bluuebunny/crossref_metadata_2025 huggingface dataset:
Citrobacter rodentiuminfection activates colonic lamina propria group 2 innate lymphoid cells
Authors: Berkachy Rita , Mishra Vishwas , Biswas Priyanka , Frankel Gad
Published: January 2025

Group 3 innate lymphoid cells (ILC3s) play a major role in protecting against infection with the enteric mouse pathogenCitrobacter rodentium,used to model infections with enteropathogenic and enterohaemorrhagicEscherichia coli. ILC3s-secreted IL-22, shown to be indispensable for protection againstC. rodentiuminfection, induces secretion of IL-18, antimicrobial peptides and nutritional immunity proteins as well as activation of tissue regeneration processes. While ILC2s have traditionally been associated with immune responses to helminth infection and allergic inflammation via the production of type 2 cytokines (e.g. IL-4, IL-5, IL-9 and IL-13), more recently they have been implicated in protection againstClostridium difficileandHelicobacter pyloriinfections. Here we show that colonic lamina propria ILC2s proliferate in response toC. rodentiuminfection and secrete IL-4, IL-5 and IL-13, which are involved in maintenance of the intestinal barrier function, tissue repair and mucus secretion. When stimulated with IL-18, colonic ILC2s from uninfected naïve mice secreted type 2 cytokines. Injection of IL-18 binding protein (IL18BP), at 2- and 3-days postC. rodentiuminfection, blocked activation of ILC2s. These data show that ILC2s are activated in response to infection with an enteric Gram-negative pathogen, where stimulation with IL-18 plays a role in inducing proliferation and secretion of type 2 cytokines.

Author Summary

While group 3 innate lymphoid cells (ILC3s) play a key role in protecting from bacterial infections, ILC2s are mainly associated with immune responses to helminth infection. Here we investigated if ILC2s are activated in responses to infection with the enteric mouse pathogenCitrobacter rodentium.We show that in infected mice, gut ILC2s expand and secreted type 2 cytokines. ILC2 isolated from uninfected mice were activated by IL-18. Consistently, administration of IL-18 binding protein intoC. rodentium-infected mice inhibited ILC2 activation. These findings suggest that gut ILC2s are activated by Gram negative enteric pathogens, which is mediated in part by IL-18.
Variational Autoencoder-based Model Improves Polygenic Prediction in Blood Cell Traits
Authors: Li Xiaoqi , Pang Minxing , Wen Jia , Zhou Laura Y. , Raffield Laura M. , Zhou Haibo , Yao Huaxiu , Chen Can , Sun Quan , Li Yun
Published: January 2025

Genetic prediction of complex traits, enabled by large-scale genomic studies, has created new measures to understand individual genetic predisposition. Polygenic Risk Scores (PRS) offer a way to aggregate information across the genome, enabling personalized risk prediction for complex traits and diseases. However, conventional PRS calculation methods that rely on linear models are limited in their ability to capture complex patterns and interaction effects in high-dimensional genomic data. In this study, we seek to improve the predictive power of PRS through applying advanced deep learning techniques. We show that the Variational AutoEncoder-based model for PRS construction (VAE-PRS) outperforms currently state-of-the-art methods for biobank-level data in 14 out of 16 blood cell traits, while being computationally efficient. Through comprehensive experiments, we found that the VAE-PRS model offers the ability to capture interaction effects in high-dimensional data and shows robust performance across different pre-screened variant sets. Furthermore, VAE-PRS is easily interpretable via assessing the contribution of each individual marker to the final prediction score through the SHapley Additive exPlanations (SHAP) method, providing potential new insights in identifying trait-associated genetic variants. In summary, VAE-PRS presents a novel measure to genetic risk prediction by harnessing the power of deep learning methods, which could further facilitate the development of personalized medicine and genetic research.
IL-21-STAT3 axis negatively regulates LAIR1 expression in B cells
Authors: Yoshida Kenji , Kurata-Sato Izumi , Atisha-Fregoso Yemil , Aranow Cynthia , Diamond Betty
Published: January 2025

LAIR1 is an inhibitory receptor broadly expressed on human immune cells, including B cells. LAIR1 has been shown to modulate BCR signaling, however, it is still unclear whether its suppressive activity can be a negative regulator for autoreactivity. In this study, we demonstrate the LAIR1 expression profile on human B cells and prove its regulatory function and relationships to B cell autoreactivity. We show that both the frequency and level of LAIR1 expression decreases during B cell differentiation. LAIR1 expressing (LAIR1+) switched memory (SWM) B cells have a transcriptional profile less differentiated toward a plasma cell (PC) phenotype, harbor more autoreactive B cells and exhibit less PC differentiationin vitrothan the LAIR1 negative (LAIR1-) counterpart. These data suggests that LAIR1 functions as a B cell tolerance checkpoint. We confirm previous data showing that patients with systemic lupus erythematosus (SLE) express less LAIR1 on B cells, implying a breakdown of the checkpoint, consistent with the enhanced PC differentiation seen in SLE. We further demonstrate that LAIR1 expression is down-regulated through the IL-21/STAT3 pathway which is known to be upregulated in SLE. These data suggest therapeutic targets that might decrease the aberrant PC differentiation observed in SLE.
Harnessing Extracellular Vesicles for Stabilized and Functional IL-10 Delivery in Macrophage Immunomodulation
Authors: Saleh Najla A. , Gagea Matthew A. , Vitija Xheneta , Janovic Tomas , Schmidt Jens C. , Deng Cheri X. , Kanada Masamitsu
Published: January 2025

Extracellular vesicles (EVs) are gaining recognition as promising therapeutic carriers for immune modulation. We investigated the potential of EVs derived from HEK293FT cells to stabilize and deliver interleukin-10 (IL-10), a key anti-inflammatory cytokine. Using minicircle (MC) DNA vectors, we achieved IL-10 overexpression and efficient incorporation into EVs, yielding superior stability compared to free, recombinant IL-10 protein. Detailed biophysical and functional analyses revealed that IL-10+EVs contain both monomeric and oligomeric forms of IL-10 on their external surface and encapsulated within vesicles. IL-10+EVs suppressed inflammatory cytokine expression in pro-inflammatory macrophages (from two to 14-fold compared to naïve EVs) without inducing anti-inflammatory polarization, demonstrating a distinct immunosuppressive mechanism. Interestingly, naïve EVs from non-transfected cells also exhibited significant anti-inflammatory effects, suggesting that the intrinsic bioactive cargo of EVs substantially contributes to their function, complicating the interpretation of IL-10-specific effects. Size-based fractionation analyses of IL-10+large EVs (lEVs), small EVs (sEVs), and non-vesicular extracellular particles (NVEPs) revealed IL-10 presence across all fractions, predominantly in monomeric form, with anti-inflammatory activity distributed among subpopulations. Anion exchange chromatography successfully enriched IL-10+exosomes while retaining immunomodulatory effects. However, the shared properties of naïve and IL-10+exosomes underscore the complexity of their immunomodulatory functions. These findings highlight the therapeutic potential of EVs while emphasizing the need to disentangle the contributions of engineered cytokines from endogenous vesicular components.
Airqtl dissects cell state-specific causal gene regulatory networks with efficient single-cell eQTL mapping
Authors: Wang Lingfei
Published: January 2025

Single-cell expression quantitative trait loci (sceQTL) mapping offers a powerful approach for understanding gene regulation and its heterogeneity across cell types and states. It has profound applications in genetics and genomics, particularly causal gene regulatory network (cGRN) inference to unravel the molecular circuits governing cell identity and function. However, computational scalability remains a critical bottleneck for sceQTL mapping, prohibiting thorough evaluation and optimization of statistical accuracy. We present airqtl, a novel method to overcome these challenges through algorithmic advances and efficient implementations of linear mixed models. Airqtl achieves superior time complexity and over eight orders of magnitude of acceleration, enabling objective method evaluation and optimization. Airqtl offersde novoinference of robust, experimentally validated cell state-specific cGRNs that reflect perturbation outcomes. Our results dissect the drivers of cGRN heterogeneity and underscore the value of natural genetic variations in primary human cell types for biologically relevant single-cell cGRN inference.
GlycoAvatars: Bead-Coated Membrane Models for Studying the Cancer-Immune Cells Interactome
Authors: Miranda Andreia , Relvas-Santos Marta , Lourenço Camila , Ferreira Eduardo , Cunha Diogo M. , Palmeira Carlos , Santos Lúcio Lara , Mattila Pieta K , Ferreira José Alexandre
Published: January 2025

ImmatureO-glycosylation of plasma membrane proteins, characterized by the presence of glycosites with a single GalNAc residue (the Tn antigen) rather than more extended and complex glycans, is a prominent feature of many advanced solid tumors across different origins and aetiologies. This form of glycosylation has been strongly associated with poor prognosis and is known to play a crucial role in the progression of the disease. Notably, it has been directly implicated in the crosstalk with the immune system, inducing tolerogenic phenotypes in both innate and adaptive immune cells. Despite this, the specific receptors involved in these interactions remain largely unidentified. To address this gap, we propose a novel high-throughput proteomics assisted strategy for characterizing the glycan interactome using plasma membrane-derived glycoprotein coated magnetic beads. Glycoproteins were isolated from plasma membranes of glycoengineered cell models with immature glycosylation and were then cloaked on the surface of magnetic beads, creating simplified cell “GlycoAvatars.” These GlycoAvatars were primarily employed to characterize the interactome between gastric and colorectal cancer cell lines and immune cells (dendritic cells and macrophages), providing a tool for identifying potentially relevant molecular nodes in glycan-mediated immune synapses, foreseeing their application in deciphering tumor-immune interactions.
Temporal Microenvironment Mapping (μMap) of Intracellular Trafficking Pathways of Cell-Penetrating Peptides Across the Blood-Brain Barrier
Authors: Morgan Danielle C. , Knutson Steve D. , Pan Chenmengxiao (Roderick) , MacMillan David W. C.
Published: January 2025

Peptides play critical roles in cellular functions such as signaling and immune regulation, and peptide-based biotherapeutics show great promise for treating various diseases. Among these, cell-penetrating peptides (CPPs) are particularly valuable for drug delivery due to their ability to cross cell membranes. However, the mechanisms underlying CPP-mediated transport, especially across the blood-brain barrier (BBB), remain poorly understood. Mapping intracellular CPP pathways is essential for advancing drug delivery systems, particularly for neurological disorders, as understanding how CPPs navigate the complex environment of the BBB could enable the development of more effective brain-targeted therapies. Here, we leverage a nanoscale proximity labeling technique, termed µMap, to precisely probe the peptide– receptor interactions and intracellular trafficking mechanisms of photocatalyst-tagged CPPs. The unique advantage of the μMap platform lies in the ability to control the timing of light exposure, which enables the collection of time-gated data, depending on when the blue light is applied to the cells. By harnessing this spatiotemporal precision, we can uncover key peptide–receptor interactions and cellular processes, setting the stage for new innovations in drug design and brain-targeted therapies.

Abstract Figure
High-yield bioproduction of virus-free virus-like P4-EKORhE multi-lysin transducing particles as an antimicrobial gene therapeutic
Authors: Ramirez-Garcia Robert , Sagona Antonia P. , Barr Jeremy J. , Jaramillo Alfonso
Published: January 2025

A description of the construction of the bioengineered P4-EKORhE and a comprehensive method for producing very high yields (up to 1012particles per millilitre) enable the use of virus-like particles to transduce genetically encoded antimicrobials through a combination of synthetic biology and optimised upstream and downstream processing. The final product, a gene-delivered antimicrobial in the form of the multi-lysins cassette, is fully functional before and after packaging within P4-EKORhE particles. The antimicrobial activity of the multilysins cassette, characterized by its lysis proteins, was testedin vivoin both pure bacterialEscherichia coli(E. coli) cultures and in a model of infection using A549 immortalised human epithelial tissue cell cultures. This work exemplifies several bioproduction methods and demonstrates how the virology of the P4 and P2 phages can be harnessed to establish a bioprocess for producing transducing particles at very high yields, avoiding contamination by the natural virus while maintaining the antimicrobial effectiveness of the final product.
Protein phosphatase 4 is required for centrosome asymmetry in fly neural stem cells
Authors: Segura Roberto Carlos , Gallaud Emmanuel , von Barnau Sythoff Adam , Aavula Kumar , Taylor Jennifer A. , Vahdat Danielle , Pielage Jan , Cabernard Clemens
Published: January 2025

Asymmetric cell division is used by stem cells to create diverse cell types while self-renewing the stem cell population. Biased segregation of molecularly distinct centrosomes could provide a mechanism to maintain stem cell fate, induce cell differentiation or both. However, the molecular mechanisms generating molecular and functional asymmetric centrosomes remain incompletely understood. Here, we show that in asymmetrically dividing fly neural stem cells, Protein phosphatase 4 (Pp4) is necessary for correct centrosome asymmetry establishment during mitosis, and microtubule organizing center (MTOC) maintenance in interphase. Usingin-vivolive cell imaging we show that while wild type neural stem cells always maintain one active MTOC,Pp4mutant neuroblasts contain two inactive centrioles in interphase. Furthermore, centrosomes ofPp4mutant neural stem cells mature in mitosis but fail to correctly transfer the centriolar protein Centrobin (Cnb) from the mother to the daughter centriole. Using superresolution imaging, we find that phosphomimetic Centrobin fails to accurately relocalize in mitosis. We propose that Pp4 regulates the timely relocalization of Cnb in mitosis to establish two molecularly distinct centrosomes. In addition, Pp4 is also necessary to maintain MTOC activity in interphase, ensuring biased centrosome segregation. Mechanistically, Pp4 could regulate centrosome asymmetry by dephosphorylating both Cnb and gamma-Tubulin.

SIGNIFICANCE STATEMENT

Asymmetric centrosome segregation occurs in stem cells and has been linked with cell fate decisions.

Protein phosphatase 4 (Pp4), a conserved Serine/Threonine phosphatase, regulates centrosome asymmetry inDrosophilaneural stem cells by acting upon gamma tubulin and Centrobin.

Pp4 regulates centrosome asymmetry establishment in mitosis and interphase, necessary for biased centrosome segregation.
Understanding the roles and experiences of mental health peer support workers in England: a qualitative study
Authors: Cooper Ruth E , Lyons Natasha , Nicholls Vicky , Foye Una , Shah Prisha , Mitchell Lizzie , Machin Karen , Chipp Beverley , Grundy Andrew , Pemovska Tamara , Ahmed Nafiso , Appleton Rebecca , Repper Julie , Lloyd-Evans Brynmor , Simpson Alan , Johnson Sonia
Published: January 2025

Background

Peer support roles in mental health services are rapidly increasing in the UK and internationally. However, there is wide variation in these roles and limited research exploring the ways in which Peer Support Workers (PSWs) are currently working. We aimed to explore: 1) the distinctive features of PSWs approaches in mental healthcare; 2) the values underpinning the role and 3) the perceived impact of the role.

Methods

We conducted semi-structured qualitative interviews with paid mental health PSWs working across a range of settings. We took a co-produced, participatory approach: interviews were carried out by researchers with lived experience of mental health conditions and data were analysed using collaborative methods, guided by general principles of thematic analysis.

Results

We interviewed 35 PSWs. Overarching themes identified from iterative analysis included: 1) The centrality of an individualised, flexible, approach, facilitating recovery through sharing lived experiences and building connection. PSWs advocated for service-user needs and most worked in non-clinical ways, offering holistic, recovery-orientated support. Tensions could arise with more clinical approaches. 2) Underpinning values included: i) Recovery is possible: bringing hope, role-modelling and encouraging change, ii) Mutuality: sharing lived experiences to bring empathy and build connection, iii) Person-centred approach: adapting ways of working to the individual, iv) Empowering instead of ‘fixing’ service users. 3) the role had benefits for participants’ own recovery, although its emotional demands could lead to burnout. Participants thought that peer support helped service users feel understood, leading to greater openness and facilitating recovery, although some felt that it may not be right for everyone. Participants felt that PSWs could bring systemic improvements to services and use their lived experience to help teams -meet service user needs.

Conclusion

PSWs work in a range of ways, but, a unifying feature is a flexible, person-centred approach, facilitating recovery through shared lived experience. A range of potential benefits of peer work were identified for PSWs and for service users, as well as reports of positive systemic change.

These could be facilitated by recovery-orientated models in services, space for shared learning with PSWs, and flexibility to incorporate PSWs’ unique ways of working.
Glymphatic Flow after Thrombectomy is Associated with Futile Recanalization in Large Vessel Occlusion Stroke
Authors: Finkelstein Alan J. , Sipple Matthew T. , Akkipeddi Sajal M. , White Racquel , Kohli Gurkirat Singh , Susa Stephen , Singh Rohin , Romiyo Prasanth , Zhong Jianhui , Bhalla Tarun , Mattingly Thomas , Nguyen Vincent , Nedergaard Maiken , Bender Matthew T. , Schartz Derrek
Published: January 2025

Background

Stroke is a leading cause of global death and disability, with mechanical thrombectomy remaining the optimal treatment approach for large vessel occlusion (LVO) ischemic stroke. Despite endovascular recanalization, nearly half of patients experience poor functional outcomes, a phenomenon termed “futile recanalization”. The cerebral glymphatic system has emerged as a potential, yet underexplored therapeutic target. In this retrospective study, we utilized glymphatic diffusion tensor analysis on post-thrombectomy MRIs scans to evaluate the association between glymphatic flow, clinical outcomes, and futile recanalization in LVO ischemic stroke.

Methods

In this retrospective study, 133 patients with anterior LVO ischemic stroke and MRI post-thrombectomy were identified. Futile recanalization was defined as a modified Rankin score >2 at 90 days, despite achieving complete or near-complete angiographic recanalization (mTICI 2b-3). We employed diffusion tensor imaging along the perivascular space (DTI-ALPS) to evaluate glymphatic function in individuals with futile recanalization and those with functional independence at 90 days. Spearman’s rank correlation was used to examine associations between the ALPS index and clinical variables. Effect sizes were calculated and reported using Cohen’s d.

Results

In total, 55 anterior circulation LVO patients (mean age 73.9, 44% male) were included with adequate post-thrombectomy MRIs for analysis. Overall, glymphatic clearance was lower in the infarct side compared to the contralateral side (p = 0.035). Patients with futile recanalization had lower glymphatic flow compared to those with functional independence (p=0.049). Additionally, glymphatic flow was significantly associated with presenting NIHSS (R=-0.46, p = 0.002).

Conclusions

These findings suggest that patients with futile recanalization have comparatively worse glymphatic clearance. Further research is required to clarify the relationship between futile recanalization and the glymphatic system, which may facilitate the development of therapeutic adjuncts.
Arc: a therapeutic hub for Alzheimer’s disease
Authors: VanDongen Antonius M.
Published: January 2025

Alzheimer’s disease (AD) is poised to reach epidemic levels as the world population ages. There is currently no treatment that halts this debilitating disease. Our recent finding that the memory gene Arc regulates the expression of many genes associated with the pathophysiology of AD sets the stage for a new therapeutic approach that is not structurally based on the amyloid hypothesis that has driven most research to date. Neuronal activity-dependent Arc expression is controlled by a chromatin-modification complex containing two enzymes: Tip60 and PHF8. Here, we show that small molecules targeting these proteins inhibit Arc expression. This finding sets the stage for a novel therapeutic approach to combat Alzheimer’s disease. Targeting Arc opens a new frontier of “multi-target” therapy designed to intervene in several aspects of the disease simultaneously. Because of Arc’s role in controlling the expression of multiple genes and pathways implicated in AD, it could serve as a therapeutic hub.
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis
Authors: Kim Hyun Young , Mizrahi Orel , Lee Wonseok , Rosenthal Sara B. , Han Cuijuan , Yee Brian A. , Blue Steven M. , Diaz Jesiel , Jonnalagadda Jyotiprakash , Hokutan Kanani , Jang Haeum , Ma Chen-Ting , Bobkov Andrey , Sergienko Eduard , Jackson Michael R. , Stefanovic Branko , Kisseleva Tatiana , Yeo Gene W. , Brenner David A.
Published: January 2025

Metabolic syndrome and excessive alcohol consumption result in liver injury and fibrosis, which is characterized by increased collagen production by activated Hepatic Stellate Cells (HSCs). LARP6, an RNA-binding protein, was shown to facilitate collagen production. However, LARP6 expression and functionality as a regulator of fibrosis development in a disease relevant model remains elusive. By using snRNA-sequencing, we show that LARP6 is upregulated mainly in HSCs of liver fibrosis patients. Moreover, LARP6 knockdown in human HSCs suppresses fibrogenic gene expression. By integrating eCLIP analysis and ribosome profiling in HSCs, we show that LARP6 interacts with mature mRNAs comprising over 300 genes, including RNA structural elements withinCOL1A1,COL1A2, andCOL3A1to regulate mRNA expression and translation. Furthermore, LARP6 knockdown in HSC attenuates fibrosis development in human liver spheroids. Altogether, our results suggest that targeting LARP6 in human HSCs may provide new strategies for anti-fibrotic therapy.

Highlights

LARP6 is upregulated in liver fibrosis, mainly in HSCs.

LARP6 knockdown in human HSCs reduces liver fibrosis development.

Of the hundreds of gene targets, LARP6 interacts most with collagen mRNAs.

LARP6 regulates mRNA translation via interaction with 5’UTRs.
Genetically encoded mechano-sensors with versatile readouts and compact size
Authors: Ren Yuan , Yang Jie , Saito Takumi , Glomb Oliver , Mousavi Sayed Iman , Naughton Brigitte , de Fontnouvelle Christina , Fujita Barbara , Schlieker Christian , Yogev Shaul , Zhang Yongli , Berro Julien
Published: January 2025

Mechanical forces are critical for virtually all fundamental biological processes, yet quantification of mechanical forces at the molecular scalein vivoremains challenging. Here, we present a new strategy using calibrated coiled-coils as genetically encoded, compact, tunable, and modular mechano-sensors to substantially simplify force measurementin vivo, via diverse readouts (luminescence, fluorescence and analytical biochemistry) and instrumentation readily available in biology labs. We demonstrate the broad applicability and ease-of-use of these coiled-coil mechano-sensors by measuring forces during cytokinesis (formin Cdc12) and endocytosis (epsin Ent1) in yeast, force distributions in nematode axons (β-spectrin UNC-70), and forces transmitted to the nucleus (mini-nesprin-2G) and within focal adhesions (vinculin) in mammalian cells. We report discoveries in intracellular force transmission that have been elusive to existing tools.
Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus-MProinhibitors with potent in vivo efficacy
Authors: Detomasi Tyler C. , Degotte Gilles , Huang Sijie , Suryawanshi Rahul K. , Diallo Amy , Lizzadro Luca , Zaptero-Belinchón Francisco J. , Taha Taha Y. , Li Jiapeng , Richards Alicia , Hantz Eric R. , Alam Zain , Mantano Mauricio , McCavitt-Malvido Maria , Gumpena Rajesh , Partridge James R. , Correy Galen J. , Charvat Annemarie F. , Glenn Isabella S. , Rosecrans Julia , Revalde Jezrael L. , Anderson Dashiell , Hultquist Judd F. , Arkin Michelle R. , Neitz R. Jeffrey , Swaney Danielle L. , Krogan Nevan J. , Shoichet Brian K. , Verba Kliment A. , Ott Melanie , Renslo Adam R. , Craik Charles S.
Published: January 2025

The main protease (MPro) of SARS-CoV-2 is crucial for viral replication and is the target of nirmatrelvir (the active ingredient of Paxlovid) and ensitrelvir. The identification of new agents with differentiated pharmacokinetic and drug resistance profiles will increase therapeutic options for COVID-19 patients and bolster pandemic preparedness generally. Starting with a lead-like dihydrouracil chemotype from a large-library docking campaign, we improved MProinhibition >1,000-fold by engaging additional sub-sites in the MProactive site, most notably by employing a latent propargyl electrophile to engage the catalytic Cys145. Advanced leads from this series, includingAVI-4516andAVI-4773show pan-coronavirus antiviral activity in cells, very low clearance in mice, and forAVI-4773a rapid reduction in viral titers more than a million-fold after just three doses, more rapidly and effectively than the approved drugs, nirmatrelvir and ensitrelvir. BothAVI-4516andAVI-4773 are well distributed in mouse tissues, including brain, where concentrations ten or fifteen-thousand times the EC90, respectively, are observed eight hours after an oral dose. As exemplar of the series,AVI-4516shows minimal inhibition of major CYP isoforms and human cysteine and serine proteases, likely due to its latent–electrophilic warhead.AVI-4516also exhibits synergy in cellular infection models in combination with the RdRp inhibitor molnupiravir, while related analogs strongly inhibit nirmatrelvir-resistant MPromutant virus in cells. Thein vivoand antiviral properties of this new chemotype are differentiated from existing clinical and pre-clinical MProinhibitors, and will advance new therapeutic development against emerging SARS-CoV-2 variants and other coronaviruses.

One sentence summary

This manuscript describes the discovery of a new class of potent inhibitors of the SARS-CoV-2 major proteases (MPro) with a unique mechanism of inhibition, pan coronaviral activityin cellulo, exquisite selectivity vs. the human proteome, and exceptionalin vivoefficacy in SARS-CoV-2 infection models that surpasses that of currently approved agents.
Self-Reported Fitness (IFIS) in Adults with Type 2 Diabetes Mellitus: Validity and Associations with Cardiometabolic and Body Composition Outcomes
Authors: Herraiz-Adillo Ángel , Rådholm Karin , Iredahl Fredrik , Carlhäll Carl-Johan , Roemkens Nahuel , Forsgren Mikael , Leinhard Olof Dahlqvist , Lundberg Peter , Kechagias Stergios , Dahlström Nils , Nasr Patrik , Ekstedt Mattias , Henriksson Pontus
Published: January 2025

This study aimed to assess the validity of the International Fitness Scale (IFIS) for evaluating cardiorespiratory fitness compared to the 6-minute walk test (criterion validity) and to examine their associations with cardiometabolic and body composition outcomes (construct validity) in adults with type 2 diabetes mellitus (T2DM). A cross-sectional analysis was conducted on 282 adults with T2DM (mean age 63.6 ± 8.1 years, 37.9% women). Self-reported fitness was assessed using IFIS, including overall fitness and cardiorespiratory fitness scores. Objective cardiorespiratory fitness was assessed using the 6-minute walk test. Associations with cardiometabolic (i.e., cardiovascular health score, metabolic dysfunction-associated steatotic liver disease [MASLD], high-sensitive C-reactive protein) and body composition outcomes (i.e., body mass index [BMI], visceral adipose tissue volume, and thigh fat-free muscle volume) were analyzed using ANCOVA and ROC curves, which were compared using DeLong tests.

Both IFIS overall and cardiorespiratory fitness strongly correlated with performance in the 6-minute walk test (p<0.001 for ANCOVA models) and were associated with all cardiometabolic and body composition outcomes. ROC analyses showed at least similar predictive performance for IFIS overall and cardiorespiratory fitness scores compared to the 6-minute walk test. Furthermore, IFIS overall outperformed the 6-minute walk test for predicting poor cardiovascular health (AUCs: 0.678 [95% CI: 0.618-0.737] versus 0.586 [95% CI: 0.517-0.654]) as well as MASLD (AUCs: 0.630 [95% CI: 0.563-0.696] versus 0.519 [95% CI: 0.443-0.595]).

This study proves that IFIS is a valid tool for assessing physical fitness in T2DM patients and that it conveys cardiometabolic and body composition outcomes at least as well as the 6-minute walk test.
Physical therapists’ perceptions of telerehabilitation for patients with musculoskeletal conditions in a post-pandemic world
Authors: McLaughlin Kevin , Minick Kate I. , Fritz Julie M. , Tannahill Nicole , Spar Anne , Feinsilver Marissa , Weber Matthew , Opoku Erika , Adams Jeff , Skolasky Richard L.
Published: January 2025

Objective

To examine physical therapists’ experience providing telerehabilitation and their perceptions of telerehabilitation for patients with musculoskeletal conditions.

Methods

Survey of members of the Academy of Orthopaedic Physical Therapy

Results

We received 208 completed responses to our survey invitation. Most physical therapists responding to our survey reported using little to no telerehabilitation prior to the pandemic but increased use during the pandemic, followed by decreased use of telerehabilitation after the pandemic. Respondents reported using telerehabilitation slightly more after the pandemic than beforehand. Physical therapists reported that they believed they could deliver effective care using telerehabilitation but that it was not as effective as in-clinic care and they would prefer to use telerehabilitation as part of a hybrid care model versus using only telerehabilitation. Physical therapists suggested that certain patients were more likely than others to benefit from telerehabilitation and identified specific factors (e.g., patient preference, self-efficacy, postoperative status) that influenced whom they would consider to be most appropriate for telerehabilitation. “Patient issues with technology” was identified as the most common barrier to telerehabilitation use. Most physical therapists reported that they planned to use telerehabilitation in the future and agreed that telerehabilitation plays an important role in expanding access to physical therapy in the United States.

Conclusions

Physical therapists believed that telerehabilitation continues to play an important role in a post-pandemic world. Although physical therapists reported that they considered telerehabilitation to be an effective method for delivering care, they did not consider it to be a replacement for in-clinic care and believed that certain patients are more likely than others to benefit from this approach.

Impact Statement

Physical therapists consider telerehabilitation to be a viable care option for patients with musculoskeletal pain.
Abdominal Myosteatosis and Cognitive Decline in a Biracial Cohort: Insights from CARDIA Study
Authors: Acevedo-Fontánez Adrianna , Rosano Caterina , Yaffe Kristine , Carr J Jeffrey , Terry James G. , Nair Sangeeta , Barinas-Mitchell Emma , Cvejkus Ryan K. , Miljkovic Iva
Published: January 2025

Objective

Skeletal muscle fat infiltration (myosteatosis) increases with age and is an emerging risk factor for dementia. We aimed to determine the association between myosteatosis and cognitive decline among middle-aged White and Black Americans.

Methods

Data were on men (n=1,080; 41.9% Black) and women (n=1,432; 49.0% Black) from the CARDIA study. CT-measured abdominal intermuscular fat (IMAT) volume was assessed at baseline. Cognition was assessed by Digit Symbol Substitution (DSST), Rey Auditory Verbal Learning (RAVLT), and Stroop Test at baseline and 5-year follow-up. Multivariable linear regression was used to assess associations of IMAT with cognitive change.

Results

Participants were aged 50.2 (3.6) years and had IMAT of 2.3 (1.6) cm3, 5-year change in DSST of -2.8% (21.8), RAVLT 2.8% (17.5) and Stroop 6.5% (49.5). Greater IMAT was associated with steeper DSST decline (β =-0.52 points per SD, p-value=0.035), but not with Stroop or RAVLT. Stratified by race, greater IMAT predicted DSST decline among White (β =-0.73, p =0.044), but not Black (β =-0.44, p =0.195), participants.

Conclusions

Abdominal myosteatosis may be a novel risk factor for decline in psychomotor speed, especially in middle-aged Whites. Further research on mechanisms, including metabolic mediators, is warranted to understand myosteatosis’s role in mid-life cognitive decline.
Vaccine demands to achieve outbreak control for MPXV Clade I with one-time mass campaign in sub-Saharan Africa: scenario-based modelling study
Authors: Jin Shihui , Asakura Toshiaki R , Murayama Hiroaki , Niyukuri David , Saila-Ngita Diafuka , Lim Jue Tao , Endo Akira , Dickens Borame L
Published: January 2025

Background

Declining cross-protection from historical smallpox vaccination campaigns and persistent zoonotic reservoirs leave many sub-Saharan countries susceptible to mpox outbreaks. With millions of vaccine doses made available to the region since late 2024, estimating the country specific impact of one-time mass vaccination strategies is crucial for ongoing outbreaks and for other countries at future risk.

Methods

We adapted a next generation matrix model to incorporate vaccination which was calibrated using mpox datasets from the Democratic Republic of Congo. We projected the effective reproduction number,Reff, for 47 sub-Saharan countries from 2025 to 2050 under four transmission scenarios with different contributions of community vs sexual contacts, informed by Clade Ia and Ib outbreaks. We then calculated country-specific minimum vaccine coverages required for outbreak control and evaluated one-time age-specific mass vaccination strategies for reducingReff.

Findings

For all 47 countries,Reffs are projected to rise. At least 20 are estimated to require vaccination in 2025, and 36 in 2050, in the event of national outbreaks. For eleven clade I-affected countries, the minimum required coverage is estimated to range from 0%–4.8% to 14.5%–19.5% in 2025 with increasing sexual transmission, increasing to 0%–10.8% and 22.6%–26.0% in 2050, respectively. The prioritised age group for vaccination shifts from 0–4 to 20–29 with additional sexual transmission.

Interpretation

With diminishing smallpox-vaccination-induced immunity, increasingReffs and potential for persistent outbreaks are expected for mpox. Policymakers may face increasing vaccine demand, which will necessitate coordinated efforts to prioritise high-risk groups under supply constraints.
Data-driven workflow for comprehensive gene expression analysis in complex microbiomes
Authors: Mameda Ryo , Bono Hidemasa
Published: January 2025

Complex microbiomes, characterized by highly diverse microbial species, are ubiquitous in the environment. However, the genomes of many constituent microbes remain uncharacterized, complicating the use of publicly available genome sequences as reference data for gene expression analysis based on next-generation sequencing (NGS) data. Consequently, selecting suitable reference sequences is critical for accurate gene expression analysis in complex microbiomes. Additionally, such analyses require precise quantitative evaluation of the genes within each microorganism. In this study, we identified appropriate reference sequences and developed a data-driven analytical workflow for gene expression analysis in complex microbiomes. Utilizing metagenomic and metatranscriptomic NGS reads from these microbiomes, the workflow evaluates gene abundance and transcriptional levels, addressing key analytical challenges. The findings demonstrate that metagenomic contigs are more suitable than conventional reference sequences for mapping both metagenomic and metatranscriptomic data. Moreover, this workflow facilitates not only the assessment of transcriptional activity but also the evaluation of gene expression potential.
Integrated analysis of protein sequence and structure redefines viral diversity and the taxonomy of theFlaviviridae
Authors: Simmonds Peter , Butković Anamarija , Grove Joe , Mayne Richard , Mifsud Jonathon C. O. , Beer Martin , Bukh Jens , Drexler J. Felix , Kapoor Amit , Lohmann Volker , Smith Donald B. , Stapleton Jack T. , Vasilakis Nikos , Kuhn Jens H.
Published: January 2025

TheFlaviviridaeare a family of non-segmented positive-sense enveloped RNA viruses containing significant pathogens including hepatitis C virus and yellow fever virus. Recent large-scale metagenomic surveys have identified many diverse RNA viruses related to classical orthoflaviviruses and pestiviruses but quite different genome lengths and configurations, and with a hugely expanded host range that spans multiple animal phyla, including molluscs, cnidarians and stramenopiles,, and plants. Grouping of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flavivirus and ‘flavi-like’ viruses into four divergent clades and multiple lineages within them was congruent with helicase gene phylogeny, PPHMM profile comparisons, and comparison of RdRP protein structure predicted by AlphFold2. These results support their classification into the established order,Amarillovirales, in three families (Flaviviridae, Pestiviridae, andHepaciviridae), and 14 genera. This taxonomic framework informed by RdRP hallmark gene evolutionary relationships provides a stable reference from which major genome re-organisational events can be understood.
Electrophysiological resting-state signatures link polygenic scores to general intelligence
Authors: Engler Rebecca , Stammen Christina , Arnau Stefan , Schneider Penate Javier , Metzen Dorothea , Digutsch Jan , Gajewski Patrick D. , Getzmann Stephan , Fraenz Christoph , Reinders Jörg , Streit Fabian , Ocklenburg Sebastian , Schneider Daniel , Burke Michael , Hengstler Jan G. , Watzl Carsten , Nitsche Michael A. , Kumsta Robert , Wascher Edmund , Genꞔ Erhan
Published: January 2025

Intelligence is associated with important life outcomes. Behavioral, genetic, structural, and functional brain correlates of intelligence have been studied for decades, but questions remain as to how genetics are related to trait expression and what intermediary role brain properties play. This study investigated these mediations in a representative sample of 434 individuals, comprising young and older adults. Polygenic scores (PGS) for intelligence were calculated. Resting-state EEG recordings were analyzed using graph theory quantifying functional connectivity across different frequencies. We tested whether global and local graph metrics like efficiency and clustering mediated the association between PGS and intelligence. PGS significantly predicted variance in intelligence and were related to frequency-specific graph metrics in areas predominantly located in parieto-frontal regions, which in turn were associated with intelligence. These findings, which are based on the first study linking PGS to intelligence using EEG-derived graph metrics, advance our understanding of the neurogenetics of intelligence.
Systematic Determination of the Impact of Structural Edits on Accumulation into Mycobacteria
Authors: Dash Rachita , Liu Zichen , Lepori Irene , Chordia Mahendra D. , Ocius Karl , Holsinger Kadie , Zhang Han , Kenyon Ryan , Im Wonpil , Siegrist M. Sloan , Pires Marcos M.
Published: January 2025

The mycomembrane of mycobacteria has long been regarded as the primary barrier to the accumulation of molecules within these bacteria. Understanding accumulation beyond the mycomembrane ofMycobacterium tuberculosis(Mtb) is crucial for developing effective antimycobacterial agents. This study investigates two design principles commonly found in natural products and mammalian cell-permeable peptides – backboneN-methylation and macrocyclization – aimed at enhancing accumulation. To assess the impact of these structural edits on accumulation, we employed our recently described Peptidoglycan Accessibility Click-Mediated Assessment (PAC-MAN) assay for live-cell analysis. Our findings indicate that peptide macrocyclization generally enhances permeability and metabolic stability, whileN-methylation modifies accumulation in a context-dependent manner. Furthermore, we applied these design principles to the peptide antibiotic Tridecaptin A1, demonstrating improved permeability and efficacy against mycobacteria, in specific contexts. This work suggests that strategic structural modifications can enhance accumulation past the mycomembrane and provide the first systematic governing rules for the rational redesign of potential antimycobacterial agents. Most importantly, our results broadly challenge the notion that large hydrophilic molecules (e.g., peptides) cannot readily bypass the mycomembrane to reach the cytosolic space.
The reasonable effectiveness of domain adaptation for inference of introgression
Authors: Cobb Kerry A. , Smith Megan L.
Published: January 2025

Supervised machine learning approaches have proven powerful in population genetics. To use such approaches, training data with known inputs and outputs are required. Since such data are generally unavailable in population genetics, researchers typically rely on simulations under the models of interest to train machine learning algorithms. While powerful, this approach depends heavily on the models used to generate training data. Because of the variety and complexity of processes shaping genetic variation, it is inevitable that not all processes important in an empirical system will be included when generating training data. This leads to a mismatch between the data used to train a machine learning algorithm and the data to which the trained model is ultimately applied–i.e., a domain shift– and can negatively impact inference. Here, we train a Convolutional Neural Network (CNN) to detect introgression between sister populations and demonstrate that it has near perfect accuracy when applied to data generated under the models used for training. To evaluate the impacts of domain shifts on inference, we generated new data with introgression from a third, unsampled population into one of the two focal populations (i.e., ghost introgression), and accuracy was substantially reduced on these data. Finally, we used domain adaptation, which aims to train a network that performs well in the presence of a domain shift. Notably, this requires no knowledge of the target or empirical domain. Our domain adaptation network was able to accurately detect introgression, even in the presence of unmodelled ghost introgression. We also applied this approach to empirical data to detect introgression between ABC Island brown bears and other populations of brown bears. Previous work has suggested that introgression between ABC Island bears and polar bears can mislead tests of introgression between populations of brown bears. We found that using domain adaptation reduced support for introgression between geographically isolated populations of brown bears, suggesting that our approach reduces false inferences of introgression due to ghost introgression.
Partial Wwox Loss of Function Increases Severity of Murine Sepsis and Neuroinflammation
Authors: De La Cruz Priscilla , Gomes Marta , Lockett Angelia , Fisher Amanda , Cook Todd , Smith Patricia , Lloyd Christopher , Twigg Homer L , Oblak Adrian , Aldaz C. Marcelo , Machado Roberto F.
Published: January 2025

Rationale

WW domain-containing oxidoreductase (WWOX) is a gene associated implicated in both neurologic and inflammatory diseases and is susceptible to environmental stressors. We hypothesize partial loss of Wwox function will result in increased sepsis severity and neuroinflammation.

Methods

WwoxWT/P47Tmice, generated by CRISPR/Cas9, andWwoxWT/WTmice were treated with intraperitoneal PBS vs LPS (10mg/kg) and euthanized 12 hours post-injection. Open Field Testing (OFT) and Murine Sepsis Severity Scores (MSS) were utilized to measure sickness behavior and sepsis severity, respectively. Brain tissue was analyzed using immunohistochemistry and PCR to measure neuroinflammation and apoptosis.

Results

WwoxWT/P47TLPS mice demonstrated a more significant response to sepsis with an increase in sickness behavior, sepsis severity, gliosis, and apoptosis compared toWwowWT/WTLPS littermates.

Conclusions

Partial loss of Wwox function increases risk for severe sepsis and neuroinflammation. Given the susceptibility ofWWOXto environmental stressors, this may be a target for future therapeutic interventions.
Differential regulation of brain-specific molecular pathways is the reason for curcumin’s adult life-phase specific DAergic neuroprotection: Insights from ALSS Drosophila model of Parkinson’s disease
Authors: Das Abhik , Yenisetti Sarat Chandra
Published: January 2025

Abstract

Curcumin (CU), a bioactive compound of turmeric, has been put forward as a “golden molecule” due to its anti-inflammatory, antioxidant, hepatoprotective, neuroprotective, and anti-cancer ability, as proven by research conducted over the decade and more. Our laboratory, developed an adult life stage specific (ALSS)Drosophilamodel of sporadic Parkinson’s disease (PD), and for first time demonstrated that dopaminergic (DAergic) neuroprotective efficacy of curcumin is limited to health phase viz. adult-young life stage and is absent during transition phase viz. adult senior life stages when PD set in. This observation suggests the limitation of curcumin as a therapeutic agent for late-onset disorders like PD. Further, our laboratory also demonstrated that despite curcumin’s ability to sequester oxidative stress during both the adult life stages, neuroprotection and brain dopamine replenishment is granted only in health stages but not in a vulnerable transition stage, which prompted to put forward the hypothesis that the molecular target(s) of CU, may be absent or inadequate in the transition stage of aging brain. With this insight, the current study was implemented to analyse the life stage-specific differential regulation of multiple molecular players of neuro-integral pathways in brain of ALSSDrosophilamodel of PD with curcumin intervention. It is discovered that curcumin-mediated health phase-specific neuroprotection underlies the correction of an altered expression of 1.dFOXO, GADD45, PucofBsk-dFOXOstress response pathway, 2.Mfn2of Mitochondrial dynamics 3.CncC, GCLC, Prx 2540 -1,2, Jafrac1, Prx3of Phase II antioxidant defense system pathway. Further, it is discovered that significant aging-associated naturally altered expression of certain molecular targets exists, that may contribute to the limitation of curcumin’s DAergic neuroprotective efficacy during the adult-transition stage. This knowledge will help in developing altered therapeutic strategies for PD as molecular targets of curcumin are conserved among fly, mice and human.