bluuebunny/crossref_metadata_2025 huggingface dataset:
Examining the feasibility of replacing ORF3a with fluorescent genes to construct SARS-CoV-2 reporter viruses
Authors: Webb Isobel , Erdmann Maximillian , Milligan Rachel , Savage Megan , Matthews David A. , Davidson Andrew D.
Published: February 2025

The SARS-CoV-2 genome encodes at least nine accessory proteins, including innate immune antagonist and putative viroporin ORF3a. ORF3a plays a role in many stages of the viral replication cycle, including immune modulation. We constructed two recombinant (r)SARS-CoV-2 viruses in which the ORF3a gene was replaced with mScarlet (mS) or mNeonGreen (mNG), denoted as rSARS-CoV-2-Δ3a-mS and rSARS-CoV-2-Δ3a-mNG, respectively. rSARS-CoV-2-Δ3a-mNG generated a fluorescent signal after infection in both A549-ACE-2-TMPRSS2 (AAT) and Vero-E6-TMPRSS2 (VTN) cells, unlike rSARS-CoV-2-Δ3a-mS. rSARS-CoV-2-Δ3a-mS mS protein could be detected immunologically in VTN but not AAT cells, indicating the expression of a non-fluorescent mS protein. The analysis of the viral transcriptomes in infected AAT cells by nanopore direct RNA sequencing (dRNAseq) revealed that the level of mS transcript was below the limit of detection in AAT cells. rSARS-CoV-2-Δ3a-mNG virus was found to be genetically stable in AAT and VTN cells, but rSARS-CoV-2-Δ3a-mS acquired partial deletions of the mS gene during sequential passaging in VTN cells, creating the virus rSARS-CoV-2-Δ3a-ΔmS. The mS deletion in VTN cells removes the chromophore coding sequence, and this may explain the presence of a non-fluorescent mS protein detected in VTN cells. The rSARS-CoV-2-Δ3a-mNG, rSARS-CoV-2-Δ3a-mS and rSARS-CoV-2-Δ3a-ΔmS viruses all replicated to a lower titre and produced smaller plaques than the parental rSARS-CoV-2-S-D614G. Interestingly, the rSARS-CoV-2-Δ3a-ΔmS virus produced higher virus titres and larger plaque sizes than rSARS-CoV-2-Δ3a-mS. This suggested that both the insertion of mS coding sequence and the deletion of ORF3a coding sequence contributed to attenuation. In comparison with rSARS-CoV-2, the rSARS-CoV-2-Δ3a-mS and rSARS-CoV-2-Δ3a-mNG viruses showed increased sensitivity to pre-treatment of cells with IFN-α but did not exhibit a dose-dependent increase in replication in the presence of the Janus kinase-signal transducer and activator of transcription signalling pathway inhibitor, ruxolitinib. In conclusion, the replacement of the ORF3a coding sequence with those of fluorescent reporter proteins attenuated the replication of SARS-CoV-2 and its ability to effectively evade the innate immune response in vitro.
Regional heterogeneity in the use of extracorporeal membrane oxygenation for heart transplant after 2018 allocation policy change
Authors: Schumer Erin M. , Endo Toyokazu , Wada Takuya , Schilling Joel D. , Kotkar Kunal D. , Faraz Masood M. , Pawale Amit
Published: February 2025

Background

The 2018 heart transplant allocation policy has changed the profile of patients receiving heart transplant, with an increased use of acute mechanical support and decreased use of durable left ventricular assist devices. We investigated the use of extracorporeal membrane oxygenation (ECMO) use pre- and post-allocation change.

Methods

Using the UNOS database, we identified adult patients who underwent heart transplant from January, 2006 - June, 2022. The study time period was divided into pre- and post-allocation change. We divided ECMO patients by region and analyzed change in the rate of ECMO use by region between eras. Differences between groups and survival comparison were analyzed.

Results

A total of 41,636 recipients were found, of which 891 (2.1%) were on ECMO at the time of transplant. Overall ECMO use increased from 231 (0.8%) to 660 (5.5%) between eras (p<0.001). There was significant regional variation in the rate of ECMO usage (p<0.001) and significant differences in postoperative dialysis (p=0.014) and acute rejection episodes (p<0.001). There was no significant difference in pacemaker rate (p=0.172), stroke (p=0.212), treatment for rejection within 1 year (p=0.358), or post-transplant survival in the current era between regions for patients on ECMO at the time of transplant (p=0.444).

Conclusion

There is increased utilization of ECMO following implementation of an allocation system which prioritizes ECMO recipients on the waitlist and thereis a differentialincrease in the use of ECMO in various regions. Further granular studies are needed to see which patients may benefit more from ECMO and what can be done to reduce post-transplant mortality from ECMO to transplant as it remains high before and after allocation change.
Exploiting Zeta potential of air borne pathogenic bacteria for effective air decontamination
Authors: Peketi Arun Sai Kumar , Sai Kushal Kumar SVL , Kennedy Kumar P , Pradeep Bulagonda Eswarappa
Published: February 2025

Background

Airborne microorganisms contribute significantly to hospital-associated infections (HAIs), particularly causing respiratory tract infections (RTIs). Multi-drug resistant (MDR) airborne pathogens pose a global clinical threat, challenging existing air decontamination technologies. While current methods effectively trap microbes, they often lack microbicidal properties. Exploitation of Zeta potential of microbes which are naturally charged could be a potential strategy for air decontamination, independent of their antimicrobial resistance. In this study, we tested the efficacy of ZeBox technology which relies on zeta potential to trap and eliminate airborne pathogens such as clinically isolated, MDRKlebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coliof respiratory origin and a non RTI isolateStaphylococcus aureus.

Methods

Five MDR bacterial pathogens which includeK. pneumoniae(2 nos),A. baumannii, P. aeruginosa, andE. colifrom patients with RTI and one pus isolate ofS. aureuswere included in the study. These isolates were aerosolized in a certified BSL-2 setting containing a ZeBox-powered Air Sterilization device. Viable bacteria were enumerated before and after exposure to the Zebox powered device. Clinical and laboratory isolated bacterial strains were assessed for zeta potential variations to understand its association with antibiotic resistance and pathogenicity.

Results

Our analyses revealed that Zeta potential is species specific, but independent of the pathogenicity and antibiotic susceptibility of the tested bacteria. Exposure to Zebox powered device for 5 mins resulted in a remarkable decline of microbial load with a minimum 5 log reduction (99.999%) of all the tested isolates, irrespective of their species. Zeta potential measurements further indicated a consistent killing mechanism of MDR pathogens by Zebox technology.

Conclusions

The current study underscores the reliability of zeta potential based air decontamination strategies for potential elimination of diverse, air borne MDR bacteria in healthcare settings.

Highlights

Zeta potential value of bacteria is not influenced by AST or pathogenicity of bacteria.

Zeta potential driven device traps and kills airborne MDR bacteria with 99.999% efficiency.

The efficacy of ZeBox technology is consistent across pathogens.
Genetic-epigenetic interactions (meQTLs) in orofacial clefts etiology
Authors: Machado-Paula LA , Romanowska J , Lie RT , Hovey L , Doolittle B , Awotoye W , Dunlay L , Xie XJ , Zeng E , Butali A , Marazita ML , Murray JC , Moreno-Uribe LM , Petrin AL
Published: February 2025

Objectives

Nonsyndromic orofacial clefts (OFCs) etiology involves multiple genetic and environmental factors with over 60 identified risk loci; however, they account for only a minority of the estimated risk. Epigenetic factors such as differential DNA methylation (DNAm) are also associated with OFCs risk and can alter risk for different cleft types and modify OFCs penetrance. DNAm is a covalent addition of a methyl (CH3) group to the nucleotide cytosine that can lead to changes in expression of the targeted gene. DNAm can be affected by environmental influences and genetic variation via methylation quantitative loci (meQTLs). We hypothesize that aberrant DNAm and the resulting alterations in gene expression play a key role in the etiology of OFCs, and that certain common genetic variants that affect OFCs risk do so by influencing DNAm.

Methods

We used genotype from 10 cleft-associated SNPs and genome-wide DNA methylation data (Illumina 450K array) for 409 cases with OFCs and 456 controls and identified 23 cleft-associated meQTLs. We then used an independent cohort of 362 cleft-discordant sib pairs for replication. We used methylation-specific qPCR to measure methylation levels of each CpG site and combined genotypic and methylation data for an interaction analysis of each SNP-CpG pair using the R package MatrixeQTL in a linear model. We also performed a Paired T-test to analyze differences in DNA methylation between each member of the sibling pairs.

Results

We replicated 9 meQTLs, showing interactions between rs13041247 (MAFB) - cg18347630 (PLCG1) (P=0.04); rs227731 (NOG) - cg08592707(PPM1E)(P=0.01); rs227731 (NOG) - cg10303698 (CUEDC1) (P=0.001); rs3758249 (FOXE1) - cg20308679 (FRZB) (P=0.04); rs8001641 (SPRY2) - cg19191560 (LGR4) (P=0.04); rs987525(8q24) - cg16561172(MYC) (P=0.00000963); rs7590268(THADA) - cg06873343 (TTYH3) (P=0.04); rs7078160 (VAX1) - cg09487139 (P=0.05); rs560426 (ABCA4/ARHGAP29) - cg25196715 (ABCA4/ARHGAP29) (P=0,03). Paired T-test showed significant differences for cg06873343 (TTYH3) (P=0.04); cg17103269 (LPIN3) (P=0.002), and cg19191560 (LGR4) (P=0.05).

Conclusions

Our results confirm previous evidence that some of the common non-coding variants detected through GWAS studies can influence the risk of OFCs via epigenetic mechanisms, such as DNAm, which can ultimately affect and regulate gene expression. Given the large prevalence of non-coding SNPs in most OFCs genome wide association studies, our findings can potentially address major knowledge gaps, like missing heritability, reduced penetrance, and variable expressivity associated with OFCs phenotypes.
Multimodal predictors of functional and cognitive decline in relapsing-remitting multiple sclerosis
Authors: Korbmacher Max , Lie Ingrid Anne , Wesnes Kristin , Westman Eric , Espeseth Thomas , Specht Karsten , Andreassen Ole A. , Westlye Lars T. , Wergeland Stig , Myhr Kjell-Morten , Torkildsen Øivind , Høgestøl Einar A.
Published: February 2025

The underlying mechanisms for neurodegeneration in multiple sclerosis are complex and incompletely understood. Multivariate and multimodal investigations integrating demographic, clinical, multi-omics, and neuroimaging data provide opportunities for nuanced analyses, aimed to define disease progression markers. We used data from a 12-year longitudinal cohort of 88 people with multiple sclerosis, to test the predictive value of multi-omics, MRI, clinical examinations, self-reports on quality of life, demographics, and general health-related variables for future functional and cognitive disability. Progressive functional loss beyond an Expanded Disability Status Scale score≥4 was used to define a functional loss group. A cognitive decline group was defined by a ≥25% decrease from the maximum (cognitive) Paced Auditory Serial Addition Test score. We used a multiverse approach to identify which baseline variables were most predictive for functional and cognitive loss group memberships, independent of analysis bias.

We identified several factors predicting an increased risk of future functional loss (FLG) and cognitive decline groups (CDG) within the next 12 years from baseline: functional score (0-10, median Odds Ratio per baseline unit increase [mORFLG=2.15±0.51; mORCDG=2.46±1.60]), cognitive scores (1-60 [mORFLG=0.98±0.03; mORCDG=0.91±0.06]), the number of previous relapses [mORFLG=1.56±0.26; mORCDG=1.44±0.60], serum vitamin A levels (umol/l [mORFLG=0.92±0.06; mORCDG=0.33±0.36]), self-reported mental health (1-100 [mORFLG=0.96±0.02; mORCDG=0.91±0.09]) and physical functioning (1-100 [mORFLG=0.99±0.01; mORCDG=0.97±0.03]). Our results suggest that clinical assessment of physical function and cognition, self-reported mental health, and potentially vitamin A levels are the best predictors for risk-group stratifications of people with MS at baseline. While these findings are promising, we also want to underscore the observed analysis-choice induced variability which necessitates both an increase in transparency when reporting study findings as well as strategies which are robust to the many researcher degrees of freedom.
Acoustofluidic patterning for improved microtissue histology
Authors: Deshmukh Dhananjay V. , Vuille-dit-Bille Emilie , Joshi Saumitra , Gerber Nicola , Fux Christine , Eichenberger Annina , Bono Epifania , Rimann Markus , Heub Sarah , Migliozzi Daniel , Boder-Pasche Stephanie , Weder Gilles , Dual Jurg , Tibbitt Mark W.
Published: February 2025

Microtissues (such as organoids or spheroids) are useful to model healthy or diseased human tissues and organs, with application in drug testing, tissue engineering, and personalized medicine. To characterize their morphology and phenotype, microtissues are often monitored using histology and high-resolution imaging. While this technique is well-established and standard for macroscopic tissue sections, it remains challenging to execute and has low throughput in the context of these sub-millimeter structures, mainly due to the fact that their size makes them difficult to locate within the embedding medium. To enhance the efficiency of microtissue histology, we developed an acoustofluidic device that arranges microtissues in a coplanar arrangement within HistoGel, a widely used embedding medium. Pre-patterning microtissues within HistoGel streamlines downstream processing by positioning the centers of mass of the microtissues at a pre-defined plan in the sample, simplifying sectioning, labeling, and imaging. We validated the method using differently sized HepG2 microtissues and tumor microtissues from osteosarcoma cells (Saos-2, MG-63, HOS), demonstrating that this method can be applied to different microtissue shapes, sizes, and types, without modifying established post-processing techniques. Our approach substantially enhances the microtissue histology workflow and broadens possibilities for microtissue analysis.
Physical Activity, Symptoms, Quality of Life and Exercise Program Preferences in People with Chronic Lymphocytic Leukemia
Authors: Miles Ellie E. , Nicol Jennifer L. , Fowler Hatti , Roberts Amelia , Hulton Andrew T. , Jeary Caitlin , Walewska Renata , Iyengar Sunil , Hanson Erik D. ,   CLL Support Association, Sitlinger Andrea , Bartlett David B.
Published: February 2025

Background

Chronic lymphocytic leukaemia (CLL) has a heterogeneous lifelong course. Most patients experience significant symptoms which negatively impact their quality of life (QoL). Although physical activity and exercise may help manage symptoms, it is unclear what disease-related factors drive physical inactivity in people with CLL.

Methods

This study explored physical activity in CLL and assessed relationships in treatment stage, symptoms, quality of life, and preferences for physical activity using an online questionnaire.

Results

128 individuals with CLL (66M/62F) completed the questionnaire. Treated CLL (N=55) exhibited worse QoL (p=0.018) and lower engagement in physical activity (p=0.045) compared to treatment naïve (N=73). Both groups reported high fatigue (∼77%) and insomnia (∼55%) which were associated with less likelihood of being physically active. Physically active participants reported better QoL (p=0.020), physical functioning (P=0.003) and role functioning (p=0.020) as well as lower levels of fatigue (p=0.036), pain (p=0.017) and symptom burden (p=0.026). Although 79% of respondents wanted to engage in exercise programs for their CLL, 70% reported never receiving exercise guidance from their healthcare professionals.

Conclusion

Findings highlight a significant need for interventions to increase physical activity in people with CLL. Furthermore, there is considerable interest from the CLL community in receiving exercise guidance.
Hierarchical Clustering with an Ensemble of Principle Component Trees for Interpretable Patient Stratification
Authors: Pfeifer Bastian , Bloice Marcus D. , Sirocchi Christel , Loecher Markus
Published: February 2025

Patient stratification plays a crucial role in personalized medicine by identifying distinct subgroups of patients based on their molecular and/or clinical characteristics. However, many unsupervised machine learning-based stratification techniques fail to identify the essential biomarker traits associated with each patient group. In this paper, we present a novel approach for interpretable patient stratification using hierarchical ensemble clustering. Our method leverages feature sampling in conjunction with principal component analysis (PCA) to capture the most significant patterns and contributing biomarkers. We demonstrate the effectiveness of our approach using machine learning benchmark datasets and real-world data from The Cancer Genome Atlas (TCGA), showcasing the improved interpretability of the detected patient clusters.
Minding the Gap in Sentinel Surveillance Networks: An Analysis of Brazilian Indigenous Areas
Authors: Oliveira Juliane F. , Vasconcelos Adriano O. , Alencar Andrêza L. , Cunha Maria Célia L. S. , Marcilio Izabel , Barral-Netto Manoel , Ramos Pablo Ivan P.
Published: February 2025

Background

Optimizing the allocation of sentinel surveillance sites, particularly aiming early pathogen detection, remains a persistent challenge. Equally critical is ensuring the inclusion of vulnerable and often underserved populations as targets when prioritizing surveillance sites.

Objective

This study assesses the current coverage of the respiratory pathogen surveillance network in Brazil and proposes an optimized rearrangement of sentinel locations that balance the coverage of Indigenous populations while integrating country-wide human mobility patterns.

Methods

We collected the locations of Indigenous populations living in Special Indigenous Sanitary Districts (DSEIs) from the Brazilian Ministry of Health, and derived mobility route estimates using the Ford-Fulkerson algorithm applied to input air, road, and water transportation data for the whole country. To optimize sentinel city selection for sample collection, we applied a linear optimization algorithm designed to maximize two key objectives: 1) representation of Indigenous regions and 2) coverage of human mobility patterns, thereby enhancing early pathogen detection. Validation of the strategy was performed by obtaining the current list of cities in Brazil’s influenza sentinel network combined with a health attraction index from the Brazilian Institute of Geography and Statistics, which enabled us to assess the suitability and potential benefits of our optimized surveillance network.

Results

Our optimization model provides actionable recommendations for pathogen sampling locations, enhancing early detection. By selecting 199 cities, we create a more representative sentinel network, covering all DSEIs by rearranging 108 cities (58.3%), addressing gaps in 9 of 34 previously uncovered regions. This improves nationwide mobility coverage by 16.8 percentage points—from 52.4% to 69.2%—compared to Brazil’s current sentinel system. Additionally, all newly selected cities serve as hubs for medium to high-complexity healthcare, with 37.9% of DSEI cities lacking coverage in the existing flu sentinel network.

Conclusions

We propose a strategic framework for sentinel site placement that maximizes DSEI coverage and aligns with human mobility patterns across Brazil, improving the overall effectiveness of disease surveillance, particularly in these critical regions and often underserved populations.
Physical Activity Phenotypes in Endometriosis Using Unsupervised Learning via Functional Mixture Models
Authors: Tricoche Bryan T. , Caceres Billy A. , Shaw Leslee , Garber Carol Ewing , Konigorski Stefan , Kolli Sahiti , Fuchs Thomas , Ensari Ipek
Published: February 2025

Introduction

Endometriosis is a chronic condition associated with severe pelvic pain, dysmenorrhea, infertility, and worsening quality of life. Regular physical activity (PA) is effective for pain management and reducing chronic disease symptoms, yet individuals with endometriosis are more likely to be insufficiently active. This study aims to investigate latent profiles of daily PA trajectories in this population via clustering.

Methods

The study sample included 173 adults (4,895 person-level days) with a confirmed diagnosis of endometriosis enrolled in theAll of Us Research Program. PA data was collected from participants using Fitbit wrist-worn trackers. We used 30 consecutive days of data from each individual, allowing up to 10 days of missingness (which were imputed using multiple imputed chained equations). Functional mixture models (FMMs) identified latent PA trajectory clusters using daily step counts as the clustering variable. The optimal number of clusters was determined using the Bayesian information criterion (BIC).

Results

The best-fitting FMM identified K=4 distinct clusters (BICK=4= –11884.442, BICK=3= –11892.236, BICK=5= –11907.917). TheHigh Activephenotype exhibited the highest volume and variability of step counts over the sample period (Mean = 12777.0, SD=5248.2) as well as the highest volume of moderate-to-vigorous PA (MVPA) minutes (Mean = 70.8). TheHigh Moderatephenotype exhibited the second highest volume and variability of step counts (Mean = 9125.4, SD = 3631.0) and second highest MVPA minutes. TheLow Moderatephenotype exhibited the second lowest volume and variability of step counts (Mean = 6067.5, SD =2797.0) and the second lowest MVPA minutes (Mean = 24.3). TheInsufficiently Activecluster exhibited the lowest volume and variability of step counts (Mean = 4235.7, SD = 2174.7) and the lowest MVPA (Mean = 16.1).

Conclusion

This is the first study to investigate and report distinct PA profiles among a national sample of individuals living with endometriosis, and via objectively estimated PA data. Identifying distinct clusters of PA patterns in endometriosis based on within– and between individual PA variance may help identify those at risk and inform the development of personalized interventions to promote PA and improve overall health outcomes.
Plant plasticity in the face of climate change – CO2offsetting effects to warming and water deficit in wheat. A review
Authors: Gawinowski Meije , Chenu Karine , Deswarte Jean-Charles , Launay Marie , Bancal Marie-Odile
Published: February 2025

Future crop production will depend on plant plasticity in response to increases in atmospheric CO2, mean temperature, heatwave and drought events. The present review intends to highlight the impact of interactions between high CO2levels, warming and water deficit in existing published experimental data in the case of wheat. To do so, we identified experiments quantifying the effects of such interactions on traits related to crop productivity and water use. We used the collected data to estimate plasticity indices assessing compensation and interaction between elevated CO2 and adverse climatic conditions, bringing a new perspective on the matter. In the studied data, even though there is an important variability, we found that crop productivity tends to decrease despite the positive effects of the rise in CO2concentration. Conversely, with elevated CO2, water consumption tends to decrease despite the warmer conditions. We hypothesized that the positive effect of CO2on crop productivity is greater under drought conditions, which is confirmed in 54% of the experiments. This review highlights the need to acquire further experimental data under possible future conditions to calibrate and validate crop models: their range of validity requires more thorough testing under the wide range of projected environmental conditions.
Evaluating Transcriptomic Integration for Cyanobacterial Constraint-based Metabolic Modelling
Authors: Pugsley Thomas , Hanke Guy , Duffy Christopher Daniel Patrick
Published: February 2025

1

Metabolic modelling has wide-ranging applications, including for the production of high-value compounds, understanding complex disease and analysing community interactions. Integrating transcriptomic data with genome-scale metabolic models is crucial for deepening our understanding of complex biological systems, as it enables the development of models tailored to specific conditions, such as particular tissues, environments, or experimental setups. Relatively little attention has been given to the assessment of such integration methods in predicting intracellular fluxes. While a few validation studies offer some insights, their scope remains limited, particularly for organisms like cyanobacteria, for which little metabolic flux data are available. Cyanobacteria hold significant biotechnological potential due to their ability to synthesize a wide range of high-value compounds with minimal resource inputs [21]. The impact of specific methodological decisions on integration, however, has scarcely been assessed beyond human models, with no thorough exploration of parameter choices in valve-based integration methods. By implementing a novel analysis pipeline, we evaluated these methodological decisions using the genome-scale model forSynechocystissp. PCC 6803 (iSynCJ816 [17]) with existing transcriptomic data in biomass-optimised scenarios. Our analyses indicate that selecting an appropriate integration method may not always be straightforward and depends on the initial model configuration - a factor which is often overlooked during integration. By evaluating sets of methods, we identified a trade-off between the buffering of light into the system and maintenance of flux near system boundaries. We suggest that the use of the lazy-step mapping function with importance-based scaling results in the best predictions, particularly when these can be validated with experimental data. When using one-size-fits-all scaling with the lazy-step mapping function, it appears preferable to use light buffering to avoid inappropriate bound changes near the photosystems, a factor which importance-based scaling may help to compensate for. In cases where no experimental data can be used for validation, the novel thresholding approach could be adopted as this showed some improvements upon the standard Lazy method.
ERGA-BGE genome ofCoenonympha oedippus: an IUCN endangered European butterfly species occurring in two ecotypes
Authors: Čelik Tatjana , Lokovšek Tjaša , Bužan Elena , Böhne Astrid , Monteiro Rita , Fernández Rosa , Escudero Nuria , Gut Marta , Aguilera Laura , Ferreira Francisco Câmara , Cruz Fernando , Gómez-Garrido Jèssica , Alioto Tyler S. , Bortoluzzi Chiara
Published: February 2025

The reference genome of the false ringlet (Coenonympha oedippus) will serve as a valuable resource for uncovering the genetic mechanism underlying the species′ adaptability to two ecologically distinct habitats. Through this genome we might be able to determine whether (i) each ecotype is monophyletic, indicating that the ecological divergence represents an early stage of speciation, (ii) the ecotypes have evolved through divergent evolution of habitat preference, or (iii) the differences between ecotypes are solely due to phenotypic plasticity or epigenetic variation. This reference genome is also a prerequisite for the planning, design, and implementation of conservation measures for this endangered species, taking into account its intraspecific diversity. Furthermore, it holds broader implications for population genomic studies of the species-rich genusCoenonympha, which includes some of the most endangered butterfly taxa in Europe. The complete genome sequence was assembled into 30 contiguous chromosomal pseudomolecules (sex chromosomes included). This chromosome-level assembly encompasses 0.39 Gb, composed of 385 contigs and 62 scaffolds, with contig and scaffold N50 values of 2.8 Mb and 14.2 Mb, respectively.
Asymmetric nature of MscL opening revealed by molecular dynamics simulations
Authors: Rogacheva Olga N. , Kopec Wojciech
Published: February 2025

We employed all-atom unbiased molecular dynamics to simulate the L17A, V21A mutant of MscL. Under a tension of 30 mN/m, the closed state adopts a funnel-like conformation. Subsequently, five chains of MscL undergo sequential transitions, leading to the formation of the asymmetric states (S1, S2, etc.). After the first chain crossed the barrier, the next transition favors the neighboring clockwise chain. This study focuses on the S1 state. Within its "open" fragment, this state is similar to the expanded state of M. acetivorans MscL, and has a conductance 10 times lower than the open state. We applied committor analysis and a nonlinear regression model to construct a reaction coordinate for the transition between the closed and the S1 state as a linear combination of interatomic distances and contacts. The main contributions to the reaction coordinate are: 1) the disruption of the "cytoplasmic" contact sites between the considered chain and two adjacent chains 2) the delipidation of the lipid-binding pocket, formed by the I82, V86, and V22 residues. The result is the pulling of the considered chain via the "cytoplasmic" tension sensor. The free energy profile along the reaction coordinate was calculated using the umbrella sampling approach. The S1 state is approximately 5 kJ/mol more favorable than the closed state under tension, and the height of the free energy barrier for the transition towards the S1 state is approximately 10 kJ/mol. This barrier is in a reasonable agreement with the corresponding average transition time, estimated to be 133 ± 13 ns.

Abstract Figure
Presaccadic modulation of lateral interactions
Authors: Mueller de Melo Gabriela , de Oliveira Pitorri Isabella , Rohenkohl Gustavo
Published: February 2025

Lateral interactions are pervasive in early visual processing, contributing directly to processes such as object grouping and segregation. This study examines whether saccade preparation - known to affect visual perception - modulates lateral interactions. In a psychophysical task, participants were instructed to detect a Gabor target flanked by two adjacent Gabors, while they either prepared a saccade to the target or maintained central fixation. Flanker gratings could be iso- or orthogonally oriented to the target and were positioned at three different distances (4λ,8λ, and 16λ). Contrast thresholds for target detection were estimated in each condition using a 3-down/1-up staircase procedure. The results showed that in both presaccadic and fixation conditions, the target was suppressed at the shortest flanker distance (4λ), revealed by markedly higher thresholds in iso-oriented compared to orthogonal flanker configurations. Lateral interaction effects were completely abolished at their largest separation (16λ. Interestingly, at the intermediate flanker distance (8λ), we observed an increase in suppression of targets presented during the presaccadic period, but not in the fixation condition. This result suggests that saccade preparation can modulate lateral interactions, promoting suppressive effects over larger distances. These findings are consistent with the visual remapping phenomenon observed before saccade execution, especially the convergent remapping of receptive fields in oculomotor and visual areas. Finally, this presaccadic expansion of inhibitory lateral interactions could assist target selection by suppressing homogeneous peripheral signals - such as iso-oriented collinear patterns - while prioritizing the processing of more salient visual information.
In pemphigus, cell detachment, but not autoantibody binding, induces cell-wide, long-lasting transcriptomic and proteomic changes
Authors: Hartmann Veronika , Guo Sen , Rahimi Siavash , Radine Uta , Malheiros Danielle , Salviano-Silva Amanda , Bumiller-Bini Hoch Valeria , Cipolla Gabriel A. , Calonga-Solis Veronica , Künstner Axel , Burmester Imke , Ludwig Ralf J. , Hariton William V.J. , Hammers Christoph M. , Müller Eliane J. , Busch Hauke , Hundt Jennifer E.
Published: February 2025

Desmoglein 1 (DSG1) and desmoglein 3 (DSG3) are adhesion molecules that maintain intercellular connections between epidermal, hair follicle, and mucosal keratinocytes. Autoantibodies (AAbs) targeting these molecules ultimately lead to the blister formation characteristic of pemphigus vulgaris (PV) or pemphigus foliaceus (PF). To investigate the molecular events following autoantibody binding up to 48 hours, we quantified transcriptome and proteome dynamics during split formation in a human skin organ culture (HSOC) model for PV and in a 2D cell-culture model for PV and endemic PF. Treatment of the cells in 2D culture with PX43, a single-chain variable fragment targeting DSG1/3, or with endemic PF anti-DSG1 IgG yielded neither a significant transcriptome nor a proteome response over time relative to the respective IgG controls. When treating the HSOC model with mouse antibody AK23 (targeting DSG3) or with PX43, only the latter induced split formation. In the absence of split formation, no differentially regulated pathways were detected at the transcriptomic level. Split formation, observed as early as 5 hours post-injection, was associated with significant and sustained upregulation of IFNγ and TNFα-related genes, mediated by upstream NFκB, MAPK, and JAK-STAT pathways. The gene expression changes, corroborated by proteomics data, were strongly correlated with early wounding and keratinocyte detachment, as well as the transcriptome profile in the skin from PV patients, while inversely associated with keratinocyte differentiation and cell stretching. The co-occurrence of well-wide and long-lasting transcriptome and proteome responses with split formation suggests that PF-IgG and PV-related AAbs neither induce downstream transcriptome nor proteome changes directly. Rather, these changes appear to be secondary effects resulting from reduced adhesion and mechanical-stress-induced split formation of keratinocytesin vitroand most likely in patient skinin vivo.
Induction of Chimera States in Hindmarsh-Rose Neurons through Astrocytic Modulation: Implications for Learning Mechanisms
Authors: Azad Fatemeh , Shouraki Saeed Bagheri , Nazari Soheila , Chan Mansun
Published: February 2025

Chimera states, a form of partial synchronization in neural networks, are characterized by the coexistence of synchronized and asynchronous regions. These states are crucial for various cognitive functions, such as learning and information processing. Conversely, abnormal synchronization—often referred to as hyper-synchronization—can lead to pathological conditions such as epilepsy and Parkinson’s disease. Understanding the mechanisms underlying synchronization can provide valuable insights for developing effective therapeutic strategies for these disorders. Astrocyte, a primary type of glial cell, plays a pivotal role in modulating neural synchrony. They influence the synchronization threshold of neurons by providing feedback through the release of gliotransmitters, promoting group firing of neurons within the astrocyte’s domain. This research aims to explore how astrocytes can facilitate the conversion of hyper-synchronized states into healthy chimera states within neural networks. This process is vital for maintaining normal brain function and may be critical to advancing treatments for neurological conditions. We analyzed how astrocytes can induce chimera states in nonlocally two-dimensional Hindmarsh-Rose neurons, which serve as realistic models of neuronal ensembles. Our findings demonstrate that astrocytes can effectively transition unhealthy hyper-synchronization states into healthy chimera states. Furthermore, by analyzing time spans, spatiotemporal patterns, inter-spike interval distributions (ISI), and phase plane diagrams of 2D H-R neurons, we validated our hypothesis about the crucial role of astrocytes in the development of chimera states. The outcomes may pave the way for innovative therapeutic approaches to restore normal neural activity patterns, ultimately improving patient outcomes in conditions such as epilepsy and Parkinson’s disease.
Do Language Models Think Like Doctors?
Authors: McCoy Liam G. , Swamy Rajiv , Sagar Nidhish , Wang Minjia , Cao James , Bacchi Stephen , Fong Nigel , Tan Nigel CK , Tan Kevin , Buckley Thomas A. , Brodeur Peter , Celi Leo Anthony , Manrai Arjun , Humbert Aloysius , Rodman Adam
Published: February 2025

Background

While large language models (LLMs) are being increasingly deployed for clinical decision support, existing evaluation methods like medical licensing exams fail to capture critical aspects of clinical reasoning including reasoning in dynamic clinical circumstances. Script Concordance Testing (SCT), a decades-old medical assessment tool, offers a nuanced way to assess how new information influences diagnostic and therapeutic decisions under uncertainty.

Methods

We developed a comprehensive and publicly available benchmark comprising 750 SCT questions from 10 internationally diverse medical datasets—9 previously unreleased—spanning multiple specialties and institutions. Each question presents a clinical scenario then asks how new information affects the likelihood of a diagnosis or management decision, scored against expert panels (Figure 1). We evaluated four state-of-the-art LLMs against the combined responses of 1070 medical students, 193 resident physicians, and 300 attending physicians in total across all datasets.

Results

LLMs demonstrated markedly lower performance on SCTs compared to their typical achievement on medical multiple choice benchmarks. GPT-4o achieved the highest performance (63.6% ± 1.2%), significantly outperforming other models (Claude-3.5 Sonnet: 58.8% ± 1.2%, o1-preview: 58.5% ± 1.3%, Gemini-1.5-Pro: 54.4% ± 1.4%). Models matched or exceeded student performance on multiple examinations, but did not reach the level of senior residents or attending physicians (Figure 2). Surprisingly, the integrated-chain-of-thought o1-preview model underperformed compared to GPT-4o, a contrast with their relative performance on other medical benchmarks.

Conclusions

SCT represents a challenging and distinctive benchmark for evaluating LLM clinical reasoning capabilities, revealing limitations not apparent in traditional MCQ-based assessments. This work demonstrates the value of SCT in providing a more nuanced evaluation of medical AI systems and highlights specific areas where current models may fall short in clinical reasoning tasks. We are making our benchmark publicly available in a secure format to foster collaborative improvement of clinical reasoning capabilities in LLMs.

Brief Summary

While large language models excel at traditional medical knowledge tests, their performance on our new public Script Concordance Test benchmark reveals important limitations in clinical reasoning capabilities, particularly in processing new information under uncertainty.
A Delphi Process to Determine the Bellwether Procedures for Trauma Systems Globally: A Study Protocol
Authors: Bath MF , Edmiston T , Amoako J , Ratnayake A , Bagaria D , Menon R , Wohlgemut J , McKenna M , Bateman K , Hancorn K , Shepherd J , Yoong S , Hobbs L , Smith BG , Whiffin C , Hardcastle TC , Morris A Conway , Weiser T , Bashford T
Published: February 2025

Introduction

Traumatic injuries are responsible for a huge amount of mortality, morbidity, and disability globally. Within global surgery, Bellwether procedures have previously been identified to measure the surgical proficiency of a hospital or a region, however traumatic injuries often have distinct epidemiological and demographic patterns, compared to routine surgical care. Using a focused set of procedures or processes to measure trauma performance could allow for improved trauma assessments and outcomes on a global scale.

Methodology

An international Delphi study will be conducted in attempt gain consensus on the optimal procedures and processes that can be used to assess the performance of trauma care within any region or hospital worldwide. Recognised guidelines for conducting the Delphi process will be followed, comprising of 3 separate rounds and participation from a public and patient involvement (PPI) group. Respondents will be identified through pre-existing collaborative networks and research partners, to ensure adequate global representation from across the trauma care pathway. The final Bellwether procedures will be those that have shown consensus in agreement and in stability throughout successive rounds

Discussion

This Delphi process aims to identify the optimal Bellwether metrics that could be used to assess trauma care worldwide. Using a focused set of procedures or processes to assess trauma performance globally will reduce complexity and improve ease of use compared to current methods.
Identification of V0g propriospinal neurons and their role in locomotor control
Authors: Toscano Elisa , Giomi Maddalena , Evtushenko Nadezhda , Santuz Alessandro , Lowenstein Elijah David , Birchmeier Carmen , Zampieri Niccolò
Published: February 2025

Propriospinal neurons relay sensory and motor information across the spinal cord and are critical components of the circuits coordinating body movements. Their diversity and roles in motor control are not clearly defined yet. In this study, by combining anatomical, molecular, and functional analyses in mice, we identified and characterized an ascending subtype of propriospinal neurons belonging to the Pitx2+V0 family of spinal neurons. We found that Pitx2+ascending neurons are integrated in spinal sensorimotor circuits and their function is important for the execution of precise limb movements required for effectively moving in challenging environments, like walking on a horizontal ladder or a balance beam. This work advances our understanding of the functional organization of propriospinal and V0 neurons, highlighting a previously unappreciated role in adjusting body movements to the more demanding needs of skilled locomotor tasks.
Differential Roles of Broadly Expressed Transcription Factors in Early Cardiac Cell Specification
Authors: Abbasi Shiva , Chrysostomou Evangelia , Tegousis Georgios , Espinosa Oscar Villasana , Conley Rie , Koromila Theodora
Published: February 2025

All developmental processes are well-orchestrated and coordinated by numerous developmentally associated genes that determine the various cell fates and tissue differentiation. The transcriptional regulation early in life is extremely dynamic and the genes implicated at those early time points work cooperatively forming multi-directional gene networks, which remain a subject of ongoing research attempting to describe their mechanisms. Previous studies have shown the gene regulation dynamics in cardiac cells, after gastrulation, but these regulatory events remained unclear before the onset of gastrulation. In this study, we focused on the role of Odd-paired (Opa/ZIC3) and Suppressor of Hairless (Su(H)/RBPJ), in regulating cardiac genes before the onset of gastrulation. Our results showed that unlike the non-significant changes in expression levels between nc14C and nc14D in Opa knockdown embryos, expression patterns were changed. Additionally, our results showed that Opa regulatesslpandoddbefore gastrulation, which confirms our hypothesis of Opa regulating important genes for cardiac cell specification during cellularization. Our findings suggested that, in low levels of Opa, Su(H) inhibits Opa activity, but at later stages, when Opa levels are elevated, Opa overcomes Su(H) repressing role and acts as an activator. These observations enhance our understanding of cell specification and may offer insights into how this regulatory mechanism influences the onset of cardiac impairments by disrupting key cardiac target genes.
Motivational control is implemented by a cingulo-prefrontal pathway
Authors: Gandaux Clémence , Sallet Jérôme , Amiez Céline , Autran-Clavagnier Delphine , Morel-Latour Valentine , Goussi-Denjean Clément , Fontanier Vincent , Misery Pierre , Lamy Camille , Lamberton Frank , Lavigne Marina , Kremer Eric J. , Wilson Charles.R. E. , Procyk Emmanuel
Published: February 2025

The neuronal connections between the midcingulate cortex (MCC) and the dorsolateral prefrontal cortex (dlPFC) are associated with multiple cognitive functions, including rapid and long-term adaptive processes. Here we show that DREADD-mediated activation of MCC to dlPFC projection in macaques led to increased engagement in a foraging task, but did not alter their trial-to-trial adaptive strategy. We conclude that a critical role for MCC-dlPFC pathway is in the temporally extended control of behaviour rather than in rapid adaptation.
Effects of treadmill exercise on retinal vascular morphology, function, and circulating immune factors in a mouse model of retinal degeneration
Authors: Haupt Hayden B. , Nickerson John M. , Boatright Jeffrey H. , Pardue Machelle T. , Bales Katie L.
Published: February 2025

Purpose

Exercise is neuroprotective in rodents undergoing retinal degeneration (RD). However, the effects of exercise on retinal vasculature remain unexplored. Here, we investigate whether treadmill exercise influences retinal vascular morphology, function, gene expression, and circulating factors in a light-induced retinal degeneration (LIRD) mouse model.

Methods

6-week-old female BALB/c mice were assigned to inactive+dim, active+dim, inactive+LIRD and active+LIRD groups (n=20 per group). Active mice were treadmill exercised (1hr/d 10m/min) for two weeks, then LIRD was induced (5000 lux/4hrs). Inactive mice were placed on a static treadmill. Retinal neurovascular coupling was measured with functional hyperemia (FH) and vascular morphology using OCT-A. Vascular gene expression was quantified from isolated retinal endothelial cells using ddPCR five days following LIRD. Serum was collected for circulating cytokine and chemokine analyses. Data were analyzed using 2-way ANOVA.

Results

Retinal vessel vasodilation was significantly increased in active+LIRD mice compared to inactive+LIRD mice. Superficial and intermediate/deep vascular plexi from inactive+LIRD mice had significantly decreased vessel density and total vessel length, with increased numbers of end points and lacunarity compared to active groups. Isolated retinal endothelial cell gene expression varied among groups. Most notably, Active+LIRD mice had a distinct immune response profile, with increased expression of IL-6, KC, and VEGF-A.

Conclusions

Treadmill exercise maintained retinal vascular morphology and function, modestly altered endothelial gene expression, and is associated with a specific circulating immune response profile in a LIRD mouse model. These data indicate therapeutic effects of exercise on retinal vasculature in RD.
CD47 prevents Rac-mediated phagocytosis through Vav1 dephosphorylation
Authors: Miller Wyatt D , Mishra Abhinava K , Sheedy Connor J , Bond Annalise , Gardner Brooke M , Montell Denise J , Morrissey Meghan A
Published: February 2025

CD47 is expressed by viable cells to protect against phagocytosis. CD47 is recognized by SIRPα, an inhibitory receptor expressed by macrophages and other myeloid cells. Activated SIRPα recruits SHP-1 and SHP-2 phosphatases but the inhibitory signaling cascade downstream of these phosphatases is not clear. In this study, we used time lapse imaging to measure how CD47 impacts the kinetics of phagocytosis. We found that targets with IgG antibodies were primarily phagocytosed through a Rac-based reaching mechanism. Targets also containing CD47 were only phagocytosed through a less frequent Rho-based sinking mechanism. Hyperactivating Rac2 eliminated the suppressive effect of CD47, suggesting that CD47 prevents activation of Rac and reaching phagocytosis. During IgG-mediated phagocytosis, the tyrosine kinase Syk phosphorylates the GEF Vav, which then activates the GTPase Rac to drive F-actin rearrangement and target internalization. CD47 inhibited Vav1 phosphorylation without impacting Vav1 recruitment to the phagocytic synapse or Syk phosphorylation. Macrophages expressing a hyperactive Vav1 were no longer sensitive to CD47. Together this data suggests that Vav1 is a key target of the CD47 signaling pathway.