bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of a Commercial Culture-free Neutralization Antibody Detection Kit for Severe Acute Respiratory Syndrome-Related Coronavirus-2 and Comparison with an Anti-RBD ELISA Assay
Authors: Papenburg Jesse , Cheng Matthew P. , Corsini Rachel , Caya Chelsea , Mendoza Emelissa , Manguiat Kathy , Lindsay L. Robbin , Wood Heidi , Drebot Michael A. , Dibernardo Antonia , Zaharatos Gerasimos , Bazin Reneée , Gasser Romain , Benlarbi Mehdi , Gendron-Lepage Gabrielle , Beaudoin-Bussières Guillaume , Prévost Jérémie , Finzi Andrés , Ndao Momar , Yansouni Cedric P 
Published: January 2021

ABSTRACTBackgroundSARS-CoV-2 surrogate neutralization assays that obviate the need for viral culture offer substantial advantages regarding throughput and cost. The cPass SARS-CoV-2 Neutralization Antibody Detection Kit (Genscript) is the first such commercially available assay, detecting antibodies that block RBD/ACE-2 interaction. We aimed to evaluate cPass to inform its use and assess its added value compared to anti-RBD ELISA assays.MethodsSerum reference panels comprising 205 specimens were used to compare cPass to plaque-reduction neutralization test (PRNT) and a pseudotyped lentiviral neutralization (PLV) assay for detection of neutralizing antibodies. We assessed the correlation of cPass with an ELISA detecting anti-RBD IgG, IgM, and IgA antibodies at a single timepoint and across intervals from onset of symptoms of SARS-CoV-2 infection.ResultsCompared to PRNT-50, cPass sensitivity ranged from 77% - 100% and specificity was 95% - 100%. Sensitivity was also high compared to the pseudotyped lentiviral neutralization assay (93% [95%CI 85-97]), but specificity was lower (58% [95%CI 48-67]). Highest agreement between cPass and ELISA was for anti-RBD IgG (r=0.823). Against the pseudotyped lentiviral neutralization assay, anti-RBD IgG sensitivity (99% [95%CI 94-100]) was very similar to that of cPass, but overall specificity was lower (37% [95%CI 28-47]). Against PRNT-50, results of cPass and anti-RBD IgG were nearly identical.ConclusionsThe added value of cPass compared to an IgG anti-RBD ELISA was modest.
Patients with Asthma and Chronic Obstructive Pulmonary Disease (COPD) have increased levels of plasma inflammatory mediators upregulated in severe COVID-19
Authors: Acevedo Nathalie , Escamilla-Gil Jose Miguel , Espinoza Héctor , Regino Ronald , Ramírez Jonathan , de Arco Lucila Florez , Dennis Rodolfo , Torres-Duque Carlos , Caraballo Luis 
Published: January 2021

AbstractBackgroundChronic obstructive pulmonary disease (COPD) is associated with increased risk of severe COVID-19, but the mechanisms are unclear. Besides, patients with severe COVID-19 have been reported to have increased levels of several immune mediators.ObjectiveTo perform an immunoproteomic profiling of dysregulated plasma proteins in patients with asthma and COPD and to evaluate their relationship with biomarkers of severe COVID-19.MethodsNinety-two proteins were quantified in 315 plasma samples from adult subjects (age 40-90 years) including 118 asthmatics, 99 COPD patients and 98 healthy controls, that have been recruited in two reference pneumology clinics in Colombia before the beginning of the COVID-19 pandemic. Protein levels were compared between each disease group and healthy controls.Significant proteins were compared to the gene signatures of SARS-CoV-2 infection reported in the “COVID-19 Drug and Gene Set Library” and with known protein biomarkers of severe COVID-19.ResultsForty-one plasma proteins showed differences between patients and controls. Asthmatic patients have increased levels in IL-6 while COPD patients have a broader systemic inflammatory dysregulation driven by HGF, OPG, and several chemokines (CXCL9, CXCL10, CXCL11, CX3CL1, CXCL1, MCP-3, MCP-4, CCL3, CCL4 and CCL11). These proteins are involved in chemokine signaling pathways related with response to viral infections and some, were found up-regulated upon SARS-CoV-2 experimental infection of Calu-3 cells as reported in the COVID-19 Related Gene Sets database. An increase of HPG, CXCL9, CXCL10, IL-6, MCP-3, TNF and EN-RAGE has also been found in patients with severe COVID-19.ConclusionsCOPD patients have altered levels of plasma proteins that have been reported increased in patients with severe COVID-19. Our study suggests that COPD patients have a systemic dysregulation in chemokine networks (including HGF and CXCL9) that could make them more susceptible to severe COVID-19. Our study also suggest that IL-6 levels are increased in some asthmatics and this may influence their immune response to COVID-19.
Preliminary Evidence on Long COVID in children
Authors: Buonsenso Danilo , Munblit Daniel , De Rose Cristina , Sinatti Dario , Ricchiuto Antonia , Carfi Angelo , Valentini Piero 
Published: January 2021

AbstractThere is increasing evidence that adult patients diagnosed with acute COVID-19 suffer from Long COVID initially described in Italy.To date, data on Long COVID in children are lacking.We assessed persistent symptoms in pediatric patients previously diagnosed with COVID-19. More than a half reported at least one persisting symptom even after 120 days since COVID-19, with 42.6% being impaired by these symptoms during daily activities. Symptoms like fatigue, muscle and joint pain, headache, insomnia, respiratory problems and palpitations were particularly frequent, as also described in adults.The evidence that COVID-19 can have long-term impact children as well, including those with asymptomatic/paucisymptomatic COVID-19, highlight the need for pediatricians, mental health experts and policy makers of implementing measures to reduce impact of the pandemic on child’s health.
Design and deployment of an affordable and long-lasting deep-water subsurface fish aggregation device
Authors: Schneider Eric VC , Brooks Edward J , Cortina Michael P , Bailey David M , Killen Shaun S , Leeuwen Travis E Van 
Published: January 2021

AbstractFish aggregation devices (FADs) are used worldwide to enhance the efficiency of various fisheries. Devices consist of a floating or subsurface component designed to exploit natural fish behavior, using species’ attraction to structure (e.g.,Sargassumspp.) to aggregate fish and increase capture success in open ocean environments. Concerns have arisen regarding the scale and management of FAD-associated fisheries, however, the efficiency of FADs to aggregate fish also introduces the possibility for FADs to be used as conservation tools to study pelagic species ecology. Building on two successful and several failed deployments of anchored deep-water (>500 m) subsurface (10 m) FADs over three years in The Bahamas, and observations from the subsequent FAD monitoring program, the objectives of the paper are to: 1) provide details and considerations for the design, construction, and deployment of an affordable and durable deep-water subsurface FAD that can be deployed using small boats; and 2) highlight the potential for a long-lasting moored FAD to be used as a sustainable and reliable scientific platform for pelagic species research and conservation, lending specifically to several research applications. This information will be useful for assessing the impacts that FADs and other anthropogenic marine infrastructure have on wild marine species, and their efficacy for conserving pelagic fish through increased encounters for study.
Gaining Insight into the Deformation of Achilles Tendon Entheses in Mice
Authors: Sartori Julian , Köhring Sebastian , Bruns Stefan , Moosmann Julian , Hammel Jörg U. 
Published: January 2021

AbstractUnderstanding the biomechanics of tendon entheses is fundamental for surgical repair and tissue engineering, but also relevant in biomimetics and palaeontology. 3D imaging is becoming increasingly important in the examination of soft tissue deformation. But entheses are particularly difficult objects for micro-computed tomography because they exhibit extreme differences in X-ray attenuation. In this article, the ex vivo examination of Achilles tendon entheses from mice using a combination of tensile tests and synchrotron radiation-based micro-computed tomography is reported. Two groups of specimens with different water content are compared with regard to strains and volume changes in the more proximal free tendon and the distal tendon that wraps around theTuber calcanei. Tomograms of relaxed and deformed entheses are recorded with propagation-based phase contrast. The tissue structure is rendered in sufficient detail to enable manual tracking of patterns along the tendon, as well as 3D optical flow analysis in a suitable pair of tomograms. High water content is found to increase strain and to change the strain distribution among proximal and distal tendon. In both groups, the volume changes are higher in the distal than in the proximal tendon. These results support the existence of a compliant zone near the insertion. They also show that the humidity of the specimen environment has to be controlled. Necessary steps to extend the automatic tracking of tissue displacements to all force steps are discussed.
Idiosyncratic learning performance in flies generalizes across modalities
Authors: Smith Matthew , Honegger Kyle S. , Turner Glenn , de Bivort Benjamin 
Published: January 2021

AbstractIndividuals vary in their innate behaviors, even when they have the same genome and have been reared in the same environment. The extent of individuality in plastic behaviors, like learning, is less well characterized. Also unknown is the extent to which intragenotypic differences in learning generalize: if an individual performs well in one assay, will it perform well in other assays? We investigated this using the fruit flyDrosophila melanogaster, an organism long-used to study the mechanistic basis of learning and memory. We found that isogenic flies, reared in identical lab conditions, and subject to classical conditioning that associated odorants with electric shock, exhibit clear individuality in their learning responses. Flies that performed well when an odor was paired with shock tended to perform well when other odors were paired with shock, or when the original odor was paired with bitter taste. Thus, individuality in learning performance appears to be prominent in isogenic animals reared identically, and individual differences in learning performance generalize across stimulus modalities. Establishing these results in flies opens up the possibility of studying the genetic and neural circuit basis of individual differences in learning in a highly suitable model organism.
Paradoxical stabilization of relative position in moving frames
Authors: Özkan Mert , Anstis Stuart , ’t Hart Bernard M. , Wexler Mark , Cavanagh Patrick 
Published: January 2021

ABSTRACTTo capture where things are and what they are doing, the visual system may extract the position and motion of each object relative to its surrounding frame of referencee.g., 1,2. Here we report a particularly powerful example where a paradoxical stabilization is produced by a moving frame. We first take a frame that moves left and right and we flash its right edge before, and its left edge after, the frame’s motion. For all frame displacements tested, the two edges are perceived as stabilized, with the left edge on the left and right edge on the right, separated by the frame’s width as if the frame were not moving. This illusory stabilization holds even when the frame travels farther than its width, reversing the actual spatial order of the two flashes. Despite this stabilization, the motion of the frame is still seen, albeit much reduced, and this hides the paradoxical standstill of relative positions. In a second experiment, two probes are flashed inside the frame at thesamephysical location before and after the frame moves. Despite being physically superimposed, the probes are perceived widely separated, again as if they were seen in the frame’s coordinates and the frame were stationary. This illusory separation is set by the distance of the frame’s travel, independently of its speed. This paradoxical stabilization suggests a link to visual constancy across eye movements where the displacement of the entire visual scene may act as a frame to stabilize the perception of relative locations.
Intelligence and academic performance: Is it all in your head?
Authors: Bottenhorn Katherine L. , Bartley Jessica E. , Riedel Michael C. , Salo Taylor , Bravo Elsa I. , Odean Rosalie , Nazareth Alina , Laird Robert W. , Musser Erica D. , Pruden Shannon M. , Brewe Eric , Sutherland Matthew T. , Laird Angela R. 
Published: January 2021

AbstractAcademic performance relies, in part, on intelligence; however, intelligence quotient (IQ) is limited in predicting academic success. Furthermore, while the search for the biological seat of intelligence predates neuroscience itself, its findings remain conflicting. Here, we assess the interplay between IQ, academic performance, and brain connectivity with behavioral and functional MRI data collected from undergraduate students as they completed an active learning or lecture-based semester-long university physics course. IQ (i.e., full-scale WAIS scores) increased significantly pre-to post-instruction, were associated with physics knowledge and reasoning measures, but were unrelated to overall course grade. IQ was related to brain connectivity during physics-related cognition, but connectivity did not mediate IQ’s association with task performance. These relations depended on students’ sex and instructional environment, providing evidence that physics classroom environment and pedagogy may have a gendered influence on students’ performance. Discussion focuses on opportunities to improve physics reasoning skills for all students.
Laser ablation of the apical sensory organ ofHydroides elegans(Polychaeta) does not inhibit detection of metamorphic cues
Authors: Nedved Brian T. , Freckelton Marnie L. , Hadfield Michael G. 
Published: January 2021

AbstractLarvae of many marine invertebrates bear an anteriorly positioned apical sensory organ (ASO) presumed to be the receptor for settlement- and metamorphosis-inducing environmental cues, based on its structure, position and observed larval behavior. Larvae of the polychaeteHydroides elegansare induced to settle by bacterial biofilms, which they explore with their ASO and surrounding anteroventral surfaces. A micro-laser was utilized to destroy the ASO and other anterior ciliary structures in competent larvae ofH. elegans. After ablation, larvae were challenged with bacterial biofilmed or clean surfaces and percent metamorphosis was determined. Ablated larvae were also assessed for cellular damage by applying fluorescently tagged FMRF-amide antibodies and observing the larvae by laser-scanning confocal microscopy. While the laser pulses caused extensive damage to the ASO and surrounding cells, they did not inhibit metamorphosis. We conclude that the ASO is not a required receptor site for cues that induce metamorphosis.Summary StatementLarvae of the polychaeteHydroides elegansretain the capacity to sense biofilm cues and metamorphose despite removal of their apical sensory organs, the supposed sensors for settlement cues.
Dynamic change and clinical relevance of post-infectious SARS-CoV-2 antibody responses
Authors: Mallon PWG , Tinago W , Leon A Garcia , McCann K , Kenny G , McGettrick P , Green S , Inzitari R , Cotter AG , Feeney ER , Savinelli S , Doran P 
Published: January 2021

AbstractBackgroundAlthough reports suggest that most individuals with COVID-19 develop detectable antibodies post infection, the kinetics, durability, and relative differences between IgM and IgG responses beyond the first few weeks after symptom onset remain poorly understood.MethodsWithin a large, well-phenotyped, diverse, prospective cohort of subjects with and without SARS-CoV-2 PCR-confirmed infection and historical controls derived from cohorts with high prevalence of viral coinfections and samples taken during prior flu seasons, we measured SARS-CoV-2 serological responses (both IgG and IgM) using commercially available assays. We calculated sensitivity and specificity, relationship with disease severity and mapped the kinetics of antibody responses over time using generalised additive models.ResultsWe analysed 1,001 samples from 752 subjects, 327 with confirmed SARS-CoV-2 (29.7% with severe disease) spanning a period of 90 days from symptom onset. Sensitivity was lower (44.1-47.1%) early (<10 days) after symptom onset but increased to >80% after 10 days. IgM positivity increased earlier than IgG-targeted assays but positivity peaked between day 32 and 38 post onset of symptoms and declined thereafter, a dynamic that was confirmed when antibody levels were analysed, with more rapid decline observed with IgM. Early (<10 days) IgM but not IgG levels were significantly higher in those who subsequently developed severe disease (signal / cut-off 4.20 (0.75-17.93) versus 1.07 (0.21-5.46), P=0.048).ConclusionsThis study suggests that post-infectious antibody responses in those with confirmed COVID-19 begin to decline relatively early post infection and suggests a potential role for higher IgM levels early in infection predicting subsequent disease severity.
Assessment of The Relationship of REMS and MEWS Scores with Prognosis in Patients Diagnosed with Covid-19 Admitted to the Emergency Department
Authors: Bas Behlul , Senturk Mucahit , Burnaz Tugce Nur , Timur Kubilay , Kalkan Asim 
Published: January 2021

ABSTRACTAimWith the rapid and global increase in COVID-19 cases, it is becoming important to identify patients with a risk of mortality and patients that need hospitalization. The aim of this study is to try to predict the mortality rate of COVID patients admitted to the emergency department with rapid scoring systems such as REMS and MEWS and their clinical termination in the emergency department at the end of the first month.MethodWe have designed this study to be a single-centered, prospective and an observational study. A total of 392 patients diagnosed with COVID-19, who were admitted to the emergency department in a 1-month period, were included in the study. REMS and MEWS scores were calculated for each case. Demographic data of patients, clinical outcomes such as discharge, service hospitalization, ICU hospitalization, and first-month mortality were analysed based on these scores. ROC curves were analysed to determine the cut-off value with the help of which REMS and MEWS scores can predict 1-month mortality and hospitalization.ResultsOut of the 392 patients included in the study, the 43.4% (n=170) were female and 56.6% (n=222) were male. The average age of our patients was 48.98±19.49 years. The 1-month mortality rate of our patients was 4.3% (n=17). At the end of the first month, the mortality of patients with a comorbid disease was higher than those who did not (p<0.01). The average of the REMS score was higher in patients with an average mortality of (7.24±3.77) than in patients without it (2.87±3.09), and there was a statistically significant difference between them (p<0.01). Similarly, the average of the MEWS score was higher in patients with an average mortality of (2.76±1.86) than in patients without it (1.65±1.35), and there was a statistically significant difference (p<0.01). The REMS score of patients admitted to the service was higher than that of patients discharged (p<0.01). When the REMS score was determined as 3 cut-off value in ROC analysis, service hospitalization was 5 times higher in patients with a REMS score of 3 and above than in those who were discharged (OR: 1:5.022 95% CI: 3.088-8.168)). REMS and MEWS scores were also higher in ICU patients than in discharged patients (p<0.01).ConclusionIn predicting the 1-month mortality of ER patients diagnosed with COVID-19, REMS and MEWS scoring systems can be useful and guiding in determining the patients who need hospitalization for emergency physicians. The use of these scoring systems in emergency departments can help predict the clinical outcomes of patients at the time of the initial evaluation, and can also be a practical method of predicting the prognosis of the patients.
Identification of COVID-19 Subtypes Based on Immunogenomic Profiling
Authors: Feng Qiushi , Wang Xiaosheng 
Published: January 2021

AbstractAlthough previous studies have shown that the host immune response is crucial in determining clinical outcomes in COVID-19 patients, the association between host immune signatures and COVID-19 patient outcomes remains unclear. Based on the enrichment levels of 11 immune signatures (eight immune-inciting and three immune-inhibiting signatures) in leukocytes of 100 COVID-19 patients, we identified three COVID-19 subtypes: Im-C1, Im-C2, and Im-C3, by clustering analysis. Im-C1 had the lowest immune-inciting signatures and high immune-inhibiting signatures. Im-C2 had medium immune-inciting signatures and high immune-inhibiting signatures. Im-C3 had the highest immune-inciting signatures while the lowest immune-inhibiting signatures. Im-C3 and Im-C1 displayed the best and worst clinical outcomes, respectively, suggesting that antiviral immune responses alleviated the severity of COVID-19 patients. We further demonstrated that the adaptive immune response had a stronger impact on COVID-19 outcomes than the innate immune response. The patients in Im-C3 were younger than those in Im-C1, indicating that younger persons have stronger antiviral immune responses than older persons. Nevertheless, we did not observe a significant association between sex and immune responses in COVID-19 patients. In addition, we found that the type II IFN response signature was an adverse prognostic factor for COVID-19. Our identification of COVID-19 immune subtypes has potential clinical implications for the management of COVID-19 patients.
Biomarkers of endothelial dysfunction and outcomes in coronavirus disease 2019 (COVID-19) patients: a systematic review and meta-analysis
Authors: Andrianto  , Al-Farabi Makhyan Jibril , Nugraha Ricardo Adrian , Marsudi Bagas Adhimurda , Azmi Yusuf 
Published: January 2021

AbstractBackgroundSeveral studies have reported that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can directly infect endothelial cells, and endothelial dysfunction is often found in severe cases of coronavirus disease 2019 (COVID-19). To better understand the pathological mechanisms underlying endothelial dysfunction in COVID-19-associated coagulopathy, we conducted a systematic review and meta-analysis to assess biomarkers of endothelial cells in patients with COVID-19.MethodsA literature search was conducted on online databases for observational studies evaluating biomarkers of endothelial dysfunction and composite poor outcomes in COVID-19 patients.ResultsA total of 1187 patients from 17 studies were included in this analysis. The estimated pooled means for von Willebrand Factor (VWF) antigen levels in COVID-19 patients was higher compared to healthy control (306.42 [95% confidence interval (CI) 291.37-321.48], p<0.001; I2:86%), with the highest VWF antigen levels was found in deceased COVID-19 patients (448.57 [95% CI 407.20-489.93], p<0.001; I2:0%). Meta-analysis showed that higher plasma levels of VWF antigen, tissue-type plasminogen activator (t-PA), plasminogen activator inhibitor-1 antigen (PAI-1) antigen, and soluble thrombomodulin (sTM) were associated with composite poor outcome in COVID-19 patients ([standardized mean difference (SMD) 0.74 [0.33-1.16], p<0.001; I2:80.4%], [SMD 0.55 [0.19-0.92], p=0.003; I2:6.4%], [SMD 0.33 [0.04-0.62], p=0.025; I2:7.9%], and [SMD 0.55 [0.10-0.99], p=0.015; I2:23.6%], respectively).ConclusionThe estimated pooled means shows increased levels of VWF antigen in COVID-19 patients. Several biomarkers of endothelial dysfunction, including VFW antigen, t-PA, PAI-1, and sTM, are significantly associated with increased composite poor outcome in patients with COVID-19.PROSPERO registration numberCRD42021228821