bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influenza A virus diffusion through mucus gel networks
Authors: Kaler Logan , Iverson Ethan , Bader Shahed , Song Daniel , Scull Margaret A. , Duncan Gregg A. 
Published: August 2020

ABSTRACTIn this study, influenza A virus (IAV) and nanoparticle diffusion in human airway mucus was quantified using fluorescent video microscopy and multiple particle tracking. In previous work, it was determined that mucin-associated sialic acid acts as a decoy receptor for IAV hemagglutinin binding, and that virus passage through the mucus gel layer is facilitated through the sialic-acid cleaving enzyme, neuraminidase (NA), also present on the IAV envelope. However, our data suggests the mobility of IAV in mucus is significantly influenced by the mesh structure of the gel, as measured by nanoparticle probes, and NA activity is not required to facilitate virus passage through mucus gels. Using newly developed analyses, the binding affinity of IAV to the 3D mucus meshwork was estimated for individual virions with dissociation constants in the mM range, indicative of weak and reversible IAV-mucus interactions. We also found IAV diffusion significantly increased in mucus when treated with a mucolytic agent to break mucin-mucin disulfide bonds. In addition, IAV diffusion was significantly limited in a synthetic mucus model as crosslink density was systematically increased and network pore size was reduced. The results of this work provide important insights on how the balance of adhesive and physical barrier properties of mucus influence the dissemination of IAV within the lung microenvironment.
Genotypic diversity and dynamic nomenclature ofParechovirus A
Authors: Parker Edyth , Han Alvin , Brouwer Lieke , Wolthers Katja , Benschop Kimberley , Russell Colin A. 
Published: August 2020

AbstractHuman parechoviruses (PeV-A) can cause severe sepsis and neurological syndromes in neonates and children and are currently classified into 19 genotypes based on genetic divergence in the VP1 gene. However, the genotyping system has notable limitations including an arbitrary distance threshold and reliance on insufficiently robust phylogenetic reconstruction approaches leading to inconsistent genotype definitions. In order to improve the genotyping system, we investigated the molecular epidemiology of human parechoviruses, including the evolutionary history of the different PeV-A lineages as far as is possible. We found that PeV-A lineages suffer from severe substitution saturation in the VP1 gene which limit the inference of deep evolutionary timescales among the extant PeV-A and suggest that the degree of evolutionary divergence among current PeV-A lineages has been substantially underestimated, further confounding the current genotyping system. We propose an alternative nomenclature system based on robust, amino-acid level phylogenetic reconstruction and clustering with the PhyCLIP algorithm which delineates highly divergent currently designated genotypes more informatively. We also describe a dynamic nomenclature framework that combines PhyCLIP’s progressive clustering with phylogenetic placement for genotype assignment.
simATAC: a single-cell ATAC-seq simulation framework
Authors: Navidi Zeinab , Zhang Lin , Wang Bo 
Published: August 2020

AbstractSingle-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) identifies regulated chromatin accessibility modules at the single-cell resolution. Robust evaluation is critical to the development of scATAC-seq pipelines, which calls for reproducible datasets for benchmarking. We hereby present the simATAC framework, an R package that generates scATAC-seq count matrices that highly resemble real scATAC-seq datasets in library size, sparsity, and chromatin accessibility signals. simATAC deploys statistical models derived from analyzing 90 real scATAC-seq cell groups. simATAC provides a robust and systematic approach to generate in silico scATAC-seq samples with known cell labels for assessing analytical pipelines.
Whole-brain mapping of monosynaptic inputs to midbrain cholinergic neurons
Authors: Huerta-Ocampo Icnelia , Dautan Daniel , Gut Nadine K. , Khan Bakhtawer , Mena-Segovia Juan 
Published: August 2020

AbstractThe cholinergic midbrain is involved in a wide range of motor and cognitive processes. Cholinergic neurons of the pedunculopontine (PPN) and laterodorsal tegmental nucleus (LDT) send long-ranging axonal projections that target sensorimotor and limbic areas in the thalamus, the dopaminergic midbrain and the striatal complex following a topographical gradient, where they influence a range of functions including attention, reinforcement learning and action-selection. Nevertheless, a comprehensive examination of the afferents to PPN and LDT cholinergic neurons is still lacking, partly due to the neurochemical heterogeneity of this region. Here we characterize the whole-brain input connectome to cholinergic neurons across distinct functional domains (i.e. PPN vs LDT) using conditional transsynaptic retrograde labeling in ChAT::Cre male and female rats. The quantification of input neurons revealed that both PPN and LDT receive similar substantial inputs from the superior colliculus and the output of the basal ganglia (i.e. substantia nigra pars reticulata). In addition, we found that PPN cholinergic neurons receive preferential inputs from basal ganglia structures than from the cortex, whereas LDT cholinergic neurons receive preferential inputs from cortical areas. Our results provide the first characterization of inputs to PPN and LDT cholinergic neurons. The differences in afferents to each cholinergic structure support their differential roles in behavior.Significance statementAcetylcholine is a widespread neuromodulator that regulates a wide variety of functions including learning, goal-directed behavior and execution of movements. In this study we characterized the distribution of presynaptic neurons that modulate the activity of functionally distinct midbrain cholinergic neurons located in the pedunculopontine nucleus (PPN) and the laterodorsal tegmental nucleus (LDT) by using a transsynaptic, modified-rabies virus strategy. We reveal that input neurons are widely distributed throughout the brain but segregated into specific functional domains. Motor related areas innervate preferentially the PPN, whereas limbic related areas preferentially innervate the LDT. Our results suggest that input neurons located along distinct functional domains have differential impact over cholinergic midbrain regions.
Developmentally regulated activation of defense allows for rapid inhibition of infection in age-related resistance toPhytophthora capsiciin cucumber fruit
Authors: Mansfeld Ben N. , Colle Marivi , Zhang Chunqiu , Lin Ying-Chen , Grumet Rebecca 
Published: August 2020

AbstractBackgroundAge-related resistance (ARR) is a developmentally regulated phenomenon conferring resistance to pathogens or pests. Although ARR has been observed in several host-pathogen systems, the underlying mechanisms are largely uncharacterized. In cucumber, rapidly growing fruit are highly susceptible toPhytophthora capsicibut become resistant as they complete exponential growth. We previously demonstrated that ARR is associated with the fruit peel and identified gene expression and metabolomic changes potentially functioning as preformed defenses.ResultsHere, we compare the response to infection in fruit at resistant and susceptible ages using microscopy, quantitative bioassays, and weighted gene co-expression analyses. We observed strong transcriptional changes unique to resistant aged fruit 2-4 hours post inoculation (hpi). Microscopy and bioassays confirmed this early response, with evidence of pathogen death and infection failure as early as 4 hpi and cessation of pathogen growth by 8-10 hpi. Expression analyses identified candidate genes involved in conferring the rapid response including those encoding transcription factors, hormone signaling pathways, and defenses such as reactive oxygen species metabolism and phenylpropanoid biosynthesis.ConclusionThe early pathogen death and rapid defense response in resistant-aged fruit provide insight into potential mechanisms for ARR, implicating both pre-formed biochemical defenses and developmentally regulated capacity for pathogen recognition as key factors shaping age-related resistance.
A data-driven epidemiological model to explain the Covid-19 pandemic in multiple countries and help in choosing mitigation strategies
Authors: Beira M. J. , Kumar A. , Perfeito L. , Gonçalves-Sá J. , Sebastião P. J. 
Published: August 2020

AbstractAccurate models are fundamental to understand the dynamics of the COVID-19 pandemic and to evaluate different mitigation strategies. Here, we present a multi-compartmental model that fits the epidemiological data for eleven countries, despite the reduced number of fitting parameters. This model consistently explains the data for the daily infected, recovered, and dead over the first six months of the pandemic. The good quality of the fits makes it possible to explore different scenarios and evaluate the impact of both individual and collective behaviors and government-level decisions to mitigate the epidemic. We identify robust alternatives to lockdown, such as self-protection measures, and massive testing. Furthermore, communication and risk perception are fundamental to modulate the success of different strategies. The fitting/simulation tool is publicly available for use and test of other models, allowing for comparisons between different underlying assumptions, mitigation measures, and policy recommendations.
Exploring the Feasibility of Using Real-World Data from a Large Clinical Data Research Network to Simulate Clinical Trials of Alzheimer’s Disease
Authors: Chen Zhaoyi , Zhang Hansi , Guo Yi , George Thomas J , Prosperi Mattia , Hogan William R , He Zhe , Shenkman Elizabeth A , Wang Fei , Bian Jiang 
Published: August 2020

ABSTRACTIn this study, we explored the feasibility of using real-world data (RWD) from a large clinical research network to simulate real-world clinical trials of Alzheimer’s disease (AD). The target trial (i.e.,NCT00478205) is a Phase III double-blind, parallel-group trial that compared the 23 mg donepezil sustained release with the 10 mg donepezil immediate release formulation in patients with moderate to severe AD. We followed the target trial’s study protocol to identify the study population, treatment regimen assignments, and outcome assessments, and to set up a number of different simulation scenarios and parameters. We considered two main scenarios: (1) a one-arm simulation: simulating a standard-of-care arm that can serve as an external control arm; and (2) a two-arm simulation: simulating both intervention and control arms with proper patient matching algorithms for comparative effectiveness analysis. In the two-arm simulation scenario, we used propensity score matching controlling for baseline characteristics to simulate the randomization process. In the two-arm simulation, higher SAE rates were observed in the simulated trials than the rates reported in original trial, and a higher SAE rate was observed in the 23mg arm than the 10 mg standard-of-care arm. In the one-arm simulation scenario, similar estimates of SAE rates were observed when proportional sampling was used to control demographic variables. In conclusion, trial simulation using RWD is feasible in this example of AD trial in terms of safety evaluation. Trial simulation using RWD could be a valuable tool for post-market comparative effectiveness studies and for informing future trials’ design. Nevertheless, such approach may be limited, for example, by the availability of RWD that matches the target trials of interest, and further investigations are warranted.
A novel stress response pathway regulates rRNA biogenesis
Authors: Szaflarski Witold , Sowiński Mateusz , Leśniczak Marta , Ojha Sandeep , Aulas Anaïs , Dave Dhwani , Malla Sulochan , Anderson Paul , Ivanov Pavel , Lyons Shawn M. 
Published: August 2020

ABSTRACTProduction of ribosomes is an energy-intensive process owing to the intricacy of these massive macromolecular machines. Each human ribosome contains 80 ribosomal proteins and four non-coding RNAs. Accurate assembly requires precise regulation of protein and RNA subunits. In response to stress, the integrated stress response (ISR) rapidly inhibits global translation. How rRNA is coordinately regulated with the rapid inhibition of ribosomal protein synthesis is not known. Here we show that stress specifically inhibits the first step of rRNA processing. Unprocessed rRNA is stored within the nucleolus, and, when stress resolves, it re-enters the ribosome biogenesis pathway. Retention of unprocessed rRNA within the nucleolus aids in the maintenance of this organelle. This response is independent of the ISR or inhibition of cellular translation but represents an independent stress-response pathway that we term Ribosome Biogenesis Stress Response (RiBiSR). Failure to coordinately regulate ribosomal protein translation and rRNA production results in nucleolar fragmentation. Our study unveils a novel stress response pathway that aims at conserving energy, preserving the nucleolus, and prevents further stress by regulation of rRNA processing.
SARS-CoV-2 ORF9b Antagonizes Type I and III Interferons by Targeting Multiple Components of RIG-I/MDA-5-MAVS, TLR3-TRIF, and cGAS-STING Signaling Pathways
Authors: Han Lulu , Zhuang Meng-Wei , Zheng Yi , Zhang Jing , Nan Mei-Ling , Wang Pei-Hui , Gao Chengjiang 
Published: August 2020

AbstractSevere acute respiratory syndrome corona-virus 2 (SARS-CoV-2), the etiologic agent of the coronavirus disease 2019 (COVID-19), has a catastrophic effect on human health and society. Clinical findings indicated that the suppression of innate antiviral immunity, especially the type I and III interferon (IFN) production, contributes to the pathogenesis of COVID-19. However, how SARS-CoV-2 evades antiviral immunity still needs further investigations. Here, we reported that the open reading frame 9b (ORF9b) protein encoded by the SARS-CoV-2 genome inhibits the activation of type I and III IFN response by targeting multiple molecules of innate antiviral signaling pathways. SARS-CoV-2 ORF9b impaired the induction of type I and III IFNs by Sendai virus or the dsRNA mimic poly (I:C). SARS-CoV-2 ORF9b inhibits the activation of type I and III IFNs induced by the components of cytosolic dsRNA-sensing pathways of RIG-I/MDA5-MAVS signaling, including RIG-I, MDA-5, MAVS, TBK1, and IKKε rather than IRF3-5D, the active form of IRF3. SARS-CoV-2 ORF9b also suppressed the induction of type I and III IFNs by TRIF and STING, the adaptor protein of endosome RNA-sensing pathway of TLR3-TRIF signaling and the adaptor protein of cytosolic DNA-sensing pathway of cGAS-STING signaling, respectively. Mechanistically, SARS-CoV-2 ORF9b protein interacts with RIG-I, MDA-5, MAVS, TRIF, STING, TBK1, and prevents TBK1 phosphorylation, thus impeding the phosphorylation and nuclear trans-localization of IRF3 activation. Overexpression of SARS-CoV-2 ORF9b facilitates the replication of the vesicular stomatitis virus. Therefore, SARS-CoV-2 ORF9b negatively regulates antiviral immunity, thus, facilitate virus replication. This study contributes to our understanding of the molecular mechanism of how SARS-CoV-2 impaired antiviral immunity and providing an essential clue to the pathogenesis of COVID-19.
Healthcare workers’ high COVID-19 infection rate: the source of infections and potential for respirators and surgical masks to reduce occupational infections
Authors: Oksanen Lotta-Maria A. H. , Sanmark Enni , Oksanen Sampo A. , Anttila Veli-Jukka , Paterno Jussi J. , Lappalainen Maija , Lehtonen Lasse , Geneid Ahmed 
Published: August 2020

AbstractObjectiveTo analyse the work-related exposure to SARS-CoV-2 and trace the source of COVID-19 infections in tertiary hospitals’ healthcare workers in light of the used PPE and their ability to maintain social distances and follow governmental restrictions.DesignCross-sectional studySettingTertiary hospitals in Uusimaa region, FinlandParticipantsOf 1072 enrolled, 866 HCWs (588 nurses, 170 doctors and 108 laboratory and medical imaging nurses) from the Helsinki University Hospital completed the questionnaire by July 15th, 2020. The average age of participants was 42.4 years and 772 (89.0%) were women. The participants answered a detailed questionnaire of their PPE usage, ability to follow safety restrictions, exposure to COVID-19, the source of potential COVID-19 infection and both mental and physical symptoms during the first wave of COVID-19 in Finland.Main outcome measuresAll participants with COVID-19 symptoms were tested with either RT-PCR or antibody tests. The infections were traced and categorised based on the location and source of infection. The possibility to maintain social distance and PPE usage during exposure were analyzed.ResultsOf the HCWs that participated, 41 (4.7%) tested positive for SARS-CoV-2, marking a substantially higher infection rate than that of the general population (0.3%); 22 (53.6%) of infections were confirmed or likely occupational, including 7 (31.8%) from colleagues. Additionally, 5 (26.3%) of other infections were from colleagues outside the working facilities. 14 (63.6%) of occupational infections occurred while using a surgical mask. No occupational infections were found while using an FFP2/3 respirator and aerosol precautions while treating suspected or confirmed COVID-19 patients.ConclusionsWhile treating suspected or confirmed COVID-19 patients, HCWs should wear an FFP2/3 respirator and recommended PPE. Maintaining safety distances in the workplace and controlling infections between HCWs should be priorities to ensure safe working conditions.
No metabolic “default mode” of human brain function
Authors: Jonasson Lars S , Grill Filip , Hahn Andreas , Rischka Lucas , Lanzenberger Rupert , Lundmark Vania Panes , Riklund Katrine , Axelsson Jan , Rieckmann Anna 
Published: August 2020

AbstractThe finding of reduced activity in the default mode network (DMN) during externally focused cognitive control has been highly influential to our understanding of human brain function, but ‘deactivations’ have also prompted major questions of interpretation. Using hybrid functional PET-MR imaging, this study shows that fMRI task activations and deactivations do not reflect antagonistic patterns of synaptic metabolism. FMRI activations were accompanied by concomitant increases in metabolism during cognitive control, but, unlike the BOLD response, metabolism in the core DMN did not change between rest and task. Metabolic increases along the borders of the DMN during task performance further revealed a set of regions that guide engagement and suppression of neighboring networks during cognitive control. Collectively, dissociations between metabolism and BOLD signal specific to the DMN reveal functional heterogeneity in this network and demonstrate that BOLD deactivations during cognitive control should not be interpreted to reflect reduced synaptic activity.
Critical role of the periplasm in copper homeostasis in Gram-negative bacteria
Authors: Ishihara Jun-ichi , Mekubo Tomohiro , Kusaka Chikako , Kondo Suguru , Aiba Hirofumi , Ishikawa Shu , Ogasawara Naotake , Oshima Taku , Takahashi Hiroki 
Published: August 2020

AbstractCopper is essential for life, but is toxic in excess; that is, cells must keep an optimal internal copper concentration. Under aerobic conditions, less toxic Cu(II) taken up by bacterial cells is reduced to more toxic Cu(I) in the cytoplasm. Copper homeostasis is achieved in the cytoplasm and the periplasm as a unique feature of Gram-negative bacteria. The copper efflux pumps, CopA and CusCBA export Cu(I) from the cytoplasm or the periplasm to outside of the cells inEscherichia coli. In addition, the periplasmic proteins, such as a multi-copper oxidase CueO, play a role in the periplasmic detoxification. While the efflux pumps are highly conserved in Gram-negative bacteria, the periplasmic proteins are diversified, indicating that copper homeostasis in the periplasm could contribute to adaptation to various living environments. However, the role of the periplasm and periplasmic proteins in regard to whole-cell copper homeostasis remains unknown. In this study, we addressed the role of the periplasm and periplasmic proteins in copper homeostasis to adapt to various ecological niches. We have used a systems approach, alternating rounds of experiments and models, to further elucidate the dynamics of copper efflux system. We measured the response to copper of the main specific copper export systems in the wild typeE. colistrain, and a series of deletion mutant strains. We interpreted these data using a detailed mathematical model and Bayesian model fitting routines, and verified copper homeostasis. Compared with the simulation and the growth in response to copper, we found that the growth was associated with copper abundance in the periplasm. In particular, CueO unique to Gram-negative bacteria contributes both to protection against Cu(I) toxicity and to incorporating copper into the periplasmic components/proteins, resulting in maximizing the growth. These results suggest that Gram-negative bacteria have evolved to utilize the periplasm as a sensor and store for copper, in order to enable Gram-negative bacteria to adapt to a wide range of environmental copper concentrations.
Baculovirus-vectored precision delivery of large DNA cargoes in human genomes
Authors: Aulicino Francesco , Pelosse Martin , Toelzer Christine , Capin Julien , Meysami Parisa , Dillingham Mark Simon , Schaffitzel Christiane , Berger Imre 
Published: August 2020

AbstractPrecise gene editing and genome engineering by CRISPR technology requires simultaneous delivery of multiple DNA-encoded components into living cells rapidly exceeding the cargo capacity of currently utilized viral vector systems. Here we exploit the unmatched heterologous DNA cargo capacity of baculovirus to resolve this bottleneck. We implement hybrid DNA techniques (MultiMate) for rapid and error-free assembly of currently up to 25 functional DNA modules in a single baculoviral vector enabling CRISPR-based genome engineering. Utilizing homology-independent targeted integration (HITI), we achieve up to 30% correct genome interventions in human cells, including precision docking of large DNA payloads in theACTBlocus. We demonstrate baculovirus-vectored delivery of prime-editing toolkits for seamless DNA search-and-replace interventions achieving, with a single vector, highly efficient cleavage-free trinucleotide insertion in theHEK3locus without any detectable indels. Our approach thus unlocks a wide range of editing and engineering applications in human cell genomes.