bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digitally immune optimised haemagglutinin with nanocage plug-and-display elicits broadly neutralising pan-H5 influenza subtype vaccine responses
Authors: Huang Chloe Qingzhou , Hills Rory A. , Carnell George W. , Vishwanath Sneha , Aguinam Ernest T. , Chan Andrew C.Y. , Palmer Phil , O’Reilly Laura , Tonks Paul , Temperton Nigel , Frost Simon D.W. , Tiley Laurence S. , Howarth Mark R. , Heeney Jonathan L. 
Published: November 2024

ABSTRACTThe increasing global spread of the highly pathogenic avian influenza (HPAI) A/H5 viruses poses a serious public health threat. Circulating clade 2.3.4.4b viruses have demonstrated rapid transcontinental dissemination, extensive reassortment, epizootic spread and potential sustained mammal-to-mammal transmission, signifying a heightened risk of becoming a human pathogen of high consequence. A broadly protective, future-proof vaccine against multiple clades of H5 influenza is urgently needed for pandemic preparedness. Here, we combine two novel vaccine technologies to generate a Digitally Immune Optimised and Selected H5 antigen (DIOSvax-H5inter) displayed multivalently on the mi3 nanocage using the SpyTag003/SpyCatcher003 conjugation system. Mice immunised with DIOSvax-H5interHomotypic Nanocages at low doses demonstrate potent, cross-clade neutralising antibody and T cell responses against diverse H5 strains. DIOSvax-H5interHomotypic Nanocages provide a scalable vaccine candidate with the potential for pan-H5 protection against drifted or newly emergent H5 strains. This World Health Organization preferred product characteristic is essential for prospective strategic stockpiling in the pre-pandemic phase.
A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation
Authors: Rodriguez Jose Manuel , Maquedano Miguel , Cerdan-Velez Daniel , Calvo Enrique , Vazquez Jesús , Tress Michael L. 
Published: November 2024

AbstractThe human genome has been the subject of intense scrutiny by experimental and manual curation projects for more than two decades. Novel coding genes have been proposed from large-scale RNASeq, ribosome profiling and proteomics experiments. Here we carry out an in-depth analysis of an entire proteomics database.We analysed the proteins, peptides and spectra housed in the human build of the PeptideAtlas proteomics database to identify coding regions that are not yet annotated in the GENCODE reference gene set. We find support for hundreds of missing alternative protein isoforms and unannotated upstream translations, and evidence of cross-contamination from other species.There was reliable peptide evidence for 34 novel unannotated open reading frames (ORFs) in PeptideAtlas. We find that almost half belong to coding genes that are missing from GENCODE and other reference sets. Most of the remaining ORFs were not conserved beyond human, however, and their peptide confirmation was restricted to cancer cell lines. We show that this is strong evidence for aberrant translation, raising important questions about the extent of aberrant translation and how these ORFs should be annotated in reference genomes.
Quantifying Cell Traction Forces at the Individual Fiber Scale in 3D: A Novel Approach Based on Deformable Photopolymerized Fiber Arrays
Authors: Ucla Pierre , Le Chesnais Joanne , Ver Hulst Henri , Ju Xingming , Calvente Isabel , Leconte Ludovic , Salamero Jean , Bonnet Isabelle , Monnot Catherine , Moreau Hélène , Landoulsi Jessem , Semetey Vincent , Coscoy Sylvie 
Published: November 2024

AbstractThe forces exerted by cells upon the fibers of the extracellular matrix play a decisive role in cell motility in development and disease. How the local physical properties of the matrix (such as density, stiffness, orientation) affect cellular forces remains poorly understood. Existing approaches to measure cell 3D traction forces within fibrous substrates lack control over the local properties and rely on continuum approaches, not suited for measuring forces at the scale of individual fibers. A novel approach is proposed here to fabricate multilayer arrays of deformable fibers with defined geometrical and mechanical properties using two-photon polymerization. The fibers are characterized using Atomic Force Microscopy and span a wide range of sizes and mechanical properties. This approach is combined with a new reference-free method for measuring traction forces in 3D, which relies on automated segmentation of the fibers coupled with finite element modeling. The force measurement pipeline is applied to study forces exerted by adherent cells, endothelial cells, fibroblasts or macrophages, and reveals how these forces are influenced by fiber density and stiffness. Additionally, coupling to fast volumetric imaging with lattice light-sheet microscopy enables the measurement of the low-intensity and short-lived tractions exerted by amoeboid cells, such as dendritic cells.
Compositional changes of the lung extracellular matrix in acute respiratory distress syndrome
Authors: Fan YW , Moser J , Jongman RM , Borghuis T , Vonk JM , Timens W , van Meurs M , Pillay J , Burgess JK 
Published: November 2024

ABSTRACTBackgroundAcute respiratory distress syndrome (ARDS) is pathologically characterized by diffuse alveolar damage (DAD) and is associated with high morbidity and mortality rates. Remodeling of the extracellular matrix (ECM), which is pivotal for both tissue repair and organ recovery, may play a large role in persistent ARDS. This study investigated the compositional changes in the ECM in different DAD stages in ARDS.MethodsParaffin-embedded lung sections collected during autopsy or from post-transplant lungs were obtained from patients with ARDS (n=28) admitted to the University Medical Center Groningen between 2010-2020. Sections were stained histochemically, and immunohistochemically for collagen III α1 chain (Col IIIa1), IV α3 chain (Col IVa3), VI α1 chain (Col VIa1), periostin (PSTN), lumican (LUM), and fibronectin (FN). The sections were divided into 118 regions based on DAD stages (54 early vs 64 advanced). The differences in the expression of selected proteins were compared between DAD stages or across ARDS duration (<7days, 7-14days, >14days). The fiber pattern of Col VIa1 was analyzed using CellProfiler.ResultsHigher tissue density, lower proportional areas of Col IIIa1, Col IVa3, and LUM, and more concentrated Col VIa1 fibers were observed in the advanced DAD stage than in the early DAD stage. Areas with higher proportions of total collagen and FN, and lower proportional areas of Col IIIa1, Col IVa3, and LUM were detected in lung regions from patients with ARDS >14days duration.ConclusionsThese findings revealed proportional changes in ECM components, strongly suggesting that dynamic changes in ECM proteins play a role in pathophysiology in ARDS during progression.
Unravelling the universal spatial properties of coral reefs
Authors: Giménez-Romero Àlex , Matías Manuel A. , Duarte Carlos M. 
Published: November 2024

AbstractCoral reefs are under rapid decline due to human pressures such as climate change. Achieving the Kunming-Montreal Global Biodiversity Framework goals, which include restoring 30% of degraded habitats like coral reefs by 2030, requires a comprehensive understanding of their extent and structure, which has been hitherto lacking. We address this limitation based on the unprecedented canonical inventory of coral reefs extracted from the Allen Coral Atlas of shallow-water tropical reefs. We identified a total of 1,579,772 individual reefs globally, extending over a total of 52,423km2of ocean area with mean and median sizes of 3.32 ha and 0.3 ha, respectively. We unravelled three universal laws that are common to all coral reef provinces: the size-frequency distribution, the inter-reef distance distribution and the area-perimeter relation, which follow power laws with an exponent of 1.8, 2.33 and 1.26, respectively. We demonstrate that coral reefs develop universal fractal patterns characterised by a perimeter fractal dimension ofDP= 1.3 and a surface fractal dimension ofDA= 1.6. Our analysis shows that coral reefs display intricate fractal-like geometries and exhibit universal macroecological patterns, largely independent of their geographical location. The universality of the observed patterns suggests that these features possibly stem from the highly conserved interactions of biological, physical, and chemical processes. Over geological scales, these processes lead to reef landscape patterns common among all provinces, providing new information relevant to reef growth modelling.
CGGBP1 from higher amniotes restricts cytosine methylation and drives a GC-bias in transcription factor binding sites at repressed promoters
Authors: Kumar Praveen , Morbia Ishani , Satish Aditi Lakshmi , Datta Subhamoy , Singh Umashankar 
Published: November 2024

AbstractCGGBP1, a 20 kDa protein, has several functions associated with its DNA-binding through a C2H2 zinc finger. A range of studies have shown that GC richness, inter-strand G/C-skew and low cytosine methylation are associated with CGGBP1 occupancy. The non-preference of any sequence motif as CGGBP1 binding site suggests widespread association of CGGBP1 with DNA including at potent transcription factor binding sites (TFBSs) in promoter regions. The evolutionary advantage of such a design remains unclear. The regulatory interference by human CGGBP1 at TFBSs is supported by purifying selection in the DNA-binding domain of CGGBP1 and its requirement for gene repression as well as restriction of cytosine methylation at GC-rich TFBSs. Here we describe an evolutionary trajectory of this property of CGGBP1 by combining global gene expression and cytosine methylation analyses on human cells expressing CGGBP1 from four different vertebrates (representatives of coelacanth, reptiles, aves and mammals). We discover a potent cytosine methylation restriction by human CGGBP1 at some GC-rich TFBSs in repressed promoters. Further, we combine a high-throughput analysis of GC compositional bias of these CGGBP1-regulated TFBSs from available orthologous sequences from a pool of over 100 species. We show that cytosine methylation restriction by CGGBP1 is tightly linked to GC retention in a set of TFBSs. Orthology analyses demonstrate that this property of CGGBP1 has evolved in higher amniotes (aves and mammals) with lineage-specific heterogeneities in lower amniotes (reptiles). CGGBP1 ChIP-seq data suggest that occupancy of CGGBP1 at these target TFBSs plays a crucial role in their low methylation, GC-biased evolution and associated functions in gene repression.
Pangenome References Improve Biomarker Estimation from Tumor Sequencing Data
Authors: Arslan Elif , Turgut Deniz , Kalay Özem , Demirkaya-Budak Sinem , Budak Gungor , Jain Amit 
Published: November 2024

AbstractIt has recently been shown that patients from non-European ancestries are at a higher risk of inappropriate clinical intervention because of inaccurate biomarker estimation, arising from the reference bias inherent in standard methods for determining the tumor genome from sequencing data. Here we demonstrate that these inaccuracies can be reduced by using a pangenome reference appropriate for the patient’s population.We constructed a novel secondary analysis workflow where the pangenome reference serves as a scaffold for mapping the sequencing reads, and is also included in the relevant ‘panel of normals’ needed to discriminate between germline and somatic mutations in tumor-only sequencing. This approach detects known somatic mutations in tumor-only sequencing more accurately than the standard GATK somatic calling workflow, prevalent in diagnostic settings for analysis of sequencing data from tumor-only assays, on a standard benchmark tumor sample, HCC1395 (33% relative increase in F1 score).We also assessed the expected clinical impact of our approach by comparing the Tumor Mutational Burden (TMB) calculated from missense somatic mutations called in tumor/normal samples from 6 patients self-reported as belonging to African, 1 to Asian and 3 to European populations respectively. We find that the TMB values calculated from the tumor-only sequencing data analyzed by our workflow more closely approximate the TMB values calculated from the tumor-normal analysis of the same sample, being 35% higher on average, whereas GATK tumor-only analysis generates TMB values 56% higher on average than the tumor-normal analysis of the same sample. Tumor-normal TMB values calculated by the two methods do not vary as drastically, GATK generated values being 13% higher on average, indicating that GATK tumor-only analysis leads to significant overestimation of TMB values, which can be largely corrected by using our workflow when tumor-normal sequencing is not available.These results indicate that pangenome based analysis has the potential to become the new standard for unbiased processing of somatic sequencing samples, following on from its increased adoption for germline sequencing analysis.
Jagged1 is a Notch-independent mechanotransducer in endothelial cells
Authors: Rodriguez Freddy Suarez , Virtanen Noora , Kiviluoto Elmeri , Driessen Rob C. H. , Zhao Feihu , Bouten Carlijn V. C. , Stassen Oscar M. J. A. , Sahlgren Cecilia M. 
Published: November 2024

AbstractFluid shear stress (FSS) from the blood flow is a crucial regulator of vascular physiology and is associated with major cardiovascular pathologies. Endothelial cells are the primary mechanotransducers of FSS. Here, we show that Jagged1, a canonical ligand of the Notch pathway, modulates biomechanical signaling in endothelial cells in response to FSS. We found that changes in FSS magnitude alter the expression and localization of Jagged1 independently of its effect on Notch expression or activation. Deletion of Jagged1 decreases FSS-induced VEGFR2 and ERK activity in vitro and causes attenuated kinase activity and cardiac defects in zebrafish embryos without significant changes in canonical Notch activity. We show that direct physical stimulation of Jagged1 induces mechanosignaling through the VEGFR2 pathway, independently of Notch signaling but mediated by Jagged1-induced Src activation. Our findings suggest a novel non-canonical role for Jagged1 as a mechanotransducer in endothelial cells with implications for cardiovascular morphogenesis and disease.One Sentence SummaryJag1 activates endothelial mechanosignaling through Src.
autoFISH - a modular toolbox for sequential smFISH experiments
Authors: Weber Christian , Defard Thomas , Lelek Mickael , Laporte Hugo , Mallick Ayan , Londoño-Vallejo José-Arturo , Walter Thomas , Fouillade Charles , Gariboldi Maria Isabella , Mueller Florian 
Published: November 2024

AbstractFluorescence in situ hybridization (FISH) allows for spatial and quantitative profiling of gene expression by visualizing individual RNA molecules. Here, we introduce automated FISH (autoFISH), a comprehensive toolbox to conduct automated single molecule FISH (smFISH) experiments that is both cost-effective and versatile. This includes detailed plans for constructing the necessary equipment, open-source software for control, reliable experimental protocols, and analysis workflows based on our FISH-quant analysis package. Validation experiments with both cell lines and tissue samples confirmed the system’s robustness. We demonstrate standard and amplified smFISH, along with a modified protocol for tissue clearing that enhances nuclear retention while preserving background reduction efficiency.
Quantifying key parameters of environmental transmission and age-specific susceptibility forMycobacterium aviumsubspeciesparatuberculosis (MAP)
Authors: Gao Yuqi , Bijma Piter , de Jong Mart C.M. 
Published: November 2024

AbstractParatuberculosis is a chronic disease in ruminants, caused byMycobacterium avium subspecies paratuberculosis(MAP). This research aims to improve the understanding of transmission dynamics on both exposure and susceptibility— factors influenced by the shedders and the recipients, respectively. We present an age-specific dose-response model, where the decrease in recipient’s susceptibility with age is quantified by a specific rate, and an environmental transmission model, where exposure from shedders is quantified by transmission rate parameters and theMAPdecay rate in the environment. Parameters of both models were estimated based on published experiments. The age-specific susceptibility decrease rate was calculated to be 0.0629 wk− 1. In the transmission model, two sub-models apply different standardization schemes for transiently infectious (Itr), low shedding (Il), high shedding (Ih): Model A standardized shedding rate at 2.29 wk− 1and varied transmission rates across states (and). Model B varied shedding rates across infectious states (and) while keeping the transmission rate constant at 0.0469 wk− 1. In both models, theMAPdecay rate was estimated at 0.424 wk− 1. Then, a scenario study was done, focusing on understanding: changes in environmental contamination levels over time, the timing of exposure, the duration of exposure, and the recipient’s age at exposure. Our findings enhance understanding ofMAPtransmission dynamics and support the development of future models that incorporate real-world complexities and interventions. The 95% confidence intervals for all estimates can be found in the main text.Author SummaryMycobacterium aviumsubspeciesparatuberculosis(MAP) causes paratuberculosis (Johne’s disease), a global concern in dairy farming that results in reduced milk production, health issues in cattle, and potential risk for food safety. In this study, we aimed to improve our understanding of MAP’s environmental transmission dynamics, including its build-up, decay, and transmission (via environmental exposure). We explored how the timing, duration of exposure, and recipient age affect infection probabilities. Our analysis of previous experimental data revealed that susceptibility to infection decreases at a specific rate as animals age. We also assess how the decay of MAP and shedding from three types of infectious animals contributes to contamination. Our findings provide new insights into the transmission dynamics of MAP and offer refined estimates of age-specific susceptibility decrease rate, three MAP shedding rates, three transmission rates and MAP natural decay rate. We hope this research can inform more effective control strategies, particularly those aimed at protecting younger animals and reducing environmental contamination.
Predicting semantic segmentation quality in laryngeal endoscopy images
Authors: Kist Andreas M. , Razi Sina , Groh René , Gritsch Florian , Schützenberger Anne 
Published: November 2024

AbstractEndoscopy is a major tool for assessing the physiology of inner organs. Contemporary artificial intelligence methods are used to fully automatically label medical important classes on a pixel-by-pixel level. This so-called semantic segmentation is for example used to detect cancer tissue or to assess laryngeal physiology. However, due to the diversity of patients presenting, it is necessary to judge the segmentation quality. In this study, we present a fully automatic system to evaluate the segmentation performance in laryngeal endoscopy images. We showcase on glottal area segmentation that the predicted segmentation quality represented by the intersection over union metric is on par with human raters. Using a traffic light system, we are able to identify problematic segmentation frames to allow human-in-the-loop improvements, important for the clinical adaptation of automatic analysis procedures.
Ranking protein-peptide binding affinities with protein language models
Authors: Chalas Charles Charbel , Dunne Michael P. 
Published: November 2024

AbstractIn this study we explore the use of protein language models for ranking protein-peptide interaction strength, extending the concept of binary protein interaction classification. We introduce a method that measures and ranks protein binding affinities in an unsupervised manner, eliminating the need for extensive labeled data, structural information, or complex biochemical features. We demonstrate the utility of our approach across five distinct protein-peptide datasets by comparing predicted interaction strength rankings with experimentally derived inhibitory concentration (IC50) values. Furthermore, we discuss limitations encountered during our study and present preliminary findings on extending our approach to more general protein-protein interactions. Finally, we highlight the need for comprehensive datasets specifically designed for ranking protein-protein interactions.
A whole-animal phenotypic drug screen identifies suppressors of atherogenic lipoproteins
Authors: Kelpsch Daniel J. , Zhang Liyun , Thierer James H. , Koren Kobe , Kumar Urmi , Lin Yuki , Hensley Monica R. , Sohn Mira , Liu Jun O. , Lectka Thomas , Mumm Jeff S. , Farber Steven A. 
Published: November 2024

AbstractLipoproteins are essential for lipid transport in all bilaterians. A single Apolipoprotein B (ApoB) molecule is the inseparable structural scaffold of each ApoB-containing lipoprotein (B-lps), which are responsible for transporting lipids to peripheral tissues. The cellular mechanisms that regulate ApoB and B-lp production, secretion, transport, and degradation remain to be fully defined. In humans, elevated levels of vascular B-lps play a causative role in cardiovascular disease. Previously, we have detailed that human B-lp biology is remarkably conserved in the zebrafish using anin vivochemiluminescent reporter of ApoB (LipoGlo) that does not disrupt ApoB function. Thus, the LipoGlo model is an ideal system for identifying novel mechanisms of ApoB modulation and, due to the ability of zebrafish to generate many progeny, is particularly amenable to large-scale phenotypic drug screening. Here, we report a screen of roughly 3000 compounds that identified 49 unique ApoB-lowering hits. Nineteen hits passed orthogonal screening criteria. A licorice root component, enoxolone, significantly lowered B-lps only in animals that express a functional allele of the nuclear hormone receptor Hepatocyte Nuclear Factor 4⍺ (HNF4⍺). Consistent with this result, inhibitors of HNF4⍺ also reduce B-lp levels. These data demonstrate that mechanism(s) of action can be rapidly determined from a whole animal zebrafish phenotypic screen. Given the well documented role of HNF4⍺ in human B-lp biology, these data validate the LipoGlo screening platform for identifying small molecule modulators of B-lps that play a critical role in a leading cause of worldwide mortality.