bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors for severe respiratory syncytial virus infection during the first year of life: development and validation of a clinical prediction model
Authors: Vartiainen Pekka , Jukarainen Sakari , Rhedin Samuel Arthur , Prinz Alexandra , Hartonen Tuomo , Vabalas Andrius , Viippola Essi , Rodosthenous Rodosthenis S. , Kuitunen Sara , Liu Aoxing , Lundholm Cecilia , Smew Awad I. , Osvald Emma Caffrey , Helle Emmi , Perola Markus , Almqvist Catarina , Heinonen Santtu , Ganna Andrea 
Published: February 2023

ABSTRACTBackgroundNovel immunisation methods against respiratory syncytial virus (RSV) are emerging, but knowledge of risk factors for severe RSV disease is insufficient for their optimal targeting. We aimed to identify predictors for RSV hospitalisation, and to develop and validate a clinical prediction model to guide RSV immunoprophylaxis for under 1-year-old infants.MethodsIn this retrospective cohort study using nationwide registries, we studied all infants born in 1997-2020 in Finland (n = 1 254 913) and in 2006-2020 in Sweden (n = 1 459 472), and their parents and siblings. We screened 1 510 candidate predictors and we created a logistic regression model with 16 predictors and compared its performance to a machine learning model (XGboost) using all 1 510 candidate predictors.FindingsIn addition to known predictors such as severe congenital heart defects (CHD, adjusted odds ratio (aOR) 2·89, 95% confidence interval 2·28-3·65), we identified novel predictors for RSVH, most notably esophageal malformations (aOR 3·11, 1·86-5·19) and lower complexity CHDs (aOR 1·43, 1·25-1·63).In validation data from 2018-2020, the C-statistic was 0·766 (0·742-0·789) in Finland and 0·737 (0·710-0·762) in Sweden. The clinical prediction model’s performance was similar to the machine learning model (C-statistic in Finland 0·771, 0·754-0·788). Calibration varied according to epidemic intensity. Model performance was similar across different strata of parental income.The infants in the 90th percentile of predicted RSVH probability hospitalisation had 3·3 times higher observed risk than the population’s average. Assuming 60% effectiveness, immunisation in this top 10% of infants at highest risk would have a number needed to treat of 23 in Finland and 40 in Sweden in preventing hospitalisations.InterpretationThe identified predictors and the prediction model can be used in guiding RSV immunoprophylaxis in infants.FundingSigrid Jusélius Foundation, European Research Council, Pediatric Research Foundation (for complete list of funding sources, see Acknowledgements).
Dissecting neuron-specific functions of circadian genes using modified cell-specific CRISPR approaches
Authors: Richhariya Shlesha , Shin Daniel , Le Jasmine Quynh , Rosbash Michael 
Published: February 2023

AbstractCircadian behavioral rhythms inDrosophila melanogasterare regulated by about 75 pairs of brain neurons. They all express the core clock genes but have distinct functions and gene expression profiles. To understand the importance of these distinct molecular programs, neuron-specific gene manipulations are essential. Although RNAi based methods are standard to manipulate gene expression in a cell-specific manner, they are often ineffective, especially in assays involving smaller numbers of neurons or weaker Gal4 drivers. We and others recently exploited a neuron-specific CRISPR-based method to mutagenize genes within circadian neurons. Here we further explore this approach to mutagenize three well-studied clock genes: the transcription factor genevrille,the photoreceptor geneCryptochrome(cry) and the neuropeptide genePdf. The CRISPR-based strategy not only reproduced their known phenotypes but also assignedcryfunction for different light mediated phenotypes to discrete, different subsets of clock neurons. We further tested two recently published methods for temporal regulation in adult neurons, inducible Cas9 and auxin-inducible gene expression system (AGES). The results were not identical, but both approaches successfully showed that the adult-specific knockout of the neuropeptidePdfreproduces the canonical loss-of-function mutant phenotypes. In summary, a CRISPR-based strategy is a highly effective, reliable, and general method to temporally manipulate gene function in specific adult neurons.Significance statementMost animals have specific brain neurons that regulate sleep-wake cycles and other aspects of circadian behavior.Drosophilahas only about 150 of these clock neurons. Despite their small numbers, they have remarkably diverse anatomy and gene expression profiles. To address the different functions of these neurons, we used highly specific and efficient CRISPR-based methods to create cell type-specific disruptions of three traditional circadian genes. We were able to assign the function of the photoreceptor cryptochrome to two tiny subsets of clock neurons. In addition, two independent methods assigned the neuropeptide PDF to the adult stage. In summary, we find that the CRISPR-based methods are very efficient at studying adult specific functions of genes in small, discrete sets of neurons.
Multi-omic screening of invasive GBM cells in engineered biomaterials and patient biopsies reveals targetable transsulfuration pathway alterations
Authors: Garcia Joseph H. , Akins Erin A. , Jain Saket , Wolf Kayla J. , Zhang Jason , Choudhary Nikita , Lad Meeki , Shukla Poojan , Gill Sabraj , Carson Will , Carette Luis , Zheng Allison , Kumar Sanjay , Aghi Manish K. 
Published: February 2023

ABSTRACTWhile the poor prognosis of glioblastoma arises from the invasion of a subset of tumor cells, little is known of the metabolic alterations within these cells that fuel invasion. We integrated spatially addressable hydrogel biomaterial platforms, patient site-directed biopsies, and multi-omics analyses to define metabolic drivers of invasive glioblastoma cells. Metabolomics and lipidomics revealed elevations in the redox buffers cystathionine, hexosylceramides, and glucosyl ceramides in the invasive front of both hydrogel-cultured tumors and patient site-directed biopsies, with immunofluorescence indicating elevated reactive oxygen species (ROS) markers in invasive cells. Transcriptomics confirmed upregulation of ROS-producing and response genes at the invasive front in both hydrogel models and patient tumors. Amongst oncologic ROS, hydrogen peroxide specifically promoted glioblastoma invasion in 3D hydrogel spheroid cultures. A CRISPR metabolic gene screen revealed cystathionine gamma lyase (CTH), which converts cystathionine to the non-essential amino acid cysteine in the transsulfuration pathway, to be essential for glioblastoma invasion. Correspondingly, supplementing CTH knockdown cells with exogenous cysteine rescued invasion. Pharmacologic CTH inhibition suppressed glioblastoma invasion, while CTH knockdown slowed glioblastoma invasionin vivo. Our studies highlight the importance of ROS metabolism in invasive glioblastoma cells and support further exploration of the transsulfuration pathway as a mechanistic and therapeutic target.
Rapid genotyping of porcine reproductive and respiratory syndrome virus (PRRSV) using MinION nanopore sequencing
Authors: Caserta Leonardo Cardia , Zhang Jianqiang , Piñeyro Pablo , Diel Diego G. 
Published: February 2023

AbstractThe global distribution and constant evolution are challenges for the control of porcine reproductive and respiratory syndrome virus (PRRSV), one of the most important viruses affecting swine worldwide. Effective control of PRRSV benefits from genotyping, which currently relies on Sanger sequencing. Here we developed and optimized procedures for real-time genotyping and whole genome sequencing of PRRSV directly from clinical samples based on targeted amplicon- and long amplicon tiling sequencing using the MinION Oxford Nanopore platform. Procedures were developed and tested on 154 clinical samples (including lung, serum, oral fluid and processing fluid) with RT-PCR Ct values ranging from 15 to 35. The targeted amplicon sequencing (TAS) approach was developed to obtain sequences of the complete ORF5 (main target gene for PRRSV genotyping) and partial ORF4 and ORF6 sequences of both PRRSV-1 and PRRSV-2 species. After only 5 min of sequencing, PRRSV consensus sequences with identities to reference sequences above 99% were obtained, enabling rapid identification and genotyping of clinical PRRSV samples into lineages 1, 5 and 8. The long amplicon tiling sequencing (LATS) approach targets type 2 PRRSV, the most prevalent viral species in the U.S. and China. Complete PRRSV genomes were obtained within the first hour of sequencing for samples with Ct values below 24.9. Ninety-two whole genome sequences were obtained using the LATS procedure. Fifty out of 60 sera (83.3%) and 18 out of 20 lung samples (90%) had at least 80% of genome covered at a minimum of 20X sequence depth per position. The procedures developed and optimized in this study here are valuable tools with potential for field application during PRRSV elimination programs.
Age-related differences in fMRI subsequent memory effects are directly linked to local grey matter volume differences
Authors: Kizilirmak Jasmin M. , Soch Joram , Richter Anni , Schott Björn H. 
Published: February 2023

AbstractEpisodic memory performance declines with increasing age, and older adults typically show reduced activation of inferior temporo-parietal cortices in functional magnetic resonance imaging (fMRI) studies of episodic memory formation. Given the age-related cortical volume loss, it is conceivable that age-related reduction of memory-related fMRI activity may be partially attributable to reduced grey matter volume (GMV). We performed a voxel-wise multimodal neuroimaging analysis of fMRI correlates of successful memory encoding, using regional GMV as covariate. In a large cohort of healthy adults (106 young, 111 older), older adults showed reduced GMV across the entire neocortex and reduced encoding-related activation of inferior temporal and parieto-occipital cortices compared to young adults. Importantly, these reduced fMRI activations during successful encoding in older adults could in part be attributed to lower regional GMV. Our results highlight the importance of controlling for structural MRI differences in fMRI studies in older adults but also demonstrate that age-related differences in memory-related fMRI activity cannot be attributed to structural variability alone.
Striatal ensemble activity in an innate naturalistic behavior
Authors: Minkowicz Samuel , Mathews Mychaela Alexandria , Mou Felicia Hoilam , Yoon Hyoseo , Freda Sara Nicole , Cui Ethan S , Kennedy Ann , Kozorovitskiy Yevgenia 
Published: February 2023

AbstractSelf-grooming is an innate, naturalistic behavior found in a wide variety of organisms. The control of rodent grooming has been shown to be mediated by the dorsolateral striatum through lesion studies and in-vivo extracellular recordings. Yet, it is unclear how populations of neurons in the striatum encode grooming. We recorded single-unit extracellular activity from populations of neurons in freely moving mice and developed a semi-automated approach to detect self-grooming events from 117 hours of simultaneous multi-camera video recordings of mouse behavior. We first characterized the grooming transition-aligned response profiles of striatal projection neuron and fast spiking interneuron single units. We identified striatal ensembles whose units were more strongly correlated during grooming than during the entire session. These ensembles display varied grooming responses, including transient changes around grooming transitions or sustained changes in activity throughout the duration of grooming. Neural trajectories computed from the identified ensembles retain the grooming related dynamics present in trajectories computed from all units in the session. These results elaborate striatal function in rodent self-grooming and demonstrate that striatal grooming-related activity is organized within functional ensembles, improving our understanding of how the striatum guides action selection in a naturalistic behavior.
A Suspension Trapping–Based Sample Preparation Workflow for Sensitive Plant Phosphoproteomics
Authors: Chen Chin-Wen , Tsai Chia-Feng , Lin Miao-Hsia , Lin Shu-Yu , Hsu Chuan-Chih 
Published: February 2023

ABSTRACTPlant phosphoproteomics provides a global view of phosphorylation-mediated signaling in plants; however, it demands high-throughput methods with sensitive detection and accurate quantification. Although protein precipitation is indispensable for removing contaminants and improving sample purity, it limits the sensitivity and throughput of plant phosphoproteomic analysis. The multiple handling steps involved in protein precipitation lead to sample loss and process variability. Herein, we developed an approach based on suspension trapping (S-Trap), termed tandem S-Trap-IMAC (immobilized metal ion affinity chromatography), by integrating an S-Trap micro column with an Fe-IMAC tip. Compared with a precipitation-based workflow, the tandem S-Trap-IMAC method deepened the coverage of the Arabidopsis (Arabidopsis thaliana) phosphoproteome by more than 30%, with improved quantification accuracy and short sample processing time. We applied the tandem S-Trap-IMAC method for studying abscisic acid (ABA) signaling in Arabidopsis seedlings. We thus identified 24,055 phosphopeptides and quantified several key phosphorylation sites on core ABA signaling components across four time points. Our results show that the optimized workflow aids high-throughput phosphoproteome profiling of low-input plant samples.
Genetic dependencies associated with transcription factor activities in human cancer cell lines
Authors: Thatikonda Venu , Supper Verena , Ravichandran Madhwesh C. , Lipp Jesse J. , Boghossian Andrew S. , Rees Matthew G. , Ronan Melissa M. , Roth Jennifer A. , Grosche Sara , Neumüller Ralph A. , Mair Barbara , Mauri Federico , Popa Alexandra 
Published: February 2023

AbstractTranscription factors (TFs) are key components of the aberrant transcriptional programs in cancer cells. In this study, we used TF activity (TFa), inferred from the downstream regulons as a potential biomarker to identify associated genetic vulnerabilities in cancer cells. Our linear model framework, integrating TFa and genome-wide CRISPR knockout datasets identified 1,770 candidate TFa-target pairs across different cancer types and assessed their survival impact in patient data. As a proof of concept, through inhibitor screens and genetic depletion assays in cell lines, we validated the dependency of cell lines on predicted targets linked to TEAD1, the most prominent TF from our analysis. Overall, these candidate pairs represent an attractive resource for early-stage targets and drug discovery programs in oncology.
Glutamine metabolism inhibition has dual immunomodulatory and antibacterial activities againstMycobacterium tuberculosis
Authors: Parveen Sadiya , Shen Jessica , Lun Shichun , Zhao Liang , Koleske Benjamin , Leone Robert D. , Rais Rana , Powell Jonathan D. , Murphy John R. , Slusher Barbara S. , Bishai William R. 
Published: February 2023

ABSTRACTAs one of the most successful human pathogens,Mycobacterium tuberculosis(Mtb) has evolved a diverse array of determinants to subvert host immunity and alter host metabolic patterns. However, the mechanisms of pathogen interference with host metabolism remain poorly understood. Here we show that a novel glutamine metabolism antagonist, JHU083, inhibitsMtbproliferation in vitro and in vivo. JHU083-treated mice exhibit weight gain, improved survival, a 2.5 log lower lung bacillary burden at 35 days post-infection, and reduced lung pathology. JHU083 treatment also initiates earlier T-cell recruitment, increased proinflammatory myeloid cell infiltration, and a reduced frequency of immunosuppressive myeloid cells when compared to uninfected and rifampin-treated controls. Metabolomics analysis of lungs from JHU083-treatedMtb-infected mice revealed reduced glutamine levels, citrulline accumulation suggesting elevated NOS activity, and lowered levels of quinolinic acid which is derived from the immunosuppressive metabolite kynurenine. When tested in an immunocompromised mouse model ofMtbinfection, JHU083 lost its therapeutic efficacy suggesting the drug’s host-directed effects are likely to be predominant. Collectively, these data reveal that JHU083-mediated glutamine metabolism inhibition results in dual antibacterial and host-directed activity against tuberculosis.
Enhanced inflammatory signaling driven by metabolic switch in Aicardi-Goutières syndrome
Authors: Batignes Maxime , Luka Marine , Jagtap Surabhi , de Cevins Camille , Nemazanyy Ivan , Fali Tinhinane , García-Paredes Víctor , Carbone Francesco , Pérot Brieuc P. , Neven Bénédicte , Bader-Meunier Brigitte , Quartier dit Maire Pierre , Hully Marie , Belot Alexandre , Lepelley Alice , Frémond Marie-Louise , Crow Yanick J. , Fischer Alain , Ménager Mickaël M. 
Published: February 2023

SummaryAicardi-Goutières syndrome (AGS) is a genetic type I interferon (IFN)-mediated disease characterised by neurological involvement with onset in childhood. Chronic inflammation in response to uncontrolled type I IFN production is, among other things, associated with IP-10 secretion. We analysed, at the single-cell transcriptomic levels, peripheral blood samples from patients bearing AGS-causing mutations inSAMHD1,RNASEH2BorADAR1genes. Using machine-learning approaches and differential gene expression we identified a drastic loss of transcription factor hypoxia induced factor 1 α (HIF-1α) expression and activity associated with features of a metabolic switch and mitochondrial stress in monocytes/dendritic cells. Chemical stabilization of HIF-1α, with a synthetic drug in anin vitromodel of AGS, allowed us to reverse the energy metabolic switch, attenuate mitochondrial stress and markedly reduce IP-10 production. We therefore propose that energy metabolic switch contributes to exacerbated chronic inflammation in AGS, and that targeting this pathway might represent a promising therapeutic approach.
Predicting the Three-dimensional Structure of the c-KITOncogene Promoter and the Dynamics of Strongly Coupled Guanine-Quadruplexes
Authors: Bignon Emmanuelle , Spinello Angelo , Miclot Tom , D’ Anna Luisa , Ducani Cosimo , Grandemange Stéphanie , Barone Giampaolo , Monari Antonio , Terenzi Alessio 
Published: February 2023

ABSTRACTGuanine-quadruplexes (G4s) are non-canonical DNA structures that play important protective and regulatory roles within cells, influencing, for instance, gene expression. Although the secondary structure of many human G4s is well characterized, in several gene-promoter regions multiple G4s are located in close proximity and may form three-dimensional structures which could ultimately influence their biological roles. In this contribution, we analyze the interplay between the three neighboring G4s present in the c-KITproto-oncogene promoter, namely WK1, WSP and WK2. In particular, we highlight how these three G4s are structurally linked and how their crosstalk favors the formation of a parallel structure for WSP, differently from what observed for this isolated G4 in solution. Relying on all-atom molecular dynamic simulations exceeding the μs time-scale and using enhanced sampling methods, we provide the first computationally-resolved structure of a well-organized G4 cluster in the promoter of a crucial gene involved in cancer development. Our results indicate that neighboring G4s influence their mutual three-dimensional arrangement and provide a powerful tool to predict and interpret complex DNA structures that ultimately can be used as starting point for drug discovery purposes.
Anesthesia suppresses gastric myoelectric power in the ferret
Authors: Tomaselli Lorenzo , Sciullo Michael , Fulton Stephanie , Yates Bill J. , Fisher Lee E. , Ventura Valérie , Horn Charles C. 
Published: February 2023

AbstractBackgroundGastrointestinal myoelectric signals have been the focus of extensive research; although it is unclear how general anesthesia affects these signals, studies have often been conducted under general anesthesia. Here, we explore this issue directly by recording gastric myoelectric signals during awake and anesthetized states in the ferret and also explore the contribution of behavioral movement to observed changes in signal power.MethodsFerrets were surgically implanted with electrodes to record gastric myoelectric activity from the serosal surface of the stomach, and, following recovery, were tested in awake and isoflurane-anesthetized conditions. Video recordings were also analyzed during awake experiments to compare myoelectric activity during behavioral movement and rest.Key ResultsA significant decrease in gastric myoelectric signal power was detected under isoflurane anesthesia compared to the awake condition. Moreover, a detailed analysis of the awake recordings indicates that behavioral movement is associated with increased signal power compared to rest.Conclusions & InferencesThese results suggest that both general anesthesia and behavioral movement can affect the amplitude of gastric myoelectric. In summary, caution should be taken in studying myoelectric data collected under anesthesia. Further, behavioral movement could have an important modulatory role on these signals, affecting their interpretation in clinical settings.
Combinatory EHMT and PARP inhibition induces an interferon response and a CD8 T cell-dependent tumor regression in PARP inhibitor-resistant models
Authors: Nguyen Lily L. , Watson Zachary L. , Ortega Raquel , Woodruff Elizabeth R. , Jordan Kimberly R. , Iwanaga Ritsuko , Yamamoto Tomomi M. , Bailey Courtney A. , Jeong Abigail D. , Guntupalli Saketh R. , Behbakht Kian , Gbaja Veronica , Arnoult Nausica , Chuong Edward B. , Bitler Benjamin G. 
Published: February 2023

ABSTRACTEuchromatic histone lysine methyltransferases 1 and 2 (EHMT1/2), which catalyze demethylation of histone H3 lysine 9 (H3K9me2), contribute to tumorigenesis and therapy resistance through unknown mechanisms of action. In ovarian cancer, EHMT1/2 and H3K9me2 are directly linked to acquired resistance to poly-ADP-ribose polymerase (PARP) inhibitors and are correlated with poor clinical outcomes. Using a combination of experimental and bioinformatic analyses in several PARP inhibitor resistant ovarian cancer models, we demonstrate that combinatory inhibition of EHMT and PARP is effective in treating PARP inhibitor resistant ovarian cancers. Ourin vitrostudies show that combinatory therapy reactivates transposable elements, increases immunostimulatory dsRNA formation, and elicits several immune signaling pathways. Ourin vivostudies show that both single inhibition of EHMT and combinatory inhibition of EHMT and PARP reduces tumor burden, and that this reduction is dependent on CD8 T cells. Together, our results uncover a direct mechanism by which EHMT inhibition helps to overcome PARP inhibitor resistance and shows how an epigenetic therapy can be used to enhance anti-tumor immunity and address therapy resistance.