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Rxivist combines biology preprints from bioRxiv and medRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 166,810 papers from 692,906 authors.

Most tweeted biology preprints, last 24 hours

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188 results found. For more information, click each entry to expand.

81: Exploring relationships between drought and epidemic cholera in Africa using generalised linear models
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Posted 19 Jul 2021

Exploring relationships between drought and epidemic cholera in Africa using generalised linear models
1 tweet medRxiv epidemiology

Gina E C Charnley, Ilan Kelman, Nathan Green, Wes Hinsley, Katy A. M. Gaythorpe, Kris A. Murray

Background: Temperature and precipitation are known to affect Vibrio cholerae outbreaks. Despite this, the impact of drought on outbreaks has been largely understudied. Africa is both drought and cholera prone and more research is needed in Africa to understand cholera dynamics in relation to drought. Methods: Here, we analyse a range of environmental and socioeconomic covariates and fit generalised linear models to publicly available national data, to test for associations with several indices of drought and make cholera outbreak projections to 2070 under three scenarios of global change, reflecting varying trajectories of CO2 emissions, socio-economic development, and population growth. Results: The best-fit model implies that drought is a significant risk factor for African cholera outbreaks, alongside positive effects of population, temperature and poverty and a negative effect of freshwater withdrawal. The projections show that following stringent emissions pathways and expanding sustainable development may reduce cholera outbreak occurrence in Africa, although these changes were spatially heterogeneous. Conclusions: Despite an effect of drought in explaining recent cholera outbreaks, future projections highlighted the potential for sustainable development gains to offset drought-related impacts on cholera risk. Future work should build on this research investigating the impacts of drought on cholera on a finer spatial scale and potential non-linear relationships, especially in high-burden countries which saw little cholera change in the scenario analysis.

82: BNT162b2 Vaccine Induces Divergent B cell responses to SARS-CoV-2 S1 and S2
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Posted 22 Jul 2021

BNT162b2 Vaccine Induces Divergent B cell responses to SARS-CoV-2 S1 and S2
1 tweet medRxiv infectious diseases

R. Camille Brewer, Nitya S Ramadoss, Lauren J Lahey, William H Robinson, Tobias V Lanz

The first ever messenger RNA (mRNA) vaccines received emergency approvals in December 2020 and are highly protective against SARS-CoV-2. However, the contribution of each dose to the generation of antibodies against SARS-CoV-2 spike (S) protein and the degree of protection against novel variants, including delta, warrant further study. Here, we investigated the B cell response to the BNT162b2 vaccine by integrating repertoire analysis with single-cell transcriptomics of B cells from serial blood collections pre- and post-vaccination. The first vaccine dose elicits highly mutated IgA+ plasmablasts against the S protein subunit S2 at day 7, suggestive of recall of a memory B cell response generated by prior infections with heterologous coronaviruses. On day 21, we observed minimally-mutated IgG+ activated switched memory B cells targeting the receptor binding domain (RBD) of the S protein, likely representing a primary response derived from naive B cells. The B cell response against RBD is specifically boosted by the second vaccine dose, and encodes antibodies that potently neutralize SARS-CoV-2 pseudovirus and partially neutralize novel variants, including delta. These results demonstrate that the first vaccine dose activates a non-neutralizing recall response predominantly targeting S2, while the second vaccine dose is vital to boosting neutralizing anti-S1 RBD B cell responses.

83: Impact of SARS-CoV-2 variant on the severity of maternal infection and perinatal outcomes: Data from the UK Obstetric Surveillance System national cohort.
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Posted 25 Jul 2021

Impact of SARS-CoV-2 variant on the severity of maternal infection and perinatal outcomes: Data from the UK Obstetric Surveillance System national cohort.
1 tweet medRxiv obstetrics and gynecology

Nicola Vousden, Rema Ramakrishnan, Kathryn Bunch, Edward Morris, Nigel Simpson, Christopher Gale, Patrick O'Brien, Maria Quigley, Peter Brocklehurst, Jennifer J Kurinczuk, Marian Knight

Background In the UK, the Alpha variant of SARS-CoV-2 became dominant in late 2020, rapidly succeeded by the Delta variant in May 2021. The aim of this study was to compare the impact of these variants on severity of maternal infection and perinatal outcomes within the time-periods in which they predominated. Methods This national, prospective cohort study collated data on hospitalised pregnant women with symptoms of confirmed SARS-CoV-2 infection and compared the severity of infection and perinatal outcomes across the Wildtype (01/03/20-30/11/20), Alpha (01/12/20-15/05/21) and Delta dominant periods (16/05/21-11/07/21), using multivariable logistic regression. Findings Of 3371 pregnant women, the proportion that experienced moderate to severe infection significantly increased between Wildtype and Alpha periods (24.4% vs. 35.8%; aOR1.75 95%CI 1.48-2.06), and between Alpha and Delta periods (35.8% vs. 45.0%; aOR1.53, 95%CI 1.07-2.17). Compared to the Wildtype period, symptomatic women admitted in the Alpha period were more likely to require respiratory support (27.2% vs. 20.3%, aOR1.39, 95%CI 1.13-1.78), have pneumonia (27.5% vs. 19.1%, aOR1.65, 95%CI 1.38-1.98) and be admitted to intensive care (11.3% vs. 7.7%, aOR1.61, 95%CI 1.24-2.10). Women admitted during the Delta period had further increased risk of pneumonia (36.8% vs. 27.5%, aOR1.64 95%CI 1.14-2.35). No fully vaccinated pregnant women were admitted between 01/02/2021 when vaccination data collection commenced and 11/07/2021. The proportion of women receiving pharmacological therapies for SARS-CoV-2 management was low, even in those critically ill. Interpretation SARS-CoV-2 infection during Alpha and Delta dominant periods was associated with more severe infection and worse pregnancy outcomes compared to the Wildtype infection, which itself increased risk compared to women without SARS-CoV-2 infection.1 Clinicians need to be aware and implement COVID-specific therapies in keeping with national guidance. Urgent action to tackle vaccine misinformation and policy change to prioritise uptake in pregnancy is essential. Funding National Institute for Health Research HS&DR Programme (11/46/12).

84: High-intensity exercise is a risk factor for renal medullary carcinoma in individuals with sickle cell trait
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Posted 01 Mar 2021

High-intensity exercise is a risk factor for renal medullary carcinoma in individuals with sickle cell trait
1 tweet medRxiv oncology

Daniel D. Shapiro, Melinda Soeung, Luigi Perelli, Eleonora Dondossola, Devaki Shilpa Surasi, Durga N. Tripathi, Jean-Philippe Bertocchio, Ruohan Xia, Michael W. Starbuck, Michael L. Van Alstine, Priya Rao, Matthew H. G. Katz, Nathan H. Parker, Amishi Y. Shah, Alessandro Carugo, Timothy P. Heffernan, Keri L. Schadler, Christopher Logothetis, Cheryl L. Walker, Christopher G. Wood, Jose A. Karam, Giulio F. Draetta, Nizar M. Tannir, Giannicola Genovese, Pavlos Msaouel

Renal medullary carcinoma (RMC) predominantly occurs in individuals with sickle cell trait (SCT). We found that patients with RMC more frequently participated in high-intensity exercise than matched controls, and renal medullary hypoxia significantly increased predominantly in the right kidney of mice with SCT following high-but not moderate-intensity exercise, consistent with the distinct predilection of RMC toward the right kidney. These results establish high-intensity exercise as a risk factor for RMC in individuals with SCT.

85: Six Month Safety and Efficacy of the BNT162b2 mRNA COVID-19 Vaccine
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Posted 28 Jul 2021

Six Month Safety and Efficacy of the BNT162b2 mRNA COVID-19 Vaccine
1 tweet medRxiv infectious diseases

Stephen J. Thomas, Edson D Moreira, Nicholas Kitchin, Judith Absalon, Alejandra Gurtman, Stephen Lockhart, John L Perez, Gonzalo Pérez Marc, Fernando P. Polack, Cristiano Zerbini, Ruth Bailey, Kena A. Swanson, Xia Xu, Satrajit Roychoudhury, Kenneth Koury, Salim Bouguermouh, Warren V. Kalina, David Cooper, Robert W Frenck, Laura L. Hammitt, Özlem Türeci, Haylene Nell, Axel Schaefer, Serhat Ünal, Qi Yang, Paul Liberator, Dina B Tresnan, Susan Mather, Philip R. Dormitzer, Uğur Şahin, William C. Gruber, Kathrin U. Jansen, C4591001 Clinical Trial Group

Background: BNT162b2 is a lipid nanoparticle-formulated, nucleoside-modified RNA vaccine encoding a prefusion-stabilized, membrane-anchored SARS-CoV-2 full-length spike protein. BNT162b2 is highly efficacious against COVID-19 and is currently authorized for emergency use or conditional approval worldwide. At the time of authorization, data beyond 2 months post-vaccination were unavailable. Methods: In an ongoing, placebo-controlled, observer-blinded, multinational, pivotal efficacy study, 44,165 [≥]16-year-old participants and 2,264 12-15-year-old participants were randomized to receive 2 doses, 21 days apart, of 30 g BNT162b2 or placebo. Study endpoints reported here are vaccine efficacy (VE) against laboratory-confirmed COVID-19 and safety data, both up to 6 months post-vaccination. Results: BNT162b2 continued to be safe and well tolerated. Few participants had adverse events leading to study withdrawal. VE against COVID-19 was 91% (95% CI 89.0-93.2) through up to 6 months of follow-up, among evaluable participants and irrespective of previous SARS-CoV-2 infection. VE of 86%-100% was seen across countries and in populations with diverse characteristics of age, sex, race/ethnicity, and COVID-19 risk factors in participants without evidence of previous SARS-CoV-2 infection. VE against severe disease was 97% % (95% CI 80.3-99.9). In South Africa, where the SARS-CoV-2 variant of concern, B.1.351 (beta), was predominant, 100% (95% CI 53.5, 100.0) VE was observed. Conclusion: With up to 6 months of follow-up and despite a gradually declining trend in vaccine efficacy, BNT162b2 had a favorable safety profile and was highly efficacious in preventing COVID-19. (ClinicalTrials.gov number, NCT04368728)

86: Reactive vaccination of workplaces and schools against COVID-19
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Posted 29 Jul 2021

Reactive vaccination of workplaces and schools against COVID-19
1 tweet medRxiv infectious diseases

Benjamin Faucher, Rania Assab, Jonathan Roux, Daniel Levy-Bruhl, Cécile Tran Kiem, Simon Cauchemez, Laura Zanetti, Vittoria Colizza, Pierre-Yves Boëlle, Chiara Poletto

As vaccination against COVID-19 stalls in some countries, increased accessibility and more adaptive approaches may be useful to keep the epidemic under control. Here we study the impact of reactive vaccination targeting schools and workplaces where cases have been detected, with an agent-based model accounting for COVID-19 natural history, vaccine characteristics, individuals' demography and behaviour and social distancing. We study epidemic scenarios ranging from sustained spread to flare-up of cases, and we consider reactive vaccination alone and in combination with mass vaccination. With the same number of doses, reactive vaccination reduces cases more than non-reactive approaches, but may require concentrating a high number of doses over a short time in case of sustained spread. In case of flare-ups, quick implementation of reactive vaccination supported by enhanced test-trace-isolate practices would limit further spread. These results provide key information to promote an adaptive vaccination plan in the months to come.

87: Evidence from imaging resilience genetics for a protective mechanism against schizophrenia in the ventral visual pathway
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Posted 30 Jul 2021

Evidence from imaging resilience genetics for a protective mechanism against schizophrenia in the ventral visual pathway
1 tweet medRxiv psychiatry and clinical psychology

Meike Dorothee Hettwer, Thomas M. Lancaster, Eva Raspor, Peter K. Hahn, Nina Roth Mota, Wolf Singer, Andreas Reif, David E. J. Linden, Robert A Bittner

Introduction: Illuminating neurobiological mechanisms underlying the protective effect of recently discovered common genetic resilience variants for schizophrenia is crucial for more effective prevention efforts. Current models implicate adaptive neuroplastic changes in the visual system and their pro-cognitive effects as a schizophrenia resilience mechanism. We investigated whether common genetic resilience variants might affect brain structure in similar neural circuits. Method: Using structural magnetic resonance imaging, we measured the impact of an established schizophrenia polygenic resilience score (PRSResilience) on cortical volume, thickness, and surface area in 101 healthy subjects and in a replication sample of 33,224 healthy subjects (UK Biobank). Finding: We observed a significant positive whole-brain correlation between PRSResilience and cortical volume in the right fusiform gyrus (FFG) (r=0.35; p=.0004). Post-hoc analyses in this cluster revealed an impact of PRSResilience on cortical surface area. The replication sample showed a positive correlation between PRSResilience and global cortical volume and surface area in the left FFG. Conclusion: Our findings represent the first evidence of a neurobiological correlate of a genetic resilience factor for schizophrenia. They support the view that schizophrenia resilience emerges from strengthening neural circuits in the ventral visual pathway and an increased capacity for the disambiguation of social and non-social visual information. This may aid psychosocial functioning, ameliorate the detrimental effects of subtle perceptual and cognitive disturbances in at-risk individuals, and facilitate coping with the cognitive and psychosocial consequences of stressors. Our results thus provide a novel link between visual cognition, the vulnerability-stress concept and schizophrenia resilience models.

88: Correlates of Neutralizing/SARS-CoV-2-S1-binding Antibody Response with Adverse Effects and Immune Kinetics in BNT162b2-Vaccinated Individuals
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Posted 30 Jul 2021

Correlates of Neutralizing/SARS-CoV-2-S1-binding Antibody Response with Adverse Effects and Immune Kinetics in BNT162b2-Vaccinated Individuals
1 tweet medRxiv infectious diseases

Kenji Maeda, Masayuki Amano, Yukari Uemura, Kiyoto Tsuchiya, Tomoko Matsushima, Kenta Noda, Yosuke Shimizu, Asuka Fujiwara, Yuki Takamatsu, Yasuko Ichikawa, Hidehiro Nishimura, Mari Kinoshita, Shota Matsumoto, Hiroyuki Gatanaga, Kazuhisa Yoshimura, Shinichi Oka, Ayako Mikami, Wataru Sugiura, Toshiyuki Sato, Tomokazu Yoshida, Shinya Shimada, Hiroaki Mitsuya

Background: While mRNA vaccines against SARS-CoV-2 have been exceedingly effective in preventing symptomatic viral infection, the features of immune response remain to be clarified. Methods: In the present prospective observational study, 225 healthy individuals in Kumamoto General Hospital, Japan, who received two BNT162b2 doses in February 2021, were enrolled. Correlates of BNT162b2-elicited SARS-CoV-2-neutralizing activity (50% neutralization titer: NT50; assessed using infectious virions and live target cells) with SARS-CoV-2-S1-binding-IgG and -IgM levels, adverse effects (AEs), ages, and genders were examined. The average half-life of neutralizing activity and the average time length for the loss of detectable neutralizing activity were determined and the potency of serums against variants of concerns was also determined. Findings: Significant rise in NT50s was seen in serums on day 28 post-1st dose. A moderate inverse correlation was seen between NT50s and ages, but no correlation was seen between NT50s and AEs. NT50s and IgG levels on day 28 post-1st dose and pain scores following the 2nd shot were greater in women than in men. The average half-life of neutralizing activity in the vaccinees was approximately 67.8 days and the average time length for their serums to lose the detectable neutralizing activity was 198.3 days. While serums from elite-responders (NT50s>1,500-fold: the top 4% among all participants' NT50s) potently to moderately blocked the infectivity of variants of concerns, some serums with moderate NT50s failed to block the infectivity of a beta strain. Interpretation: BNT162b2-elicited immune response has no significant association with AEs. BNT162b2-efficacy is likely diminished to under detection limit by 6-7 months post-1st shot. High-level neutralizing antibody-containing serums potently to moderately block the infection of SARS-CoV-2 variants; however, a few moderate-level neutralizing antibody-containing serums failed to do so. If BNT162b2-elicited immunity memory is short, an additional vaccine or other protective measures would be needed.

89: Hibernation slows epigenetic aging in yellow-bellied marmots
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Posted 08 Mar 2021

Hibernation slows epigenetic aging in yellow-bellied marmots
1 tweet bioRxiv evolutionary biology

Gabriela Medeiros Pinho, Julien G. A. Martin, Colin Farrell, Amin Haghani, Joseph Alan Zoller, Joshua Zhang, Sagi Snir, Matteo Pellegrini, Robert K. Wayne, Daniel T Blumstein, Steve Horvath

Species that hibernate live longer than would be expected based solely on their body size. Hibernation is characterized by long periods of metabolic suppression (torpor) interspersed by short periods of increased metabolism (arousal). The torpor-arousal cycles occur multiple times during hibernation, and it has been suggested that processes controlling the transition between torpor and arousal states cause aging suppression. Metabolic rate is also a known correlate of longevity, we thus proposed the hibernation-aging hypothesis whereby aging is suspended during hibernation. We tested this hypothesis in a well-studied population of yellow-bellied marmots (Marmota flaviventer), which spend 7-8 months per year hibernating. We used two approaches to estimate epigenetic age: the epigenetic clock and the epigenetic pacemaker. Variation in epigenetic age of 149 samples collected throughout the life of 73 females were modeled using generalized additive mixed models (GAMM), where season (cyclic cubic spline) and chronological age (cubic spline) were fixed effects. As expected, the GAMM using epigenetic ages calculated from the epigenetic pacemaker was better able to detect nonlinear patterns in epigenetic age change over time. We observed a logarithmic curve of epigenetic age with time, where the epigenetic age increased at a higher rate until females reached sexual maturity (2-years old). With respect to circannual patterns, the epigenetic age increased during the summer and essentially stalled during the winter. Our enrichment analysis of age-related CpG sites revealed pathways related to development and cell differentiation, while the season-related CpGs enriched pathways related to central carbon metabolism, immune system, and circadian clock. Taken together, our results are consistent with the hibernation-aging hypothesis and may explain the enhanced longevity in hibernators.

90: Efficacy and safety of Ivermectin and Hydroxychloroquine in patients with severe COVID-19. A randomized controlled trial
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Posted 23 Feb 2021

Efficacy and safety of Ivermectin and Hydroxychloroquine in patients with severe COVID-19. A randomized controlled trial
1 tweet medRxiv infectious diseases

Jose Lenin Beltran Gonzalez, Mario González Gámez, Emanuel Antonio Mendoza Enciso, Ramiro Josue Esparza Maldonado, Daniel Hernández Palacios, Samuel Dueñas Campos, Itzel Ovalle Robles, Mariana Jocelyn Macías Guzmán, Andrea Lucia García Díaz, César Mauricio Gutiérrez Peña, Lucila Martinez Medina, Victor Antonio Monroy Colin, Arreola Guerra Jose Manuel

BackgroundIn the search for active drugs against COVID-19, the indications of many have been redirected. Ivermectin and Hydroxychloroquine are drugs that inhibit viral replication in vitro and that have been used in several medical centers. ObjectivesThis clinical trial analyzes the efficacy of Ivermectin and Hydroxychloroquine in patients with moderate COVID-19 and in need of hospitalization. MethodsThis a controlled, clinical, randomized, double-blind trial that included patients with COVID-19-induced pneumonia and hospitalization criteria, but no severe respiratory failure. Patients were randomized to one of three groups: Group1-hydroxychloroquine, 400 mg every 12 hours on the first day and subsequently, 200 mg every 12 hours for 4 days, Group 2-ivermectin, 12 mg or 18 mg, according to patient weight and, Group 3-placebo. At inclusion, blood samples for arterial blood gases and biochemical markers associated with a poor prognosis were obtained. The primary outcome was established as the duration of hospitalization until discharge due to patient improvement, the total duration of hospitalization, and the safety outcomes were either respiratory deterioration or death. ResultsDuring the month of August, the admission of patients requiring hospitalization mostly encompassed cases with severe respiratory failure, so we ended the recruitment process and analyzed the data that was available at the time. One hundred and six (106) patients with an average age of 53 yrs. ({+/-}16.9) were included, with a greater proportion of males (n=66, 62.2 %). Seventy-two percent (72%) (n= 76) had an associated comorbidity. Ninety percent (90 %) of patients were discharged due to improvement (n=96). The average duration of hospitalization was 6 days (IQR, 3 - 10). No difference in hospitalization duration was found between the treatment groups (Group1: 7 vs Group 2: 6 vs Group 3: 5, p=0.43) nor in respiratory deterioration or death (Group 1: 18 % vs Group 2: 22.2 % vs Group 3: 24.3 %, p =0.83). ConclusionsIn non-critical hospitalized patients with COVID-19 pneumonia, neither ivermectin nor hydroxychloroquine decreases the number of in-hospital days, respiratory deterioration, or deaths. ClinicalTrials identifier NCT04391127

91: SARS-CoV-2 causes brain inflammation and induces Lewy body formation in macaques
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Posted 23 Feb 2021

SARS-CoV-2 causes brain inflammation and induces Lewy body formation in macaques
1 tweet bioRxiv neuroscience

Ingrid H.C.H.M. Philippens, Kinga P. Boszormenyi, Jacqueline A. Wubben, Zahra C Fagrouch, Nikki van Driel, Amber Q. Mayenburg, Diana Lozovagia, Eva Roos, Bernadette Schurink, Marianna Bugiani, Ronald E Bontrop, Jinte Middeldorp, Willy M Bogers, Lioe-Fee de Geus-Oei, Jan A.M. Langermans, Marieke A Stammes, Babs E Verstrepen, Ernst J Verschoor

SARS-CoV-2 may cause acute respiratory disease, but the infection can also initiate neurological symptoms. Here we show that SARS-CoV-2 infection causes brain inflammation in the macaque model. An increased metabolic activity in the pituitary gland of two macaques was observed by longitudinal positron emission tomography-computed tomography (PET-CT). Post-mortem analysis demonstrated infiltration of T-cells and activated microglia in the brain, and viral RNA was detected in brain tissues from one animal. We observed Lewy bodies in brains of all rhesus macaques. These data emphasize the virus' capability to induce neuropathology in this nonhuman primate model for SARS-CoV-2 infection. As in humans, Lewy body formation is an indication for the development of Parkinson's disease, this data represents a warning for potential long-term neurological effects after SARS-CoV-2 infection.

92: Diagnostic Efficacy of Rapid Antigen Testing for SARS-CoV-2: The COVid-19 AntiGen (COVAG) study
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Posted 07 Aug 2021

Diagnostic Efficacy of Rapid Antigen Testing for SARS-CoV-2: The COVid-19 AntiGen (COVAG) study
1 tweet medRxiv public and global health

Christoph Wertenauer, Geovana Brenner-Michael, Alexander Dressel, Caroline Pfeifer, Ulrike Hauser, Eberhard Wieland, Christian Mayer, Caren Mutschmann, Martin Roskos, Hans-Joerg Wertenauer, Winfried Maerz

Abstract Background: Widely available rapid testing is pivotal to the fight against COVID-19. Real-time reverse transcription-polymerase chain reaction (rRT-PCR) remains the gold standard. We compared two frequently used commercial rapid diagnostic tests (RDTs) for SARS-CoV-2-antigens, the SD Biosensor SARS-CoV-2 Rapid Antigen Test (Roche Diagnostics) and the Panbio COVID-19 Ag Rapid Test (Abbott Diagnostics), against rRT-PCR for SARS-CoV-2 detection. Methods: We compared the tests in 2215 all-comers at a diagnostic centre between February 1 and March 31, 2021. rRT-PCR-positive samples were examined for SARS-CoV-2 variants. Findings: 338 participants (15%) were rRT-PCR-positive for SARS-CoV-2. The sensitivities of Roche-RDT and Abbott-RDT were 60.4% and 56.8% (P<0.0001) and specificities 99.7% and 99.8% (P=0.076), respectively. Sensitivity inversely correlated with rRT-PCR-derived Ct values. Unadjusted, the RDTs had higher sensitivities in individuals referred by treating physicians and health departments than those tested for other reasons, in persons without comorbidities compared to those with comorbidities, in individuals with symptoms suggesting COVID-19, and in the absence of SARS-CoV-2 variants compared to Alpha variant carriers. The associations of sensitivity with clinical symptoms and the SARS-CoV-2 genotype were robust against adjustment for Ct values. Assuming that 10 000 symptomatic individuals are tested, 500 of which are truly positive, the RDTs would generate 38 false-positive and 124 false-negative results. Assuming that 10 000 asymptomatic individuals are tested, including 50 true positives, 18 false-positives and 34 false- negatives would be generated. Interpretation: The sensitivities of the two RDTs are unsatisfactory. This calls into question whether their widespread use is effective in the ongoing SARS-CoV-2 pandemic. Funding: SYNLAB Holding Deutschland GmbH Key words COVID-19, SARS-Cov-2, antibodies, rapid detection, antigen testing

93: Modelling the effectiveness and social costs of daily lateral flow antigen tests versus quarantine in preventing onward transmission of COVID-19 from traced contacts
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Posted 08 Aug 2021

Modelling the effectiveness and social costs of daily lateral flow antigen tests versus quarantine in preventing onward transmission of COVID-19 from traced contacts
1 tweet medRxiv epidemiology

Luca Ferretti, Chris Wymant, Anel Nurtay, Lele Zhao, Robert Hinch, David Bonsall, Michelle Kendall, Joanna Masel, John Bell, Susan Hopkins, A. Marm Kilpatrick, Tim Peto, Lucie Abeler-Dörner, Christophe Fraser

Quarantining close contacts of individuals infected with SARS-CoV-2 for 10 to 14 days is a key strategy in reducing transmission. However, quarantine requirements are often unpopular, with low adherence, especially when a large fraction of the population has been vaccinated. Daily contact testing (DCT), in which contacts are required to isolate only if they test positive, is an alternative to quarantine for mitigating the risk of transmission from traced contacts. In this study, we developed an integrated model of COVID-19 transmission dynamics and compared the strategies of quarantine and DCT with regard to reduction in transmission and social/economic costs (days of quarantine/self-isolation). Specifically, we compared 10-day quarantine to 7 days of self-testing using rapid lateral flow antigen tests, starting 3 days after exposure to a case. We modelled both incomplete adherence to quarantine and incomplete adherence to DCT. We found that DCT reduces transmission from contacts with similar effectiveness, at much lower social/economic costs, especially for highly vaccinated populations. The findings were robust across a spectrum of scenarios with varying assumptions on the speed of contact tracing, sensitivity of lateral flow antigen tests, adherence to quarantine and uptake of testing. Daily tests would also allow rapid initiation of a new round of tracing from infected contacts.

94: Machine learning detects SARS-CoV-2 and variants rapidly on DNA aptamer metasurfaces
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Posted 08 Aug 2021

Machine learning detects SARS-CoV-2 and variants rapidly on DNA aptamer metasurfaces
1 tweet medRxiv infectious diseases

Hulya Torun, Buse Bilgin, Muslum Ilgu, Cenk Yanik, Sukru Numan Batur, Suleyman Celik, Meric Ozturk, Ozlem Dogan, Onder Ergonul, Ihsan Solaroglu, Fusun Can, Mehmet Cengiz Onbasli

COVID-19 is detected using reverse transcription polymerase chain reaction (RT-PCR) of nasal swabs. A very sensitive and rapid detection technique using easily-collected fluids like saliva must be developed for safe and precise mass testing. Here, we introduce a metasurface platform for direct sensing of COVID-19 from unprocessed saliva. We computationally screen gold metasurfaces out of a pattern space of 2100 combinations for strongly-enhanced light-virus interaction with machine learning and use it to investigate the presence and concentration of the SARS-CoV-2. We use machine learning to identify the virus from Raman spectra with 95.2% sensitivity and specificity on 36 PCR positive and 33 negative clinical samples and to distinguish wild-type, alpha, and beta variants. Our results could pave the way for effective, safe and quantitative preventive screening and identification of variants.

95: Psilocybin induces rapid and persistent growth of dendritic spines in frontal cortex in vivo
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Posted 17 Feb 2021

Psilocybin induces rapid and persistent growth of dendritic spines in frontal cortex in vivo
1 tweet bioRxiv neuroscience

Ling-Xiao Shao, Clara Liao, Ian Gregg, Pasha A Davoudian, Neil Savalia, Kristina Delagarza, Alex C Kwan

Psilocybin is a serotonergic psychedelic with untapped therapeutic potential. There are hints that the use of psychedelics can produce neural adaptations, although the extent and time scale of the impact in a mammalian brain are unknown. In this study, we used chronic two-photon microscopy to image longitudinally the apical dendritic spines of layer 5 pyramidal neurons in the mouse medial frontal cortex. We found that a single dose of psilocybin led to ~10% increases in spine size and density, driven by an elevated spine formation rate. The structural remodeling occurred quickly within 24 hours and was persistent 1 month later. Psilocybin also ameliorated stress-related behavioral deficit and elevated excitatory neurotransmission. Overall, the results demonstrate that psilocybin-evoked synaptic rewiring in the cortex is fast and enduring, potentially providing a structural trace for long-term integration of experiences and lasting beneficial actions.

96: Pandemic excess mortality in Spain, Sweden, and Switzerland during the COVID-19 pandemic in 2020 was at its highest since 1918
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Posted 13 Aug 2021

Pandemic excess mortality in Spain, Sweden, and Switzerland during the COVID-19 pandemic in 2020 was at its highest since 1918
1 tweet medRxiv public and global health

Kaspar Staub, Radoslaw Panczak, Katarina L Matthes, Joel Floris, Claudia Berlin, Christoph Junker, Rolf Weitkunat, Svenn-Erik Mamelund, Matthias Egger, Marcel Zwahlen, Julien Riou

Estimating excess mortality allows quantification of overall pandemic impact. For recent decades, mortality data are easily accessible for most industrialized countries, but only a few countries have continuous data available for longer periods. Since Spain, Sweden, and Switzerland were militarily neutral and not involved in combat during both world wars, these countries have monthly all-cause mortality statistics available for over 100 years with no interruptions. We show that during the COVID-19 pandemic in 2020, Spain, Sweden and Switzerland recorded the highest aggregated monthly excess mortality (17%, 9% and 14%) since the 1918 influenza pandemic (53%, 33% and 49%), when compared to respective expected values. For Sweden and Switzerland, the highest monthly spikes in 2020 almost reached those of January 1890. These findings emphasize the historical dimensions of the ongoing pandemic and support the notion of a pandemic disaster memory gap.

97: Parasite co-opts a ubiquitin receptor to induce a plethora of developmental changes
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Posted 15 Feb 2021

Parasite co-opts a ubiquitin receptor to induce a plethora of developmental changes
1 tweet bioRxiv molecular biology

Weijie Huang, Allyson Marie MacLean, Akiko Sugio, Abbas Maqbool, Macro Busscher, Shu-Ting Cho, Sophien Kamoun, Chih-Horng Kuo, Richard G.H. Immink, Saskia A Hogenhout

Obligate parasites can induce complex and substantial phenotypic changes in their hosts in ways that favour their transmission to other trophic levels. However, mechanisms underlying these changes remain largely unknown. Here, we demonstrate how SAP05 protein effectors from insect-vectored plant pathogenic phytoplasmas take control of several plant developmental processes to simultaneously prolong host lifespan and induce witch's broom-like proliferations of leaf and sterile shoots, organs colonized by phytoplasmas and vectors. SAP05 acts by mediating the concurrent degradation of SPL and GATA developmental regulators via a process that uniquely relies on hijacking the plant ubiquitin receptor RPN10 independently of substrate lysine ubiquitination. RPN10 is highly conserved among eukaryotes, but SAP05 does not bind insect vector RPN10. A two-amino-acid substitution within plant RPN10 generates a functional variant that is resistant to SAP05 activities. Therefore, one effector protein enables obligate parasitic phytoplasmas to induce a plethora of developmental phenotypes in their hosts.

98: Initial real world evidence for lower viral load of individuals who have been vaccinated by BNT162b2
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Posted 08 Feb 2021

Initial real world evidence for lower viral load of individuals who have been vaccinated by BNT162b2
1 tweet medRxiv epidemiology

Ella Petter, Orna Mor, Neta Zuckerman, Danit Oz-Levi, Asaf Younger, Dvir Aran, Yaniv Erlich

One of the key questions regarding COVID19 vaccines is whether they can reduce viral shedding. To date, Israel vaccinated substantial parts of the adult population, which enables extracting real world signals. The vaccination rollout started on Dec 20th 2020, utilized mainly the BNT162b2 vaccine, and focused on individuals who are 60 years or older. By now, more than 75% of the individuals of this age group have been at least 14 days after the first dose, compared to 25% of the individuals between ages 40-60 years old. Here, we traced the Ct value distribution of 16,297 positive qPCR tests in our lab between Dec 1st to Jan 31st that came from these two age groups. As we do not have access to the vaccine status of each test, our hypothesis was that if vaccines reduce viral load, we should see a difference in the Ct values between these two age groups in late January but not before. Consistent with this hypothesis, until Jan 15th, we did not find any statistically significant differences in the average Ct value between the groups. In stark contrast, our results in the last two weeks of January show a significant weakening in the average Ct value of 60+ individuals to the 40-60 group. To further corroborate these results, we also used a series nested linear models to explain the Ct values of the positive tests. This analysis favored a model that included an interaction between age and the late January time period, consistent with the effect of vaccination. We then used demographic data and the daily vaccination rates to estimate the effect of vaccination on viral load reduction. Our estimate suggests that vaccination reduces the viral load by 1.6x to 20x in individuals who are positive for SARS-CoV-2. This estimate might improve after more individuals receive the second dose. Taken together, our findings indicate vaccination is not only important for individual's protection but can reduce transmission.

99: Decreased SARS-CoV-2 viral load following vaccination
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Posted 08 Feb 2021

Decreased SARS-CoV-2 viral load following vaccination
1 tweet medRxiv infectious diseases

Matan Levine-Tiefenbrun, Idan Yelin, Rachel Katz, Esma Herzel, Ziv Golan, Licita Schreiber, Tamar Wolf, Varda Nadler, Amir Ben-Tov, Jacob Kuint, Sivan Gazit, Tal Patalon, Gabriel Chodick, Roy Kishony

Beyond their substantial protection of individual vaccinees, it is hoped that the COVID-19 vaccines would reduce viral load in breakthrough infections thereby further suppress onward transmission. Here, analyzing positive SARS-CoV-2 test results following inoculation with the BNT162b2 mRNA vaccine, we find that the viral load is reduced 4-fold for infections occurring 12-28 days after the first dose of vaccine. These reduced viral loads hint to lower infectiousness, further contributing to vaccine impact on virus spread.

100: The Specious Art of Single-Cell Genomics
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Posted 26 Aug 2021

The Specious Art of Single-Cell Genomics
1 tweet bioRxiv genomics

Tara Chari, Joeyta Banerjee, Lior Pachter

Dimensionality reduction is standard practice for filtering noise and identifying relevant dimensions in large-scale data analyses. In biology, single-cell expression studies almost always begin with reduction to two or three dimensions to produce 'all-in-one' visuals of the data that are amenable to the human eye, and these are subsequently used for qualitative and quantitative analysis of cell relationships. However, there is little theoretical support for this practice. We examine the theoretical and practical implications of low-dimensional embedding of single-cell data, and find extensive distortions incurred on the global and local properties of biological patterns relative to the high-dimensional, ambient space. In lieu of this, we propose semi-supervised dimension reduction to higher dimension, and show that such targeted reduction guided by the metadata associated with single-cell experiments provides useful latent space representations for hypothesis-driven biological discovery.

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