bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of in-house, indirect ELISAs for the detection of SARS-CoV-2 spike protein-associated serology in COVID-19 patients in Panama
Authors: de la Guardia Carolina , Rangel Giselle , Villarreal Alcibiades , Goodridge Amador , Fernández Patricia L , Lleonart Ricardo 
Published: May 2021

AbstractCOVID-19 is the name of the acute respiratory disease caused by the new coronavirus SARS-CoV-2, a close relative of those that caused the severe outbreaks of SARS and MERS several years ago. Since first appearance on December of 2019, the COVID-19 pandemic has cause extremely high levels of mortality, morbidity, global economic breakdown and the consequent human suffering. While vaccination efforts are not extensive and rapid enough, the main tools to keep the virus under control are still keeping physical distancing, reinforce personal hygiene measures, using masks and early diagnosis of virus infected persons, either symptomatic or not. The main diagnostic test for the confirmation of symptomatic individuals is the detection of viral RNA by reverse transcriptase – quantitative real time PCR (RT-PCR). Additionally, serology techniques, such as ELISA are extremely useful to measure the antibodies generated in humans after virus contact, as well as the direct presence of viral antigens. In this study we aim to assemble and evaluate four ELISAs assays to measure the presence of IgG or IgM specific for the viral Spike protein in COVID-19 patients, using either the full recombinant SARS-CoV-2 Spike protein or the fragment corresponding to the receptor binding domain. As a control, we also analyzed a group of prepandemic serum samples obtained before 2017.Strong reactivity was observed against both antigens. A few prepandemic samples displayed high OD values, suggesting the possibility of some crossreactivity. All four assays show very good repeatability, both intra- and inter-assay; however, no clear relationship could be detected between positivity and time of sample collection for serology. Receiver operating characteristic analysis allowed the definition of cutoffs and evaluation of performance for each ELISA by estimation of the area under the curve. This performance parameter was high for all tests (AUC range: 0.98-0.995). Multiple comparisons between tests revealed no significant difference between each other (P values: 0.24-0.95). Our results show that both antigens are very effective to reveal both specific IgG and IgM antibodies, with high sensitivity (range 0.929-0.99) and specificity (range 0.933-0.977). The estimated congruence with the RT-PCR test, as estimated by Cohen’s Kappa, indicates a high agreement in all cases (range 0.874-0.937). This test will allow health authorities to have a new tool to estimate seroprevalence, and to manage and improve the serious sanitary situation created by this virus.
Possible role of accessory proteins in the viral replication for the 20I/501Y.V1 (B.1.1.7) SARS-CoV-2 variant
Authors: Nyayanit Dimpal A. , Sarkale Prasad , Shete-Aich Anita , Kumar Abhinendra , Patil Savita , Majumdar Triparna , Baradkar Shreekant , Gawande Pranita , Mohandas Sreelekshmy , Yadav Pragya D 
Published: May 2021

AbstractThe study investigates the replication cycle and transcriptional pattern of the B.1.1.7 variant. It was observed that the B.1.1.7 variant required a longer maturation time. The transcriptional response demonstrated higher expression of ORF6 and ORF8 compared to nucleocapsid transcript till the eclipse period which might influence higher viral replication. The number of infectious viruses titer is higher in the B.1.1.7, despite a lesser copy number than B.1, indicating higher infectivity.
Point of care testing for detection of coronaviruses including SARS-CoV-2 from saliva without treating RNA in advance
Authors: Muraoka Masaaki , Kawaguchi Osamu , Mizukoshi Mikio , Sejima Shunsuke 
Published: May 2021

ABSTRACTCoronavirus disease 2019 (COVID-19) outbreak was reported to the WHO (World Health Organization) as an outbreak on end of 2019, afterwards pandemic on the worldwide in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has be reported it to cause COVID-19, and highly transmissible. Therefore, it is important that it is rapidly and continuously detected and monitored on site so that the infection is prevented. Namely, POCT (point of care testing) may be important to control cross infection of SARS-CoV-2. At present, the routine confirmation of SARS-CoV-2 is based on detection of sequence unique in the virus RNA by nucleic acid amplification tests (NAATs) such as rRT-PCR. Taking POCT into account, it is clear that it takes time and labour very much or much. Thus, it was our purpose this time to contribute to develop POCT for microbes such as SARS-CoV-2, and thus needed to improve NAATs method.First, combining the mobile real-time RT-PCR (rRT-PCR) device PCR1100 with the appropriate rRT-PCR reagent, we found that it is possible to detect RNA of SARS-CoV-2 for less 14 minutes with equivalent accuracy to conventional devices. Next, we found that the above method made it possible for us to detect coronaviruses by direct rRT-PCR without pre-treatments. Furthermore, it also made clear that coronaviruses in saliva could be detected by the similar direct rRT-PCR method.Hence, it was concluded that this method made it possible to detect virus in saliva without treating in advance (extraction, purification, concentration, etc.), and moreover, samples would be able to be collected with non-invasive. For this reason, we suggest that this method is useful for POCT of coronaviruses including SARS-CoV-2.
Forecasting COVID-19 Spreading in Canada using Deep Learning
Authors: Khennou Fadoua , Akhloufi Moulay A. 
Published: May 2021

AbstractThe novel coronavirus disease 2019 (COVID-19) is disrupting all aspects of our lives as the global spread of the virus continues. In this difficult period, various research projects are taking place to study and analyse the dynamics of the pandemic. In the present work, we firstly present a deep overview of the main forecasting models to predict the new cases of COVID-19. In this context, we focus on univariate time series models in order to analyze the dynamic change of this pandemic through time. We secondly shed light on multivariate time series forecasting models using weather and daily tests data, to study the impact of exogenous features on the progression of COVID-19. In the final stage of this paper, we present our proposed approach based on LSTM and GRU ensemble learning model and evaluate the results using the MAE, RMSE and MAPE for the prediction of new cases. The results of our experiments using the Canadian dataset show that the ensemble model performs well in comparison to other models. In addition, this research provides us with a new outcome regarding the dynamic correlation between temperature, humidity and daily test data and its impact on the new contaminated cases.
Signaling through FcγRIIA and the C5a-C5aR pathway mediates platelet hyperactivation in COVID-19
Authors: Apostolidis Sokratis A. , Sarkar Amrita , Giannini Heather M. , Goel Rishi R. , Mathew Divij , Suzuki Aae , Baxter Amy E. , Greenplate Allison R. , Alanio Cécile , Abdel-Hakeem Mohamed , Oldridge Derek A. , Giles Josephine , Wu Jennifer E. , Chen Zeyu , Huang Yinghui Jane , Pattekar Ajinkya , Manne Sasikanth , Kuthuru Oliva , Dougherty Jeanette , Weiderhold Brittany , Weisman Ariel R. , Ittner Caroline A. G. , Gouma Sigrid , Dunbar Debora , Frank Ian , Huang Alexander C. , Vella Laura A. ,   The UPenn COVID Processing Unit, Reilly John P. , Hensley Scott E. , Rauova Lubica , Zhao Liang , Meyer Nuala J. , Poncz Mortimer , Abrams Charles S. , Wherry E. John 
Published: May 2021

AbstractPatients with COVID-19 present with a wide variety of clinical manifestations. Thromboembolic events constitute a significant cause of morbidity and mortality in patients infected with SARS-CoV-2. Severe COVID-19 has been associated with hyperinflammation and pre-existing cardiovascular disease. Platelets are important mediators and sensors of inflammation and are directly affected by cardiovascular stressors. In this report, we found that platelets from severely ill, hospitalized COVID-19 patients exhibit higher basal levels of activation measured by P-selectin surface expression, and have a poor functional reserve upon in vitro stimulation. Correlating clinical features to the ability of plasma from COVID-19 patients to stimulate control platelets identified ferritin as a pivotal clinical marker associated with platelet hyperactivation. The COVID-19 plasma-mediated effect on control platelets was highest for patients that subsequently developed inpatient thrombotic events. Proteomic analysis of plasma from COVID-19 patients identified key mediators of inflammation and cardiovascular disease that positively correlated with in vitro platelet activation. Mechanistically, blocking the signaling of the FcγRIIa-Syk and C5a-C5aR pathways on platelets, using antibody-mediated neutralization, IgG depletion or the Syk inhibitor fostamatinib, reversed this hyperactivity driven by COVID-19 plasma and prevented platelet aggregation in endothelial microfluidic chamber conditions, thus identifying these potentially actionable pathways as central for platelet activation and/or vascular complications in COVID-19 patients. In conclusion, we reveal a key role of platelet-mediated immunothrombosis in COVID-19 and identify distinct, clinically relevant, targetable signaling pathways that mediate this effect. These studies have implications for the role of platelet hyperactivation in complications associated with SARS-CoV-2 infection.Cover illustrationOne-sentence summaryThe FcγRIIA and C5a-C5aR pathways mediate platelet hyperactivation in COVID-19
ACE2 expression in rat brain: implications for COVID-19 associated neurological manifestations
Authors: Hernández Vito S , Zetter Mario A , Guerra Enrique C. , Hernández-Araiza Ileana , Karuzin Nikita , Hernández-Pérez Oscar R. , Eiden Lee E , Zhang Limei 
Published: May 2021

AbstractWe examined cell type-specific expression and distribution of rat brain angiotensin converting enzyme 2 (ACE2), the receptor for SARS-CoV-2, in rodent brain. ACE2 is ubiquitously present in brain vasculature, with the highest density of ACE2 expressing capillaries found in the olfactory bulb, the hypothalamic paraventricular, supraoptic and mammillary nuclei, the midbrain substantia nigra and ventral tegmental area, and the hindbrain pontine nucleus, pre-Bötzinger complex, and nucleus oftractus solitarius. ACE2 was expressed in astrocytes and astrocytic foot processes, pericytes and endothelial cells, key components of the blood-brain-barrier. We found discrete neuronal groups immunopositive for ACE2 in brainstem respiratory rhythm generating centers including the pontine nucleus, the parafascicular/retrotrapezoid nucleus, the parabrachial nucleus, the Bötzinger and pre-Bötzinger complex and the nucleus of tractus solitarius; in arousal-related pontine reticular nucleus and in gigantocellular reticular nuclei; in brainstem aminergic nuclei, including substantia nigra, ventral tegmental area, dorsal raphe, and locus coeruleus; in the epithalamic habenula, hypothalamic paraventricular and suprammamillary nuclei; and in the hippocampus. Identification of ACE2-expressing neurons in rat brain within well-established functional circuits facilitates prediction of possible neurological manifestations of brain ACE2 dysregulation during and after COVID-19 infection.HighlightsACE2 is present in astrocytes, pericytes, and endothelia of the blood brain barrier.Neuronal ACE2 expression is shown in discrete nuclei through the brain.Brainstem breathing, arousal-related, hypothalamic and limbic nuclei express ACE2.ACE2 is expressed in circuits potentially involved in COVID-19 pathophysiology.
Inhibiting LSD1 suppresses coronavirus-induced inflammation but spares innate antiviral activity
Authors: Mazzarella Luca , Santoro Fabio , Ravasio Roberto , Massa Paul E. , Rodighiero Simona , Gavilán Elena , Romanenghi Mauro , Duso Bruno Achutti , Bonetti Emanuele , Pallavi Rani , Trastulli Deborah , Pallavicini Isabella , Gentile Claudia , Leonardi Tommaso , Pasqualato Sebastiano , Buttinelli Gabriele , Martino Angela Di , Fedele Giorgio , Schiavoni Ilaria , Stefanelli Paola , Meroni Giuseppe , Steinkuhler Christian , Fossati Gianluca , Minucci Saverio , Pelicci Pier Giuseppe 
Published: May 2021

AbstractTissue-resident macrophages exert critical but conflicting effects on the progression of coronavirus infections by secreting both anti-viral type I Interferons and tissue-damaging inflammatory cytokines. Steroids, the only class of host-targeting drugs approved for Covid19, indiscriminately suppress both responses, possibly impairing viral clearance, and provide limited clinical benefit. Here we set up a mousein vitroco-culture system that reproduces the macrophage response to SARS-CoV2 seen in patients and allows quantitation of inflammatory and antiviral activities. We show that the NFKB-dependent inflammatory response can be selectively inhibited by ablating the lysine-demethylase LSD1, which additionally unleashed interferon-independent ISG activation and blocked viral egress through the lysosomal pathway. These results provide a rationale for repurposing LSD1 inhibitors, a class of drugs extensively studied in oncology, for Covid-19 treatment.One-Sentence SummaryTargeting a chromatin-modifying enzyme in coronavirus infections curbs tissue-damage without affecting antiviral response
Vitamin C Binds to SARS Coronavirus-2 Main Protease Essential for Viral Replication
Authors: Malla Tek Narsingh , Pandey Suraj , Aldama Luis , Feliz Dennisse , Noda Moraima , Poudyal Ishwor , Phillips George N. , Stojković Emina A. , Schmidt Marius 
Published: May 2021

AbstractThere is an urgent need for anti-viral agents that treat and/or prevent Covid-19 caused by SARS-Coronavirus (CoV-2) infections. The replication of the SARS CoV-2 is dependent on the activity of two cysteine proteases, a papain-like protease, PL-pro, and the 3C-like protease known as main protease Mpro or 3CLpro. The shortest and the safest path to clinical use is the repurposing of drugs with binding affinity to PLpro or 3CLpro that have an established safety profile in humans. Several studies have reported crystal structures of SARS-CoV-2 main protease in complex with FDA approved drugs such as those used in treatment of hepatitis C. Here, we report the crystal structure of 3CLpro in complex Vitamin C (L-ascorbate) bound to the protein’s active site at 2.5 Ångstrom resolution. The crystal structure of the Vitamin C 3CLpro complex may aid future studies on the effect of Vitamin C not only on the coronavirus main protease but on related proteases of other infectious viruses.
City-wide school-located influenza vaccination: a retrospective cohort study
Authors: Benjamin-Chung Jade , Arnold Benjamin F. , Mishra Kunal , Kennedy Chris J. , Nguyen Anna , Pokpongkiat Nolan N. , Djajadi Stephanie , Seth Anmol , Klein Nicola P. , Hubbard Alan E. , Reingold Arthur , Colford John M. 
Published: May 2021

AbstractBackgroundWe measured the effectiveness of a city-wide school-located influenza vaccination (SLIV) program implemented in over 102 elementary schools in Oakland, California.MethodsWe conducted a retrospective cohort study among Kaiser Permanente Northern California (KPNC) members of all ages residing in either the intervention or a multivariate-matched comparison site from September 2011 - August 2017. Outcomes included medically attended acute respiratory illness (MAARI), influenza hospitalization, and Oseltamivir prescriptions. We estimated difference-in-differences (DIDs) in 2014-15, 2015-16, and 2016-17 using generalized linear models and adjusted for race, ethnicity, age, sex, health plan, and language.ResultsPre-intervention member characteristics were similar between sites. Among school-aged children, SLIV was associated with lower Oseltamivir prescriptions per 1,000 (DIDs: −3.5 (95% CI −5.5, −1.5) in 2015-16; −4.0 (95% CI −6.5, −1.6) in 2016-17) but not with other outcomes. SLIV was associated with lower MAARI per 1,000 in adults 65+ years (2014-15: −13.2, 95% CI −23.2, −3.2; 2015-16: −21.5, 95% CI −31.1, −11.9; 2016-17: −13.0, 95% CI −23.2, −2.9). There were few significant associations with other outcomes among adults.ConclusionsA city-wide SLIV intervention was associated with lower Oseltamivir prescriptions in school-aged children and lower MAARI among people over 65 years, suggesting possible indirect effects of SLIV among older adults.
Optimization of AAV6 transduction enhances site-specific genome editing of primary human lymphocytes
Authors: Rogers Geoffrey L. , Huang Chun , Clark Robert , Seclen Eduardo , Chen Hsu-Yu , Cannon Paula M. 
Published: May 2021

AbstractAdeno-associated virus serotype 6 (AAV6) is a valuable reagent for genome editing of hematopoietic cells due to its ability to serve as a homology donor template. However, a comprehensive study of AAV6 transduction of hematopoietic cells in culture, with the goal of maximizingex vivogenome editing, has not been reported. Here, we evaluated how the presence of serum, culture volume, transduction time, and electroporation parameters could influence AAV6 transduction. Based on these results, we identified an optimized protocol for genome editing of human lymphocytes based on a short, highly concentrated AAV6 transduction in the absence of serum, followed by electroporation with a targeted nuclease. In human CD4+T cells and B cells, this protocol improved editing rates up to 7-fold and 21-fold respectively, when compared to standard AAV6 transduction protocols described in the literature. As a result, editing frequencies could be maintained using 50-100-fold less AAV6, which also reduced cellular toxicity. Our results highlight the important contribution of cell culture conditions forex vivogenome editing with AAV6 vectors and provide a blueprint for improving AAV6-mediated homology-directed editing of human T and B cells.
Metagenomic and Metatranscriptomic Analysis Reveals Enrichment for Xenobiotic-Degrading Bacterial Specialists and Xenobiotic-Degrading Genes in a Canadian Prairie Two-Cell Biobed System
Authors: Russell J. N. , Perry B. J. , Bergsveinson J. , Freeman C. N. , Sheedy C. , Nilsson D. , Braul L. , Yost C. K. 
Published: May 2021

AbstractBiobeds are agriculture-based bioremediation tools used to safely contain and microbially degrade on-farm pesticide waste and rinsate, thereby reducing the negative environmental impacts associated with pesticide use. While these engineered ecosystems demonstrate efficient pesticide removal, their microbiome dynamics remain largely understudied both taxonomically and functionally. As such, further characterization of these parameters may aid in the optimization of biobed management and deployment. This study used metagenomic and metatranscriptomic techniques to characterize the microbial community in a two-cell Canadian biobed system before and after a field season of pesticide application. These culture-independent approaches identified an enrichment of xenobiotic-degrading bacteria, such asAfipia,SphingopyxisandPseudomonas, and enrichment and transcription of xenobiotic-degrading genes, such as peroxidases, oxygenases, and hydroxylases, among others; we were able to directly link the transcription of these genes toPseudomonas,Oligotropha,Mesorhizobium,Rhodopseudomonas, andStenotrophomonastaxa.
Structures of the active HER2/HER3 receptor complex reveal dynamics at the dimerization interface induced by binding of a single ligand
Authors: Diwanji Devan , Trenker Raphael , Thaker Tarjani M. , Wang Feng , Agard David A. , Verba Kliment A. , Jura Natalia 
Published: May 2021

AbstractThe Human Epidermal Growth Factor Receptor 2 (HER2) and HER3 form a potent pro-oncogenic heterocomplex upon binding of growth factor neuregulin-1β (NRG1β)1–3. The mechanism by which HER2 and HER3 interact remains unknown in the absence of any structures of the complex. We isolated the NRG1β-bound near full-length HER2/HER3 dimer and obtained a 2.9Å cryo-electron microscopy (cryo-EM) reconstruction of the extracellular domain module which reveals unexpected dynamics at the HER2/HER3 dimerization interface. We show that the dimerization arm of NRG1β-bound HER3 is unresolved likely because the apo HER2 monomer fails to undergo a ligand-induced conformational change needed to establish a HER3 dimerization arm binding pocket. In a second structure of an oncogenic extracellular domain mutant of HER2, S310F, we observe a compensatory interaction with the HER3 dimerization arm that stabilizes the dimerization interface. We show that both HER2/HER3 and HER2-S310F/HER3 retain the capacity to bind to the HER2-directed therapeutic antibody, trastuzumab, but the mutant complex does not bind to pertuzumab. Our 3.5Å structure of the HER2-S310F/HER3/NRG1β/trastuzumab Fragment antigen binding (Fab) complex shows that the receptor dimer undergoes a conformational change to accommodate trastuzumab. Thus, like oncogenic mutations, therapeutics exploit the intrinsic dynamics of the HER2/HER3 heterodimer. The unique features of a singly liganded HER2/HER3 heterodimer underscore the allosteric sensing of the ligand occupancy by the dimerization interface and explain why extracellular domains of HER2 do not homo-associate via canonical active dimer interface.
Increased alpha-helicity of a supercharged coiled-coil protein increases siRNA delivery efficiency of protein-lipid hybrid vehicle
Authors: Thomas Joseph , Monkovic Julia , Frezzo Joseph A. , Katyal Priya , Punia Kamia , Montclare Jin K. 
Published: May 2021

AbstractGene therapy has the potential to treat various diseases and has recently gained new interest due to the deployment nucleic acid based vaccines for COVID-19. Despite these developments, there still remains a need for further development of gene delivery vehicles to increase their safety and efficacy.. We have recently developed a lipoproteoplex (LPP) consisting of a super-charged coiled-coil protein (CSP) and a cationic liposomal carrier, that has the ability to condense nucleic acids and deliver themin vivo. The LPP is distinct from other liposomal gene delivery systems in that it utilizes a modular protein component to drive transfection activity as opposed to relying on the passive effects of the cationic lipids. A CSP library has been rationally designed to improve the efficacy of the LPP compared to the parent protein via improved alpha-helical structure and increased nucleic acid binding through the use of extended histidine tags and increased positive charge. The secondary structure and nucleic acid binding ability of each library member was assessed, then compared to functional transfection data in NIH-3T3 mouse fibroblasts. Structural and functional data suggests that increasing alpha-helicity of the protein component of the LPP compared to the parent sequence doubles nucleic acid binding affinity and increases transfection activity almost 3-fold with a favorable safety profile.