpression of either OPN (p < .0001) or MMP-7 (p < .001) improved tumor infiltration in a xenograft model of NB. This resulted in improved tumor control (94% reduction in tumor burden, p < .05) and a survival extension in OPN-GD2.CAR T treated mice compared to unmodified GD2.CAR Ts (median of 148 days, p < .05). OPN overexpression did not increase off-target infiltration into healthy tissues or promote tumor metastasis, highlighting its potential for safe therapeutic application. Our study provides a framework for further exploration of gene modifications to improve CAR T infiltration and efficacy in solid tumors and identifies SPP1 as a candidate gene to improve GD2.CAR T treatment of bulky tumors.
SVCROWS: A User-Defined Tool for Delineating Biologically Significant Structural Variants in Heterogeneous Datasets
Authors: Brown Noah , Danis Charles , Ahmedjonova Vazira , Guler Jennifer L.
Published: January 2025

SVCROWS is an option-rich R package that generates summarized and quantified structural variant (SV) regions from large and heterogeneous datasets. By using a size-weighted reciprocal overlap framework for comparisons, SVCROWS ensures that regions are delineated without size bias. User input directs stringency of comparisons, exhibiting different levels of resolution in complex regions of the genome.

Availability

SVCROWS can be downloaded as a Package or R-Markdown file athttps://github.com/A-Crow-Nowhere/SVCROWS.git

Contact

jlg5fw@virginia.edu;njb8sg@virginia.edu
Multi-modal analysis of satellite cells reveals early impairments at pre-contractile stages of myogenesis in Duchenne muscular dystrophy
Authors: Franzmeier Sophie , Chakraborty Shounak , Mortazavi Armina , Stöckl Jan B. , Jiang Jianfei , Pfarr Nicole , Sabass Benedikt , Fröhlich Thomas , Kaufhold Clara , Stirm Michael , Wolf Eckhard , Schlegel Jürgen , Matiasek Kaspar
Published: January 2025

Recent studies on the role of myogenic satellite cells (SC) in Duchenne muscular dystrophy (DMD) documented altered division capacities and impaired regeneration potential of SC in DMD patients and animal models. It remains unknown, however, if SC-intrinsic effects trigger these deficiencies at pre-contractile stages of myogenesis rather than resulting from the pathologic environment. Addressing this, we isolated SC from muscle biopsies of a porcine DMD model for characterization. Traction force microscopy (TFM) revealed that DMD SC produce a significantly higher strain energy than wild-type cells (WT; 0.136 ± 0.016 µJ vs. 0.057 ± 0.008 µJ). By RNA-seq, we identified 1,390 differentially expressed genes and proteomics measurements detected 1,261 proteins with altered abundance in DMD vs. WT. Dysregulated pathways uncovered by Gene Ontology (GO) enrichment analysis included sarcomere organization, focal adhesion, and response to hypoxia. We integrated the data using multi-omics factor analysis (MOFA) and identified five factors accounting for the variance with an overall higher contribution of the transcriptomic (61.95 %) than the proteomic data (54.02 %). Our findings suggest SC impairments result from their inherent genetic abnormality rather than environmental influences. The observed biological changes are independent and not reactive to the pathological surrounding of DMD muscle.
Atomic scale description of the allosteric coupling between a lipid bilayer and a membrane protein
Authors: Fourel Clarisse , Gautier Yanna , Pozza Alexandre , Giraud François , Point Elodie , Le Bon Christel , Moncoq Karine , Stirnemann Guillaume , Hénin Jérôme , Lescop Ewen , Catoire Laurent J.
Published: January 2025

Biological membranes are complex environments whose functions are closely tied to the dynamic interactions between lipids and proteins. Here, we utilize high-pressure NMR of lipid nanodiscs paired with molecular dynamics simulations to elucidate at the atomic scale the allosteric dialog between the lipid bilayer and a bacterial model membrane protein, OmpX. We discover that OmpX delays the gelation process by liquefying the annular shell of lipids through hydrophobic and roughness matching processes at the protein surface. Furthermore, the alteration of the mechanical properties of the lipid bilayer directly impacts the energy landscape of amino acid side chains at the lipid/protein interface, but also, unexpectedly, at the protein core. Our work highlights a potential thermodynamically coupled but kinetically uncoupled allosteric pathway linking lipid dynamics with the interior of membrane proteins, directly impacting our understanding of membrane function.

Graphical Abstract
A pancrustacean brain and its visual systems define a Cambrian great appendage arthropod.
Authors: Strausfeld Nicholas James , Hirth Frank , Hou Xianguang
Published: January 2025

Early Cambrian fossils from the Chengjiang biota demonstrate that over half a billion years ago early stem euarthropods existed coevally with representatives of already recognizable crown groups. Prominent stem taxa were Fuxianhuia protensa and Alalcomenaeus whose cerebral and ganglionic traits identify them as, respectively, stem mandibulates and stem chelicerates. Here we report features of the visual systems and brain of the enigmatic lower Cambrian stem euarthropod Jianfengia multisegmentalis, which despite the absence of trunk tagmatization reveals neural traits that justify its inclusion within stem Pancrustacea also known as Tetraconata. The sutured eyestalks of Jianfengia, typifying crown Malacostraca, terminate as compound eyes populated by ommatidia that reveal tetradic structures indicative of cone-building Semper cells. Preserved neuropils and tracts in the eyestalks of Jianfengia resolve nested optic neuropils as occur in eucrustaceans. The nauplius-like eyes of Jianfengia and their associated nerves supply a discrete forebrain region, as they do in pancrustaceans. These attributes distinguish Pancrustacea from stem Chelicerata and extant Myriapoda as does the organization of the jianfengiid deutocerebrum and tritocerebrum. In the absence of external traits that differentiate identities amongst stem euarthropods, neuroanatomical traits provide a powerful tool for discerning characteristic distinctions and correspondences for elucidating euarthropod relationships. Here, we demonstrate that cerebral arrangements in Jianfengia correspond to those of pancrustaceans existing today.
The cause-effect conundrum of local-scale site and soil factors in acute oak decline (AOD)
Authors: Shaw Liz J , Rabiey Mojgan , Garcia Mateo S.J. , Clarke Toni , Broome Alice , Corbett Luci J , Booth Oliver R , Barrett Glyn A , Preston Gail M , Barsoum Nadia , Schonrogge Karsten , Jackson Robert W , Ray Duncan
Published: January 2025

Background and aims: Acute oak decline (AOD), a decline syndrome affecting mature oaks, involves bacterial pathogens which likely act as opportunists under host stress. Trees displaying symptoms (bleeding cankers) appear in localized clusters, not whole stands. This study investigates the potential involvement of local scale factors, in interaction with large scale environmental drivers, in influencing onset and progression of AOD. Methods: AOD-symptomatic (n=30) and asymptomatic trees (n=30) across three UK oak woodlands were assessed for tree characteristics, their surrounding context, and soil properties. Results: Tree health status was linked to significant differences in soil and tree properties across sites. Symptomatic trees exhibited greater loss of crown density, lower local stand (0 to 20 m) basal area and shallower depth to gleying. Significant differences in soil properties included lower concentrations of Olsen P, total N, and exchangeable Mg in symptomatic trees, alongside higher exchangeable Fe, especially at 40 to 50 cm depth. Depth to gleying and exchangeable Fe were identified as the most influential predictors of AOD. Conclusions: AOD symptomatic trees may experience seasonal soil water saturation closer to the surface compared to asymptomatic trees, resulting in a higher proportion of their roots being exposed to an anoxic, iron reducing environment. This study is the first to report such an association between gleying depth, likely seasonal water saturation, and symptom status for AOD. It is unclear whether water balance and associated soil nutrient variations are predisposing factors or consequences of declining tree health, though the identified local scale factors likely contribute to AOD. A feedback loop is conceptualised where declining tree health worsens soil conditions, creating a negative cycle that accelerates tree decline.
Deciphering Multiway Multiscale Brain Network Connectivity: Insights from Birth to 6 Months
Authors: Li Qiang , Fu Zening , Walum Hasse , Seraji Masoud , Bajracharya Prerana , Calhoun Vince , Shultz Sarah , Iraji Armin
Published: January 2025

Converging evidence suggests that understanding the human brain requires more than just examining pairwise functional brain interactions. The human brain is a complex, nonlinear system, and focusing solely on linear pairwise functional connectivity often overlooks important nonlinear and higher-order relationships. Infancy is a critical period marked by significant brain development that could contribute to future learning, health, and life success. Exploring higher-order functional relationships in the brain can provide insight into brain function and development. To the best of our knowledge, there is no existing research on multiway, multiscale brain network interactions in infants. In this study, we comprehensively investigate the interactions among brain intrinsic connectivity networks (ICNs), including both pairwise (pair-FNC) and triple relationships (tri-FNC). We focused on an infant dataset collected between birth and six months, a critical period for brain maturation. Our results revealed significant hierarchical, multiway, multiscale brain functional network interactions in the infant brain. These findings suggest that tri-FNC provide additional insights beyond what pairwise interactions reveal during early brain development. The tri-FNC predominantly involve the default mode, sensorimotor, visual, limbic, language, salience, and central executive domains. Notably, these triplet networks align with the classical triple network model of the human brain, which includes the default mode network, the salience network, and the central executive network. This suggests that the brain network system might already be initially established during the first six months of infancy. Interestingly, tri-FNC in the default mode and salience domains showed significantly stronger nonlinear interactions with age compared to pair-FNC. We also found that pair-FNC were less effective at detecting these networks. The present study suggests that exploring tri-FNC can offer additional insights beyond pair-FNC by capturing higher-order nonlinear interactions, potentially yielding more reliable biomarkers to characterize developmental trajectories.
Epigenetic small molecule screening identifies a new HDACi compound for ameliorating Duchenne muscular dystrophy
Authors: Louie Ke’ale W. , Hasegawa Eva H. , Farr Gist H. , Ignacz Amanda , Paguio Alison , Maenza Alyssa , Paquette Alison G. , Henry Clarissa , Maves Lisa
Published: January 2025

Duchenne muscular dystrophy (DMD) is the most common inherited muscle disease. There are currently few effective therapies to treat the disease, although many approaches are being pursued. Certain histone deacetylase inhibitors (HDACi) have been shown to ameliorate DMD phenotypes in mouse and zebrafish animal models, and the HDACi givinostat has recently gained FDA approval for DMD. Our goal was to identify additional HDACi, or other classes of epigenetic small molecules, that are beneficial for DMD. Using an established animal model for DMD, the zebrafishdmdmutant strainsapje, we screened a library of over 800 epigenetic small molecules of various classes. We used a quantitative muscle birefringence assay to assess and compare the effects of these small molecule treatments ondmdmutant zebrafish skeletal muscle. Our screening identified a new HDACi, SR-4370, that ameliorateddmdmutant zebrafish skeletal muscle degeneration, in addition to HDACi previously shown to improvedmdzebrafish. We find that a single early treatment of HDACi can amelioratedmdzebrafish. Furthermore, we find that HDACi that improvedmdmuscle also cause increased histone acetylation in zebrafish larvae, whereas givinostat does not appear to increase histone acetylation or improve zebrafishdmdmuscle. Our results add to the growing evidence that HDACi are promising candidates for treating DMD. Our study also provides further support for the effectiveness of small-molecule screening indmdzebrafish.

Graphical abstract
HMG box-containing protein 1 (HBP1) prevents pancreatic injury in experimental pancreatitis but accelerates pancreatic neoplasia progression
Authors: Lee Seung-Won , Ekstrom Taelor , Manalo Elise C. , Ye Shangyuan , Berry Mark , Grygoryev Dmytro , Szczepaniak Malwina , Marmolejo Carlos Origel , Haverlack Syber , Lee Jinho , Shah Vidhi M. , Keith Dove , Muschler John L. , Chin Koei , Sears Rosalie C , Weisberg Stuart P. , Morgan Terry , Kim Jungsun
Published: January 2025

Background & Aims

Pancreatitis is an inflammatory disease of the exocrine pancreas and is a known risk factor for pancreatic ductal adenocarcinoma (PDAC). We previously identified HMG-box transcription factor 1 (HBP1) as a potential master transcription factor (TF) involved in the early progression of PDAC and associated with poor patient survival. However, the functional role of HBP1 in the pathophysiological mechanism for progression from acute to chronic pancreatitis to PDAC remains unclear.

Methods

We examined HBP1 expression in human chronic pancreatitis samples and cerulein-induced acute pancreatitis mouse model. We generated mice with pancreatic-specific conditional HBP1 knockout, without or with an oncogenic Kras mutation, and their corresponding controls. Then, we employed spatial proteomic and transcriptomics, histology, and immunostaining to characterize pathological changes in these mice. We validated findings from mouse models using inducible HBP1-overexpressing human pancreatic ductal epithelial cells.

Results

HBP1 was upregulated in pancreatic acinar cells in human chronic and mouse acute pancreatitis, and the expression of HBP1 in human chronic pancreatitis was associated with the presence of PDAC. Ablation of HBP1 in the pancreas disrupted acinar homeostasis by impairing the autophagic influx and exacerbated inflammation upon injury. However, in the presence of an oncogenic KRAS, HBP1 ablation delayed the formation of pancreatic intraepithelial neoplasia (PanINs), precursors of PDAC, and their progression into higher grades.

Conclusions

Upregulated HBP1 in normal acinar cells limits pancreatic inflammatory injury, but HBP1 is essential for PanIN progression in the presence of an oncogenic KRAS. Thus, HBP1 is a key regulator in both pancreatitis and early neoplastic changes and a potential target for therapeutic intervention in pancreatitis and PanIN progression.
TargetingRunx1 protects against heart failure with preserved ejection fraction
Authors: Elbassioni Ali Ali Mohamed , Raheem Anmar A , Song Jian , Johnston Alexander S , Trivett Cara , Lin Hong , Zhang Haobo , Bradley Ashley , Higgins Erin , Mooney Leanne , Koay Yen Chin , O’Toole Dylan , Herzyk Pawel , Nixon Colin , Blyth Karen , O’Sullivan John F , Lang Ninian N , Berry Colin , Braun Thomas , Schiattarella Gabriele G , Giacca Mauro , McBride Martin W , Nicklin Stuart A , Cameron Ewan R , Loughrey Christopher M , MacDonald Eilidh A
Published: January 2025

Heart failure with preserved ejection fraction (HFpEF) is a public health problem and an elusive illness for which there are few treatment options. HFpEF is a systemic condition with a broad phenotype including diastolic dysfunction, pulmonary oedema, exercise intolerance, and left ventricular (LV) hypertrophy, collectively resulting in enhanced morbidity and mortality. Master-regulator transcription factor RUNX1 has recently been identified as a mediator of pathological changes in many cardiac diseases, however its role in HFpEF was unknown. Here we show that inhibition ofRunx1 limits adverse cardiac remodelling in a clinically relevant mouse model of HFpEF. Cardiomyocyte-specific tamoxifen-inducibleRunx1-deficient mice with HFpEF are protected, with preservation of diastolic function, and attenuation of pulmonary oedema, exercise intolerance, and hypertrophy. Furthermore, targetingRunx1 in HFpEF by using gene transfer or small molecule inhibitors improves diastolic function, both in female and male mice. Overall, our research enhances our understanding of RUNX1 in cardiac disease and demonstrates a novel translational target for the treatment of HFpEF. Keywords: Heart failure with preserved ejection fraction, metabolic heart failure, diastolic dysfunction, hypertrophy, pulmonary oedema, exercise intolerance

CLINICAL PERSPECTIVE

Heart failure (HF) is a leading cause of death world-wide and traditionally divided into different subtypes according to cardiac ejection fraction (EF). In contrast to HF with reduced EF (HFrEF), there are limited treatment options for HF with preserved EF which is of considerable concern given that HFpEF is projected to become the dominant HF subtype in the future1. RUNX1 has been demonstrated to play an important role in the development of many cardiac and non-cardiac diseases. As a result, the potential for RUNX1 inhibitors as therapeutic agents across various conditions has become increasingly evident. In this study we established the therapeutic potential of targeting RUNX1 in the context of HFpEF. Targeting RUNX1 in cardiomyocytes markedly attenuates the development of the HFpEF phenotype and therefore this novel translational therapeutic target has great potential to address one of the biggest challenges in cardiac research.
Scd1 diffuses end to end along the cytoplasm to facilitate Cdc42 activation and bipolar growth
Authors: Harrell Marcus , Chinsen Olivia , Das Maitreyi E
Published: January 2025

The conserved GTPase Cdc42 is a major regulator of polarized growth in most eukaryotes. In Schizosaccharomyces pombe, Cdc42 activity displays anticorrelated oscillatory dynamics between the growing ends enabling bipolarity. Cdc42 at each end is activated only when the opposite end loses activity. This suggests that a regulator of Cdc42 likely travels end-to-end to activate Cdc42. The oscillatory dynamics between the growing ends have also been observed in Cdc42 activator Scd1, its scaffold Scd2. It is unclear how these proteins move between the ends to facilitate bipolarity. We find that Scd1 does not travel between the cell ends via actin-mediated delivery. Instead, we show that Scd1 is mostly cytoplasmic and diffuses between the cell ends. The rate of diffusion is not entirely proportional to increasing the mass of Scd1 and cells lacking the inhibitor Pak1 kinase show decreased diffusion. Moreover, we show that Scd1 diffuses at a much faster rate compared to its scaffold Scd2. These findings suggest that Scd1 diffusion is not random and is regulated by Pak1 kinase. We find that decreasing the rate of diffusion disrupts Cdc42 oscillatory dynamics and results in monopolarity. Our results show that end-to-end Scd1 diffusion drives Cdc42 oscillatory dynamics and regulates cell polarity.
Bioenergetic reprogramming of macrophages reduces drug tolerance inMycobacterium tuberculosis
Authors: Yadav Vikas , Sahoo Sarthak , Malhotra Nitish , Mishra Richa , Rajmani Raju S , Shanmugam Siva , Shandil Radha K , Narayanan Shridhar , Thacker Vivek V. , Jolly Mohit , Seshasayee Aswin Sai Narain , Singh Amit
Published: January 2025

Eradication ofMycobacterium tuberculosis(Mtb) requires strategies targeting bacteria inside the host.Mtbexhibits heterogeneity in redox metabolism inside macrophages to evade killing by anti-TB drugs. If and how macrophage physiology correlates with bacterial redox heterogeneity and drug tolerance remains unclear. Using a fluorescent reporter of mycobacterial redox potential, flow sorting, and RNA sequencing of infected macrophages, we characterized transcriptional and metabolic responses of macrophages harboring redox-diverseMtbpopulations. We found that macrophages with suppressed glycolysis and elevated oxidative phosphorylation (OXPHOS) correlated withMtbpopulations exhibiting reductive stress and drug tolerance. Conversely, macrophages with elevated glycolysis and suppressed OXPHOS displayed higher mitochondrial reactive oxygen species through reverse electron transport, resulting in oxidative stress inMtband enhancing drug efficacy. Computational and genetic approaches identified Nrf2 as a key regulator of macrophage bioenergetics driving redox heterogeneity and drug tolerance inMtb. Redirecting macrophage metabolism from OXPHOS to glycolysis using an FDA- approved antiemetic drug, meclizine, subverted redox heterogeneity and diminished drug tolerance in macrophages and mice. The pharmacological profile of meclizine (Cmaxand AUClast) indicated no adverse interactions with first-line anti-TB drugs in mice. Our data demonstrate the feasibility of reprogramming macrophage metabolism to reduce drug tolerance inMtbinfection.
Algorithms to Improve Fairness in Medicare Risk Adjustment
Authors: Reitsma Marissa B. , McGuire Thomas G. , Rose Sherri
Published: January 2025

Importance

Payment system design creates incentives that impact healthcare spending, access, and outcomes. With Medicare Advantage accounting for more than half of Medicare spending, changes to its risk adjustment algorithm have the potential for broad consequences.

Objective

To develop risk adjustment algorithms that can achieve fair spending targets, and compare their performance to a baseline that emulates the least squares regression approach used by the Centers for Medicare and Medicaid Services.

Design

Retrospective analysis of Traditional Medicare enrollment and claims data between January 2017 and December 2020. Diagnoses in claims were mapped to Hierarchical Condition Categories (HCCs). Algorithms used demographic indicators and HCCs from one calendar year to predict Medicare spending in the subsequent year.

Setting

Data from Medicare beneficiaries with documented residence in the United States or Puerto Rico.

Participants

A random 20% sample of beneficiaries enrolled in Traditional Medicare. Included beneficiaries were aged 65 years and older, and did not have Medicaid dual eligibility. Race/ethnicity was assigned using the Research Triangle Institute enhanced indicator.

Main Outcome and Measures

Prospective healthcare spending by Medicare. Overall performance was measured by payment system fit and mean absolute error. Net compensation was used to assess group-level fairness.

Results

The main analysis included 4,398,035 Medicare beneficiaries with a mean age of 75.2 years and mean annual Medicare spending of $8,345. Out-of-sample payment system fit for the baseline regression was 12.7%. Constrained regression and post-processing both achieved fair spending targets, while maintaining payment system fit values of 12.6% and 12.7%, respectively. Whereas post-processing only increased mean payments for beneficiaries in minoritized racial/ethnic groups, constrained regression increased mean payments for beneficiaries in minoritized racial/ethnic groups and beneficiaries in other groups residing in counties with greater exposure to socioeconomic factors that can adversely affect health outcomes.

Conclusions and Relevance

Constrained regression and post-processing can incorporate fairness objectives in the Medicare risk adjustment algorithm with minimal reduction in overall fit.
Apraxia as a Predictor of Post-Stroke Recovery: Insights from the Birmingham Cognitive Screening Program
Authors: Rounis Elisabeth , Ramanan Siddharth , Bickerton Wai-Ling , Demeyere Nele , Ralph Matthew A. Lambon
Published: January 2025

Our study highlights cognitive measures underlying post-stroke recovery using the ‘Birmingham Cognitive Screening’ (BCOS) program—the only dataset with comprehensive assessments of cognition, praxis, and stroke outcomes. We analysed 256 stroke patients tested for cognitive deficits, which uniquely included apraxia and the Barthel Index for daily living activities at subacute and chronic stages. Using step-wise multivariate linear regression, we identified significant predictive factors—praxis, language, orientation, and baseline independence—linked to improved daily activities, and validated our model with 4-fold cross-validation. This research underscores the vital role of specific cognitive measures including apraxia as key cognitive predictors for stroke recovery.
Seasonal variations and time trends of deaths from COVID-19 in Italy, September 2021 - September 2024: a segmented linear regression study
Authors: Roccetti Marco , De Rosa Eugenio Maria
Published: January 2025

Objectives: To investigate the occurrence of seasonal variations of COVID-19 deaths in Italy over a period during which the SARS-CoV-2 Omicron and post-Omicron variants were predominant: September 2021 - September 2024. Design: We examined the seasonal profiles of weekly COVID-19 deaths data, over a three-year long period, using a segmented linear regression model. Comparing the slopes of the regression segments, we are able to discuss the variation in steepness of the Italian COVID-19 mortality trend, identifying the corresponding growth/decline profile for each considered season. Settings: Public data of weekly COVID-19 deaths over a three-year long period in Italy. Participants: Only publicly available data were utilized for this study, patients and/or the public were not involved in any phase of this study. Interventions: Not applicable, not being proposed any interventions. Primary and secondary outcome measures: Not applicable, being this study not based on a protocol with preliminary planned measures. Results: Although the COVID-19 weekly death mortality has been in a declining trend in Italy since the end of 2021 until the end of 2024, we have identified increasing variations of the COVID-19 deaths for all winters and summers of that period. These increasing mortality variations were more pronounced in winters (average slope coefficient of the regression segments: 55.75, average and SD values of the coefficient of determination r2: 0.74 and 0.05) than in summers (average slope coefficient of the regression segments: 22.90, average and SD values of the coefficient of determination r2: 0.63 and 0.19). We found that COVID-19 deaths were, instead, less frequent in the intermediate periods between winters and summers (average slope coefficient of the regression segments: -38.01, average and SD values of the coefficient of determination r2: 0.70 and 0.06). Conclusion: Favored by a declining COVID-19 mortality trend in Italy in the period from September 2021 to September 2024, the occurrence of increasing alterations (from serious to moderate) received little attention. These transient rises of the trend have been present both in winters and in summers, but more pronounced in winters. Since these increasing seasonal alterations of the COVID-19 mortality trend have been always compensated by consistent downward drifts occurring during the intermediate periods between winters and summers, they have been considered cause for concern, only occasionally.
Insights on improving accessibility and usability of functional data to unlock its potential for variant interpretation
Authors: Park Min Seon , Kumar Runjun D. , Ovadiuc Cristian , Folta Andrew , McEwen Abbye E. , Snyder Ashley , Fowler Douglas M. , Rubin Alan F. , Shirts Brian H. , Starita Lea M. , Stergachis Andrew B.
Published: January 2025

Introduction: Variant-level functional data is a core component of clinical variant classification and can aid in reinterpreting variants of uncertain significance (VUS). However, the usage of functional data by genetics professionals is currently unknown. Methods: An online survey was developed and distributed in spring of 2024 to individuals actively engaged in variant interpretation. Quantitative and qualitative methods were used to assess responses. Results: 190 eligible individuals responded, with 93% reporting interpreting 26 or more variants per year. The median respondent reported 11-20 years of experience. The most common professional roles were laboratory medical geneticists (23%) and variant review scientists (23%). 77% reported using functional data for variant interpretation in a clinical setting and overall respondents felt confident in assessing functional data. However, 67% indicated that functional data for variants of interest was rarely or never available, and 91% considered insufficient quality metrics or confidence in the accuracy of data as barriers to its use. 94% of respondents noted that better access to primary functional data and standardized interpretation of functional data would improve usage. Respondents also indicated that handling conflicting functional data is a common challenge in variant interpretation that is not performed in a systematic manner across institutions. Discussion: The results from this survey showed a demand for a comprehensive database with reliable quality metrics to support use of functional evidence in clinical variant interpretation. The results also highlight a need for guidelines regarding how putatively conflicting functional data should be used for variant classification.
Not Such a Long Way Off? Contemporary Artificial intelligence Performance Evaluation on Adult Medicine Long Cases
Authors: Gao Christina , Bellinge Jamie , El-Masri Shaddy , Chim Ivana , Sorich Michael , Seth Ishish , Gorcilov James , Lim Matthew , McCoy Liam , Vanlint Andrew , Lim Lauren , Stranks Jessica , Zannettino Andrew , Maddison John , Bacchi Stephen
Published: January 2025

The Royal Australasian College of Physicians (RACP) "Long Cases" assess a trainee's clinical reasoning beyond what is tested in multiple-choice questions, which large language models (LLMs) have already demonstrated proficiency in. This study evaluated a LLM's ability to perform a "Long Case" assessment, including history-taking, case presentation, and answering examiner questions. The LLM achieved passing consensus scores of 4-5 out of 6 on five cases, suggesting potential for LLMs in complex clinical evaluations.
De novo expression of neuropeptide Y in sensory neurons does not contribute to peripheral neuropathic pain
Authors: Cooper Andrew H , Nie Al , Hedden Naomi , Herzog Herbert , Taylor Bradley K
Published: January 2025

Nerve damage induces a robust de novo expression of the pain-modulatory peptide neuropeptide Y (NPY) in large-diameter primary afferent neurons that innervate the dorsal horn of the spinal cord and the dorsal column nuclei. To determine whether this functions to modulate peripheral neuropathic pain, we selectively deleted the Npy gene in neurons of the dorsal root ganglion (DRG), without disruption of its expression in brain or dorsal horn neurons. We then subjected sensory neuron-specific NPY deletion mutant mice (Pirt-NPY) and their wild-type controls to either sham surgery, spared sural nerve injury (SNI) or spared tibial nerve injury (tSNI). Conditional Npy deletion did not change the severity or duration of static mechanical, dynamic mechanical, or cold allodynia in SNI or tSNI models, nor ongoing neuropathic pain as assessed with conditioned place preference to gabapentin. When injected after the resolution of tSNI-induced mechanical hypersensitivity (a latent pain sensitization model of chronic neuropathic pain), the NPY Y1 receptor-specific antagonist BIBO3304 equally reinstated mechanical hypersensitivity in Pirt-NPY mice and their wildtype controls. We conclude that nerve injury-induced upregulation of NPY in sensory neurons does not cause mechanical or cold hypersensitivity or ongoing pain, and that tonic inhibitory control of neuropathic pain by NPY in the spinal cord is mediated by release from dorsal horn interneurons rather than sensory neurons.
A pan-respiratory virus attachment inhibitor with high potency in human airway models and in vivo
Authors: Mathez Gregory , Jacob Silva Paulo , Carlen Vincent , Deloizy Charlotte , Prompt Clémentine , Hubart Anaïs , Rocha-Pereira Joana , Galloux Marie , Le Goffic Ronan , Stellacci Francesco , Cagno Valeria
Published: January 2025

Respiratory viruses can cause severe infections, including bronchiolitis and pneumonia, often leading to hospitalization or death. Due to their ease of transmission, they are also scrutinized for their pandemic potential. No broad-spectrum antiviral is currently available. However most respiratory viruses use sialic acid or heparan sulfates as attachment receptors. Here, we report the identification of a pan-respiratory antiviral strategy based on mimicking both glycans. We synthesized and characterized a unique modified cyclodextrin that simultaneously mimics heparan sulfate and sialic acid. This novel compound demonstrated broad-spectrum antiviral activity against important human pathogens: parainfluenza virus 3, respiratory syncytial virus, influenza virus H1N1, SARS-CoV-2. Additionally, the compound is active against different avian strains of influenza virus, revealing its importance for pandemic preparedness. The compound retains broad- spectrum activity in ex vivo models of respiratory tissues and in vivo experiments against RSV and Influenza virus, using both prophylactic and therapeutic strategies. These findings represent a significant step forward in the development of future treatments and preventive measures for respiratory viral infections.

Significance Statement

Following the SARS-CoV-2 pandemic, Influenza A H5N1 has become widespread in poultry and has already begun to spill over into mammals, posing a potential risk for the next pandemic. Indeed, respiratory viruses represent a major threat for future global health crises. Unfortunately, there is a significant lack of broad-spectrum antivirals available for such scenarios. To address this gap, our study developed a single molecule with the capacity to inhibit a wide range of clinically relevant human respiratory viruses including avian strains of influenza virus. This antiviral demonstrated verified efficacy not only in cellular systems but also in human-derived respiratory tissues and animal models.
Structural Basis of Lipid Membrane Binding by Human Ferlins
Authors: Cretu Constantin , Chernev Aleksandar , Kibedi Szabo Csaba Zoltan , Pena Vladimir , Urlaub Henning , Moser Tobias , Preobraschenski Julia
Published: January 2025

Ferlins, ancient membrane proteins with a unique architecture, are central to multiple essential, Ca2+-dependent vesicle fusion processes. Despite numerous functional studies and their link to burdening human diseases, a mechanistic understanding of how these multi-C2domain proteins interact with lipid membranes to promote their remodeling and fusion is currently lacking. Here, we elucidate the near-complete cryo-electron microscopy structures of human myoferlin and dysferlin in their Ca2+and lipid-bound states. We show that ferlins adopt compact, ring-like tertiary structures achieved upon membrane binding. The top arch of the ferlin ring, comprising the C2C-C2D region, is rigid and varies little across the observed functional states. In contrast, the N-terminal C2B and the C-terminal C2F-C2G domains cycle between alternative conformations and, in response to Ca2+, close the ferlin ring, promoting tight interaction with the target membrane. Probing key domain interfaces validates the observed architecture and informs a model of how ferlins engage lipid bilayers in a Ca2+- dependent manner. This work reveals the general principles of human ferlin structures and provides a framework for future analyses of ferlin-dependent cellular functions and disease mechanisms.
Cancer cells transfer invasive properties through microRNAs contained in collagen-tracks
Authors: Normand Léa , Rouyer Lucile , Richard Elodie , Allain Nathalie , Giraud Julie , Di-Tommaso Sylvaine , Dourthe Cyril , Raymond Anne-Aurélie , Dupuy Jean-William , Moreau Kevin , Iggo Richard , McGrogan Gaetan , Dugot-Senant Nathalie , Bouter Anthony , Tan Sisareuth , Favereaux Alexandre , Moreau Violaine , Luco Reini F. , Ros Manon , Saltel Frédéric
Published: January 2025

Invasion is a prerequisite for metastasis formation. During tumor development, the extracellular matrix (ECM) is remodeled in part through overexpression of type I collagen, increasing tumor microenvironment stiffness, and facilitating cancer dissemination. During breast cancer cell migration, we observed membrane debris left behind, attached to the collagen fibrils, along the migration path. We named these structures collagen-tracks. These collagen-tracks can be deposited in 3D matricesin vitroandin vivoand their formation is stimulated by the interaction between the ECM and matrix receptors, such as the discoidin-domain receptor (DDR1). However, they are different from structures already known to be involved in cell-cell communication such as exosomes and migrasomes, due to their specific nucleic acid and protein contents. When deposited by highly invasive breast cancer cells, internalized collagen-tracks reprogram non-invasive cells into highly pro-metastatic ones by inducing a partial epithelial–mesenchymal transition (EMT). This cell reprogramming is dependent on specific miRNAs present in the collagen-tracks, that are necessary to promote ECM degradation, increase cell motility and invasiveness. Collagen-tracks thus represent a new form of cell-cell communication important for driving tumor invasion that could be targeted to prevent metastasis.
Targeted delivery of mRNA to the heart via extracellular vesicles or lipid nanoparticles
Authors: Nawaz Muhammad , Tangruksa Benyapa , Heydarkhan-Hagvall Sepideh , Kohl Franziska , González-King Garibotti Hernán , Jing Yujia , Payandeh Zahra , Reyahi Azadeh , Jennbacken Karin , Wiseman John , Hultin Leif , Lindfors Lennart , Synnergren Jane , Valadi Hadi
Published: January 2025

Targeted mRNA transport plays a crucial role in enhancing the therapeutic efficacy of the molecule, reducing its side effects, and minimizing off-target effects. Systemic administration of mRNA through lipid nanoparticles (LNPs) or extracellular vesicles (EVs) predominantly results in mRNA accumulation in the liver. We hypothesized that cardiac-specific EVs could more effectively target the transport of mRNA to the heart, in comparison to non-cardiac-specific EVs or LNPs. In mice, after intravenous administration, EVs from cardiac progenitor cells (CPC-EVs) were the most efficient to transport the modified mRNA, encoding vascular endothelial growth factor A (VEGF-A), to mouse heart, with minimal liver accumulation compared to non-cardiac-specific EVs or LNPs. Additionally, intracardiac injections of CPC-EVs not only demonstrate that they are the most adapted vehicle for interacting with heart tissue, delivering the mRNA to cells, and inducing maximal VEGF-A protein production, but RNA-seq analyses also revealed their minimal impact on overall gene expression, compared to LNPs or non-cardiac-specific EVs. Furthermore, immunofluorescence staining of CD31 and α-SMA, markers of microvascular density, showed increased vessel density in mouse aortic rings following the delivery ofVEGF-AmRNA via CPC-EVs. These findings suggest that CPC-EVs are superior in mRNA targeting to heart, communication with cardiac cells, and causing minimal transcriptomic changes duringVEGF-AmRNA delivery. Therefore, CPC-EVs could be promising vectors for heart-targeted mRNA delivery, potentially reducing liver accumulation.
Glycan-Mediated Mechanosensing Regulates Megakaryocyte-Biased Hematopoietic Stem Cell Subsets
Authors: Roisman Alejandro , Rivadeneyra Leonardo , Conroy Lindsey , Lee-Sundlov Melissa M. , Weich Natalia , Glabere Simon , Zheng Shikan , Rosenbalm Katelyn E. , Zogg Mark , Steinhardt George , Veltri Anthony J. , Lau Joseph T. , Gu Tongjun , Weiler Hartmut , Sun Ramon C. , Hoffmeister Karin M.
Published: January 2025

Definitive hematopoietic stem and progenitor cells (HSPCs) development relies on intrinsic and extrinsic programs to meet homeostatic and stress-related demands. The comprehensive mechanisms governing HSPC’s fate remain poorly understood. Our study identifies B4GALT1, a glycosyltransferase essential for N-glycosylation, as a key modulator of HSPC lineage decisions. We demonstrate that B4GALT1 deficiency disrupts glycosylation patterns within the bone marrow (BM) niche, resulting in oncogenic glycan signatures and altered expression of Mucin13 in HSPCs. Loss of B4GALT1 expands HSPC pools and promotes megakaryocyte priming in HSPCs through transcriptional and chromatin modifications, enhancing the Wnt-Mucin13 axis. Mucin13, an oncogene characterized by aberrant glycosylation, underscores the critical role of B4GALT1 in sustaining BM glycosylation and mechanosensing, thereby regulating HSPC fate through functional, transcriptional, and chromatin dynamics. These observations provide insights into the impact of glycan structures on HSPC function, lineage reprogramming, and malignant transformation.
Task-specific changes in representation and connectivity between parietal and occipito-temporal areas following left hemisphere stroke
Authors: Zhang Zuo , Halai Ajay , Bracci Stefania , Pizzamiglio Gloria , Ralph Matthew Lambon , Rounis Elisabeth
Published: January 2025

Recent studies highlight a critical role of the human lateral occipitotemporal cortex (LOTC) in action understanding, particularly in how we perceive and interpret movements and interactions with tools and bodies. This region, along with connected fronto-parietal areas, has been implicated in limb apraxia, a disorder that affects skilled movement after stroke.

In this study, we focused on whether there were any changes in brain activity or connectivity in areas involving the LOTC and its interconnected perceptuo-motor network after left hemisphere stroke, a common cause of limb apraxia.

We recruited 29 stroke patients and 19 age-matched healthy participants. Using functional neuroimaging, we asked participants to observe static photographs of familiar tools, bodies, non-tool objects, and scrambled images while performing a simple attention task (1-back task). The goal was to map the brain areas specifically involved in tool-related and body-related visual processing. Whole-brain analysis revealed activity changes related to tool and body stimuli in the LOTC and fronto-parietal regions. Interestingly, there were no significant differences in activation between stroke patients and controls based on the overall whole-brain analysis. However, deeper analyses revealed critical group-related differences. Using representational similarity analysis (RSA), we found that stroke patients showed reduced ability to discriminate between tools and non-tools within the right LOTC. Psychophysiological interactions (PPI) analysis further indicated increased connectivity between the left inferior parietal sulcus (IPS) and the left LOTC in stroke patients during tool-related tasks, a finding that correlated with their performance on meaningless imitation apraxia task.

Our findings suggest that limb apraxia after stroke is associated with altered representation of tools and functional connectivity in the perceptuo-motor network, particularly involving parietal and occipitotemporal regions. These results suggest perceptual deficits may be more relevant than previously reported in limb apraxia after stroke.

Highlights

Consistent activations in the lateral occipitotemporal cortex (LOTC) were identified during tool and body localizer tasks in both stroke patients and healthy controls.

Representational similarity analysis (RSA) revealed reduced discrimination between tools and non-tools in the right LOTC of stroke patients.

Differential task-related functional connectivity was observed between the LOTC and intraparietal sulcus (IPS) regions in stroke patients compared to controls during the tools localizer task.

These findings provide insights into altered neural representations and connectivity underlying limb apraxia following left hemisphere stroke.