bluuebunny/crossref_metadata_2025 huggingface dataset:
Barriers to Developmental Care in the NICU
Authors: Logsdon Shelby , Arter Sara
Published: January 2025

Background:

Variability in developmental care implementation in the neonatal intensive care unit (NICU) highlights the need to explore barriers to care delivery, yet few studies addressed these challenges.

Purpose:

Drawing from NICU literature, this integrative review identifies barriers to implementing developmental care with premature infants.

Methods:

A systematic search of CINAHL and PubMed (2014-2024) was conducted, yielding 2 qualitative and 5 quantitative studies.

Results:

Thematic analysis revealed 3 key barriers based on the theory of planned behavior: attitude, subjective norm, and perceived control.

Conclusions:

To improve developmental care, a multi-pronged approach engaging stakeholders is recommended. Future research should apply rigorous implementation science methods to overcome these barriers.
Avian telencephalon and cerebellum volumes can be accurately estimated from digital brain endocasts
Authors: Keirnan Aubrey R. , Cunha Felipe , Citron Sara , Prideaux Gavin , Iwaniuk Andrew N. , Weisbecker Vera
Published: January 2025

For studies of the evolution of vertebrate brain anatomy and potentially associated behaviours, reconstructions of digital brain endocasts from computed tomography scans have revolutionized our capacity to collect neuroanatomical data. However, measurements from digital endocasts must be validated as reflecting actual brain anatomy, which is difficult because the collection of soft tissue information through histology is laborious and time-consuming. In birds, the reliability of digital endocast measurements as volume proxies for the two largest brain regions—the telencephalon and cerebellum—remains to be validated despite their use as proxies, e.g. of cognitive performance or flight ability. We here use the largest dataset of histology and digital endocasts to date, including 136 species from 25 avian orders, to compare digital endocast surface area measurements with actual brain volumes of the telencephalon, cerebellum and whole-brain endocast. Using linear and phylogenetically informed regression analyses, we demonstrate that endocast surfaces are strongly correlated with their brain volume counterparts for both absolute and relative size. This provides empirical support for using endocast-derived cerebellar and telencephalic surface areas in existing and future studies of living and extinct birds, with potential to expand to the dinosaur—bird transition in the future.
CryoEM structure and small-angle X-ray scattering analyses of porcine retinol-binding protein 3
Authors: Kaushik Vineeta , Gessa Luca , Kumar Nelam , Pinkas Matyáš , Czarnocki-Cieciura Mariusz , Palczewski Krzysztof , Nováček Jiří , Fernandes Humberto
Published: January 2025

The vertebrate visual cycle hinges on enzymatically converting all-
trans
-retinol (at-ROL) into 11-
cis
-retinal (11c-RAL), the chromophore that binds to opsins in photoreceptors, forming light-responsive pigments. When struck by a photon, these pigments activate the phototransduction pathway and initiate the process of vision. The enzymatic isomerization of at-ROL, crucial for restoring the visual pigments and preparing them to receive new light stimuli, relies on various enzymes found in both the photoreceptors and retinal pigment epithelium cells. To function effectively, retinoids must shuttle between these two cell types. Retinol-binding protein 3 (RBP3), located in the interphotoreceptor matrix, probably plays a pivotal role in this transport mechanism. Comprised of four retinoid-binding modules, RBP3 also binds fatty acids, potentially aiding retinal function by facilitating the loading and unloading of different retinoids at specific cell types thereby directing the cycle. In this study, we present a 3.67 Å cryoEM structure of porcine RBP3, along with molecular docking analysis and corroborative in-solution small-angle X-ray scattering data for titration of RBP3 with relevant ligands, that also give insights on RBP3 conformational adaptability.
The role of expansion and adaptability of face-space for individual differences in face identity processing
Authors: Ficco Linda , Ramon Meike , Schroeger Anna , Kaufmann Jürgen M. , Schweinberger Stefan R.
Published: January 2025

Individuals can strongly vary in their ability to process face identity. Understanding the mechanisms driving these differences is important for theoretical development, and in clinical and applied contexts. Here we investigate the role of face-space properties in relation to individual face identity processing skills. We consider two fundamental properties of face-space:
expansion
(how distant from each other similar faces are located in such space) and
adaptability
(the degree to which these distances change over time). Fifty-two participants performed a face detection task, with faces systematically varying in their location in face-space, and a comprehensive face identity processing test battery. We replicate previous results indicating a detection advantage for typical, as compared with distinctive faces. Critically, we find that neither our measure of face-space expansion nor that of face-space adaptability are related to individual face processing abilities. While future studies might benefit from the use of more sensitive measures of face-space properties, these results suggest that the two examined here do not contribute to individual differences in face processing abilities as previous studies suggest.
Human-interpretable clustering of short text using large language models
Authors: Miller Justin K. , Alexander Tristram J.
Published: January 2025

Clustering short text is a difficult problem, owing to the low word co-occurrence between short text documents. This work shows that large language models (LLMs) can overcome the limitations of traditional clustering approaches by generating embeddings that capture the semantic nuances of short text. In this study, clusters are found in the embedding space using Gaussian mixture modelling. The resulting clusters are found to be more distinctive and more human-interpretable than clusters produced using the popular methods of doc2vec and latent Dirichlet allocation. The success of the clustering approach is quantified using human reviewers and through the use of a generative LLM. The generative LLM shows good agreement with the human reviewers and is suggested as a means to bridge the ‘validation gap’ which often exists between cluster production and cluster interpretation. The comparison between LLM coding and human coding reveals intrinsic biases in each, challenging the conventional reliance on human coding as the definitive standard for cluster validation.
Submarine groundwater discharge drives both direct and indirect effects on organismal and community metabolism on coral reefs
Authors: Barnas Danielle M. , Zeff Maya , Silbiger Nyssa J.
Published: January 2025

Coral reefs experience numerous environmental gradients affecting organismal physiology and species biodiversity, which ultimately impact community metabolism. This study shows that submarine groundwater discharge (SGD), a common natural environmental gradient in coastal ecosystems associated with decreasing temperatures, salinity and pH with increasing nutrients, has both direct and indirect effects on coral reef community metabolism by altering individual growth rates and community composition. Our data revealed that SGD exposure hindered the growth of two algae,
Halimeda opuntia
and
Valonia fastigiata,
by 67 and 200%, respectively, and one coral,
Porites rus,
by 20%. Community metabolic rates showed altered community production, respiration and calcification between naturally high and low exposure areas mostly due to differences in community identity (i.e. species composition), rather than a direct effect of SGD on physiology. Production and calcification were 1.5 and 6.5 times lower in assemblages representing high SGD communities regardless of environment. However, the compounding effect of community identity and SGD exposure on respiration resulted in the low SGD community exhibiting the highest respiration rates under higher SGD exposure. By demonstrating SGD’s role in altering community composition and metabolism, this research highlights the critical need to consider compounding environmental gradients (i.e. nutrients, salinity and temperature) in the broader context of ecosystem functions.
The role of exploration and exploitation in primate communication
Authors: Fröhlich Marlen , Boeckx Cedric , Tennie Claudio
Published: January 2025

The concepts of social learning and exploration have been central to debates in comparative cognition research. While their roles in the origins of human cumulative culture on the one hand and creativity on the other have been highlighted, the two concepts have mostly been studied separately. In this article, we examine the relationship between adopting similar or different behaviours within a group, focusing on how exploration and exploitation shape primate communication systems. Using a comparative approach, we discuss how similarity and differentiation of communicative behaviour can be viewed as two endpoints on a continuum, impacting both individual- and group-level behavioural variation. While group-level variation is evident in some ape behaviours (e.g. foraging traditions), individual variation in communicative behaviour appears to outweigh group-level differences, making a widespread communicative culture in apes unlikely. Drawing parallels to language acquisition in human infants, we propose that ape communication follows an exploration–exploitation trajectory, with initial exploration gradually giving way to focused exploitation of genetically predisposed and/or individually developed communicative repertoires. By integrating the individual and social learning processes underlying communicative behaviour, we can gain a deeper understanding of how exploration–exploitation tensions shape communication systems across species.
Wild recognition: conducting the mark test for mirror self-recognition on wild baboons
Authors: Ahmad Esa A. , Reiderman Helen , Huchard Elise , Delaunay Axelle , Roatti Vittoria , Cowlishaw Guy , Carter Alecia
Published: January 2025

The distribution of self-awareness across species is important to understand, not only as a matter of scientific interest but also because of its implications for the ethical standing of non-human animals. The prevailing methodology for determining self-awareness is to test for visual self-recognition using mirror-image stimulation and a ‘mark test’. However, most studies have involved very small sample sizes, omitted a control condition and been conducted on captive animals. Here, we designed and implemented the first controlled mark test in a wild setting, conducting the mark test using a laser pointer on a large (
n
= 51 individuals, 135 mark tests) sample of wild chacma baboons (
Papio ursinus
)
in situ
. Control tests showed that baboons were interested in the mark, but this interest decreased with age, and was greater in males and towards green (cf. red) marks. However, as predicted, subjects showed no evidence of visual self-recognition, which, given the control, cannot be attributed to a lack of motivation in the mark. Our study proposes a novel, controlled mark test
in situ
and contributes to the evidence that, without extensive training, non-hominid primates are not capable of full visual self-recognition.
Covert variations of a musician’s loudness during collective improvisation capture other musicians’ attention and impact their interactions
Authors: Schwarz Armand , Faraco Arthur , Vincent Coralie , Susini Patrick , Ponsot Emmanuel , Canonne Clément
Published: January 2025

While research on auditory attention in complex acoustical environment is a thriving field, experimental studies thus far have typically treated participants as passive listeners. The present study—which combined real-time covert loudness manipulations and online probe detection—investigates for the first time to our knowledge, the effects of acoustic salience on auditory attention during live interactions, using musical improvisation as an experimental paradigm. We found that musicians were more likely to pay attention to a given co-performer when this performer was made sounding louder or softer; that such salient effect was not owing to the local variations introduced by our manipulations but rather likely to be driven by the more long-term context; and that improvisers tended to be more strongly and more stably coupled when a musician was made more salient. Our results thus demonstrate that a meaningful change of the acoustical context not only captured attention but also impacted the ongoing musical interaction itself, highlighting the tight relationship between attentional selection and interaction in such social scenarios and opening novel perspectives to address whether similar processes are at play in human linguistic interactions.
The Apoprotein E4 isotype does not affect the severity of COVID-19 infection and other flu-like syndromes
Authors: Carvalho-Rassbach Marina , Ventura Lucas Haniel Araujo , Assis Larissa Oliveira , Fabrini Sabrina , Natividade Manuelle Maria Pereira , Silva Janayne Luihan , Gomes Karina Braga , Faria Ana Maria Caetano , Alvarez-Leite Jacqueline I.
Published: January 2025

Impact of e4 allele on flu-like syndromes

The ɛ4 allele has no influence on flu-like syndrome, including COVID-19. COVID-19 severity was associated with BMI, male sex, comorbidities and IL-4 levels.
Oncogenic Stress is a Novel Immunogenic Signal Driven by the Unfolded Protein Response and Detected by Neutrophils
Authors: Debiesse Antoine , Moudombi Lyvia , Voissière Aurélien , Lefèvre Leïla , Malfroy Marine , Moskalevska Iryna , Pereira Abrantes Manuela , Vanacker Hélène , Hubert Margaux , Pommier Roxane , Assaf Cassandra , Jacquet Emmanuelle , Laurent Marie , Belluco Sara , Goutagny Nadège , Petrilli Virginie , Cherfils-Vicini Julien , Caux Christophe , Bendriss-Vermare Nathalie , Michallet Marie-Cécile
Published: January 2025

Cellular transformation is initiated by a driver mutation, resulting in the abnormal expression of an oncogene or the loss of a tumor suppressor gene in a normal cell. This event leads to oncogenic stress (OS), describing a disruption of cellular homeostasis which activates stress response pathways and transcriptomic programs that can either promote tumor development or trigger intrinsic safeguards such as senescence or apoptosis. While the immunogenicity of senescent cells is well established, the immunogenic potential of cells at the early OS stage and the mechanisms by which they are sensed by the immune system remain unknown. We developed an originalin vitroOS model using primary human mammary epithelial cells to investigate this process. Our results show that OS cells display an immunoactive secretome associated with OS (SOS), as well as immunogenic membrane ligands. Intrinsically, OS cells activate the PERK and IRE1 branches of the unfolded protein response (UPR) that regulate their immunogenic features. Extrinsically, we demonstrated that neutrophils can detect OS-induced immunogenic signals, leading to their recruitment and their activation in co-culturein vitro. We validated this observation in two spontaneous murine models of breast cancer, where the earliest preneoplastic stages exhibit both UPR activation in epithelial cells and neutrophil infiltration. Altogether, our work identifies OS as the first immunogenic event in carcinogenesis and neutrophils as the first immune cell involved in immunosurveillance, paving the way for potential therapeutic approaches intercepting early steps of tumorigenesis.
Global transcriptome analysis identifies nicotinamide metabolism to play key roles in IFN-γ and nitric oxide modulated responses
Authors: Chattopadhyay Avik , Shyam Sai , Das Shreyasee , Nandi Dipankar
Published: January 2025

Interferon-gamma (IFN-γ) is a key regulator of immune responses. A hallmark of the IFN-γ response is inducible nitric oxide (NO) production, driven primarily by nitric oxide synthase 2 (NOS2). In this study, we investigated the influence of NO on the IFN-γ-induced transcriptomic and metabolic changes in the RAW 264.7 macrophage cell line. IFN-γ activation led to NO-dependent lactate production and lower cell survival. Bulk RNA sequencing analysis identified genes differentially expressed early by IFN-γ that were either NO-independent or NO-dependent. Inhibition of NO modulated a minor subset of the transcriptome, notably affectingKlf6(a tumor suppressor) andZfp36(a regulator of pro-inflammatory cytokines). Interestingly, bothKlf6andZfp36correlatively showed high expression in most cancers. The PPI network exhibited dense clustering with scale-free and small-world properties, identifyingStat1,Irf7,Irf1,Cxcl10, andIsg15as top five hubs. The top IFN-γ signalling genes exhibited deficient expression in the brain but were highly expressed in lung, spleen, and EBV-transformed lymphocytes. Gene-disease associations linked the IFN-γ-regulated genes to immunodeficiencies, chronic inflammatory responses and malignancies. Interestingly, IFN-γ upregulated genes were involved in nicotinamide metabolism, suggesting a transcriptional basis for modulation of metabolic pathways. This novel aspect was experimentally tested to show that IFN-γ induced NAD amounts. Importantly, the inhibition of purine nucleoside phosphorylase (using Forodesine hydrochloride) which is involved in the endogenous pathway for NAD generation, lowered IFN-γ induced nitrite and increased cell survivalin vitro. Functionally, enriched nicotinamide metabolism by IFN-γ may regulate inflammatory responses and the implications of our findings are discussed.
In vivodeletion of a GWAS-identifiedMybdistal enhancer acts onMybexpression, globin switching, and clinical erythroid parameters in β-thalassemia
Authors: Deleuze Virginie , Stephen Tharshana , Salma Mohammad , Orfeo Cédric , Jorna Ruud , Maas Alex , Barroca Vilma , Arcangeli Marie-Laure , Andrieu-Soler Charlotte , Grosveld Frank , Soler Eric
Published: January 2025

Genome-wide association studies (GWAS) have identified numerous genetic variants linked to human diseases, mostly located in non-coding regions of the genome, particularly in putative enhancers. However, functional assessment of the non-coding GWAS variants has progressed at slow pace, since the functions of the vast majority of genomic enhancers have not been defined, impeding interpretation of disease-susceptibility variants. TheHBS1L-MYBintergenic region harbors multiple SNPs associated with clinical erythroid parameters, including fetal hemoglobin levels, a feature impacting disease severity of beta-hemoglobinopathies such as sickle cell anemia and beta-thalassemia. HBS1L-MYB variants cluster in the vicinity of severalMYBenhancers, altering MYB expression and globin switching. We and others have highlighted the conserved humanMYB-84kb enhancer, known as the -81kb enhancer in the mouse, as likely candidate linked to these traits. We report here the generation of aMyb-81kb enhancer knock-out mouse model, and shed light for the first time on its impact on steady state erythropoiesis and in beta-thalassemiain vivo.
Understanding RNA Chaperone Activity of ProQ Protein
Authors: Singh Shilpi , Kumari Nisha , Dutta Tanmay , Karmakar Tarak
Published: January 2025

RNA-binding proteins (RBPs) are crucial in recognizing and binding small RNAs that modulate gene expression. RBPs often act as RNA chaperones facilitating the sRNA-mRNA duplex formation. One of the most studied sRNA chaperones is Hfq, the post-transcriptional gene regulator in bacteria. Recently a new RNA-chaperone protein, ProQ has been discovered, which binds to a novel sRNARaiZ, derived from the 3’-end of mRNA encoding ribosome-inactivating protein, and promotes its base pairing with the ribosome binding site of hupA mRNA leading to the repression of HU-α protein synthesis. Despite these studies, the RNA binding mechanism in ProQ has not been well explored in detail to date. In this work, we studied the binding ofraiZRNA to ProQ using atomistic long-timescale molecular dynamics and on-the-fly probability-based enhanced sampling (OPES) simulations. TheraiZRNA binds to ProQ’s concave surface mostly decorated with polar and positively charged residues like arginine and lysine exerting electrostatic stabilization to the RNA.In-silicomutations of these crucial residues lead to significant loss of the intermolecular interactions resulting in the detachment of the RNA from the protein. The free energy surface obtained from the OPES simulation helps identify stableraiZbound ProQ structures as well as intermediate states. The pertinent atomistic insights into the protein-RNA interactions and deciphering the binding mechanism of theraiZRNA to ProQ enrich our knowledge about ProQ and its RNA chaperone activity.
Weighted gene co-expression network analysis reveals key genes and lncRNAs in desi cattle chronically infected with Johne’s disease
Authors: Sahu Abhisek , Abdullah Mohd , Gupta Saurabh , Singh Shoor Vir , Dhillon Ankush , Yadav Prabhati , Azam Sarwar
Published: January 2025

Johne’s disease (JD), caused byMycobacterium aviumsubsp.paratuberculosis(MAP), is a chronic enteric disease with significant economic impacts on the dairy industry. To elucidate molecular mechanisms underlying MAP infection indesicattle (Bos indicus), we conducted a comprehensive transcriptomic study. This revealed 1,905 protein-coding and 3,123 lncRNA genes as differentially expressed in MAP-infected samples, alongside the first comprehensive annotation of 45,947 lncRNAs indesicattle. Weighted Gene Co-expression Network Analysis identified 11 co-expressed gene modules, with the turquoise module comprising 870 protein- coding genes and 934 lncRNAs, highly correlated with clinical traits. Functional enrichment analysis of this key module revealed significant involvement in defense response, inflammatory processes, and NK cell-mediated immunity and cytotoxicity. GSE analysis revealed suppressed pathways, including NK cell immunity and lectin response, facilitating bacterial persistence in chronic infection, while activated pathways included G-protein-coupled receptor signaling and metabolic pathways. Network approach identified 12 hub genes (IL7R, TLR4, KLRK1, IFNG, TGFB1, CD68, CXCR6, GZMB, KLRG1, MMP9, GZMA, SELL) associated with immune suppression, inflammation, and tissue remodeling. Additionally, 22 lncRNAs co-expressed with hub genes suggesting roles in modulating immune regulation. By identifying critical genes and lncRNAs, our study offers potential targets for developing innovative diagnostic and therapeutic strategies for JD.
The Genome ofChenopodium ficifolium: Developing Genetic Resources and a Diploid Model System for Allotetraploid Quinoa
Authors: Ludwig Clayton D. , Maughan Peter J. , Jellen Eric N. , Davis Thomas M.
Published: January 2025

High-quality nuclear, chloroplast, and preliminary mitochondrial genomes have been assembled and annotated for the B-genome diploid (BB: 2n = 2x = 18) figleaf goosefoot (Chenopodium ficifolium). The primary objective was to advance a simplified model system for genetic characterization and improvement of allotetraploid (AABB: 2n = 4x = 36) quinoa (Chenopodium quinoa), a nutritionally valuable, halophytic orphan crop. In addition to its diploidy and favorably small genome size, theC. ficifoliummodel provides a shorter generational period and smaller overall plant size as compared toC. quinoa, while displaying relevant agronomic trait variations amenable to gene-trait association studies. TheC. ficifolium‘Portsmouth’ nuclear genome was sequenced using PacBio HiFi Long Read technology and assembled using Hifiasm. After manual adjustments, the final ChenoFicP_1.0 assembly consisted of nine pseudochromosomes spanning 711.5 Mbp, while 22,617 genes were identified and annotated. BUSCO analyses indicated a nuclear genome completeness of 97.5%, and a proteome and transcriptome completeness of 98.4 percent. The chloroplast genome assembly detected two equally represented structural haplotypes differing in the orientation of the Short Single Copy region relative to the Long Single Copy region. Phylogenetic and parentage analyses pointed to an unspecified AA diploid species and away fromC. ficifoliumas the likely maternal chloroplast and mitochondrial genome donor(s) during the initial tetraploidization event in theC. quinoalineage. Using the new ChenoFicP_1.0 reference genome, a GWAS was performed on a previously studiedC. ficifoliumF2 population to further define region(s) implicated in the control of three key agronomic traits: days to flowering, plant height, and branch number. This analysis localized control of all three traits to a 7 Mb interval on pseudochromosome Cf4. This region contains approximately 770 genes, including theFTL1locus, thus confirming and extending our prior, single-marker analysis showing association of these three traits with anFTL1amplicon length polymorphism. The use of these data to further developC. ficifoliumas a model species for genetics and breeding of quinoa serves to expand knowledge and germplasm resources for quinoa improvement.
Delivery of a chemically modified noncoding RNA domain improves dystrophic myotube function
Authors: Niasse-Sy Zeinabou , Zhao Bo , Lenardič Ajda , Luong Huyen Thuc Tran , Bar-Nur Ori , Auwerx Johan , Wohlwend Martin
Published: January 2025

Fast twitch, type II muscle fibers are particularly prone to degradation in skeletal muscle pathologies, such as sarcopenia and muscular dystrophies. We previously showed that endogenous activation of the exercise-induced long noncoding RNA CYTOR promotes fast-twitch myogenesis. In the present study, we identify an independent pro-myogenic element within human CYTOR and optimize its RNA delivery. In human primary myoblasts exogenous, vector-based CYTORexon2recapitulates the effect of full-length CYTOR by enhancing fast-twitch myogenic differentiation. Furthermore, chemically modified CYTORexon2RNAΨU(N1-me-PseudoU, 7-methyl guanosine 5’Cap, polyA tail) enhanced RNA stability and reduced the immunogenic response to CYTORexon2RNA. We demonstrate that viral- or chemically optimized RNA-mediated CYTORexon2administration enhances the commitment towards myogenic maturation in Duchenne muscular dystrophy-derived primary myoblasts, induced myogenic progenitor cells and mouse embryonic stem cells. Furthermore, chemically optimized CYTORexon2improves key disease characteristics in dystrophic myotubes, including calcium handling and mitochondrial bioenergetics. In summary, our findings identify CYTOR exon 2 as the pro-myogenic domain of CYTOR that can be delivered in a disease context using chemical modifications. This is of particular importance given the susceptibility of type II muscle fibers in different muscle pathologies such as aging and dystrophies, and the reported oncogenic effect of CYTOR exon 1. Our study, therefore, highlights the potential of identifying functional domains in noncoding RNAs. Delivery, or targeting of such RNA domains could constitute next-generation RNA therapeutics.
Systems biology framework for rational design of operational conditions forin vitro / in vivotranslation of microphysiological systems
Authors: Cadavid Jose L. , Meimetis Nikolaos , Griffith Linda G. , Lauffenburger Douglas A.
Published: January 2025

Preclinical models are used extensively to study diseases and potential therapeutic treatments. Complexin vitroplatforms incorporating human cellular components, known as microphysiological systems (MPS), can model cellular and microenvironmental features of diseased tissues. However, determining experimental conditions -- particularly biomolecular cues such as growth factors, cytokines, and matrix proteins -- providing most effective translatability of MPS-generated information toin vivohuman subject contexts is a major challenge. Here, using metabolic dysfunction-associated fatty liver disease (MAFLD) studied using the CNBio PhysioMimix as a case study, we developed a machine learning framework called LatentIn VitrotoIn VivoTranslation (LIV2TRANS) to ascertain how MPS data map toin vivodata, first sharpening translation insights and consequently elucidating experimental conditions that can further enhance translation capability. Our findings in this case study highlight TGFβ as a crucial cue for MPS translatability and indicate that adding JAK-STAT pathway perturbations via interferon stimuli could increase the predictive performance of this MPS in MAFLD studies. Finally, we developed an optimization approach that identified androgen and EGFR signaling as key for maximizing the capacity of this MPS to capturein vivohuman biological information germane to MAFLD. More broadly, this work establishes a mathematically principled approach for identifying experimental conditions most beneficially capturingin vivohuman-relevant molecular pathways and processes, generalizable to preclinical studies for a wide range of diseases and potential treatments.
ORF1ab Codon Frequency Model Predicts Host-Pathogen Relationship in Orthocoronavirinae
Authors: Davis Phillip E. , Russell Joseph A.
Published: January 2025

Predicting phenotypic properties of a virus directly from its sequence data is an attractive goal for viral epidemiology. Here, we focus narrowly on the Orthocoronavirinae clade and demonstrate models that are powerfully predictive for a human-pathogen phenotype with >86% average precision and >99% average recall on the withheld test set groups, using only Orf1ab codon frequencies. We show alternative examples for other viral coding sequences and feature representations that do not perform well and discuss what distinguishes the models that are performant. These models point to a small subset of features, specifically 5 codons, that are critical to the success of the models. We discuss and contextualize how this observation may fit within a larger model for the role of translation in virus-host agreement.
A Simple and Scalable Chopped-Thallus Transformation Method forMarchantia polymorpha
Authors: Batth Rituraj , Poormassalehgoo Andisheh , Bhardwaj Kritika , Kaniecka Elżbieta , Goto-Yamada Shino
Published: January 2025

The liverwortMarchantia polymorphahas emerged as a valuable model for studying fundamental biological processes and the evolutionary history of land plants. Agrobacterium-mediated transformation is widely used for genetic modification ofM. polymorphausing spores, thalli, and gemmae. While spores offer high transformation efficiency, they result in diverse genetic backgrounds due to sexual reproduction. Conversely, thallus- and gemma-based methods maintain genetic consistency but are impractical for large-scale applications. To address these limitations, we developed a novel chopped-thallus transformation method. This technique involves generating numerous plant fragments by chopping thalli, eliminating the need for complex preprocessing. The method demonstrated superior transformation efficiency compared to traditional approaches and achieved sufficient numbers of transformants using simplified Gamborg’s B5 medium, previously considered suboptimal. This scalable and straightforward method enables the generation of large numbers of genetically consistent transformants, facilitating high-throughput experiments, including mutant screening and other large-scale applications.
SCAN-ACT: Adoptive T Cell Therapy Target Discovery Through Single-Cell Transcriptomics
Authors: Testa Stefano , Pal Aastha , Subramanian Ajay , Varma Sushama , Tang Jack Pengfei , Graham Danielle , Arfan Sara , Pan Minggui , Bui Nam Q. , Ganjoo Kristen N. , Dry Sarah , Huang Paul , van de Rijn Matt , Jiang Wei , Kalbasi Anusha , Moding Everett J.
Published: January 2025

The FDA approval of T cell receptor-engineered T cells (TCR-T) for synovial sarcoma demonstrates the potential for adoptive T cell therapies (ACTs) in solid tumors. However, the paucity of tumor-specific targets without expression in normal tissues remains a major bottleneck, especially in rare cancer subtypes. Here, we present a comprehensive computational pipeline called SCAN-ACT that leverages single cell RNA sequencing and multi-omics data from tumor and normal tissues to nominate and prioritize targets for both chimeric antigen receptor (CAR)- and TCR-T cells. For surface membrane targets, SCAN-ACT proposes target pairs for bispecific Boolean logic-gated CAR T cells. For peptide-MHC targets, SCAN-ACT proposes intracellular peptides bound to a diverse set of human leukocyte antigens. We applied the SCAN-ACT pipeline to soft tissue sarcoma (STS), analyzing 986,749 single cells to identify and prioritize 395 monospecific CAR-T targets, 14,192 bispecific CAR-T targets, and 5,020 peptide-MHC targets for TCR-T cells. Selected targets were validated experimentally by protein expression and for peptide-MHC binding. Proposed targets and target pairs reflected the mesenchymal, neuronal, and hematopoietic ontogeny of STS. This work provides a robust data repository along with a web-based and user-friendly set of analysis tools to accelerate ACT development for solid tumors.
Simplifying species interaction matrices by grouping: optimal groupings differ between effects and responses
Authors: Brown Christopher R. P. , Stouffer Daniel B.
Published: January 2025

Most dynamic models of ecological communities require many parameters, making them expensive to fit to experimental or observational data. To reduce the number of parameters, species are often divided into groupsa priori, using phylogenetic or functional groups, and species within a group are assumed to behave identically. Here, we assess the validity of such grouping by deriving the optimal groupingsa posterioribased on the fit of the Beverton–Holt model to experimental data from six species ofDrosophilacompeting in laboratory conditions. We find evidence that grouping can indeed improve the parsimony of species interaction models, but we also observe that there is no single optimal grouping. Further, those groupings that did prove beneficial could not have been easily predicted from available species attributes, calling into question the prevailing method ofa priorispecies grouping. Lastly, we find that species did not group equivalently in their competitive effect and in their response to competition, invalidating a key assumption often made implicitly when defining species groupings. Our study suggests the need for a different, more data-informed, approach to grouping in species interaction models.
The Distribution of Elastin and Collagen Underpinning the Smart Properties of the Interosseous Membrane
Authors: Anastopolous Sotiria , Knothe Tate Melissa L.
Published: January 2025

The interosseous membrane (IOM), a ligament-like structure spanning the radius and ulna, reduces strain in the ulna and structurally stiffens the radio-ulnar complex of the forearm. Using two-photon and second-harmonic-imaging we measured collagen and elastin signal intensity to test the hypothesis that their spatial distributions correspond to predominant loading patterns in the IOM. Distinct spatial gradients in collagen and elastin, as well as cruciate ligament-like architectures, were observed at the submicron and the micron to mesoscopic length scales. Quantitative analysis revealed anisotropies in the elastin-collagen composite comprising the IOM, with elastin 4-6 times higher than collagen concentrations at radius/ulna - IOM interfaces, and organized in the tensile loading direction,i.e. along the major Centroidal Axis, of the IOM. Hence, the IOM exhibits a composite structure comprising elastin and collagen, with spatial distribution of elastin higher than collagen at bone-IOM interfaces and decreasing from the interface with the ulna to that of the radius. These increased concentrations of elastin at interfaces are expected to confer elasticity (spring function). In contrast, peaks in collagen concentrations represent collagens’ organization into fibers, parallel to the length of the IOM, bridging the radius and ulna, and conferring toughness and damping function to the IOM and forearm construct. Mapping the cross-scale elastin and collagen composition of the IOM gives unprecedented insight into its emergent properties and associated mechanical function, an understanding of which may guide future surgical treatments, implant and medical textile design and manufacture, as well as physical therapy protocols to promote healing.
Risk Prediction of RNA Off-Targets of CRISPR Base Editors in Tissue-Specific Transcriptomes Using Language Models
Authors: Nakamae Kazuki , Suzuki Takayuki , Yonezawa Sora , Yamamoto Kentaro , Kakuzaki Taro , Ono Hiromasa , Naito Yuki , Bono Hidemasa
Published: January 2025

Base-editing technologies, particularly cytosine base editors (CBEs), allow precise gene modification without introducing double-strand breaks; however, unintended RNA off-target effects remain a critical concern and are under-studied. To address this gap, we developed PiCTURE, a standardized computational pipeline for detecting and quantifying transcriptome-wide CBE-induced RNA off-target events. PiCTURE identifies both canonical ACW (W = A or T/U) motif-dependent and non-canonical RNA off-targets, revealing a broader WCW motif that underlies many unanticipated edits. Additionally, we developed two machine learning models based on the DNABERT-2 language model, termed STL and SNL, which outperformed motif-only approaches in terms of accuracy, precision, recall, and F1 score. To demonstrate the practical application of our predictive model for CBE-induced RNA off-target risk, we integrated PiCTURE outputs with the PROTECTiO pipeline and estimated RNA off-target risk for each transcript showing tissue-specific expression. The analysis revealed differences among tissues: while the brain and ovaries exhibited relatively low off-target burden, the colon and lungs displayed relatively high risks. Our study provides a comprehensive frame-work for RNA off-target profiling, emphasizing the importance of advanced machine learning-based classifiers in CBE safety evaluations and offering valuable insights for the development of safer genome-editing therapies.
Understanding Telomere Biology in Hematopoietic Cell Transplantation: A Dynamical Systems Perspective
Authors: Toor Amir A. , Horton Morgan , Khalid Haniya , Krieger Elizabeth , Lai Tsung-Po , Spellman Stephen R. , Levine John E. , Saber Wael , Aviv Abraham , Stewart Valerie , Gadalla Shahinaz M
Published: January 2025

Background.

T cell proliferation and repertoire reconstitution is a hallmark of successful hematopoietic cell transplantation (HCT). This process may be modeled as a dynamical system and in such a system, precise telomere length (TL) measurement may reflect the proliferative capacity of donor T cells. TL for different chromosomes span a few orders of magnitude, and different T cell clones will display variable TL; these differences across the population are not represented when examining average TL. This study aims to develop a method that integrates the entire spectrum of TL observed within a sample to better understand the influence on clinical outcomes following HCT.

Methods.

To better reflect the entire span of TL , we used data generated using the TeLSA PCR technique that provided discrete measurments of individual telomeres for each DNA sample for 72 stem cell transplant (SCT) donor-recipient pairs. Donor and recipient TeSLA TL measurements was performed on samples taken before and 90 days post HCT, respectively. Set correspondence mathematical techniques and area under the curve (AUC) calculations were used to measured donor-recipient TL differences (delta-TL) incorporating the full distribution of measured TL from each sample.

Results.

Telomere band lengths ranged from 350 basepairs (BP) to 16.7 kilobases with a logarithmically declining distribution in all samples when arrayed in a descending order. Set correspondence methods yielded TL averages which were highly correlated with AUC calculations (r >0.9, p<0.001 for all) TheAUC delta-TLmethod predicted patient overall survival (P-log rank <0.0001). HCT recipients with intermediate degrees of telomere attrition (25th-75thpercentile) post-HCT experienced the best outcomes (2 years overall survival; OS=92%), whilst donors with the least (<25thpercentile; 2 years OS=33%; adjusted HRvs.intermediate shortening=9.3, p=0.001) and the greatest (>75thpercentile; 2 years OS=59%; adjusted HR=6.0, p=0.01) shortening had worse outcomes. By contrast, using the traditional method based on donor-recipient difference in TeSLA mean telomere length did not demonstrate survival association in this small sample set (p log-rank=0.95).

Conclusion.

The findings described herein suggest that the degree of donor telomere attrition may reflect T cell proliferation and alloreactivity following transplant. Accounting for the entire span of telomere lengths, could better identify post-transplant risk groups.
CAR T cell engineering impacts antigen-independent activation and co-inhibition
Authors: Stücheli Simon , Schultheiß Christoph , Schmidt-Barbo Paul , Zingg Andreas , Franz Natascha , Adamo Sarah , Fischer Claudia , Läubli Heinz , Binder Mascha
Published: January 2025

Viral vectors have successfully modified T cells to express chimeric antigen receptors (CAR), leading to clinical approvals. However, their high cost and regulatory challenges hinder rapid and broad clinical translation. Here, we demonstrate that our lentivirally (LV) manufactured R110-CAR T cells, targeting a leukemia neoepitope, can also be engineered using non-viral Sleeping Beauty (SB) transposition with minimal-sized DNA vectors. Flow cytometry and single-cell sequencing was used to compare the two production modes using healthy donor and CLL patient-derived T cells and a CD19-CAR T cell control. SB products were shifted towards CD8+subsets with expression of activation/co-inhibition markers (CD69, LAG-3, TIM-3) despite their naïve-like phenotype and lack of antigenic challenge. The CAR binding moiety modulated these patterns with R110-CAR T cells showing more aberrant phenotypes. Moreover, SB engineering resulted in inflammatory signatures along with RIG-I-like and TOLL-like nucleotide sensing potentially resulting from the transfection procedure. Patient-derived products showed significantly fewer CAR-expressing cells, reduced proliferation clusters, and lower T cell diversity, particularly with SB manufacturing, pointing at potential challenges with this method when engineering CLL T cells. Together, our data suggest that the engineering mode may substantially influence T cell properties and that these are further modulated by the CAR binding moiety and the type of T cell donor.
RAS-PI3K Pathway in CAFs Shapes Physicochemical Properties of Tumor ECM to Impact Tumor progression
Authors: Cuesta Cristina , Alcon-Perez Marta , Zheng Jie , Procel Nicole , Cota Rosa Ramirez , Fennema Dirk , Rosell Alejandro , Meson Diana Loa , Martinez-Castedo Belen , Arafat Youssef , Sanz-Fraile Hector , Rajeeve Vinothini , Alonso Diego , Hynds Robert E. , Swanton Charles , Alcaraz Jordi , Cutillas Pedro , Reyes-Aldasoro Constantino C , Wang Haiyun , Castellano Esther
Published: January 2025

Cancer-associated fibroblasts (CAFs) are key regulators of the tumor microenvironment, promoting tumor progression through extracellular matrix (ECM) remodeling and paracrine signaling, but the signaling pathways controlling CAF function remain incompletely defined. Here, we demonstrate that RAS-PI3K signaling plays a central role in CAF activation and ECM remodeling by promoting collagen crosslinking, fibronectin organization, and glycoprotein deposition at least partially through the activation of YAP. Disruption of RAS-PI3K interaction in CAFs leads to structurally and mechanically defective ECMs that impair tumor cell adhesion, migration, and proliferation. In vivo, fibroblast-specific deletion of RAS-PI3K reduces tumor burden in different models of KRAS-driven lung cancer, limits ECM deposition, and enhances the response to chemotherapy in lung adenocarcinoma models. These findings position RAS-PI3K signaling as a critical regulator of CAF function and ECM remodeling, highlighting a drug repurposing therapeutic strategy to disrupt tumor-stroma interactions and improve treatment outcomes.
Bulk segregant analysis reveals genomic regions associated with imidacloprid resistance in the Colorado potato beetle
Authors: Edison Alitha , Narimanov Nijat , Duchen Pablo , Xu Shuqing
Published: January 2025

Given the increased accessibility of genomic techniques, the speed of evolution of resistance, and the large number of genes involved in resistance, investigations into the genetic basis of resistance in more species are pertinent. Despite being an important agricultural pest, only a limited number of genetic mapping studies based on crossed populations have been performed to identify genes involved in resistance in the Colorado potato beetle (Leptinotarsa decemlineata, CPB). Here, we performed bulk segregant analysis on a mapping population generated by creating advanced intercross lines from five European strains of CPB. We identified eight peaks across chromosomes 1,8,10, and 16 involved in resistance against the neonicotinoid, imidacloprid. We identified 337 genes within these peaks and shortlisted three candidates based on gene expression and functional annotation. Among the three candidates thus identified, we found that an ABC transporter and a galactosyl transferase are expressed in relatively higher amounts in a relatively more susceptible strain than in a resistant strain. We attempted to validate the role of these two genes in insecticide resistance by knocking them down in a resistant strain using RNA interference (RNAi) and performing toxicity experiments. Surprisingly, our results showed that the activation of RNAi machinery reduced imidacloprid resistance and the effect is not specific to the tested candidate genes, which raised a concern on the suitability of using RNAi for validating insecticide resistance mechanisms in CPB.
STAT3 phosphorylation in the rheumatoid arthritis immunological synapse
Authors: Kotzer Hila Novak , Capera Jesusa , Jainarayanan Ashwin , Mayya Viveka , Zanin-Zhorov Alexandra , Valvo Salvatore , Macdonald Joanne , Taylor Peter C. , Dustin Michael L
Published: January 2025

Targeting the JAK/STAT pathway has emerged as a key therapeutic strategy for managing Rheumatoid Arthritis (RA). JAK inhibitors suppress cytokine-mediated signaling, including the critical IL-6/STAT3 axis, thereby effectively targeting different aspects of the pathological process. However, despite their clinical efficacy, a subset of RA patients remains refractory to JAK inhibition, underscoring the need for alternative approaches. Here, we identify a novel JAK-independent mechanism of STAT3 activation, which is triggered by the formation of the immunological synapse (IS) in naïve CD4+ T cells. Our data demonstrates that Lck mediates the TCR-dependent phosphorylation of STAT3 at the IS, highlighting this pathway as a previously unrecognized hallmark of early T cell activation. Furthermore, we show that the synaptic Lck/TCR-STAT3 pathway is compromised in RA. This discovery highlights a new therapeutic target for RA beyond JAK inhibitors, offering potential avenues for treating patients resistant to current therapies.