bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of saliva specimens for the molecular detection of SARS-CoV-2 in the community setting: does sample collection method matter?
Authors: Fernández-González Marta , Agulló Vanesa , de la Rica Alba , Infante Ana , Carvajal Mar , García José Alberto , Gonzalo-Jiménez Nieves , Cuartero Claudio , Ruiz Montserrat , de Gregorio Carlos , Sánchez Manuel , Masiá Mar , Gutiérrez Félix 
Published: December 2020

AbstractBackgroundData on the performance of saliva specimens for diagnosing COVID-19 in ambulatory patients are scarce and inconsistent. We assessed saliva-based specimens for detecting SARS-CoV-2 by RT-PCR in the community setting and compared three different collection methods.MethodProspective study conducted in three primary care centres. RT-PCR was performed in paired nasopharyngeal swabs (NPS) and saliva samples collected from outpatients with a broad clinical spectrum of illness. To assess differences in collection methods, saliva specimens were obtained in a different way in each of the participating centres: supervised collection (SVC), oropharyngeal washing (OPW) and self-collection (SC).ResultsNPS and saliva pairs of samples from 577 patients (median age 39 years, 44% men, 42% asymptomatic) were collected and tested, and 120 (20.8%) gave positive results. The overall agreement with NPS and kappa coefficients (KƘ) for SVC, OPW and SC were 95% (Ƙ=0.85), 93.4% (Ƙ=0.76), and 93.3% (Ƙ=0.76), respectively. The sensitivity (95% CI) of the saliva specimens varied from 86% (72.6-93.7) for SVC to 66.7% (50.4-80) for SC samples. The sensitivity was higher in samples with lower cycle threshold (Ct) values. The best performance of RT-PCR was observed for SVC, with sensitivity (95% CI) for Ct values ≤32 of 97% (82.5-99.8) in symptomatic, and 88.9% (50.7-99.4) in asymptomatic individuals.ConclusionsSaliva is an acceptable specimen for the detection of SARS-CoV-2 in the community setting. Specimens collected under supervision perform comparably to NPS and can effectively identify individuals with higher risk of transmission in real life conditions.
Short-term outcomes of pubertal suppression in a selected cohort of 12 to 15 year old young people with persistent gender dysphoria in the UK
Authors: Carmichael Polly , Butler Gary , Masic Una , Cole Tim J , De Stavola Bianca L , Davidson Sarah , Skageberg Elin M. , Khadr Sophie , Viner Russell 
Published: December 2020

AbstractBackgroundIn adolescents with severe and persistent gender dysphoria (GD), gonadotropin releasing hormone analogues (GnRHa) are used from early/middle puberty with the aim of delaying irreversible and unwanted pubertal body changes. Evidence of outcomes of pubertal suppression in GD is limited.MethodsWe undertook an uncontrolled prospective observational study of GnRHa as monotherapy in 44 12-15 year olds with persistent and severe GD. Prespecified analyses were limited to key outcomes: bone mineral content (BMC) and bone mineral density (BMD); Child Behaviour CheckList (CBCL) total t-score; Youth Self-Report (YSR) total t-score; CBCL and YSR self-harm indices; at 12, 24 and 36 months. Semistructured interviews were conducted on GnRHa.Results44 patients had data at 12 months follow-up, 24 at 24 months and 14 at 36 months. All had normal karyotype and endocrinology consistent with birth-registered sex. All achieved suppression of gonadotropins by 6 months. At the end of the study one ceased GnRHa and 43 (98%) elected to start cross-sex hormones.There was no change from baseline in spine BMD at 12 months nor in hip BMD at 24 and 36 months, but at 24 months lumbar spine BMC and BMD were higher than at baseline (BMC +6.0 (95% CI: 4.0, 7.9); BMD +0.05 (0.03, 0.07)). There were no changes from baseline to 12 or 24 months in CBCL or YSR total t-scores or for CBCL or YSR self-harm indices, nor for CBCL total t-score or self-harm index at 36 months. Most participants reported positive or a mixture of positive and negative life changes on GnRHa. Anticipated adverse events were common.ConclusionsOverall patient experience of changes on GnRHa treatment was positive. We identified no changes in psychological function. Changes in BMD were consistent with suppression of growth. Larger and longer-term prospective studies using a range of designs are needed to more fully quantify the benefits and harms of pubertal suppression in GD.
CDH26 amplifies airway epithelial IL-4 receptor α signaling in asthma
Authors: Feng Yuchen , Chen Shengchong , Chang Chenli , Wu Wenliang , Chen Dian , Gao Jiali , Chen Gongqi , Yi Lingling , Zhen Guohua 
Published: December 2020

ABSTRACTBackgroundActivation of interleukin (IL)-4 receptor (R) signaling in airway epithelial cells leads to airway hyperresponsiveness and mucus overproduction in asthma. Cadherin-26 (CDH26), a cadherin implicated in polarization of airway epithelial cells, is upregulated in asthma. However, the role of CDH26 in asthma remains unknown. We hypothesize that CDH26 plays a role in airway epithelial IL-4R signaling in asthma.MethodsWe measured airway resistance, mucus production, airway inflammation, and Il-4Rα expression in Cdh26-/- and WT mice after allergen sensitization and challenge. We explored the role of CDH26 in IL-4R signaling, mucin genes and eosinophilic chemokine expression in cultured bronchial epithelial cells and bronchial brushings from asthma patients.ResultsCdh26 deficiency nearly blocked airway mucus overproduction, and suppressed AHR and airway eosinophilia in a murine model of allergic airway disease. Interestingly, Il-4Rα expression in airway epithelium was markedly reduced in Cdh26-/- mice. In cultured human bronchial epithelial cells, CDH26 knockdown inhibited IL-13, a ligand for IL-4R, -induced IL-4Rα and IL-13Rα1 expression, and suppressed the downstream Jak1 and Stat6 phosphorylation. Moreover, CDH26 knockdown inhibited IL-13-induced MUC5AC, MUC5B and eosinophilic chemokines CCL11, CCL24, CCL26 expression. In contrast, CDH26 overexpression intensified IL-13-induced activation of IL-4Rα signaling. In asthma patients, CDH26 was the only one upregulated of 11 cadherins in bronchial brushings. CDH26 expression significantly correlated with epithelial IL-4Rα, MUC5AC expression, sputum eosinophilia and fractional exhaled nitric oxide (FeNO).ConclusionTaken together, CDH26 is an amplifier of epithelial IL-4R signaling in asthma, and may represent a therapeutic target for airway mucus overproduction.
Behavioral Inhibition and Dual Mechanisms of Anxiety Risk: Disentangling Neural Correlates of Proactive and Reactive Control
Authors: Valadez Emilio A. , Troller-Renfree Sonya V. , Buzzell George A. , Henderson Heather A. , Chronis-Tuscano Andrea , Pine Daniel S. , Fox Nathan A. 
Published: December 2020

AbstractBackgroundBehavioral inhibition (BI) is a temperament style characterized by heightened reactivity and negative affect in response to novel people and situations, and it is a strong predictor of anxiety problems later in life. However, not all BI children develop anxiety problems and mounting evidence suggests that how one manages their cognitive resources (cognitive control) influences anxiety risk. The present study tests whether more (proactive control) or less (reactive control) planful cognitive strategies moderate relations between BI and anxiety.MethodsParticipants included 144 adolescents (55.9% female) whose temperament was assessed during toddlerhood. In adolescence (Mage= 15.4 years), participants completed an AX Continuous Performance Test while EEG was recorded in order to disentangle neural activity related to proactive (cue-locked P3b) and reactive (probe-locked N2) control.ResultsBI was associated with greater total anxiety scores only among adolescents with smaller ΔP3bs and larger ΔN2s – a pattern consistent with decreased reliance on proactive strategies and increased reliance on reactive strategies. Additionally, a larger ΔP3b was associated with greater total anxiety scores.ConclusionsBI relates to risk for anxiety specifically among adolescents who rely less on proactive strategies and more on reactive control strategies. Results further suggest that proactive control differentiates a BI-related etiological pathway to anxiety from a more general pathway to anxiety occurring regardless of BI level. Thus, developmental context (i.e., temperament) moderates the association between anxiety and proactive control. The present study is the first to characterize how proactive and reactive control uniquely relate to pathways toward anxiety risk.
Antigen-driven clonal selection shapes the persistence of HIV-1 infected CD4+T cellsin vivo
Authors: Simonetti Francesco R. , Zhang Hao , Soroosh Garshasb P. , Duan Jiayi , Rhodehouse Kyle , Hill Alison L. , Beg Subul A. , McCormick Kevin , Raymond Hayley , Nobles Christopher L. , Everett John , Kwon Kyungyoon J. , White Jennifer A. , Lai Jun , Margolick Joseph B. , Hoh Rebecca , Deeks Steven G. , Bushman Frederic D. , Siliciano Janet D. , Siliciano Robert F. 
Published: December 2020

AbstractClonal expansion of infected CD4+T cells is a major mechanism of HIV-1 persistence and a barrier to cure. Potential causes are homeostatic proliferation, effects of HIV-1 integration, and interaction with antigens. Here we show that it is possible to link antigen responsiveness, full proviral sequence, integration site, and T cell receptor β-chain (TCRβ) sequence to examine the role of recurrent antigenic exposure in maintaining the HIV-1 reservoir. We isolated Cytomegalovirus (CMV)- and Gag-responding CD4+T cells from 10 treated individuals. Proviral populations in CMV-responding cells were dominated by large clones, including clones harboring replication-competent proviruses. TCRβ repertoires showed high clonality driven by converging adaptive responses. Although some proviruses were in genes linked to HIV-1 persistence (BACH2,STAT5B, MKL1), proliferation of infected cells under antigenic stimulation occurred regardless of the site of integration. Paired TCRβ-integration site analysis showed that infection could occur early or late in the course of a clone’s response to antigen and could generate infected cell populations too large to be explained solely by homeostatic proliferation. Together these findings implicate antigen-driven clonal selection as a major factor in HIV-1 persistence, a finding that will be a difficult challenge to eradication efforts.
The N-glycosylation sites and Glycan-binding ability of S-protein in SARS-CoV-2 Coronavirus
Authors: Chen Wentian , Hui Ziye , Ren Xiameng , Luo Yijie , Shu Jian , Yu Hanjie , Li Zheng 
Published: December 2020

AbstractThe emerging acute respiratory disease, COVID-19, caused by SARS-CoV-2 Coronavirus (SARS2 CoV) has spread fastly all over the word. As a member of RNA viruses, the glycosylation of envelope glycoprotein plays the crucial role in protein folding, evasing host immune system, invading host cell membrane, even affecting host preference. Therefore, detail glyco-related researches have been adopted in the Spike protein (S-protein) of SARS2 CoV from the bioinformatic perspective. Phylogenic analysis of S-protein sequences revealed the evolutionary relationship of N-glycosylation sites in different CoVs. Structural comparation of S-proteins indicated their similarity and distributions of N-glycosylation sites. Further potential sialic acid or galactose affinity domains have been described in the S-protein by docking analysis. Molecular dynamic simulation for the glycosylated complexus of S-protein-ACE2 implied that the complicate viral binding of receptor-binding domain may be influenced by peripheric N-glycans from own and adjacent monoers. These works will contribute to investigate the N-glycosylation in S-protein and explain the highly contagious of COVID-19.
Synergistic stabilization of a double mutant in CI2 from anin-celllibrary screen
Authors: Hamborg Louise , Granata Daniele , Olsen Johan G. , Roche Jennifer Virginia , Pedersen Lasse Ebdrup , Nielsen Alex Toftgaard , Lindorff-Larsen Kresten , Teilum Kaare 
Published: December 2020

AbstractMost single point mutations destabilize folded proteins. Mutations that stabilize a protein typically only have a small effect and multiple mutations are often needed to substantially increase the stability. Multiple point mutations may act synergistically on the stability, and it is not straightforward to predict their combined effect from the individual contributions. Here, we have applied an efficientin-cellassay to select variants of the barley chymotrypsin inhibitor 2 with increased stability. We find two variants that are more than 3.8 kJ/mol more stable than the wild-type. In one case the increased stability is the effect of the single substitution D55G. The other case is a double mutant, L49I/I57V, which is 5.1 kJ/mol more stable than the sum of the effects of the individual mutations. In addition to demonstrating the strength of our selection system for finding stabilizing mutations, our work also demonstrate how subtle conformational effects may modulate stability.
A pomegranate peel extract as inhibitor of SARS-CoV-2 Spike binding to human ACE2 (in vitro): a promising source of novel antiviral drugs
Authors: Tito Annalisa , Colantuono Antonio , Pirone Luciano , Pedone Emilia , Intartaglia Daniela , Giamundo Giuliana , Conte Ivan , Vitaglione Paola , Apone Fabio 
Published: December 2020

AbstractPlant extracts are rich in bioactive compounds, such as polyphenols, sesquiterpenes and triterpenes, with potential antiviral activities. As the dramatic outbreak of the pandemic COVID-19, caused by the SARS-CoV-2 virus, thousands of scientists are working tirelessly trying to understand the biology of this new virus and the disease pathophysiology, with the main goal to discover effective preventive treatments and therapeutic agents. Plant-derived secondary metabolites may play key roles in preventing and counteracting the rapid spread of SARS-CoV-2 infections by inhibiting the activity of several viral proteins, in particular those involved in the virus entry into the host cells and its replication. In this study, by using differentin vitroapproaches, we uncovered the role of a pomegranate peel extract in attenuating the interaction between the SARS-CoV-2 Spike glycoprotein and the human Angiotensin-Converting Enzyme 2 (ACE2) receptor, and in inhibiting the activity of the virus 3CL protease. Although further studies will be determinant to assess the efficacy of this extractin vivo, our results open up new promising opportunities to employ natural extracts for the development of effective and innovative therapies in the fight against SARS-CoV-2.
Disease related mutations in PI3Kγ disrupt regulatory C-terminal dynamics and reveals a path to selective inhibitors
Authors: Rathinaswamy Manoj K , Gaieb Zied , Fleming Kaelin D , Borsari Chiara , Harris Noah J , Moeller Brandon E , Wymann Matthias P , Amaro Rommie E , Burke John E 
Published: December 2020

AbstractClass I Phosphoinositide 3-kinases (PI3Ks) are master regulators of cellular functions, with the p110γ subunit playing a key role in immune signalling. PI3Kγ is a key factor in inflammatory diseases, and has been identified as a therapeutic target for cancers due to its immunomodulatory role. Using a combined biochemical/biophysical approach, we have revealed insight into regulation of kinase activity, specifically defining how immunodeficiency and oncogenic mutations of R1021 in the c-terminus can inactivate or activate enzyme activity. Screening of small molecule inhibitors using HDX-MS revealed that activation loop binding inhibitors induce allosteric conformational changes that mimic those seen for the R1021C mutant. Structural analysis of clinically advanced PI3K inhibitors revealed novel binding pockets that can be exploited for further therapeutic development. Overall this work provides unique insight into the regulatory mechanisms that control PI3Kγ kinase activity, and shows a framework for the design of PI3K isoform and mutant selective inhibitors.
Single cell profiling reveals novel tumor and myeloid subpopulations in small cell lung cancer
Authors: Chan Joseph M , Quintanal-Villalonga Álvaro , Gao Vianne , Xie Yubin , Allaj Viola , Chaudhary Ojasvi , Masilionis Ignas , Egger Jacklynn , Chow Andrew , Walle Thomas , Mattar Marissa , Yarlagadda Dig VK , Wang James L. , Uddin Fathema , Offin Michael , Ciampricotti Metamia , Bhanot Umesh K , Lai W Victoria , Bott Matthew J , Jones David R , Ruiz Arvin , Hollmann Travis , Poirier John T , Nawy Tal , Mazutis Linas , Sen Triparna , Pe’er Dana , Rudin Charles M 
Published: December 2020

ABSTRACTSmall cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined by differential expression ofASCL1,NEUROD1, andPOU2F3(SCLC-A, -N, and -P, respectively), which are associated with distinct therapeutic vulnerabilities. To define the heterogeneity of tumors and their associated microenvironments across subtypes, we sequenced 54,523 cellular transcriptomes from 21 human biospecimens. Our single-cell SCLC atlas reveals tumor diversity exceeding lung adenocarcinoma, driven by canonical, intermediate, and admixed subtypes. We discovered aPLCG2-high tumor cell population with stem-like, pro-metastatic features that recurs across subtypes and predicts worse overall survival, and manipulation ofPLCG2expression in cells confirms correlation with key metastatic markers. Treatment and subtype are associated with substantial phenotypic changes in the SCLC immune microenvironment, with greater T-cell dysfunction in SCLC-N than SCLC-A. Moreover, the recurrent,PLCG2-high subclone is associated with exhausted CD8+ T-cells and a pro-fibrotic, immunosuppressive monocyte/macrophage population, suggesting possible tumor-immune coordination to promote metastasis.
Glycan-Protein Interactions Determine Kinetics ofN-Glycan Remodeling
Authors: Mathew Corina , Weiß R. Gregor , Giese Christoph , Lin Chia-wei , Losfeld Marie-Estelle , Glockshuber Rudi , Riniker Sereina , Aebi Markus 
Published: December 2020

AbstractA hallmark ofN-linked glycosylation in the secretory compartments of eukaryotic cells is the sequential remodeling of an initially uniform oligosaccharide to a site-specific, heterogeneous ensemble of glycostructures on mature proteins. To understand site-specific processing, we used protein disulfide isomerase (PDI), a model protein with five glycosylation sites, for molecular dynamics (MD) simulations and compared the result to a biochemicalin vitroanalysis with four different glycan processing enzymes. As predicted by an analysis of the accessibility of theN-glycans for their processing enzymes derived from the MD simulations,N-glycans at different glycosylation sites showed different kinetic properties for the processing enzymes. In addition, altering the tertiary structure context ofN-glycan substrates affectedN-glycan remodeling in a site-specific way. We propose that differential, tertiary structure context dependentN-glycan reactivities lead to different glycan structures in the same protein through kinetically controlled processing pathways.
Rac guanine nucleotide exchange factors promoting Lgl1 phosphorylation in glioblastoma
Authors: Lavictoire Sylvie J , Jomaa Danny , Gont Alexander , Jardine Karen , Cook David P , Lorimer Ian AJ 
Published: December 2020

ABSTRACTThe protein Lgl1 has key roles in the regulation of cell polarity. We have shown that Lgl1 is inactivated by hyperphosphorylation in glioblastoma as a consequence ofPTENloss and aberrant activation of the PI 3-kinase pathway; this contributes to glioblastoma pathogenesis both by promoting invasion and repressing glioblastoma cell differentiation. Lgl1 is phosphorylated by atypical protein kinase C in a complex with Par6 and activated Rac. Here we have investigated the role of specific Rac guanine nucleotide exchange factors in Lgl1 hyperphosphorylation in glioblastoma. We used CRISPR/Cas9 to knockout PREX1, a PI 3-kinase pathway-responsive Rac guanine nucleotide exchange factor, in patient-derived glioblastoma cells. Knockout cells had reduced Lgl1 phosphorylation which could be reversed by re-expressing PREX1. PREX1 knockout cells showed reduced motility and an altered phenotype suggestive of partial neuronal differentiation; consistent with this, RNA-seq analyses identified sets of PREX1-regulated genes associated with changes in cell motility and neuronal differentiation. PREX1 knockout in glioblastoma cells from a second patient did not affect Lgl1 phosphorylation. These cells overexpressed a short isoform of the Rac guanine nucleotide exchange factor TIAM1; knockdown of TIAM1 in PREX1-knockout cells from this patient reduced Lgl1 phosphorylation. These data show that PREX1 links aberrant PI 3-kinase signaling to Lgl1 phosphorylation in glioblastoma, but that TIAM1 can also promote Lgl phosphorylation in a subset of patients. While this shows redundant mechanisms for Lgl1 phosphorylation, PREX1 appears to have a non-redundant role in glioblastoma cell motility, as this was impaired in PREX1 knockout cells from both patients.
Mechanisms of antibody binding revealed by asymmetric Fab-virus complexes
Authors: Goetschius Daniel J. , Hartmann Samantha R. , Organtini Lindsey J. , Callaway Heather , Huang Kai , Bator Carol M. , Ashley Robert E. , Makhov Alexander M. , Conway James F. , Parrish Colin R. , Hafenstein Susan 
Published: December 2020

AbstractOverlap on the surface of parvovirus capsids between the antigenic epitope and the receptor binding site contributes to species jumping. Mab 14 strongly binds and neutralizes canine, but not feline parvovirus. The high resolution map of the canine parvovirus capsid complexed with Fab 14 was used to solve local structures of the Fab-bound and -unbound antigenic sites extracted from the same complex. The subsequent analysis includes a new method for using cryo EM to investigate complementarity of antibody binding.