bluuebunny/crossref_metadata_2025 huggingface dataset:
Respiratory virus genomic epidemiology during post-pandemic re-emergence of influenza in Australia
Authors: Rockett Rebecca J , Agius Jessica E , Chandra Shona , Fong Winkie , Aziz Ammar , Suster Carl JE , Basile Kerri , Lam Connie , Chen Sharon CA , Dwyer Dominic E , Kok Jen , Sullivan Sheena G , Barr Ian G , Sintchenko Vitali , Golubchik Tanya
Published: February 2025

Simultaneous genomic sequencing of multiple respiratory pathogens from clinical samples can provide real-time data on viral evolution, co-circulation and co-infection during seasonal epidemics. Influenza is a major global respiratory pathogen, with a mature genomic epidemiology framework, that has yet to be integrated with genomic surveillance of other co-circulating respiratory viruses. Leveraging existing well-integrated community influenza sampling during the first major Australian winter influenza season after the lifting of the COVID-19 pandemic restrictions in 2022, we examined the genomic epidemiology of influenza alongside co-infections of common human respiratory viruses. Using a commercial respiratory viral sequencing method, Respiratory Virus Oligo Panel (RVOP, Illumina), we recovered full-length human influenza A genomes from 75% (117/157) of samples with nucleic acid amplification test-confirmed influenza, as well as 19 genomes of co-infecting viruses from 17 samples, including respiratory syncytial virus (RSV-B), human bocavirus, SARS-CoV-2, human metapneumovirus, and coronaviruses 229E and OC43. The observed incidence of co-infecting viruses was temporally consistent with national epidemic trends (RSV and SARS-CoV-2). In all co-infections, the viral abundance was predominated by one of the infecting viruses, suggesting either consecutive infections, or within-host dynamics favouring the dominance of one of the infecting viruses. The dominant influenza subtype was A/H3N2, with a persistent minority of A/H1N1 infections, consistent with national surveillance. We contextualise our representative sample set within the global genomic diversity of A/H3N2 and the ongoing evolution of influenza A/H3N2 in the following Northern Hemisphere 2022/2023 winter. In addition to influenza genomic epidemiology, multi-pathogen methodology enables simultaneous detection and characterisation of co-infecting respiratory pathogens, providing insights into the role of viral dynamics during overlapping epidemics.
Linker histone H1.0 loads onto nucleosomes through multiple pathways that are facilitated by histone chaperones
Authors: Akbari Ehsan , Burge Nathanial L , Poirier Michael G
Published: February 2025

Linker histone H1 is an essential chromatin architectural protein that compacts chromatin into transcriptionally silent regions by interacting with nucleosomal and linker DNA, while rapidly exchanging in vivo. How H1 targets nucleosomes while being dynamic remains unanswered. Using a single-molecule strategy, we investigated human H1.0 interactions with DNA and nucleosomes. H1.0 directly binds nucleosomes and naked DNA with a preference toward nucleosomes. DNA-bound H1.0 exhibited a range of bound state lifetimes with both mobile and immobile states, where the mobile H1.0 did not load onto nucleosomes. The histone chaperone Nap1 facilitated H1.0-nucleosome loading by enabling H1.0 loading through DNA sliding, reducing DNA resident times without impacting nucleosome resident times, increasing mobility along DNA, and targeting H1.0 loading onto the nucleosome dyad. These findings reveal linker histones load onto nucleosomes through multiple distinct mechanisms that are facilitated by chaperones to regulate chromatin accessibility.
CD11c+ CD8 T cells cause IFN-g-dependent autoimmune neuroinflammation that is restrained by PD-1 signaling.
Authors: Hwang Daniel , Ishikawa Larissa Lumi Watanabe , Seyedsadr Maryam S. , Jang Soohwa , Kasimoglu Ezgi , Rostami Abdolmohamad , Zhang Guang-Xian , Ciric Bogoljub
Published: February 2025

In multiple sclerosis (MS) lesions, CD8 T cells outnumber CD4 T cells, suggesting that they contribute to MS pathology. However, little is known on the role of CD8 T cells in MS, partially due to the nearly ubiquitous use of experimental autoimmune encephalomyelitis (EAE) models that are mediated by CD4 T cells, with no CD8 T cell contribution. Importantly, MS and EAE differ in both their distribution of CNS lesions and their symptoms, indicating differences in CNS inflammation. MS lesions are more prevalent in the brain, while EAE lesions are more frequent in the spinal cord. Additionally, neurologic deficits in MS rarely parallel the paralysis typical for CD4 T cell-mediated EAE (CD4-EAE). In contrast, CD8-EAE models suggest that CD8 T cells preferentially cause brain inflammation, but little is known regarding how brain and spinal cord inflammation may differ, and how CD8 T cells may contribute to those differences. We have established an adoptive CD8-EAE mouse model characterized by brain-centered inflammation, severe ataxia, and weight loss. CNS inflammation in the brain and spinal cord differed in immune cell numbers, cellular composition, and inflammatory signatures. CD8-EAE could be suppressed by blocking IFN-g, and exacerbated by blocking PD-1, with concomitant changes in numbers of CNS-infiltrating monocytes. Most CD8 T cells in the CNS were CD11c+, suggesting that they are the pathogenic subset. We describe a robust CD8-EAE model, identify differences between brain and spinal cord inflammation, and characterize mechanisms that control CD8 T cell-mediated neuroinflammation, thereby furthering understanding of these cells in EAE/MS.
Development and Pilot Testing for a Novel Shared Decision-Making Tool for Tracheostomy Decision-Making
Authors: Mehta Anuj B , Lockhart Steven , Douglas Ivor S , Mealer Meredith , Matlock Daniel D
Published: February 2025

Background: Tracheostomy and prolonged mechanical ventilation decision-making is one of the most emotionally difficult decisions facing surrogate decision-makers in health care. Often, surrogates face decisions between the potential for prolonged life support verses transitions to comfort measures and possible death. Despite more than two decades of research, major gaps exist in improving the decision-making process. Objective: Develop and pilot testing a novel shared decision-making tool for tracheostomy and prolonged mechanical ventilation. Methods: Development of the novel web-based conversation tool called TRACH-Support was an iterative process engaging key stakeholders (patients, surrogates, critical care providers, and shared decision-making experts) at multiple points. Development of the website used a Human-Centered Design approach with modern graphics and website interfaces. Pragmatic pilot testing was a mixed methods approach recruiting surrogates, providers, nurses, and respiratory therapists. Primary quantitative outcomes included Usability (System Usability Scale (SUS)) and Acceptability (Acceptability of Intervention (AIM)) measures with multiple secondary outcomes. Qualitative interviews used a Think Aloud approach and matrix analysis methodology. Results: A total of 86 participants were recruited for the quantitative survey with 10 surrogates and 10 providers completing qualitative interviews. Mean SUS score among all participants was 68.2/100 (SD=10.7) but surrogates specifically had a mean SUS=74.2/100 (74.2). The overall mean AIM score was 4.2/5 (SD=0.8) and 79.4% of all participants viewed TRACH-Support as Acceptable or Very Acceptable. Qualitative interviews indicated that TRACH-Support had high Usability and Acceptability. Customizability, pictures, novel outcomes, and the organization were all features that contributed to participant views. Participants also suggested several modifications including reducing the word count, adding video testimonials, and adding information on how faith/religion may play a role in decision-making for some. Conclusions: TRACH-Support, a novel, web-based, customizable and personalizable conversation tool for tracheostomy and prolonged mechanical ventilation was developed according to the most rigorous standards for decision-support tools. It had high Usability and Acceptability as assessed by quantitative and qualitative measures. Future large-scale testing is needed to assess real-world effectiveness and implementation.
Transcription factor binding and individual genetic risk for valproate teratogenicity
Authors: Anderson Alison May , Perucca Piero , Vianca Elena , Sandvik Daniel , Antonic-Baker Ana , Krause Roland , Jazayeri Dana , Hitchcock Alison , Graham Janet , Todaro Marian , Tomson Torbjorn , Battino Dina , Perucca Emilio , Martinez Ferri Meritxell , Rochtus Anne , Lagae Lieven , Canevini Maria Paola , Zambrelli Elena , Campbell Ellen , Rakitin Aleksei , Koeleman Bobby P. C , Scheffer Ingrid E , Berkovic Samuel F , Kwan Patrick , Sisodiya Sanjay M , Craig John , Vajda Frank J. E , O'Brien Terence ,   EpiPGX,   EPIGEN
Published: February 2025

Valproate (VPA) use during pregnancy is associated with a wide range of birth defects and adverse neurodevelopmental outcomes, but not all exposed children are affected and there is evidence for a genetic predisposition. We hypothesised that genomic variants that impact on the binding affinity of transcription factors (TFs) are integral to VPA-associated teratogenicity and a plausible explanation for variance in interindividual risk. We interrogated maternal exomes from women recruited through international epilepsy genomics consortia. The variant burden within genes associated with 32 different birth defect types was higher for those exposed to VPA as compared to other antiseizure medications (OR 1.73 [95% CI 1.40 to 2.14], p = 2.25E-07). Variants in women exposed to VPA were predicted to impact the binding affinity of 359 TFs and network analysis of encoded proteins indicated that a master regulator, EP300, interacts with 42% (151/359) of all variant sensitive TFs. We then profiled coexpression between EP300 and other TFs in differentiating neurons derived from human embryonic stem cells (hESCs) exposed to VPA at 300 µM and 700 µM, or unexposed, and a reference map generated using public data. We found strong overlap in EP300-TF coexpressed pairs between the reference and all comparison groups (99%,900/911) but only 32% (134/422) of pairs observed in unexposed cells were evident following VPA exposure, and over half of all pairs (489/911) were observed in VPA-exposed cells only. Our findings suggest that VPA-induced disruption of EP300-related regulation is common across birth defect types and that genetic variation can modify subsequent transcriptional dysregulation, explaining why only some pregnancies are affected. The results have implications for the development of genetic risk biomarkers and safer drugs.
Detection of inertial effects in capillary flows in open and closed channels
Authors: Berthier Jean , Tokihiro Jodie C , McManamen Anika M , Caira TJ , Shin Albert , Lee Jing J , Theberge Ashleigh B , Berthier Erwin
Published: February 2025

The Lucas-Washburn-Rideal law is commonly applied to describe capillary flow dynamics in closed or open channels, microporous media, such as paper pads and fiber threads or even granulous soil. It assumes a viscous flow regime where capillary forces are counteracted by friction with the solid structure, a valid assumption given the small flow velocities and device dimensions. However, scenarios exist outside the viscous regime, where inertial effects become significant, meaning capillary and friction forces do not fully balance. One well-documented case is the transient inertial regime at the onset of capillary motion. With the advancement of capillary devices, other configurations also raise the possibility of inertia influencing flow behavior. This study introduces a criterion to identify inertial contributions in capillary-driven flows in spatially varying geometries within open or closed channels and demonstrates how the Bosanquet equation can account for inertial effects in rectangular open-channel configurations.
Dynamics of blood NAD and glutathione in health, disease, aging and under NAD-booster treatment
Authors: Euro Liliya , Haimilahti Kimmo , Jansson Sonja , Forsström Saara , Buzkova Jana , Suomalainen Anu
Published: February 2025

Nicotinamide adenine dinucleotide (NAD) and glutathione are vital molecules that control redox-state, enzyme functions and metabolic flux in hundreds of cellular metabolic reactions. High NAD+ level occurs in fasting and has been associated with health outcomes in model systems, while low NAD+/NADH ratio occurs in specific diseases. Still, the normal, booster-treated or disease-related levels of NADs or glutathiones are not well known in humans. Here, we present a standardized technology for high-throughput quantitative measurement of NAD+, NADH, NADP+, NADPH, GSH, and GSSG from a single whole-blood sample. In healthy population (n=299;18-70 year-olds) redox metabolites follow normal distribution in blood and remain unchanged during aging. NAD-boosting increased 4-6 fold the blood NAD+ depending on individual, pointing to need of personalized dose adjustment in treatment trials. In patients with cancer, diabetes or neurodegeneration, NADs and glutathiones showed disease-dependent ″redox fingerprints″. The evidence highlights the potential of redox profiling as an indicator of metabolic pathology and as a measure of treatment response.
The keratin cortex stabilizes cells at high strains
Authors: Meyer Ruth , Rölleke Ulrike , Schwarz Nicole , Perez-Tirado Amaury , Schepers Anna V. , Janshoff Andreas , Köster Sarah
Published: February 2025

The eukaryotic cytoskeleton consists of three filament types: actin filaments, microtubules and intermediate filaments (IFs). IF proteins are expressed in a cell-type specific manner, and keratins are found in epithelial cells. In certain cell types, the keratins form a layer close to the membrane which may be referred to as an ``IF-cortex''. It is hypothesized that this IF-cortex arranges with radial bundles in a ``rim-and-spokes'' structure in epithelia. Based on this hypothesis, IFs and actin filaments might add complementary mechanical properties to the cortex. It was previously shown that single IFs in vitro remain undamaged at high strains. We now ask the question of whether this unique force-extension behavior of single IFs is also relevant in the filament network within a cell. Here, we show the influence of equibiaxial strain on wild-type (WT) and keratin-deficient (KO) cells comparing the viscoelastic properties close to the cell membrane using atomic force microscopy, in a spatially resolved manner. We find that cells without keratin exhibit a higher pre-stress than the WT cells. The compressibility modulus is increased at the cell rim, compared to the inside region, due to the geometry of the cell layer. Interestingly, both the pre-stress and the fluidity of the KO cells are altered already at low strains, whereas the WT cells show a response only at large strain. Our results indicate that KO cells compensate for the missing keratin, but are nevertheless very sensitive to external strain, whereas the intricate interplay between the actin and keratin cortices preserves the mechanical state and cell stability.
Powerful flowers: Public perception of grassland aesthetics is strongly related to management and biodiversity
Authors: Klaus Valentin H. , Fox Nathan , Richter Franziska J. , Andreatta Davide , Chai-allah Abdesslam
Published: February 2025

Temperate grasslands provide various cultural ecosystem services that are appreciated in diverse ways. Capturing these diverse appreciations requires different methodological approaches, such as questionnaire surveys and social media analyses. In this study, we combined the potential of both approaches to capture two aspects of what people appreciate in agricultural grasslands, i.e., the aesthetic quality of differently managed plant communities and the objects frequently found in grassland-based social media images. The two complementary approaches showed that people preferred colourful flower- and species-rich grasslands over grass-dominated and fertilised swards. Social media analysis highlighted that people mainly photographed flowers, followed by livestock and/or wildlife, but this depended also on the social media platform used. In conclusion, people's appreciation was clearly related to the intensity of grassland management and to the level of biodiversity, with a preference for extensively managed grasslands with diverse flowers and wildlife. Yet, we also found significant differences between (i) conservationists and agricultural professionals in the aesthetic appreciation of the plant communities, and (ii) between common visitors and naturalists in their social media content. Our results suggest that extensive management and ecological restoration can be used to increase cultural grassland ecosystem services by enhancing the richness of forbs, flowers and other attractive wildlife. Thus, targeted management is necessary to maintain and enhance the attractiveness of grassland landscapes and subsequently increase the health benefits that can be associated with these cultural grassland ecosystem services and human-nature contacts.
Orthosteric interactions with PIP2 activate TMEM16A channels
Authors: Xu Jie , Santa Cruz Ana , Chandrashekar Aishwarya , Kawano Takeharu , Zaka Mehreen , Cui Meng , Logothetis Diomedes E. , Plant Leigh D.
Published: February 2025

TMEM16A channels pass Ca2+ activated Cl- currents that drive a plethora of fundamental physiological processes. TMEM16A channels are activated by a rise in intracellular Ca2+ levels but also require interactions with the signaling phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) to gate open. Although PIP2 is essential for the activity of many types of ion channels, its precise binding site and role in channel gating remain poorly understood in most cases, limiting efforts to study channel dynamics and design targeted modulators. In this study, we identify the PIP2 binding interactions that govern TMEM16A gating and permeation. Using a combination of gating molecular dynamics (GMD) simulations and electrophysiological assays, we reveal how the α4 helix of TMEM16A interacts with both the phosphate headgroups and acyl chains of PIP2 to open an electrostatic ring within the channel and stabilize the extracellular opening of the Cl- conduction pathway. These findings provide key insights into the dynamic role of PIP2 in membrane protein function and shed light on the activation mechanism of TMEM16A. This work establishes a framework for rational targeting of TMEM16A in drug development, with potential therapeutic applications in a variety of diseases.
Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment
Authors: Moses Lambda , Huseynov Alik , Rich Joseph , Pachter Lior
Published: February 2025

SpatialFeatureExperiment is a Bioconductor package that leverages the versatility of Simple Features for spatial data analysis and SpatialExperiment for single-cell -omics to provide an expansive and convenient S4 class for working with spatial -omics data. SpatialFeatureExperiment can be used to store and analyze a variety of spatial -omics data types, including data from the Visium, Xenium, MERFISH, SeqFish, and Slide-seq platforms, bringing spatial operations to the SingleCellExperiment ecosystem.
Calcium stabilization of a flexible N-terminal domain in a pentameric ligand-gated ion channel
Authors: Fan Chen , Lycksell Marie , Zhuang Yuxuan , Howard Rebecca J , Lindahl Erik
Published: February 2025

Pentameric ligand-gated ion channels (pLGICs) are responsible for the rapid conversion of chemical to electrical signals. In addition to the canonical extracellular and transmembrane domains, some prokaryotic pLGICs contain an N-terminal domain (NTD) of unclear structure and function. In one such case, the calcium-sensitive channel DeCLIC, the NTD appears to accelerate gating; however, its evident flexibility has posed a challenge to model building, and its role in calcium sensitivity is unclear. Here we report cryo-EM structures of DeCLIC to the highest resolutions thus far, in circularized lipid nanodiscs. Application of refinement tools enabled definition of multiple calcium-binding sites in each symmetric subunit. Under calcium-free conditions, both symmetric and asymmetric classes could be reconstructed, implicating a heterogeneous ensemble. Behavior of these structures in molecular dynamics simulations was consistent with calcium stabilization of the NTD, an effect that may be conserved in structurally homologous domains across evolution.
Improving Patient Engagement in Phase 2 Clinical Trials with a Trial-specific Patient Decision Aid (tPDA): A Development and Usability Study
Authors: Halilaj Iva , Lieverse Relinde , Oberije Cary , Hendriks Lizza , Billiet Charlotte , Joye Ines , Van Eeckhout Brice , Wind Anke , Ankolekar Anshu , Lambin Philippe
Published: February 2025

Background: Making informed decisions about clinical trial participation can be overwhelming for patients due to the complexity of trial information, potential risks and benefits, and the emotional burden of a recent diagnosis. Patient decision aids (PDAs) simplify this process by providing clear information on treatment options, empowering patients to actively participate in shared decision-making (SDM) with their doctors. While PDAs have shown promise in various healthcare contexts, their use in clinical trials, particularly in the form of trial-specific PDAs (tPDAs), remains underutilized. Objective: To address the challenge of patient comprehension of traditional clinical trial materials, we developed a freely accessible, user-friendly tPDA within the context of the ImmunoSABR phase 2 trial. The tPDA aimed to enhance informed decision-making regarding trial participation. The primary endpoint was usability, quantitatively measured by the System Usability Scale (SUS). Secondary endpoints included time spent on the tPDA, patient satisfaction ratings, and participants self-reported level of understanding of the trial. Methods: We developed the tPDA following the International Patient Decision Aid Standards (IPDAS) and validated through a structured, three-phase iterative evaluation process. Initial evaluation was performed with 17 computer scientists who had expertise in biomedical applications, ensuring technical robustness. The content and usability were further refined through evaluations involving 10 clinicians and 8 medical students, focusing on clinical accuracy and user-friendliness. Lastly, the tool was tested by six patients eligible for the ImmunoSABR trial, to assess real-world applicability and patient-centered design. Results: Evaluations demonstrated the tPDA's effectiveness in enhancing informed decision-making, directly addressing our primary endpoint of usability with an overall mean SUS score of 79.4, indicative of good usability. Addressing our secondary endpoints, patients completed the tPDA efficiently, with the majority (four out of six) finishing in under 30 minutes, and all but one within 60 minutes. The mean satisfaction rating was 9.5 out of 10. Qualitative feedback highlighted significant improvements in patients understanding of the trial details, reinforcing the tPDA's role in facilitating better patient engagement and comprehension. Conclusion: Our study demonstrates the feasibility and potential of tPDAs to enhance patient comprehension and engagement in clinical trials. Integrating tPDAs offers a valuable addition to traditional paper-based and verbal communication methods, promoting informed decision-making and patient-centered care.
AS04 in a bivalent HPV vaccine drives superior cross-protective antibody response by increased NOTCH signaling of cDC1 leading to increased proliferation of adaptive immune cells
Authors: D’Onofrio Valentino , Santana Ana-Carolina , Pauwels Marthe , Waerlop Gwenn , Willems Anthony , Boever Fien De , Sehr Peter , Waterboer Tim , Leroux-Roels Isabel , Sharma Ashish , Sékaly Rafick Pierre , Leroux-Roels Geert
Published: February 2025

Introduction

Cervarix® and Gardasil® are two HPV vaccines with differing antigen and adjuvant compositions. Gardasil-4 contains HPV types 6, 11, 16 and 18 type-specific L1 viral like particles (VLPs) formulated with amorphous AlHO9PS-3 adjuvant, while Cervarix targets HPV types 16 and 18 using AS04 (Al(OH)3 + TLR4 agonist MPL) to enhance immune response and cross-protection against other high-risk HPV types, not included in the vaccine.

Methods

To investigate mechanisms of cross-neutralizing potential of Cervarix, six monozygotic twins (12 females aged 9-13 years) were vaccinated with either Cervarix or Gardasil-4 (2 doses, 6 months apart). Serum neutralizing antibody titers against HPV 6,16,18,31,33,45,52, and 58, were assessed pre-vaccination and 7 days post-second dose. Multi-omic single cell RNA and ATAC sequencing of PBMCs were performed at the latter timepoint.

Results

Cervarix generated higher cross-neutralizing antibody titers than Gardasil-4. Higher frequencies of plasmacytoid (pDC) and conventional dendritic cells (cDC1, cDC2), CD4+ T effector memory (Tem) and B memory cells were also observed after Cervarix. Cervarix-vaccinated subjects showed increased DC-to-CD4+ Tem and B memory cell signaling, through increased antigen presentation and upregulation of NOTCH pathway. Gene Set Enrichment Analysis indicated enhanced pathways related to cell migration and NOTCH2 signaling in DCs and cell cycling/RNA translation in CD4+ T and B cells, correlating positively with cross-neutralizing antibody titers. Increased chromatin accessability in genes related to NOTCH signaling in cDC1 was also observed. Engagement of MHC and NOTCH induced FOS in CD4+ Tem cells and BCL2 in B memory cells, supporting proliferative and anti-apoptotic states. This also resulted in an increase in Th2 cells in Cervarix-vaccinated subjects, and increased IgG4 expression in B memory cells.

Conclusion

Increased DC signaling, including NOTCH, through AS04 in Cervarix supports cell survival and sustained RNA translation in adaptive immune cells, 7 days post-vaccination, especially memory T and B cells. This increased cell metabolism and activation may enhance cell maturation of adaptive immune cells, providing a mechanism triggered by Cervarix that can lead to improved cross-reactivity.
Neurophysiological dysconnectivity across multiple resting state brain networks and cognitive impairment in children with Prader-Willi Syndrome
Authors: Dunkley Benjamin T , Solar Kevin G , Zamyadi Rouzbeh , Reichelt Amy C , Morrison Ellie , Scratch Shannon E , Hamilton Jill
Published: February 2025

Prader-Willi Syndrome (PWS) is a rare genetic condition with multifaceted physical, behavioural and cognitive difficulties that is characterized by hyperphagia and low executive functioning. Food-seeking behaviours may be moderated by hormonal, cognitive, and psychological factors, and are thought to be mediated in part by functional brain abnormalities. Here, we used an experimental protocol integrating eyes opens resting state magnetoencephalography (MEG) - a high-resolution neurophysiological imaging technique - and neuropsychological profiling to understand the relationship between executive functioning, and intrinsic brain activity & functional connectivity in a prospective, cross-sectional cohort with PWS, and a sex-, age- and BMI-matched control group. We observed lower executive functioning in PWS as well as functional dysconnectivity across multiple channels of brain synchrony - in other words, across multiple frequency bands that mediate communication within and between brain networks - in the visual, attentional, and the default mode networks. Moreover, we found ‘brain-wide’ changes in the topological structure of brain networks in those with PWS, with increased ‘hubness’ of functional networks, but decreased centrality. However, none of these measures survived multiple comparison correction after correlating with neuropsychological outcomes, although there were moderate effect sizes (degree of association). This is the first study to combine neuropsychology and neurophysiological imaging to show that functional synchrony in multiple brain networks is dysregulated in PWS.
Development of Interactive Nomograms for Predicting Short-Term Survival in ICU Patients with Aplastic Anemia
Authors: Fan Junyi , Chen Shuheng , Alaei Kamiar , Placencia Greg , Pishgar Elham , Pishgar Maryam
Published: February 2025

Background:Aplastic anemia is a severe hematologic disorder marked by pancytopenia and bone marrow failure. ICU admission often reflects disease progression or complications requiring critical care. Predicting short-term survival in these patients is vital for individualized treatment and resource optimization. Nomograms provide a practical tool for integrating clinical parameters, offering accurate visualized survival predictions to guide decision-making in patients with aplastic anemia in the ICU. Methods:Using the MIMIC-IV database, we identified ICU patients diagnosed with aplastic anemia. From thousands of available variables, we extracted data across five dimensions: demographic, synthetic indicators, laboratory events, comorbidities, and drug usage. Based on existing studies of aplastic anemia, more than 400 variables were further refined and machine learning techniques were applied to identify the seven most effective predictors for modeling. Preprocessing was performed using machine learning approaches, and the feasibility of these predictors was validated through additional classification and regression models, the verification method is AUROC. Furthermore, external validation was performed using data from the eICU Collaborative Research Database to assess the generalizability of our models.The interactive nomograms were constructed using logistic regression (LR) to predict mortality rates at 7 days, 14 days, and 28 days in patients with aplastic anemia. Results: A total of 1,662 patients diagnosed with aplastic anemia were included in this study, with a 7:3 ratio split into training and testing cohorts. The logistic regression model demonstrated strong predictive performance, achieving AUC values of 0.8227, 0.8311, and 0.8298 for 7-day, 14-day, and 28-day mortality predictions, respectively. External validation using the eICU database further confirmed the model's generalizability, with AUC values of 0.7391, 0.7119, and 0.7093. These results highlight the model's stability and effectiveness in predicting short-term survival in aplastic anemia patients. Conclusion:A set of seven predictors, led by APS III, proved effective for modeling short-term survival in aplastic anemia patients. Using these predictors, Cox and logistic regression models generated nomograms that accurately predict 7-day, 14-day, and 28-day mortality. These tools can support clinicians in personalized risk assessment and decision-making.
Structural and Conformational Impact of Deleterious Spike Protein Mutations in SARS-CoV-2 Omicron Lineages
Authors: Khalid Aqsa , Ahmed Kumail , Kanji Akbar , Munir Tania , Bukhari Ali Raza , Hasan Zahra , Van Voorhis Wes , Iqbal Najeeha Talat
Published: February 2025

Background: A large number of mutations in the Spike (S) protein of the SARS-CoV-2 omicron variant have been noted to alter the receptor binding domain (RBD) and increase the binding surface and enhance the opening of the binding pocket. The cumulative effect of S1 and S2 subunit mutations can influence the conformational dynamics of the binding surface, facilitating the release of viral genome into host cells. Aim: This study investigates the deleterious mutations across all Omicron lineages identified in our analysis and their effect on the conformational stability of RBD opening. Methods: Whole Genome Sequencing of 231 SARS-CoV-2 positive patients in Karachi, Pakistan, were performed using Illumina Miseq instrument and raw reads were analyzed using viralrecon pipeline. The mutational effects of omicron variant on the stability of S protein, including wild-type (7FG7), close (6VXX) and open (6VYB) states, were assessed through MD simulations. Results: Four deleterious missense mutations (Tyr505His, Asn764Lys, Asp950Asn, Asn969Lys) were identified in the S1 and S2 subunit of the S protein of omicron variant. In the wildtype and open state mutant models, Tyr505His, Asp950Asn and Asn969Lys caused destabilizing effects, higher RMSDs vs. wild-type, and fluctuations in the RBD (438-510) region and S2 subunit (946-1010), compared to the native structure. These mutations increased the binding pocket propensity to open in mutant model compared to the native open conformation (6VYB). This structural change promoted trimer opening in the open state through α-helix movement in the S2 subunit away from the RBD region. In the closed state, only S2 subunit mutations (Asp950Asn and Asn969Lys) lead to predicted destabilization through the movement of protomer C towards protomer B (RBD region). These S2 subunit mutations are predicted to stabilize the RBD ″down″ conformation potentially enhancing spike antigenic heterogeneity. Conclusion: This study highlighted the cumulative effect of S1 (Tyr505His) and S2 (Asp950Asn and Asn969Lys) subunit mutations on different S protein states, potentially controlling its conformational dynamics and presentation to host receptors. Future experimental studies are needed to elucidate the biological significance of these alterations, particularly by establishing a link between the identified mutations and their impact on viral biology.
A database for large-scale docking and experimental results
Authors: Hall Brendan W , Tummino Tia A , Tang Khanh , Irwin John J , Shoichet Brian K.
Published: February 2025

The rapid expansion of readily accessible compounds over the past six years has transformed molecular docking, improving hit rates and affinities. While many millions of molecules may score well in a docking campaign, the results are rarely fully shared, hindering the benchmarking of machine learning and chemical space exploration methods that seek to explore the expanding chemical spaces. To address this gap, we develop a website providing access to recent large library campaigns, including poses, scores, and in vitro results for campaigns against 11 targets, with 6.3 billion molecules docked and 3729 compounds experimentally tested. In a simple proof-of-concept study that speaks to the new library's utility, we use the new database to train machine learning models to predict docking scores and to find the top 0.01% scoring molecules while evaluating only 1% of the library. Even in these proof-of-concept studies, some interesting trends emerge: unsurprisingly, as models train on larger sets, they perform better; less expected, models could achieve high correlations with docking scores and yet still fail to enrich the new docking-discovered ligands, or even the top 0.01% of docking-ranked molecules. It will be interesting to see how these trends develop for methods more sophisticated than the simple proof-of-concept studies undertaken here; the database is openly available at lsd.docking.org.
Repeatable phenotypic but not genetic response to selection on body size in the black soldier fly
Authors: Generalovic Tomas N , Zhou Wenjun , Zhao Leia Chengcheng , Leonard Sam , Warren Ian A , Pipan Miha , Jiggins Chris D
Published: February 2025

Polygenic traits are expected to show high genetic redundancy and therefore low repeatability in the genomic response to selection. We tested this prediction by selecting for large body size in the black soldier fly (Hermetia illucens). Over three replicate experiments selected for large body size, we found a strong and repeatable phenotypic response, with a mean 15% increase in body size. Selected lines also increased in larval growth rate (+19%) and average protein content (+14%), suggesting that selection on large body size does not result in strong trade-offs. In contrast to the predictability of the phenotypic response across replicates, whole genome sequencing identified a highly polygenic and non-repeatable genomic response. We identified 120, 301 and 157 outlier genomic regions in the three replicates, but high redundancy with only four shared regions. Among 12 candidate genes found in these regions, the insulin-like receptor gene (HiInR) was confirmed as regulating larval growth using a CRISPR knockout experiment. In summary, polygenic quantitative traits show high genetic redundancy, even where the phenotypic response to selection is highly repeatable.
Interactions between parasites within the host: helminth infection reduces lice abundance in feral pigeons (Columba livia)
Authors: JEANTET Aurélie , Audebert Fabienne , Agostini Simon , Decencière Beatriz , Chéreau Maxence , Grasset Maïa , Federici Pierre , Rozen-Rechels David , Gasparini Julien
Published: February 2025

1. Within a host, parasites form a community and interact with each another. They can interact directly through competition for space or indirectly through competition for resources, or even via the host′s immune response. These interactions can influence infection patterns within the host. In particular, helminths are capable of facilitating the infection of other parasites through their immunosuppressive effects or hindering it by activating immune responses that reduce the ability of other species to infest the host. 2. In this study, we aimed to test the existence of parasite interactions in the wild pigeon host (Columba livia). More specifically, we experimentally tested whether helminth infestation influences the infestation dynamics of ecto- and endoparasites in pigeons. 3. Our predictions were tested on a sample of pigeons captured in Paris, half of them were exposed to an anthelmintic treatment. We then assessed the effects of this deworming treatment on the abundance of blood parasites (hemosporidian parasites,Haemoproteusspp.,Plasmodiumspp., andLeucocytozoonspp.), lice (Columbicola columbaeandCampanulote compar), as well as on the intensity of antiparasitic behavioral responses (preening). 4. We detected a negative relationship between helminth presence and lice abundance, with higher lice abundance when helminths were reduced (with anthelmintic treatment) and lower lice abundance when helminths were more abundant (without anthelmintic treatment), indicating inhibitory effects of helminths on ectoparasite abundance. However, these results were not supported by differences in preening activity between the two experimental groups, suggesting that other mechanisms are involved. Our results showed no effect of anthelmintic treatment on the abundance of blood parasites. The mechanism by which helminths induced ectoparasite repulsion remains to be demonstrated.
Unveiling the Complete Spectrum of SARS-CoV-2 Fusion Stages by In Situ Cryo-ET
Authors: Akil Caner , Xu Jialu , Shen Juan , zhang peijun
Published: February 2025

SARS-CoV-2 entry into host cells is mediated by the spike protein, which drives membrane fusion. While cryo-EM has revealed stable prefusion and postfusion conformations of the spike, the transient intermediate states during the fusion process have remained poorly understood. Here, we designed a near-native viral fusion system that recapitulates SARS-CoV-2 entry and used cryo-electron tomography (cryo-ET) to capture fusion intermediates leading to complete fusion. The spike protein undergoes extensive structural rearrangements, progressing through extended, partially folded, and fully folded intermediates prior to fusion-pore formation, a process that is dependent on protease cleavage and inhibited by the WS6 S2 antibody. Upon interaction with ACE2 receptor dimer, spikes cluster at membrane interfaces and following S2' cleavage concurrently transition to postfusion conformations encircling the hemifusion and pre-fusion pores in a distinct conical arrangement. Subtomogram averaging revealed that the WS6 S2 antibody binds to the spike's stem-helix, crosslinks and clusters prefusion spikes and inhibits refolding of fusion intermediates. These findings elucidate the complete process of spike-mediated fusion and SARS-CoV-2 entry, highlighting the neutralizing mechanism of S2-targeting antibodies.
Deciphering the Molecular Mechanisms of BPTF Interactions with Nucleosomes via Molecular Simulations
Authors: Hebert Ryan , Wereszczynski Jeff
Published: February 2025

Many transcription factors regulate DNA accessibility and gene expression by recognizing post-translational modifications on histone tails within nucleosomes. These interactions are often studied in vitro using short peptide mimics of histone tails, which may overlook conformational changes that occur in the full nucleosomal context. Here, we employ molecular dynamics simulations to investigate the binding dynamics of the PHD finger and bromodomain of BPTF, both in solution and bound to either a histone H3 peptide or a full nucleosome. Our results show that BPTF adopts distinct conformational states depending on its binding context, with nucleosome-bound BPTF exhibiting altered histone core interactions. Electrostatic repulsion limits direct reader-DNA contacts, while histone-DNA hydrogen bonding decreases, suggesting a shift in nucleosome stability. Our findings indicate that BPTF binding to nucleosomes alters local chromatin architecture, potentially contributing to nucleosome remodeling and gene regulation.
Biallelic variants in SREK1 downregulating SNORD115 and SNORD116 cause a novel Prader-Willi-like syndrome
Authors: Saeed Sadia , Siegert Anna-Maria , Tung Y.C. Loraine , Khanam Roohia , Janjua Qasim M , Manzoor Jaida , Derhourhi Mehdi , Toussaint Benedicte , Lam Brian Y.H. , Mahmoud Sherine Awad , Vaillant Emmanuel , Buse Falay Emmanuel , Amanzougarene Souhila , Ayesha Hina , Khan Waqas I , Ramazan Nosheen , Saudek Vladimir , o'rahilly stephen , Goldstone Anthony P , Arslan Muhammad , Bonnefond Amelie , Froguel Philippe , Yeo Giles S.H.
Published: February 2025

Up to 10% of patients with severe early-onset obesity carry pathogenic variants in known obesity-related genes, mostly affecting the leptin-melanocortin pathway. Studying children with severe obesity from consanguineous populations provides a unique opportunity to uncover novel molecular mechanisms. Using whole-exome sequencing, followed by a rigorous analytical and filtration strategy, we identified three different homozygous missense variants in SREK1 (encoding Splicing Regulatory glutamic acid and lysine rich protein) in Pakistani children with severe obesity, from three unrelated consanguineous pedigrees. The wild type SREK1 gene of human induced pluripotent stem cell (iPSC)-derived hypothalamic neurons was individually replaced by each of the three variants and the impact of these changes on global gene expression was studied. Neurons expressing the two variants in the SREK1 RNA recognition domain p.P95L and p.T194M, but not the C-terminally located p.E601K, had markedly reduced expression of the small nucleolar RNA clusters SNORD115 and SNORD116, deficiency of which has been implicated in Prader-Willi syndrome (PWS). In addition to hyperphagic obesity the carriers of these two variants had other features of PWS, such as neonatal hypotonia. In conclusion, homozygous variants in SREK1 result in a subtype of severe early onset obesity sharing features with PWS.
Detection and genotyping of enteric foodborne viruses with high (NoV, HAV, HEV) and low (RV, AdV) health impact in ready-to-eat leafy vegetables and berries from Córdoba, Argentina
Authors: Di Cola Guadalupe , Prez Verónica E. , Fantilli Anabella C. , Frydman Camila , Mozgovoj Marina , Luque Liliana , Ferreyra Leonardo , Nates Silvia V. , Pisano María Belén , Ré Viviana E.
Published: February 2025

The global consumption of ready-to-eat (RTE) leafy green vegetables and berries has risen as consumers perceive them as safe and nutritious options. However, these foods have also been identified as sources of enteric viruses that infect the human gastrointestinal system, which are then excreted and can spread through the fecal-oral route. In Argentina, there is limited evidence on the detection of enteric viruses in food, and no legislation currently requires their detection in frozen or fresh produce intended for domestic consumption. This study aimed to identify and characterize five foodborne viruses with high and low health impact (norovirus, hepatitis A virus, hepatitis E virus, rotavirus, and adenovirus) in berries and RTE leafy vegetables marketed in central Argentina. A total of 242 samples (145 berries and 97 leafy greens) were collected from retail sources in Córdoba and processed according to ISO 15216-2:2019 standard. Viral detection was performed by qPCR or RT-qPCR, followed by viral characterization through specific RT-PCR assays or Sanger sequencing. Results indicate that 4.1% of berry samples, primarily frozen strawberries, tested positive for norovirus or rotavirus, while 10.3% of leafy green samples were positive for norovirus, rotavirus and adenovirus. Genotyping indicated the same strains to those involved in local gastroenteritis outbreaks. The absence of hepatitis A and E viruses suggests limited transmission of these pathogens through these foods. This study highlights the need to strengthen hygiene and monitoring protocols for RTE products, as viral contamination poses potential health risks to consumers, underscoring a critical area for improving food safety.
Metagenomic Profiling of Airborne Microbial Communities from Aircraft Filters and Face Masks
Authors: Oumer Oliyad Jeilu , Sumner Jack T. , Moghadam Anahid Amani , Thompson Kelsey N. , Huttenhower Curtis , Catlett Charles Edward , Hartmann Erica M
Published: February 2025

Airborne microbial communities, although often challenging to study due to low biomass, play crucial roles in public health and pathogen transmission. Through shotgun metagenomics, this study utilizes non-invasive air sampling of face masks and aircraft cabin filters to investigate microbial diversity in environments with frequent human interactions, including hospitals and airplanes. A comprehensive sampling and analysis workflow was developed, incorporating environmental and enrichment protocols to enhance microbial DNA recovery and diversity profiling. Despite limitations in biomass, optimized extraction methods allowed for the successful identification of 407 species, with dominant taxa including Cutibacterium acnes, Staphylococcus epidermidis, Sphingomonas hankookensis, and Methylobacterium radiotolerans. Enrichment processing resulted in greater metagenome-assembled genome (MAG) recovery and higher antimicrobial resistance gene (ARG) identification. The findings highlight the presence of ARGs in high-occupancy public spaces, suggesting the importance of monitoring and the potential for mitigating airborne transmission risks in such environments. This study demonstrates the utility of combining environmental and enrichment sampling to capture comprehensive microbial and ARG profiles in confined spaces, providing a framework for enhanced pathogen monitoring in public health contexts.