bluuebunny/crossref_metadata_2025_split huggingface dataset:
#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol
Authors: Dommer Abigail , Casalino Lorenzo , Kearns Fiona , Rosenfeld Mia , Wauer Nicholas , Ahn Surl-Hee , Russo John , Oliveira Sofia , Morris Clare , Bogetti Anthony , Trifan Anda , Brace Alexander , Sztain Terra , Clyde Austin , Ma Heng , Chennubhotla Chakra , Lee Hyungro , Turilli Matteo , Khalid Syma , Tamayo-Mendoza Teresa , Welborn Matthew , Christensen Anders , Smith Daniel G. A. , Qiao Zhuoran , Sirumalla Sai Krishna , O’Connor Michael , Manby Frederick , Anandkumar Anima , Hardy David , Phillips James , Stern Abraham , Romero Josh , Clark David , Dorrell Mitchell , Maiden Tom , Huang Lei , McCalpin John , Woods Christopher , Gray Alan , Williams Matt , Barker Bryan , Rajapaksha Harinda , Pitts Richard , Gibbs Tom , Stone John , Zuckerman Daniel , Mulholland Adrian , Miller Thomas , Jha Shantenu , Ramanathan Arvind , Chong Lillian , Amaro Rommie 
Published: November 2021

ABSTRACTWe seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus ob-scure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.ACM Reference FormatAbigail Dommer1†, Lorenzo Casalino1†, Fiona Kearns1†, Mia Rosenfeld1, Nicholas Wauer1, Surl-Hee Ahn1, John Russo,2Sofia Oliveira3, Clare Morris1, AnthonyBogetti4, AndaTrifan5,6, Alexander Brace5,7, TerraSztain1,8, Austin Clyde5,7, Heng Ma5, Chakra Chennubhotla4, Hyungro Lee9, Matteo Turilli9, Syma Khalid10, Teresa Tamayo-Mendoza11, Matthew Welborn11, Anders Christensen11, Daniel G. A. Smith11, Zhuoran Qiao12, Sai Krishna Sirumalla11, Michael O’Connor11, Frederick Manby11, Anima Anandkumar12,13, David Hardy6, James Phillips6, Abraham Stern13, Josh Romero13, David Clark13, Mitchell Dorrell14, Tom Maiden14, Lei Huang15, John McCalpin15, Christo- pherWoods3, Alan Gray13, MattWilliams3, Bryan Barker16, HarindaRajapaksha16, Richard Pitts16, Tom Gibbs13, John Stone6, Daniel Zuckerman2*, Adrian Mulholland3*, Thomas MillerIII11,12*, ShantenuJha9*, Arvind Ramanathan5*, Lillian Chong4*, Rommie Amaro1*. 2021. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy ofDeltaSARS-CoV-2 in a Respiratory Aerosol. InSupercomputing ‘21: International Conference for High Perfor-mance Computing, Networking, Storage, and Analysis. ACM, New York, NY, USA, 14 pages.https://doi.org/finalDOI
“Addressing the core trait of bipolar disorder”: a concept analysis of mood stabilizing drugs
Authors: Estivalete Marchionatti Lauro , Blaya-Rocha Paula , Magalhães Pedro Vieira da Silva 
Published: November 2021

ABSTRACTBackgroundThe term “mood stabilizer” is controversial in the literature. As there is no consensual meaning, its retirement has been suggested to avoid misuse. Nevertheless, it remains largely employed, and may carry an important meaning. This issue has not been approached using a validated qualitative inquiry.MethodsWe employed document analysis for reviewing definitions for mood stabilizer. Then, we used concept analysis as a qualitative methodology to clarify the meanings associated with the term. Based on its results, we built a theoretical model for a mood stabilizer, matching it with evidence for drugs used in the treatment of bipolar disorder.ResultsConcept analysis of documents defining the term unearthed four attributes of a mood stabilizer that were nested into the following ascending hierarchy: “not worsening”, “acute effects”, “prophylactic effects”, and “advanced effects”. To be considered a mood stabilizer, a drug had to reach the “prophylactic effects” tier, as this was discussed by authors as the core aspect of the class. After arranging drugs according to this scheme, “lithium” and “quetiapine” received the label, but only the former fulfilled all four attributes, as evidence indicates it has neuroprotective action.ConclusionThe proposed model uses a hierarchy of attributes that take into account the complexity of the term and help to determine whether a drug is a mood stabilizer. Prophylaxis is pivotal to the concept, whose utility lies in implying a drug able to truly treat bipolar disorder, as opposed to merely targeting symptoms. This could modify long-term outcomes and illness trajectory.
Naloxone Buyers Club: Overlooked Critical Public Health Infrastructure for Preventing Overdose Deaths
Authors: Doe-Simkins Maya , Wheeler Eliza Jane , Figgatt Mary C. , Jones T. Stephen , Bell Alice , Davidson Peter J. , Dasgupta Nabarun 
Published: November 2021

ABSTRACTBackgroundCommunity-based naloxone distribution is an evidence-based pillar of overdose prevention. Since 2012, the naloxone Buyers Club facilitated purchase of low-cost naloxone by harm reduction and syringe service programs, the primary conduits for reaching people who use drugs. This innovative purchasing and mutual aid network has not been previously described.MethodsWe analyzed transactional records of naloxone orders (2017-2020, n=965), a survey of current Buyers Club members (2020, n=104), and mutual aid requests (2021, n=86).ResultsBetween 2017 and 2020, annual orders for naloxone increased 2.6-fold. 114 unique harm reduction programs from 40 states placed orders for 3,714,110 vials of 0.4 mg/mL generic naloxone through the Buyers Club. States with most orders were: Arizona (600,000 vials), Illinois (576,800), Minnesota (347,450), California (317,200), North Carolina (315,040). Among programs that ordered naloxone in 2020, 52% (n=32) received no federal funding and ordered half as much as funded programs. During the 2021 shortage, mutual aid redistribution was common, with 80% participating as either a donor or recipient. Among 59 mutual aid requestors, 59% (n=35) were willing to accept expired naloxone; the clear preference was for generic injectable naloxone, 95% (n=56).ConclusionsThe naloxone Buyers Club is a critical element of overdose prevention infrastructure. Yet, barriers from corporate compliance officers and federal prescription-only status impede access. These barriers can be reduced by FDA removing the prescription requirement for naloxone and government funding for harm reduction programs.
Safety and immunogenicity of anti-SARS CoV-2 vaccine SOBERANA 02 in homologous or heterologous scheme
Authors: Eugenia-Toledo-Romani Maria , Verdecia-Sánchez Leslihana , Rodriguez-González Meybis , Rodríguez-Noda Laura , Valenzuela-Silva Carmen , Paredes-Moreno Beatriz , Sanchez-Ramirez Belinda , Perez-Nicado Rocmira , González-Mugica Raul , Hernández-Garcia Tays , Bergado-Baez Gretchen , Pi-Estopiñán Franciscary , Cruz-Sui Otto , Fraga-Quintero Anitza , García-Montero Majela , Palenzuela-Diaz Ariel , Baro-Roman Gerardo , Mendosa-Hernández Ivis , Fernandez-Castillo Sonsire , Climent-Ruiz Yanet , Santana-Mederos Darielys , Gonzalez Ubel Ramírez , García-Vega Yanelda , Perez-Massón Beatriz , Guang-Wu-Chen  , Boggiano-Ayo Tammy , Ojito-Magaz Eduardo , Rivera Daniel G. , Valdés-Balbín Yury , García-Rivera Dagmar , Vérez-Bencomo Vicente ,   SOBERANA Research Group
Published: November 2021

AbstractBackgroundSOBERANA 02 is a COVID-19 conjugate vaccine candidate based on SARS-CoV-2 recombinant RBD conjugated to tetanus toxoid. SOBERANA Plus antigen is dimeric-RBD. Here we report safety, reactogenicity and immunogenicity from phase I and IIa clinical trials using two-doses SOBERANA 02 (homologous protocol) and three-doses (homologous) or heterologous (with SOBERANA Plus) protocols.MethodWe performed an open-label, monocentric, sequential and adaptive phase I for evaluating safety, reactogenicity and exploring immunogenicity of SOBERANA 02 in two formulations (15 and 25 μg) in 40 subjects, 19–59 years old. Phase IIa was open-label including 100 volunteers 19–80 years, receiving two doses of SOBERANA 02-25 μg. In both trials, half of volunteers received a third dose of SOBERANA 02, half received a heterologous dose of SOBERANA Plus-50 μg. Primary outcomes were safety and reactogenicity. The secondary outcome was vaccine immunogenicity evaluated by anti-RBD IgG ELISA, molecular neutralization test of RBD:hACE2 interaction, live-virus neutralization test and specific T-cells response.ResultsThe most frequent AE was local pain, other AEs had frequencies ≤ 5%. No serious related AEs were reported. Phase IIa confirmed the safety results in 60–80 years subjects. In phase-I SOBERANA 02-25µg elicited higher immune response than SOBERANA 02-15 µg; in consequence, the higher dose progressed to phase IIa. Phase IIa results confirmed the immunogenicity of SOBERANA 02-25 μg even in 60–80 age range. Two doses of SOBERANA02-25 μg elicited an immune response similar to that of the Cuban Convalescent Serum Panel; it was higher after both the homologous and heterologous third doses; the heterologous scheme showing a higher immunological response.ConclusionsSOBERANA 02 was safe and immunogenic in persons aged 19–80 years, eliciting neutralizing antibodies and specific T cell response. Highest immune responses were obtained in the heterologous three doses protocol. Trial registry: https://rpcec.sld.cu/trials/RPCEC00000340 and https://rpcec.sld.cu/trials/RPCEC00000347
Comparison and aggregation of event sequences across ten cohorts to describe the consensus biomarker evolution in Alzheimer’s disease
Authors: Khatami Sepehr Golriz , Salimi Yasamin , Hofmann-Apitius Martin , Oxtoby Neil P. , Birkenbihl Colin ,   for the Alzheimer’s Disease Neuroimaging Initiative,   the Japanese Alzheimer’s Disease Neuroimaging Initiative,   the Alzheimer’s Disease Repository Without Borders Investigators
Published: November 2021

AbstractBackgroundPrevious models of Alzheimer’s disease (AD) progression were primarily hypothetical or based on data originating from single cohort studies. However, cohort datasets are subject to specific inclusion and exclusion criteria that influence the signals observed in their collected data. Furthermore, each study measures only a subset of AD relevant variables. To gain a comprehensive understanding of AD progression, the heterogeneity and robustness of estimated progression patterns must be understood, and complementary information contained in cohort datasets be leveraged.MethodsWe compared ten event-based models that we fit to ten independent AD cohort datasets. Additionally, we designed and applied a novel rank aggregation algorithm that combines partially overlapping, individual event sequences into a meta-sequence containing the complementary information from each cohort.ResultsWe observed overall consistency across the ten event-based model sequences (Kendall’s tau correlation coefficient of 0.78±0.13), despite variance in the positioning of mainly imaging variables. The changes described in the aggregated meta-sequence are broadly consistent with current understanding of AD progression, starting with cerebrospinal fluid amyloid beta, followed by memory impairment, tauopathy, FDG-PET, and ultimately brain deterioration and impairment of visual memory.ConclusionOverall, the event-based models demonstrated similar and robust disease cascades across independent AD cohorts. Aggregation of data-driven results can combine complementary strengths and information of patient-level datasets. Accordingly, the derived meta-sequence draws a more complete picture of AD pathology compared to models relying on single cohorts.
Should we Mitigate or Suppress the next Pandemic? Time-Horizons and Costs shape optimal Social Distancing Strategies
Authors: Nowak Sarah , de Lima Pedro Nascimento , Vardavas Raffaele 
Published: November 2021

AbstractThe COVID-19 pandemic has called for swift action from local governments, which have instated Nonpharmaceutical Interventions (NPIs) to curb the spread of SARS-Cov-2. The quick and decisive decision to save lives through blunt instruments has raised questions about the conditions under which decision-makers should employ mitigation or suppression strategies to tackle the COVID-19 pandemic. More broadly, there are still debates over which set of strategies should be adopted to control different pandemics, and the lessons learned for SARS-Cov-2 may not apply to a new pathogen. While curbing SARS-Cov-2 required blunt instruments, it is unclear whether a less-transmissible and less-deadly emerging pathogen would justify the same response. This paper illuminates this question using a parsimonious transmission model by formulating the social distancing lives vs. livelihoods dilemma as a boundary value problem. In this setup, society balances the costs and benefits of social distancing contingent on the costs of reducing transmission relative to the burden imposed by the disease. To the best of our knowledge, our approach is distinct in the sense that strategies emerge from the problem structure rather than being imposed a priori. We find that the relative time-horizon of the pandemic (i.e., the time it takes to develop effective vaccines and treatments) and the relative cost of social distancing influence the choice of the optimal policy. Unsurprisingly, we find that the appropriate policy response depends on these two factors. We discuss the conditions under which each policy archetype (suppression vs. mitigation) appears to be the most appropriate.
Higher Vaccination Rate Predicts Reduction in SARS-CoV-2 Transmission across the United States
Authors: Au Jacky 
Published: November 2021

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began proliferating widely throughout the world in late 2019/early 2020, creating a global pandemic and health crisis. Although vaccines became available to the public approximately one year after the onset of the pandemic, there still remains much hesitancy surrounding vaccination even two years into the pandemic. One key concern comes from reports of breakthrough infections among the vaccinated that show comparable levels of peak viral load as the unvaccinated, calling into question the ability of vaccines to slow or prevent transmission. Therefore young, healthy individuals who are at low risk of serious complications themselves have little incentive to receive a vaccine that they are not convinced will protect others around them. To address this important concern, this article analyzes COVID-19 incidence in the United States as a function of each state’s vaccination rate. Results show that states with higher percentages of fully vaccinated individuals report fewer new cases among the remaining unvaccinated population. These data add to accumulating evidence that COVID-19 vaccinations can indeed slow the spread of SARS-CoV-2, and are an important tool in society’s arsenal to put this pandemic behind us.
Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2
Authors: Chen Irene P. , Longbotham James E. , McMahon Sarah , Suryawanshi Rahul K. , Carlson-Stevermer Jared , Gupta Meghna , Zhang Meng Yao , Soveg Frank W. , Hayashi Jennifer M. , Taha Taha Y. , Lam Victor L. , Li Yang , Yu Zanlin , Titus Erron W. , Diallo Amy , Oki Jennifer , Holden Kevin ,   QCRG Structural Biology Consortium, Krogan Nevan , Galonić Fujimori Danica , Ott Melanie 
Published: November 2021

SUMMARYInhibitors of Bromodomain and Extra-terminal domain (BET) proteins are possible anti-SARS-CoV-2 prophylactics as they downregulate angiotensin-converting enzyme 2 (ACE2). Here, we show that BET proteins should not be inactivated therapeutically as they are critical antiviral factors at the post-entry level. Knockouts of BRD3 or BRD4 in cells overexpressing ACE2 exacerbate SARS-CoV-2 infection; the same is observed when cells with endogenous ACE2 expression are treated with BET inhibitors during infection, and not before. Viral replication and mortality are also enhanced in BET inhibitor-treated mice overexpressing ACE2. BET inactivation suppresses interferon production induced by SARS-CoV-2, a process phenocopied by the envelope (E) protein previously identified as a possible “histone mimetic.” E protein, in an acetylated form, directly binds the second bromodomain of BRD4. Our data support a model where SARS-CoV-2 E protein evolved to antagonize interferon responses via BET protein inhibition; this neutralization should not be further enhanced with BET inhibitor treatment.
Presence of SARS-CoV-2 in food surfaces and public space surfaces in 3 districts of Lima, Peru
Authors: Alvis-Chirinos Katherine , Angulo-Bazán Yolanda , Escalante-Maldonado Oscar , Fuentes Duilio , Rodriguez Miryam Guillermina Palomino , Gonzales-Achuy Elena , Mormontoy Henry , Hinojosa Paul , Huamán-Espino Lucio , Aparco Juan Pablo 
Published: November 2021

ResumeObjectiveThe goal of this study is to determine the presence of SARS-CoV-2 in food surfaces and public space surfaces in 3 districts of Lima, Peru.Material and methodsCross-sectional descriptive study, carried out in the districts of San Juan de Lurigancho, San Martin de Porres and Villa el Salvador. Surfaces that were exposed to the greatest user manipulation were selected, samples were swabbed for 4 weeks and transported to the laboratory to determine the presence of the virus.Results1095 inert surface samples and 960 food surface samples were evaluated for the identification of SARS-CoV-2 by the RT-PCR molecular test, whereby only one sample from an ATM (Automated Teller Machine) was positive.ConclusionsMost of the inert and food surfaces evaluated did not show the presence of SARS-CoV-2 during the time of sample collection. Despite the negative results, the frequency of disinfection measures should be maintained and increased, especially on inert high-contact surfaces, and hygiene measures on food should be continue.
Fecal genomic DNA extraction method impacts outcome of MinION based metagenome profile of tuberculosis patients
Authors: Sahu Sukanya , Kaushik Sandeep Rai , Goswami Bidhan , Dasgupta Arunabha , Guha Hritusree , Das Ranjit , Saha Sourav , Das Anjan , Nanda Ranjan Kumar 
Published: November 2021

ABSTRACTIn the present era, emergence of next generation sequencing approaches has revolutionized the field of gut microbiome study. However, the adopted DNA extraction step used in metagenomics experiments and its efficiency may play a critical role in their reproducibility and outcome. In this study, fecal samples from active and non-tuberculosis subjects (ATB/NTB, n=7) were used. Fecal samples of a subgroup of these subjects were subjected to Mechanical enzymatic lysis (MEL) and Phenol: Chloroform: Isoamyl Alcohol (PCIA) methods of DNA extraction and a third-generation sequencing platform i.e. MinION was employed for microbiome profiling. Findings of this study demonstrated that DNA extraction method significantly impacts the DNA yield and microbial diversity. Irrespective of the adopted method of DNA extraction, ATB patients showed altered microbial diversity compared to NTB controls. Also, the fecal microbial diversity details are better captured in samples processed by MEL method and may be suitable to be adopted for high-throughput gut microbiome studies.
Positive end expiratory pressure in invasive and non-invasive ventilation of COVID-19 acute respiratory distress syndrome: computational modeling illuminates the data
Authors: Weaver Liam , Bates Declan G. , Camporota Luigi 
Published: November 2021

AbstractPositive end expiratory pressure (PEEP) is routinely used as part of lung protective ventilation strategies in the treatment of acute respiratory distress syndrome (ARDS). In the case of ARDS arising due to COVID-19 (CARDS), there is some debate as to whether the atypical pathophysiological characteristics of the disease which lead to hypoxaemia could warrant a modified approach to ventilator management, particularly with regards to PEEP settings. Here we review the available evidence for the existence of a unique underlying lung pathophysiology in CARDS, and for the suitability of standard approaches to setting PEEP, in both the invasive and non-invasive ventilation settings. We show how detailed computational models informed by this evidence can shed light on the available data, and help to interpret recent results in the literature.
Mental and social wellbeing and the UK Coronavirus Job Retention Scheme: evidence from nine longitudinal studies
Authors: Wels Jacques , Booth Charlotte , Wielgoszewska Bożena , Green Michael , Di Gessa Giorgio , Huggins Charlotte F. , Griffith Gareth J. , Kwong Alex S. F. , Bowyer Ruth C. E. , Maddock Jane , Patalay Praveetha , Silverwood Richard J. , Fitzsimons Emla , Shaw Richard , Thompson Ellen J. , Steptoe Andrew , Hughes Alun , Chaturvedi Nishi , Steves Claire J. , Katikireddi Srinivasa Vittal , Ploubidis George B. 
Published: November 2021

AbstractBackgroundThe COVID-19 pandemic has led to major economic disruptions. In March 2020, the UK implemented the Coronavirus Job Retention Scheme – known as furlough – to minimize the impact of job losses. We investigate associations between change in employment status and mental and social wellbeing during the early stages of the pandemic.MethodsData were from 25,670 respondents, aged 17 to 66, across nine UK longitudinal studies. Furlough and other employment changes were defined using employment status pre-pandemic and during the first lockdown (April-June 2020). Mental and social wellbeing outcomes included psychological distress, life satisfaction, self-rated health, social contact, and loneliness. Study-specific modified Poisson regression estimates, adjusting for socio-demographic characteristics and pre-pandemic mental and social wellbeing measures, were pooled using meta-analysis.ResultsCompared to those who remained working, furloughed workers were at greater risk of psychological distress (adjusted risk ratio, ARR=1.12; 95% CI: 0.97, 1.29), low life satisfaction (ARR=1.14; 95% CI: 1.07, 1.22), loneliness (ARR=1.12; 95% CI: 1.01, 1.23), and poor self-rated health (ARR=1.26; 95% CI: 1.05, 1.50), but excess risk was less pronounced than that of those no longer employed (e.g., ARR for psychological distress=1.39; 95% CI: 1.21, 1.59) or in stable unemployment (ARR=1.33; 95% CI: 1.09, 1.62).ConclusionsDuring the early stages of the pandemic, those furloughed had increased risk for poor mental and social wellbeing. However, their excess risk was lower in magnitude than that of those who became or remained unemployed, suggesting that furlough may have partly mitigated poorer outcomes.