bluuebunny/crossref_metadata_2025_split huggingface dataset:
K18-hACE2 Mice for Studies of COVID-19 Treatments and Pathogenesis Including Anosmia
Authors: Zheng Jian , Roy Wong Lok-Yin , Li Kun , Verma Abhishek K. , Ortiz Miguel , Wohlford-Lenane Christine , Leidinger Mariah R. , Knudson C. Michael , Meyerholz David K. , McCray Paul B. , Perlman Stanley 
Published: August 2020

ABSTRACTThe ongoing COVID-19 pandemic is associated with substantial morbidity and mortality. While much has been learned in the first months of the pandemic, many features of COVID-19 pathogenesis remain to be determined. For example, anosmia is a common presentation and many patients with this finding show no or only minor respiratory signs. Studies in animals experimentally infected with SARS-CoV-2, the cause of COVID-19, provide opportunities to study aspects of the disease not easily investigated in human patients. COVID-19 severity ranges from asymptomatic to lethal. Most experimental infections provide insights into mild disease. Here, using K18-hACE2 mice that we originally developed for SARS studies, we show that infection with SARS-CoV-2 causes severe disease in the lung, and in some mice, the brain. Evidence of thrombosis and vasculitis was detected in mice with severe pneumonia. Further, we show that infusion of convalescent plasma (CP) from a recovered COVID-19 patient provided protection against lethal disease. Mice developed anosmia at early times after infection. Notably, while treatment with CP prevented significant clinical disease, it did not prevent anosmia. Thus K18-hACE2 mice provide a useful model for studying the pathological underpinnings of both mild and lethal COVID-19 and for assessing therapeutic interventions.
Worldwide tracing of mutations and the evolutionary dynamics of SARS-CoV-2
Authors: Zhou Zhong-Yin , Liu Hang , Zhang Yue-Dong , Wu Yin-Qiao , Peng Min-Sheng , Li Aimin , Irwin David M. , Li Haipeng , Lu Jian , Bao Yiming , Lu Xuemei , Liu Di , Zhang Ya-Ping 
Published: August 2020

AbstractUnderstanding the mutational and evolutionary dynamics of SARS-CoV-2 is essential for treating COVID-19 and the development of a vaccine. Here, we analyzed publicly available 15,818 assembled SARS-CoV-2 genome sequences, along with 2,350 raw sequence datasets sampled worldwide. We investigated the distribution of inter-host single nucleotide polymorphisms (inter-host SNPs) and intra-host single nucleotide variations (iSNVs). Mutations have been observed at 35.6% (10,649/29,903) of the bases in the genome. The substitution rate in some protein coding regions is higher than the average in SARS-CoV-2 viruses, and the high substitution rate in some regions might be driven to escape immune recognition by diversifying selection. Both recurrent mutations and human-to-human transmission are mechanisms that generate fitness advantageous mutations. Furthermore, the frequency of three mutations (S protein, F400L; ORF3a protein, T164I; and ORF1a protein, Q6383H) has gradual increased over time on lineages, which provides new clues for the early detection of fitness advantageous mutations. Our study provides theoretical support for vaccine development and the optimization of treatment for COVID-19. We call researchers to submit raw sequence data to public databases.
SARS-CoV-2 neutralization and serology testing of COVID-19 convalescent plasma from donors with non-severe disease
Authors: Gniadek Thomas J. , Thiede Joshua M. , Matchett William E. , Gress Abigail R. , Pape Kathryn A. , Jenkins Marc K. , Menachery Vineet D. , Langlois Ryan A. , Bold Tyler D. 
Published: August 2020

AbstractWe determined the antigen binding activity of convalescent plasma units from 47 individuals with a history of non-severe COVID-19 using three clinical diagnostic serology assays (Beckman, DiaSorin, and Roche) with different SARS-CoV-2 targets. We compared these results with functional neutralization activity using a fluorescent reporter strain of SARS-CoV-2 in a microwell assay. This revealed positive correlations of varying strength (Spearman r = 0.37-0.52) between binding and neutralization. Donors age 48-75 had the highest neutralization activity. Units in the highest tertile of binding activity for each assay were enriched (75-82%) for those with the highest levels of neutralization.
Hydrogen Peroxide Levels in Freshly Brewed Coffee and the Effects of Storage
Authors: Uppu Sannihith N. , London Bianca K. 
Published: August 2020

SummaryOne of the world’s most consumed beverages, coffee has its origins as early as the 15thcentury Ethiopia. Although there are studies on caffeine and other components of coffee such as cafestol and kahweol, up until recently knowledge of the presence of hydrogen peroxide (H2O2) in coffee was confined to the scientific community and some informed public. It is a general belief that H2O2is formed only after long periods of storage or with certain roasting practices. The present study is focused on dispelling the myths of H2O2in coffee. We first measured H2O2in freshly brewed coffee from different companies using the ferrous oxidation-xylenol orange binding (FOX) assay. Following this, we examined the time-dependent accumulation of H2O2and its changes with temperature. Further, H2O2was estimated in coffee obtained from several local vendors. Contrary to the general belief that the accumulation of H2O2is an aging phenomenon of coffee, we found this toxicant even in freshly brewed coffee. This was true for all brands tested, and the H2O2content increased upon storage. The highest increase was seen in coffee stored on the hot plate compared to the ones kept at room temperature (22-25 °C) or in the cold (0-4 °C). The H2O2content of coffee from different vendors ranged between 0.29 and 0.82 mM, which is 5- to 20-fold higher than the typical H2O2concentrations at which significant cytotoxic effects have been reported for assay systems using the human Fanconi deficient (PD20 FANCD2−/−) fibroblasts and other cell types. Our findings are deemed to shine new light on the probable toxic effects of a commonly consumed beverage like coffee, and the time and temperature dependent variations of keeping. While there are documented benefits of consumption of coffee, the possible H2O2-medicated toxic effects are critical and should be considered. Future studies are warranted to delineate the contribution of H2O2in the healthy wellbeing of individuals who consume coffee extensively.
Input-output signal processing plasticity of vagal motorneurons in response to cardiac ischemic injury
Authors: Gorky Jonathan , Moss Alison , Balycheva Marina , Vadigepalli Rajanikanth , Schwaber James S. 
Published: August 2020

AbstractVagal stimulation is emerging as the next frontier in bioelectronic medicine to modulate peripheral organ health and treat disease. The neuronal molecular phenotypes in the dorsal motor nucleus of the vagus (DMV) remain largely unexplored, limiting the potential for harnessing the DMV plasticity for therapeutic interventions. We developed a mesoscale single cell transcriptomics data from hundreds of DMV neurons under homeostasis and following physiological perturbations. Our results revealed that homeostatic DMV neuronal states can be organized into distinguishable input-output signal processing units. Remote ischemic preconditioning induced a distinctive shift in the neuronal states towards diminishing the role of inhibitory inputs, with concomitant changes in regulatory microRNAs miR-218a and miR-495. Chronic cardiac ischemic injury resulted in a dramatic shift in DMV neuronal states suggestive of enhanced neurosecretory function. We propose a DMV molecular network mechanism that integrates combinatorial neurotransmitter inputs from multiple brain regions and humoral signals to modulate cardiac health.
A potent neutralizing nanobody against SARS-CoV-2 with inhaled delivery potential
Authors: Gai Junwei , Ma Linlin , Li Guanghui , Zhu Min , Qiao Peng , Li Xiaofei , Zhang Haiwei , Zhang Yanmin , Chen Yadong , Ji Weiwei , Zhang Hao , Cao Huanhuan , Li Xionghui , Gong Rui , Wan Yakun 
Published: August 2020

AbstractThe outbreak of COVID-19 has emerged as a global pandemic. The unprecedented scale and severity call for rapid development of effective prophylactics or therapeutics. We here reported Nanobody (Nb) phage display libraries derived from four camels immunized with the SARS-CoV-2 spike receptor-binding domain (RBD), from which 381 Nbs were identified to recognize SARS-CoV-2-RBD. Furthermore, seven Nbs were shown to block interaction of human angiotensin converting enzyme 2 (ACE2) with SARS-CoV-2-RBD-variants, bat-SL-CoV-WIV1-RBD and SARS-CoV-1-RBD. Among the seven candidates, Nb11-59 exhibited the highest activity against authentic SARS-CoV-2 with ND50 of 0.55 μg/mL. Nb11-59 can be produced on a large-scale in Pichia pastoris, with 20 g/L titer and 99.36% purity. It also showed good stability profile, and nebulization did not impact its stability. Overall, Nb11-59 might be a promising prophylactic and therapeutic molecule against COVID-19, especially through inhalation delivery.Graphical Abstract
Brain-wide mapping of neural activity mediating collicular-dependent behaviors
Authors: Sans-Dublanc Arnau , Chrzanowska Anna , Reinhard Katja , Lemmon Dani , Montaldo Gabriel , Urban Alan , Farrow Karl 
Published: August 2020

AbstractNeuronal cell-types are arranged in brain-wide circuits to guide behavior. In mice, the superior colliculus is comprised of a set of cell-types that each innervate distinct downstream targets. Here we reveal the brain-wide networks downstream of four collicular cell-types by combining functional ultrasound imaging (fUSi) with optogenetics to monitor neural activity at a resolution of ~100 μm. Each neuronal group triggered different behaviors, and activated distinct, partially overlapping sets of brain nuclei. This included regions not previously thought to mediate defensive behaviors, e.g. the posterior paralaminar nuclei of the thalamus (PPnT), that we show to play a role in suppressing habituation. Electrophysiological recordings support the fUSi findings and show that neurons in the downstream nuclei preferentially respond to innately threatening visual stimuli. This work provides insight into the functional organization of the networks governing defensive behaviors and demonstrates an experimental approach to explore the whole-brain neuronal activity downstream of targeted cell-types.
DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist
Authors: Thépaut Michel , Luczkowiak Joanna , Vivès Corinne , Labiod Nuria , Bally Isabelle , Lasala Fátima , Grimoire Yasmina , Fenel Daphna , Sattin Sara , Thielens Nicole , Schoehn Guy , Bernardi Anna , Delgado Rafael , Fieschi Franck 
Published: August 2020

SummaryThe efficient spread of SARS-CoV-2 resulted in a pandemic that is unique in modern history. Despite early identification of ACE2 as the receptor for viral spike protein, much remains to be understood about the molecular events behind viral dissemination. We evaluated the contribution of C-type lectin receptors (CLRS) of antigen-presenting cells, widely present in air mucosa and lung tissue. DC-SIGN, L-SIGN, Langerin and MGL bind to diverse glycans of the spike using multiple interaction areas. Using pseudovirus and cells derived from monocytes or T-lymphocytes, we demonstrate that while virus capture by the CLRs examined does not allow direct cell infection, DC/L-SIGN, among these receptors, promote virus transfer to permissive ACE2+ cells. A glycomimetic compound designed against DC-SIGN, enable inhibition of this process. Thus, we described a mechanism potentiating viral capture and spreading of infection. Early involvement of APCs opens new avenues for understanding and treating the imbalanced innate immune response observed in COVID-19 pathogenesis
The tiny Cretaceous stem-birdOculudentavisrevealed as a bizarre lizard
Authors: Bolet Arnau , Stanley Edward L. , Daza Juan D. , Arias J. Salvador , Čerňanský Andrej , Vidal-García Marta , Bauer Aaron M. , Bevitt Joseph J. , Peretti Adolf , Evans Susan E. 
Published: August 2020

AbstractOculudentavis khaungraaewas described based on a tiny skull trapped in amber. The slender tapering rostrum with retracted osseous nares, large eyes, and short vaulted braincase led to its identification as the smallest avian dinosaur on record, comparable to the smallest living hummingbirds. Despite its bird-like appearance,Oculudentavisshowed several features inconsistent with its original phylogenetic placement. Here we describe a more complete, specimen that demonstratesOculudentavisis actually a bizarre lizard of uncertain position. The new interpretation and phylogenetic placement highlights a rare case of convergent evolution rarely seen among reptiles. Our results re-affirm the importance of Myanmar amber in yielding unusual taxa from a forest ecosystem rarely represented in the fossil record.
Identification of spacer and protospacer sequence requirements in theVibrio choleraeType I-E CRISPR/Cas System
Authors: Bourgeois Jacob , Lazinski David W. , Camilli Andrew 
Published: August 2020

AbstractThe prokaryotic adaptive immune system CRISPR/Cas serves as defense against bacteriophage and invasive nucleic acid. A Type I-E CRISPR/Cas system has been detected in classical biotype isolates ofVibrio cholerae, the causative agent of the disease cholera. Experimental characterization of this system revealed a functional immune system that operates using a 5’-TT-3’ protospacer-adjacent motif (PAM) for interference. However, several designed spacers against the 5’-TT-3’ PAM do not interfere as expected, indicating further investigation of this system is necessary. In this study, we identified additional sequence requirements of a pyrimidine in the 5’ position of the spacer and purine in the complementary position of the protospacer using 873 unique spacers and 2267 protospacers mined from CRISPR arrays in deposited sequences ofV. cholerae. We present bioinformatic evidence that during acquisition the protospacer purine is captured in the prespacer and that a 5’-RTT-3’ PAM is necessary for spacer acquisition. Finally, we demonstrate experimentally that a 5’-RTT-3’ PAM is necessary for CRISPR interference by designing and manipulating spacer and cognate PAMs in a plasmid conjugation assay and discover functional consequences of base pairing with the 5’ spacer pyrimidine in spacer efficacy.ImportanceBacterial CRISPR/Cas systems provide immunity by defending against phage and other invading elements. A thorough comprehension of the molecular mechanisms employed by these diverse systems will improve our understanding of bacteriophage-bacterial interactions and bacterial adaptation to foreign DNA. TheVibrio choleraeType I-E system was previously identified in an extinct classical biotype and was partially characterized for its function. Here, using both bioinformatic and functional assays, we extend that initial study. We have found that the Type I-E system still exists in modern strains ofV. cholerae. Furthermore, we defined additional sequence elements in both the CRISPR array and in target DNA that are required for immunity. CRISPR/Cas systems are now commonly used as precise and powerful genetic engineering tools. Knowledge of the sequences required for CRISPR/Cas immunity is a prerequisite for the effective design and experimental use of these systems. Our results greatly facilitate the effective use of one such system. Furthermore, we provide a publicly available script that assists in the detection and validation of CRISPR/Cas immunity requirements when such a system exists in any bacterial species.
Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization
Authors: Goren Emily , Wang Chong , He Zhulin , Sheflin Amy M , Chiniquy Dawn , Prenni Jessica E , Tringe Susannah , Schachtman Daniel P , Liu Peng 
Published: August 2020

AbstractBackgroundMicrobiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and optimization of crop yields which requires identification of microbiome features that impact the outcome in the population of interest. That task is challenging because of the high dimensionality of microbiome data and the confounding that results from the complex and dynamic interactions among host, environment, and microbiome. In the presence of such confounding, variable selection and estimation procedures may have unsatisfactory performance in identifying microbial features with an effect on the outcome.ResultsIn this manuscript, we aim to estimate population-level effects of individual microbiome features while controlling for confounding by a categorical variable. Due to the high dimensionality and confounding-induced correlation between features, we propose feature screening, selection, and estimation conditional on each stratum of the confounder followed by a standardization approach to estimation of population-level effects of individual features.Comprehensive simulation studies demonstrate the advantages of our approach in recovering relevant features. Utilizing a potential-outcomes framework, we outline assumptions required to ascribe causal, rather than associational, interpretations to the identified microbiome effects. We conducted an agricultural study of the rhizosphere microbiome of sorghum in which nitrogen fertilizer application is a confounding variable. In this study, the proposed approach identified microbial taxa that are consistent with biological understanding of potential plant-microbe interactions.ConclusionsStandardization enables more accurate identification of individual microbiome features with an effect on the outcome of interest compared to other variable selection and estimation procedures when there is confounding by a categorical variable.
Discovery of COVID-19 Inhibitors Targeting the SARS-CoV2 Nsp13 Helicase
Authors: White Mark Andrew , Lin Wei , Cheng Xiaodong 
Published: August 2020

ABSTRACTThe raging COVID-19 pandemic caused by SARS-CoV2 has infected millions of people and killed several hundred thousand patients worldwide. Currently, there are no effective drugs or vaccines available for treating coronavirus infections. In this study, we have focused on the SARS-CoV2 helicase (Nsp13), which is critical for viral replication and the most conserved non-structural protein within the coronavirus family. Using homology modeling and molecular dynamics approaches, we generated structural models of the SARS-CoV2 helicase in its apo- and ATP/RNA-bound conformations. We performed virtual screening of ~970,000 chemical compounds against the ATP binding site to identify potential inhibitors. Herein, we report docking hits of approved human drugs targeting the ATP binding site. Importantly, two of our top drug hits have significant activity in inhibiting purified recombinant SARS-CoV-2 helicase, providing hope that these drugs can be potentially repurposed for the treatment of COVID-19.
Comparison of polygenic risk scores for coronary artery disease highlights obstacles to overcome for clinical use
Authors: Trochet Holly , Pelletier Justin , Tadros Rafik , Hussin Julie G 
Published: August 2020

AbstractPolygenic risk scores, or PRS, are a tool to estimate individuals’ liabilities to a disease or trait measurement based solely on genetic information. One commonly discussed potential use is in the clinic to identify people who are at greater risk of developing a disease. In this paper, we compare three PRS models that incorporate a large number of genetic markers for coronary artery disease (CAD). In the UK Biobank, the cohort which was used at some point in the creation or validation of each score, we calculated the association between CAD, the scores, and population structure for the white British subset. After adjusting for geographic and socioeconomic factors, CAD was not associated with the first principal components of genetic diversity, which reflect fine-scale population structure. In contrast, all three scores were confounded by these genetic components, highlighting that PRS may be influenced by genetic factors not directly causal for CAD, thereby raising concerns about their biases in clinical application.Furthermore, we investigated the differences in risk stratification using four different UK Biobank assessment centers as separate cohorts, and tested how missing genetic data affected risk stratification through simulation. We show that missing data impact classification for extreme individuals for high- and low-risk, and quantiles of risk are sensitive to individual-level genotype missingness. Distributions of scores varied between assessment centers, revealing that thresholding based on quantiles can be problematic for consistency across centers and populations. Based on these results, we discuss potential avenues of improvements of PRS methodologies for usage in clinical practice.
Anatomical modeling of brain vasculature in two-photon microscopy by generalizable deep learning
Authors: Tahir Waleed , Kura Sreekanth , Zhu Jiabei , Cheng Xiaojun , Damseh Rafat , Tadesse Fetsum , Seibel Alex , Lee Blaire S. , Lesage Frédéric , Sakadžié Sava , Boas David A. , Tian Lei 
Published: August 2020

AbstractObjective and Impact StatementSegmentation of blood vessels from two-photon microscopy (2PM) angiograms of brains has important applications in hemodynamic analysis and disease diagnosis. Here we develop a generalizable deep learning technique for accurate 2PM vascular segmentation of sizable regions in mouse brains acquired from multiple 2PM setups. The technique is computationally efficient, thus ideal for large-scale neurovascular analysis.IntroductionVascular segmentation from 2PM angiograms is an important first step in hemodynamic modeling of brain vasculature. Existing segmentation methods based on deep learning either lack the ability to generalize to data from different imaging systems, or are computationally infeasible for large-scale angiograms. In this work, we overcome both these limitations by a method that is generalizable to various imaging systems, and is able to segment large-scale angiograms.MethodsWe employ a computationally efficient deep learning framework with a loss function that incorporates a balanced binary-cross-entropy loss and a total variation regularization on the network’s output. Its effectiveness is demonstrated on experimentally acquired in-vivo angiograms from mouse brains of dimensions up to 808×808×702 μm.ResultsTo demonstrate the superior generalizability of our framework, we train on data from only one 2PM microscope, and demonstrate high-quality segmentation on data from a different microscope without any network tuning. Overall, our method demonstrates 10× faster computation in terms of voxels-segmented-per-second and 3× larger depth compared to the state-of-the-art.ConclusionOur work provides a generalizable and computationally efficient anatomical modeling framework for brain vasculature, which consists of deep learning based vascular segmentation followed by graphing. It paves the way for future modeling and analysis of hemodynamic response at much greater scales that were inaccessible before.