bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling effectiveness of testing strategies to prevent COVID-19 in nursing homes —United States, 2020
Authors: See Isaac , Paul Prabasaj , Slayton Rachel B. , Steele Molly K. , Stuckey Matthew J. , Duca Lindsey , Srinivasan Arjun , Stone Nimalie , Jernigan John A. , Reddy Sujan C. 
Published: December 2020

AbstractBackgroundSARS-CoV-2 outbreaks in nursing homes can be large with high case fatality. Identifying asymptomatic individuals early through serial testing is recommended to control COVID-19 in nursing homes, both in response to an outbreak (“outbreak testing” of residents and healthcare personnel) and in facilities without outbreaks (“non-outbreak testing” of healthcare personnel). The effectiveness of outbreak testing and isolation with or without non-outbreak testing was evaluated.MethodsUsing published SARS-CoV-2 transmission parameters, the fraction of SARS-CoV-2 transmissions prevented through serial testing (weekly, every three days, or daily) and isolation of asymptomatic persons compared to symptom-based testing and isolation was evaluated through mathematical modeling using a Reed-Frost model to estimate the percentage of cases prevented (i.e., “effectiveness”) through either outbreak testing alone or outbreak plus non-outbreak testing. The potential effect of simultaneous decreases (by 10%) in the effectiveness of isolating infected individuals when instituting testing strategies was also evaluated.ResultsModeling suggests that outbreak testing could prevent 54% (weekly testing with 48-hour test turnaround) to 92% (daily testing with immediate results and 50% relative sensitivity) of SARS-CoV-2 infections. Adding non-outbreak testing could prevent up to an additional 8% of SARS-CoV-2 infections (depending on test frequency and turnaround time). However, added benefits of non-outbreak testing were mostly negated if accompanied by decreases in infection control practice.ConclusionsWhen combined with high-quality infection control practices, outbreak testing could be an effective approach to preventing COVID-19 in nursing homes, particularly if optimized through increased test frequency and use of tests with rapid turnaround.SummaryMathematical modeling evaluated the effectiveness of serially testing asymptomatic persons in a nursing home in response to a SARS-CoV-2 outbreak with or without serial testing of asymptomatic staff in the absence of known SARS-CoV-2 infections.
Cell-type specific analysis of physiological action of estrogen in mouse oviducts
Authors: McGlade Emily A. , Herrera Gerardo G. , Stephens Kalli K. , Olsen Sierra L. W. , Winuthayanon Sarayut , Guner Joie , Hewitt Sylvia C. , Korach Kenneth S. , DeMayo Francesco J. , Lydon John P. , Monsivais Diana , Winuthayanon Wipawee 
Published: December 2020

AbstractOne of the endogenous estrogens, 17β-estradiol (E2) is a female steroid hormone secreted from the ovary. It is well established that E2causes biochemical and histological changes in the uterus. The oviduct response to E2is virtually unknown in anin vivoenvironment. In this study, we assessed the effect of E2on each oviductal cell type, using an ovariectomized-hormone-replacement mouse model, single cell RNA-sequencing (scRNA-seq),in situhybridization, and cell-type-specific deletion in mice. We found that each cell type in the oviduct responded to E2distinctively, especially ciliated and secretory epithelial cells. The treatment of exogenous E2did not drastically alter the transcriptomic profile from that of endogenous E2produced during estrus. Moreover, we have identified and validated genes of interest in our datasets that may be used as cell- and region-specific markers in the oviduct. Insulin-like growth factor 1 (Igf1) was characterized as an E2-target gene in the mouse oviduct and was also expressed in human Fallopian tubes. Deletion ofIgf1in progesterone receptor (Pgr)-expressing cells resulted in female subfertility, partially due to an embryo developmental defect and embryo retention within the oviduct. In summary, we have shown that oviductal cell types are differentially regulated by E2and support gene expression changes that are required for normal embryo development and transport in mouse models.
The distribution of onion virulence gene clusters among Pantoea spp
Authors: Stice Shaun P. , Shin Gi Yoon , De Armas Stefanie , Koirala Santosh , Galván Guillermo A. , Siri María Inés , Severns Paul M. , Coutinho Teresa , Dutta Bhabesh , Kvitko Brian H. 
Published: December 2020

AbstractPantoea ananatis is a gram-negative bacterium and the primary causal agent of center rot of onions in Georgia. Previous genomic studies identified two virulence gene clusters, HiVir and alt, associated with center rot. The HiVir gene cluster is required to induce necrosis on onion tissues via synthesis of a predicted small molecule toxin. The alt gene cluster aids in tolerance to thiosulfinates generated during onion tissue damage. Whole genome sequencing of other Pantoea species suggest that these gene clusters are present outside of P. ananatis. To assess the distribution of these gene clusters, two PCR primer sets were designed to detect the presence of HiVir and alt. Two hundred fifty-two strains of Pantoea spp. were phenotyped using the red onion scale necrosis (RSN) assay and were assayed using PCR for the presence of these virulence genes. A diverse panel of strains from three distinct culture collections comprised of 24 Pantoea species, 41 isolation sources, and 23 countries, collected from 1946-2019, were tested. There is a significant association between the alt PCR assay and Pantoea strains recovered from symptomatic onion (P<0.001). There is also a significant association of a positive HiVir PCR and RSN assay among P. ananatis strains but not among Pantoea spp., congeners. This may indicate a divergent HiVir cluster or different pathogenicity and virulence mechanisms. Last, we describe natural alt positive [RSN+/HiVir+/alt+] P. ananatis strains, which cause extensive bulb necrosis in a neck-to-bulb infection assay compared to alt negative [RSN+/HiVir+/alt-] P. ananatis strains. A combination of assays that include PCR of virulence genes [HiVir and alt] and an RSN assay can potentially aid in identification of onion-bulb-rotting pathogenic P. ananatis strains.
Spatiotemporal Control of Pathway Sensors and Cross-Pathway Feedback Regulate a Cell Differentiation MAPK Pathway in Yeast
Authors: Prabhakar Aditi , Gonzalez Beatriz , Dionne Heather , Basu Sukanya , Cullen Paul J. 
Published: December 2020

ABSTRACTMitogen-Activated Protein Kinase (MAPK) pathways control cell differentiation and the response to stress. MAPK pathways can share components with other pathways yet induce specific responses through mechanisms that remain unclear. InSaccharomyces cerevisiae, the MAPK pathway that controls filamentous growth (fMAPK) shares components with the MAPK pathway that regulates the response to osmotic stress (HOG). By exploring temporal regulation of MAPK signaling, we show here that the two pathways exhibited different patterns of activity throughout the cell cycle. The different patterns resulted from different expression profiles of genes encoding the mucin sensors (MSB2for fMAPK andHKR1for HOG). We also show that positive feedback through the fMAPK pathway stimulated the HOG pathway, presumably to modulate fMAPK pathway activity. By exploring spatial regulation of MAPK signaling, we found that the shared tetraspan protein, Sho1p, which has a dynamic localization pattern, induced the fMAPK pathway at the mother-bud neck. A Sho1p-interacting protein, Hof1p, which also localizes to the mother-bud neck and regulates cytokinesis, also regulated the fMAPK pathway. Therefore, spatial and temporal regulation of pathway sensors, and cross-pathway feedback, regulate a MAPK pathway that controls a cell differentiation response in yeast.
Cross-reactive coronavirus antibodies with diverse epitope specificities and extra-neutralization functions
Authors: Shiakolas Andrea R. , Kramer Kevin J. , Wrapp Daniel , Richardson Simone I. , Schäfer Alexandra , Wall Steven , Wang Nianshuang , Janowska Katarzyna , Pilewski Kelsey A. , Venkat Rohit , Parks Rob , Manamela Nelia P. , Raju Nagarajan , Fechter Emilee Friedman , Holt Clinton M. , Suryadevara Naveenchandra , Chen Rita E. , Martinez David R. , Nargi Rachel S. , Sutton Rachel E. , Ledgerwood Julie E. , Graham Barney S. , Diamond Michael S. , Haynes Barton F. , Acharya Priyamvada , Carnahan Robert H. , Crowe James E. , Baric Ralph S. , Morris Lynn , McLellan Jason S. , Georgiev Ivelin S. 
Published: December 2020

ABSTRACTThe continual emergence of novel coronavirus (CoV) strains, like SARS-CoV-2, highlights the critical need for broadly reactive therapeutics and vaccines against this family of viruses. Coronavirus spike (S) proteins share common structural motifs that could be vulnerable to cross-reactive antibody responses. To study this phenomenon in human coronavirus infection, we applied a high-throughput sequencing method called LIBRA-seq (Linking B cell receptor to antigen specificity through sequencing) to a SARS-CoV-1 convalescent donor sample. We identified and characterized a panel of six monoclonal antibodies that cross-reacted with S proteins from the highly pathogenic SARS-CoV-1 and SARS-CoV-2 and demonstrated a spectrum of reactivity against other coronaviruses. Epitope mapping revealed that these antibodies recognized multiple epitopes on SARS-CoV-2 S, including the receptor binding domain (RBD), N-terminal domain (NTD), and S2 subunit. Functional characterization demonstrated that the antibodies mediated a variety of Fc effector functionsin vitroand mitigated pathological burdenin vivo. The identification of cross-reactive epitopes recognized by functional antibodies expands the repertoire of targets for pan-coronavirus vaccine design strategies that may be useful for preventing potential future coronavirus outbreaks.
Genomic instability is an early event driving chromatin reorganization and escape from oncogene-induced senescence
Authors: Zampetidis C , Galanos P , Angelopoulou A , Zhu Y , Karamitros T , Polyzou A , Mourkioti I , Lagopati N , Mirzazadeh R , Polyzos A , Garnerone S , Gusmao EG , Sofiadis K , Pefani DE , Demaria M , Crosetto N , Maya-Mendoza A , Evangelou K , Bartek J , Papantonis A , Gorgoulis VG 
Published: December 2020

SUMMARYOncogene-induced senescence (OIS) is an inherent and important tumor suppressor mechanism. However, if not timely removed via immune surveillance, senescent cells will also present a detrimental side. Although this has mostly been attributed to the senescence-associated-secretory-phenotype (SASP) of these cells, we recently proposed that “escape” from the senescent state represents another unfavorable outcome. Here, we exploit genomic and functional data from a prototypical human epithelial cell model carrying an inducibleCDC6oncogene to identify an early-acquired recurrent chromosomal inversion, which harbors a locus encoding the circadian transcription factor BHLHE40. This inversion alone suffices for BHLHE40 activation uponCDC6induction and for driving cell cycle re-entry and malignant transformation. In summary, we now provide strong evidence in support of genomic instability underlying “escape” from oncogene-induced senescence.HIGHLIGHTSOncogene driven error-prone repair produces early genetic lesions allowing escape from senescenceCells escaping oncogene-induced senescence display mutational signatures observed in cancer patientsA single recurrent inversion harboring a circadian TF gene suffices for bypassing oncogene-induced senescenceChromatin loop and compartment remodeling support the “escape” transcriptional program
Mathematical Models for Assessing Vaccination Scenarios in Several Provinces in Indonesia
Authors: Nuraini N. , Khairudin K. , Hadisoemarto P. , Susanto H. , Hasan A. , Sumarti N. 
Published: December 2020

AbstractTo mitigate more casualties from the COVID-19 outbreak, this study assessed optimal vaccination scenarios, considering some existing healthcare conditions and some assumptions, by developing SIQRD (Susceptible-Infected-Quarantine-Recovery-Death) models for Jakarta, West Java, and Banten, in Indonesia. The models included an age-structured dynamic transmission model that naturally could give different treatments among age groups of population. The simulation results show that the timing and period’s length of the vaccination should be well planned and prioritizing particular age groups will give significant impact on the total number of casualties.
Immunological and pathological outcomes of SARS-CoV-2 challenge after formalin-inactivated vaccine immunisation of ferrets and rhesus macaques
Authors: Bewley Kevin R. , Gooch Karen , Thomas Kelly M. , Longet Stephanie , Wiblin Nathan , Hunter Laura , Chan Kin , Brown Phillip , Russell Rebecca A. , Ho Catherine , Slack Gillian , Humphries Holly E. , Alden Leonie , Allen Lauren , Aram Marilyn , Baker Natalie , Brunt Emily , Cobb Rebecca , Fotheringham Susan , Harris Debbie , Kennard Chelsea , Leung Stephanie , Ryan Kathryn , Tolley Howard , Wand Nadina , White Andrew , Sibley Laura , Sarfas Charlotte , Pearson Geoff , Rayner Emma , Xue Xiaochao , Lambe Teresa , Charlton Sue , Gilbert Sarah , Sattentau Quentin J. , Gleeson Fergus , Hall Yper , Funnell Simon , Sharpe Sally , Salguero Francisco J. , Gorringe Andrew , Carroll Miles 
Published: December 2020

AbstractThere is an urgent requirement for safe and effective vaccines to prevent novel coronavirus disease (COVID-19) caused by SARS-CoV-2. A concern for the development of new viral vaccines is the potential to induce vaccine-enhanced disease (VED). This was reported in several preclinical studies with both SARS-CoV-1 and MERS vaccines but has not been reported with SARS-CoV-2 vaccines. We have used ferret and rhesus macaques challenged with SARS-CoV-2 to assess the potential for VED in animals vaccinated with formaldehyde-inactivated SARS-CoV-2 (FIV) formulated with Alhydrogel, compared to a negative control vaccine in ferrets or unvaccinated macaques. We showed no evidence of enhanced disease in ferrets or rhesus macaques given FIV except for mild transient enhanced disease seen at seven days post infection in ferrets. This increased lung pathology was observed early in the infection (day 7) but was resolved by day 15. We also demonstrate that formaldehyde treatment of SARS-CoV-2 reduces exposure of the spike receptor binding domain providing a mechanistic explanation for suboptimal immunity.
Protective effect ofMorus macrouraMiq. fruit extract against acetic acid-induced ulcerative colitis in rats: Involvement of miRNA-223 and TNFα/NFκB/NLRP3 inflammatory pathway
Authors: Salama Rania M. , Darwish Samar F. , Shaffei Ismail El , Elmongy Noura F. , Afifi Manal S. , Abdel-Latif Ghada A. 
Published: December 2020

AbstractTumor necrosis factor receptor (TNFR) activation and nuclear factor kappa B (NFκB) expression play a significant role in the activation of nod-like receptor pyrin domain-1 containing 3 (NLRP3) inflammasome inflammatory pathway, which is involved in the pathogenesis of ulcerative colitis (UC). Furthermore, miRNA-223 expression was shown to exert counter-regulatory effect on NLRP3 expression. Interestingly, polyphenols are attaining increased importance for their potential effectiveness in ameliorating certain diseases owing to their antioxidant and anti-inflammatory activity. In accord, our study attempted to investigate the effect of mulberry tree (Morus macroura) fruit extract (MFE) against acetic acid (AA)- induced UC in rats, which is not previously investigated, based on previous promising results for MFE in alleviating gastric ulcer in rats. First, total phenolic (TPC), total flavonoid (TFC), and total anthocyanin content (TAC) were determined in MFE. Then, MFE (300 mg/kg) and sulfasalazine (Sulfa), as a standard treatment (100 mg/kg), were given orally for seven days before intra-rectal induction of UC by AA (2 ml, 4% v/v) on day eight. The extent of UC was evaluated macroscopically and microscopically. Biochemically, the colonic TNFR1, NLRP3, p- NFκB p65, TNFα, interleukin-1 beta (IL-1β), IL-18 levels, miRNA-223 expression and caspase-1 activity were assayed. MFE significantly reduced macroscopic and microscopic scores, colonic levels of TNFR1, NLRP3, p-NFκB p65, TNFα, IL-1β, IL-18, and caspase-1 activity, and showed increased miRNA-223 expression, almost similarly to Sulfa effects. In conclusion, our study provided a novel impact for MFE against AA-induced UC in rats through affecting miRNA-223 expression and halting TNFα/NFκB/NLRP3 inflammatory pathway.
Trends of and implications for the diffusion of lesson study: thematic analysis of WALS2019 conference presentations
Authors: Fang Yanping , Wang Hongyan 
Published: December 2020

PurposeA first post-WALS attempt at a thematic analysis of the conference presentations since its first annual meeting in 2007, this paper aims to achieve two major purposes: first, to capture the trends of spread and diffusion of lesson and learning studies globally and second, to draw useful implications for future conferences.Design/methodology/approachA thematic analysis using NVIVO12.0 coding on all forms of conference presentations found in the WALS 2019 Conference Programme was conducted. Representative cases were selected from paper and symposiums sessions to support the claims generated from the analysis.FindingsThe study provides an evidence-based confirmation of the global spread and diffusion of lesson and learning studies. It uncovers findings key to the initial spread and continued diffusion; examines funding as a mechanism enabling university–school research relationships, models of adaptations and issues of sustainability; surfaces the theoretical models and methods adopted in paper and symposia presentations. The current situation, lessons learned and possible implications for future WALS conferences are discussed.Research limitations/implicationsInform research on practical cases.Practical implicationsLessons learned are discussed.Social implicationsThese are possible implications for future WALS conferences.Originality/valueThe originality lies in its being the first WALS post-conference analysis aiming at identifying substantive themes with potential to draw important implications for future research and subsequent years' conferences.
A novel model of constrictive pericarditis associated with myocardial fibrosis in rats
Authors: Qiao Wei , Xiao Yang‐jie , Wang Xin , Sun Li‐juan , Chen Yi‐xin , Ren Wei‐dong 
Published: December 2020

AbstractAn efficient animal model is fundamental for studies on the underlying mechanisms of constrictive pericarditis (CP). A novel CP rat model was established by pericardial injection composing of lipopolysaccharides (LPS) and talcum powder without thoracotomy. Pathological changes were confirmed by histological staining. E‐flow Doppler of mitral valve, tissue Doppler E′ in the medial mitral annular (E′sep) and the lateral mitral annular (E′lat) were measured to assess ventricular filling function. Circumferential, longitudinal, and radial strains (SC, SL and SR) and the respective strain rates (SrC, SrL and SrR) were analyzed in interventricular septum (IVS) and left ventricular free wall (LVFW). Rat cardiac fibroblasts (CFs) were treated with LPS. The activation of transforming growth factor β1 (TGF‐β1) was confirmed by Q‐PCR and western blot assays. Thickening of pericardium and fibrosis in pericardium and subepicardial myocardium were showed in the model group. Diastolic dysfunction in the CP group was indicated by decreased E′lat and E′lat/E′sep, increased E/E′lat, decreased EFW of SrC and SrL, increased AIVS and decreased E/A of SrC, SrL and SrR. Systolic dysfunction was indicated by decreased SCFW and SLFW in CP rats. The levels of TGF‐β1, p‐Smad2/3, α‐smooth muscle actin (α‐SMA), and collagen‐I/III (COL‐I/III) were increased in the CP group. The increased TGF‐β1 that induced by LPS activated and phosphorylated Smad2/3 resulting in the secretion of α‐SMA and COL‐I/III. This model is of vital importance in studying the pathogenesis of CP.
Opportunistic use of catecholamine neurotransmitters as siderophores to access iron by Pseudomonas aeruginosa
Authors: Perraud Quentin , Kuhn Lauriane , Fritsch Sarah , Graulier Gwenaëlle , Gasser Véronique , Normant Vincent , Hammann Philippe , Schalk Isabelle J. 
Published: December 2020

SummaryIron is an essential nutrient for bacterial growth and the cause of a fierce battle between the pathogen and host during infection. Bacteria have developed several strategies to access iron from the host, the most common being the production of siderophores, small iron‐chelating molecules secreted into the bacterial environment. The opportunist pathogen Pseudomonas aeruginosa produces two siderophores, pyoverdine and pyochelin, and is also able to use a wide panoply of xenosiderophores, siderophores produced by other microorganisms. Here, we demonstrate that catecholamine neurotransmitters (dopamine, l‐DOPA, epinephrine and norepinephrine) are able to chelate iron and efficiently bring iron into P. aeruginosa cells via TonB‐dependent transporters (TBDTs). Bacterial growth assays under strong iron‐restricted conditions and with numerous mutants showed that the TBDTs involved are PiuA and PirA. PiuA exhibited more pronounced specificity for dopamine uptake than for norepinephrine, epinephrine and l‐DOPA, whereas PirA specificity appeared to be higher for l‐DOPA and norepinephrine. Proteomic and qRT‐PCR approaches showed pirA transcription and expression to be induced in the presence of all four catecholamines. Finally, the oxidative properties of catecholamines enable them to reduce iron, and we observed ferrous iron uptake via the FeoABC system in the presence of l‐DOPA.
Interweaving the Fabric of Urban Infrastructure: Senegalese City‐making in Rio de Janeiro
Authors: Heil Tilmann 
Published: December 2020

AbstractThis article reveals how newcomers weave their own threads into the fabric of urban infrastructure. Entangling their own with other urban assemblages, newcomers generate multi‐layered dynamics situationally in order to render possible the lives to which they aspire. They forge openings where there seemed none before and keep negative potentialities in check. To offer an ethnography of how the Senegalese presence in Rio de Janeiro has grown dynamically between 2014 and 2019, I draw analytical strength from the double meaning of agencement: the action of interweaving varied socio‐material components—agencer—so that they work together well, and the resulting assemblage of social and material components. Two case studies act as a starting point: how Senegalese came to inhabit an urban architectural landmark and how they regularize their residence status. Their transformative power of city‐making is generated both through the mutual intertwining of a dahira, a religious group of Senegalese migrants, and a diasporic Senegalese association and through the ways in which the Senegalese interweave themselves and their institutionalized collective forms with ever more socio‐material components of the urban space. Beyond the better‐known transnational embeddedness of the Senegalese, their complex infrastructuring practices upon arrival become constitutive of new urban realities, moulding the city fabric of which they are becoming part.