bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the Effectiveness of a Population-Level Health Intervention to Increment HCV Treatment Coverage in Tuscany Region, Italy: An Interrupted Time Series Analysis
Authors: Seghieri Chiara , Ceccarelli Luca , Tortù Costanza , Tavoschi Lara 
Published: June 2024

AbstractWorldwide, an estimated 71.1 million people are chronically infected with the Hepatitis C virus (HCV). The advent of direct-acting antivirals (DAAs) has made possible the definition of elimination targets by 2030. This study aimed to evaluate the effectiveness of a population-level health intervention to expand access to HCV treatment in the Tuscany Region, Italy.We used individual-level administrative data from the Tuscany region, collected between January 2015 and December 2022. Data include monthly observations on i) the number of serological tests to detect HCV, ii) the number of PCR tests to detect HCV and, iii) the number of prescriptions of direct-acting antivirals against HCV.We implemented an Interrupted Time Series (ITS) model, where the primary outcome was the number of monthly prescriptions of direct-acting antivirals, while the number of tests to detect HCV were included as control variables. The analysis was implemented i) in the general population, ii) in specific sub-population groups.Results show that the health intervention promoted by the Tuscany Regional Health Authority was highly effective in increasing DAAs treatment coverage in the general population, while no significant effects were observed among sub-population groups.Findings of this study provide evidence to support policies at national and subnational levels to booster HCV screening and simplify access to DAA prescriptions.
A Bayesian Survival Analysis on Long COVID and non Long COVID patients: A Cohort Study Using National COVID Cohort Collaborative (N3C) Data
Authors: Jiang Sihang , Loomba Johanna , Zhou Andrea , Sharma Suchetha , Sengupta Saurav , Liu Jiebei , Brown Donald 
Published: June 2024

AbstractSince the outbreak of COVID-19 pandemic in 2020, numerous researches and studies have focused on the long-term effects of COVID infection. The Centers for Disease Control (CDC) implemented an additional code into the International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) for reporting ‘Post COVID-19 condition, unspecified (U09.9)’ effective on October 1st 2021, representing that Long COVID is a real illness with potential chronic conditions. The National COVID Cohort Collaborative (N3C) provides researchers with abundant electronic health records (EHR) data by aggregating and harmonizing EHR data across different clinical organizations in the United States, making it convenient to build up a survival analysis on Long COVID patients and non Long COVID patients among large amounts of COVID positive patients.
High confidence and demand for hepatitis E vaccine during an outbreak in Bentiu, South Sudan: A qualitative study
Authors: Koyuncu Aybüke , Asilaza Kinya Vincent , Rumunu John , Wamala Joseph , Gitahi Priscillah , Antier Zelie , Duncker Jetske , Nkemenang Patrick , Gakima Primitive , Haile Melat , Gignoux Etienne , Albela Manuel , Loro Frederick Beden , Biem Duol , Rull Monica , Azman Andrew S , Ciglenecki Iza , Nesbitt Robin 
Published: June 2024

AbstractIntroductionIn 2021 in response to an outbreak of hepatitis E in Bentiu internally displaced persons camp the South Sudanese Ministry of Health with support from Médecins Sans Frontières implemented the first-ever mass reactive vaccination campaign with HEV239 (Hecolin; Innovax, Xiamen, China). As part of an evaluation of the feasibility of hepatitis vaccination as part of an epidemic response, we conducted qualitative research to assess knowledge, attitudes, and practices related to hepatitis E and the hepatitis E vaccine.MethodsWe conducted 8 focus group discussions (FGDs) with community leaders, the general population of vaccine-eligible adults, vaccine-eligible pregnant women (vaccinated and non-vaccinated), and healthcare workers. FGDs were separate by gender and were audio recorded, transcribed, and translated to English by trained research assistants. Two coders used inductive thematic analysis to organize emergent themes.ResultsData were collected in November 2022. Most individuals had personal experiences with hepatitis E. Hepatitis E was perceived as a dangerous disease, and almost everyone was knowledgeable about transmission pathways. Participants believed children, pregnant women, and the elderly were the highest risk groups. Participants frequently made requests for additional hepatitis E vaccination campaigns and expanded eligibility criteria for vaccination. The primary barriers to vaccination were practical issues related to being away from the camp at the time of the campaign, but participants shared that some in the community were unvaccinated due to fears about injections, social pressure, misinformation about side effects such as infertility, concerns about why some groups were eligible for vaccination and not others (e.g. young children), and a lack of information about the vaccine/vaccination campaigns.ConclusionPersonal experiences with hepatitis E illness, perceived severity of illness, and confidence in organizations recommending the vaccine were drivers of high demand for hepatitis E vaccines in the first-ever use of the vaccine in an outbreak setting.
Divergent roles of SOX2 in human and mouse germ cell specification related to X-linked gene dosage effects
Authors: He Wenteng , Luo Qing , Zhao Jian , Wang Mengting , Feng Luohua , Zhao Allan , Reda Ahmed , Lindgren Eva , Strukenborg Jan-Bernd , Chen Jiayu , Deng Qiaolin 
Published: June 2024

SummaryHuman primordial germ cell-like cells (hPGCLCs) can be generated from pluripotent stem cells (PSCs) but the differentiation efficiency of female hPSCs is often lower than that of male hPSCs. Moreover, Klinefelter Syndrome (KS), a condition characterized by an extra X-chromosome in males, often presents the failure of germline specification and infertility. In this study, we investigate how X-linked gene dosage affects hPGCLCs specification potential in both healthy and diseased conditions. We reveal that the X-chromosome plays a multifaceted role in modulating hPGCLCs induction. The inhibitory effects on TGF-beta/Activin A and BMP pathways by escape genes IGSF1 and CHRDL1, respectively, are demonstrated by the increased yield of hPGCLCs with knockdown experiments. Importantly, our results identified the intriguing role of SOX2 that is upregulated by the escape geneUSP9Xin hPGCLCs specification, highlighting a species-specific difference from the mouse model. The elevatedUSP9X-SOX2regulatory axis profoundly influences cellular metabolism, mitochondrial morphology, and progenitor competence, thereby affecting hPGCLCs induction. Furthermore, the inability to downregulate SOX2 and upregulate SOX17 in response to BMP signaling impedes downstream gene activation due to motif binding competition. These findings shed novel insights into the hPGC specification by elucidating the differential roles of SOX2 versus SOX17 between mice and humans, influenced by X-linked gene dosage effects. Additionally, our results offer potential applications for improving the induction and survival efficiency of hPGCLCs from hPSCs, facilitating disease modeling and mechanistic studies.HighlightsDownregulation of three X-linked genes, i.e. IGSF1, CHRDL1 and USP9X, enhanced the differentiation efficiency of hPGCLCsSOX2 as a downstream of human-specific escape gene USP9X plays a multifacet role against hPGCLCs specificationFailure to timely downregulate SOX2 and upregulate SOX17 interferes downstream gene activation likely due to motif binding competition
Epigenetic memory of Lateral Ganglionic Eminence derived hiPSCs cannot overcome barriers in authentic MSN differentiation
Authors: Bartley O. J. M. , Vinh N. N. , Lelos M.J. , Williams N. M. , Precious S. V. , Rosser A. E. 
Published: June 2024

AbstractInduced pluripotent stem cells (iPSCs) have previously been shown to retain some of the epigenetic features associated with the tissues from which they were derived, which in turn can help the iPSCs to differentiate towards similar cell fates. Here we investigate whether human iPSCs (hiPSC) derived from the lateral ganglionic eminence (LGE) retain sufficient epigenetic features of their original tissue to enhance their capacity to differentiate into striatal medium spiny neurons (MSN) compared to isogenic controls. We identify a subtle methylation signature within these isogenic hiPSCs, and observe line specific capacities to produce MSN-like cells and their subtypes. We directly compare these cells to authentic LGE derived MSNs and identify large differences in DNA methylation between these populations. Using single cell RNA sequencing, we also find subpopulations that do not reflect the transcriptional profile of authentic MSNs. While we observe some potential epigenetic “benefits” within our LGE derived hiPSC-MSNs (e.g. reduced hypomethylation of off-target pathways), we did not observe an improved propensity to differentiate towards an MSN-like fate. Overall, this work highlights that pluripotent stem cells are unique in their individual capacity for differentiation, that subtle differences between cell lines can have far reaching effects on the final cell product, and that while hPSC-MSNs can model many aspects of MSN development, there are still epigenetic and transcriptional differences that limit the full recapitulation of the authentic LGE-derived MSN phenotype.
Fibrillarin modulates fetal hemoglobin silencing
Authors: Wu Dongliang , Li Qixiang , Qiu Sipei , Guo Chan , Li Feng , Shangguan Wenbing , Li Wenyang , Yang Dongjun , Meng Xingjun , Xing Mengying , Chen Bing , Kong Lingdong , Huang David C. S. , Zhao Quan 
Published: June 2024

AbstractDecoding the molecular mechanisms underlying human fetal (γ) globin gene silencing impacts therapeutic strategies for β-thalassemia and sickle cell disease. Here, we identified a nucleolar protein, fibrillarin (FBL), which mediates the methylation of glutamine104 in histone H2A and functions as a repressor of the γ-globin gene in cultured erythroid cells, including those from β-thalassemia patients. ConditionalFbldepletion in adult β-YAC transgenic mice or in βIVS-2-654-thalassemic mice reactivated the human γ-globin gene or murine embryonic globin expression, respectively, which corrects hematologic and pathologic defects in β-thalassemic mice. We showed that FBL plays a dual role in activatingBCL11Aexpression and repressing γ-globin gene expression, which is dependent on its histone methyltransferase activity. Our study may provide an alternative strategy for therapeutic targeted treatment of β-hemoglobinopathies.
Structural basis of nucleotide selectivity in pyruvate kinase
Authors: Taguchi Atsushi , Nakashima Ryosuke , Nishino Kunihiko 
Published: June 2024

ABSTRACTNucleoside triphosphates are indispensable in numerous biological processes, with enzymes involved in their biogenesis playing pivotal roles in cell proliferation. Pyruvate kinase (PYK), commonly regarded as the terminal glycolytic enzyme that generates ATP in tandem with pyruvate, is also capable of synthesizing a wide range of nucleoside triphosphates from their diphosphate precursors. Despite their substrate promiscuity, some PYKs show preference towards specific nucleotides, suggesting an underlying mechanism for differentiating nucleotide bases. However, the thorough characterization of this mechanism has been hindered by the paucity of nucleotide-bound PYK structures. Here, we present crystal structures ofStreptococcus pneumoniaePYK in complex with four different nucleotides. These structures facilitate direct comparison of the protein-nucleotide interactions and offer structural insights into its pronounced selectivity for GTP synthesis. Notably, this selectivity is dependent on a sequence motif in the nucleotide recognition site that is widely present among prokaryotic PYKs, particularly in Firmicutes species. We show that pneumococcal cell growth is significantly impaired when expressing a PYK variant with compromised GTP and UTP synthesis activity, underscoring the importance of PYK in maintaining nucleotide homeostasis. Our findings collectively advance our understanding of PYK biochemistry and prokaryotic metabolism.
Natural Variation in HIV-1 Entry Kinetics Map to Specific Residues and Reveal an Interdependence Between Attachment and Fusion
Authors: Webb Nicholas E. , Sevareid Colin M. , Sanchez Carolina , Tobin Nicole H. , Aldrovandi Grace M. 
Published: June 2024

AbstractHIV-1 entry kinetics reflect the fluid motion of the HIV envelope glycoprotein through at least three major structural configurations that drive virus-cell membrane fusion. The lifetime of each state is an important component of potency for inhibitors that target them. We used the time-of-addition inhibitor assay and a novel analytical strategy to define the kinetics of pre-hairpin exposure (using T20) and co-receptor engagement (via. maraviroc), through a characteristic delay metric, across a variety of naturally occurring HIV Env isolates. Among 257 distinct HIV-1 envelope isolates we found a remarkable breadth of T20 and maraviroc delays ranging from as early as 30 seconds to as late as 60 minutes. The most extreme delays were observed among transmission-linked clade C isolates. We identified four single-residue determinants of late T20 and maraviroc delays that are associated with either receptor engagement or gp41 function. Comparison of these delays with T20 sensitivity suggest co-receptor engagement and fusogenic activity in gp41 act cooperatively but sequentially to drive entry. Our findings support current models of entry where co-receptor engagement drives gp41 eclipse and have strong implications for the design of entry inhibitors and antibodies that target transient entry states.Author Summary.The first step of HIV-1 infection is entry, where virus-cell membrane fusion is driven by the HIV-1 envelope glycoprotein through a series of conformational changes. Some of the most broadly active entry inhibitors work by binding conformations that exist only transiently during entry. The lifetimes of these states and the kinetics of entry are important elements of inhibitor activity for which little is known. We demonstrate a remarkable range of kinetics among 257 diverse HIV-1 isolates and find that this phenotype is highly flexible, with multiple single-residue determinants. Examination of the kinetics of two conformational landmarks shed light on novel kinetic features that offer new details about the role of co-receptor engagement and provide a framework to explain entry inhibitor synergy.
Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth: a conserved metabolic switch
Authors: Medini Hadar , Mishmar Dan 
Published: June 2024

AbstractInteractions between mitochondrial and nuclear factors are essential to life. Nevertheless, the importance of coordinated regulation of mitochondrial-nuclear gene expression (CMNGE) to changing physiological conditions is poorly understood, and is limited to certain tissues and certain organisms. We hypothesized that CMNGE is important for development across vertebrates, and hence will be conserved. As a first step, we analyzed >1400 RNA-seq experiments performed during embryo development, neonates and adults across vertebrate evolution. We found conserved sharp elevation after birth of CMNGE, including oxidative phosphorylation (OXPHOS) and mitochondrial ribosome genes, in heart, hindbrain, forebrain and kidney across mammals,Gallus gallusand in the lizardAnolis carolinensis. This was accompanied by elevated expression of TCA cycle enzymes, and reduction in hypoxia response genes, suggesting a conserved cross-tissue metabolic switch after birth/hatching. Analysis of ∼70 known regulators of mitochondrial gene expression revealed consistently elevated expression of PGC-1a and C/EBPB after birth/hatching across organisms and tissues, thus highlighting them as candidate regulators of CMNGE upon transition to the neonate. Analyses ofDanio rerio,Xenopus tropicalisandDrosophila melanogasterrevealed elevated CMNGE prior to hatching, coinciding with the development of motor neurons. Lack of such ancient pattern in mammals and in the chicken suggests that it was lost during radiation of terrestrial vertebrates. Taken together, our results suggest that regulated CMNGE during embryogenesis and after birth, alludes to metabolic switch which is under strong selective constraints and hence essential.
Presynaptic GABAAreceptors control integration of nicotinic input onto dopaminergic axons in the striatum
Authors: Brill-Weil Samuel G. , Kramer Paul F. , Yanez Anthony , Clever Faye H. , Zhang Renshu , Khaliq Zayd M. 
Published: June 2024

ABSTRACTAxons of dopaminergic neurons express gamma-aminobutyric acid type-A receptors (GABAARs) and nicotinic acetylcholine receptors (nAChRs) which are both independently positioned to shape striatal dopamine release. Using electrophysiology and calcium imaging, we investigated how interactions between GABAARs and nAChRs influence dopaminergic axon excitability. Direct axonal recordings showed that benzodiazepine application suppresses subthreshold axonal input from cholinergic interneurons (CINs). In imaging experiments, we used the first temporal derivative of presynaptic calcium signals to distinguish between direct- and nAChR-evoked activity in dopaminergic axons. We found that GABAAR antagonism with gabazine selectively enhanced nAChR-evoked axonal signals. Acetylcholine release was unchanged in gabazine suggesting that GABAARs located on dopaminergic axons, but not CINs, mediated this enhancement. Unexpectedly, we found that a widely used GABAAR antagonist, picrotoxin, inhibits axonal nAChRs and should be used cautiously for striatal circuit analysis. Overall, we demonstrate that GABAARs on dopaminergic axons regulate integration of nicotinic input to shape presynaptic excitability.
Dopamine increases protein synthesis in hippocampal neurons enabling dopamine-dependent LTP
Authors: Fuchsberger T. , Stockwell I. , Woods M. , Brzosko Z. , Greger I. , Paulsen O. 
Published: June 2024

AbstractThe reward and novelty related neuromodulator dopamine plays an important role in hippocampal long- term memory, which is thought to involve protein synthesis-dependent synaptic plasticity. However, the direct effects of dopamine on protein synthesis, and the functional implications of newly synthesized proteins for synaptic plasticity, have not yet been investigated. We have previously reported that timing- dependent synaptic depression (t-LTD) can be converted into potentiation by dopamine application during synaptic stimulation (Brzosko et al., 2015) or postsynaptic burst activation (Fuchsberger et al., 2022). Here we show that dopamine increases protein synthesis in mouse hippocampal CA1 neurons, enabling dopamine-dependent long-term potentiation (DA-LTP), which is mediated via the Ca2+-sensitive adenylate cyclase (AC) subtypes 1/8, cAMP, and cAMP-dependent protein kinase (PKA). We found that neuronal activity is required for the dopamine-induced increase in protein synthesis. Furthermore, dopamine induced a protein synthesis-dependent increase in the AMPA receptor subunit GluA1, but not GluA2. We found that DA-LTP is absent in GluA1 knock-out mice and that it requires calcium-permeable AMPA receptors. Taken together, our results suggest that dopamine together with neuronal activity controls synthesis of plasticity-related proteins, including GluA1, which enable DA-LTP via a signalling pathway distinct from that of conventional LTP.
Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells
Authors: Love Kasey S. , Johnstone Christopher P. , Peterman Emma L. , Gaglione Stephanie , Galloway Kate E. 
Published: June 2024

AbstractTo realize the potential of engineered cells in therapeutic applications, transgenes must be expressed within the window of therapeutic efficacy. Differences in copy number and other sources of extrinsic noise generate variance in transgene expression and limit the performance of synthetic gene circuits. In a therapeutic context, supraphysiological expression of transgenes can compromise engineered phenotypes and lead to toxicity. To ensure a narrow range of transgene expression, we design and characterizeCompactmicroRNA-MediatedAttenuator ofNoise andDosage (ComMAND), a single-transcript, microRNA-based incoherent feedforward loop. We experimentally tune the ComMAND output profile, and we model the system to explore additional tuning strategies. By comparing ComMAND to two-gene implementations, we highlight the precise control afforded by the single-transcript architecture, particularly at relatively low copy numbers. We show that ComMAND tightly regulates transgene expression from lentiviruses and precisely controls expression in primary human T cells, primary rat neurons, primary mouse embryonic fibroblasts, and human induced pluripotent stem cells. Finally, ComMAND effectively sets levels of the clinically relevant transgenes FMRP1 and FXN within a narrow window. Together, ComMAND is a compact tool well-suited to precisely specify expression of therapeutic cargoes.
ThePlasmodium falciparumhistone methyltransferase PfSET10 is dispensable for the regulation of antigenic variation and gene expression in blood stage parasites
Authors: Wyss Matthias , Kanyal Abhishek , Niederwieser Igor , Bartfai Richard , Voss Till S. 
Published: June 2024

AbstractThe malaria parasitePlasmodium falciparumemploys antigenic variation of the virulence factorP. falciparumerythrocyte membrane protein 1 (PfEMP1) to escape adaptive immune responses during blood infection. Antigenic variation of PfEMP1 occurs through epigenetic switches in the mutually exclusive expression of individual members of the multi-copyvargene family.vargenes are located in perinuclear clusters of transcriptionally inactive heterochromatin. Singularvargene activation is linked to locus repositioning into a dedicated zone at the nuclear periphery and deposition of histone 3 lysine 4 di-/trimethylation (H3K4me2/3) and H3K9 acetylation marks in the promoter region. While previous work identified the putative H3K4-specific methyltransferase PfSET10 as an essential enzyme and positive regulator ofvargene expression, a recent study reported conflicting data. Here, we used iterative genome editing to engineer a conditional PfSET10 knockout line tailored to study the function of PfSET10 invargene regulation. We demonstrate that PfSET10 is not required for mutually exclusivevargene expression and switching. We also show that PfSET10 is dispensable not only for asexual parasite proliferation but also for sexual conversion and gametocyte differentiation. Furthermore, comparative RNA-seq experiments revealed that PfSET10 plays no obvious role in regulating gene expression during asexual parasite development and gametocytogenesis. Interestingly, however, PfSET10 shows different subnuclear localization patterns in asexual and sexual stage parasites and female-specific expression in mature gametocytes. In summary, our work confirms in detail that PfSET10 is not involved in regulatingvargene expression and not required for blood stage parasite viability, indicating PfSET10 may be important for life cycle progression in the mosquito vector or during liver stage development.