bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the limits of experimental knowledge
Authors: Evans P. W. , Thébault K. P. Y. 
Published: July 2020

To demarcate the limits of experimental knowledge, we probe the limits of what might be called an experiment. By appeal to examples of scientific practice from astrophysics and analogue gravity, we demonstrate that the reliability of knowledge regarding certain phenomena gained from an experiment is not circumscribed by the manipulability or accessibility of the target phenomena. Rather, the limits of experimental knowledge are set by the extent to which strategies for what we call ‘inductive triangulation’ are available: that is, the validation of the mode of inductive reasoning involved in the source-target inference via appeal to one or more distinct and independent modes of inductive reasoning. When such strategies are able to partially mitigate reasonable doubt, we can take a theory regarding the phenomena to be well supported by experiment. When such strategies are able to fully mitigate reasonable doubt, we can take a theory regarding the phenomena to be established by experiment. There are good reasons to expect the next generation of analogue experiments to provide genuine knowledge of unmanipulable and inaccessible phenomena such that the relevant theories can be understood as well supported.
This article is part of a discussion meeting issue ‘The next generation of analogue gravity experiments’.
Dynamics landscape for acoustic superradiance
Authors: Gooding Cisco 
Published: July 2020

We analyse the behaviour of acoustic vortex beams interacting with rotating, fluid-saturated porous materials. Regions of the parameter space that exhibit distinct dynamical features are identified, with a focus on features that are relevant to the characterization of rotational superradiance. We discuss the similarities and differences between two recent proposals to observe acoustic superradiance with rotating, air-saturated sound absorbers. Finally, theoretical predictions for macroscopic acoustic scattering, obtained by averaging over interactions between the fluid and the porous material at the microscopic level, are compared with predictions of the first-Born approximation.
This article is part of a discussion meeting issue ‘The next generation of analogue gravity experiments’.
Aeromicrobium chenweiae sp. nov. and Aeromicrobium yanjiei sp. nov., isolated from Tibetan antelope (Pantholops hodgsonii) and plateau pika (Ochotona curzoniae), respectively
Authors: Li Junqin , Lei Wenjing , Yang Jing , Lu Shan , Jin Dong , Lai Xin-He , Zhang Sihui , Cheng Yanpeng , Mi Fei , Huang Yuyuan , Pu Ji , Dong Kui , Tian Zhi , Wu Xiaomin , Huang Ying , Wang Suping , Xu Jianguo 
Published: July 2020

Four novel strains (592T, S592, MF47T and SMF47) were isolated from Tibetan antelopes (Pantholops hodgsonii) and plateau pikas (Ochotona curzoniae), respectively. The cells were aerobic, non-motile, Gram-stain- and catalase-positive, rod-shaped bacteria. The 16S rRNA gene sequences of the four strains showed highest similarities to

Aeromicrobium fastidiosum

DSM 10552T (98.1, 98.6, 98.7 and 98.7 %, respectively), and the phylogenetic analyses based on 16S rRNA gene and genomic sequences indicated that strains 592T and MF47T represent two novel species. The four isolates produced acid from l-rhamnose, d-xylose and cellobiose, but were unable to reduce nitrate. The DNA G+C contents of strains 592T and MF47T were 70.3 and 69.8 mol%, respectively. The digital DNA–DNA hybridization value between strains 592T and MF47T was 32.6 %, lower than the threshold of 70 %, indicating they belong to different species. The four strains’ genomes displayed less than 24.6 % DNA–DNA relatedness with all available genomes of the genus

Aeromicrobium

in the NCBI database, including

Aeromicrobium fastidiosum

NBRC 14897T and

Aeromicrobium ginsengisoli

JCM 14732T. The major fatty acids of the four strains were C18 : 1
ω9c and C18 : 0 10-methyl, and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant respiratory quinones were MK-9(H4) and MK-8(H4). The cell-wall peptidoglycan contained ll-diaminopimelic acid. Based on these genotypic, phenotypic and biochemical analyses, it is proposed that the four unidentified bacteria be classified as two novel species, Aeromicrobium chenweiae sp. nov. and Aeromicrobium yanjiei sp. nov. The type strains are 592T (=CGMCC1.16526T=DSM 106289T) and MF47T (=CGMCC 1.17444T=JCM 33790T), respectively.
A privacy-preserving Bayesian network model for personalised COVID19 risk assessment and contact tracing
Authors: Fenton Norman E , McLachlan Scott , Lucas Peter , Dube Kudakwashe , Hitman Graham A , Osman Magda , Kyrimi Evangelia , Neil Martin 
Published: July 2020

AbstractConcerns about the practicality and effectiveness of using Contact Tracing Apps (CTA) to reduce the spread of COVID19 have been well documented and, in the UK, led to the abandonment of the NHS CTA shortly after its release in May 2020. One of the key non-technical obstacles to widespread adoption of CTA has been concerns about privacy. We present a causal probabilistic model (a Bayesian network) that provides the basis for a practical CTA solution that does not compromise privacy. Users of the model can provide as much or little personal information as they wish about relevant risk factors, symptoms, and recent social interactions. The model then provides them feedback about the likelihood of the presence of asymptotic, mild or severe COVID19 (past, present and projected). When the model is embedded in a smartphone app, it can be used to detect new outbreaks in a monitored population and identify outbreak locations as early as possible. For this purpose, the only data needed to be centrally collected is the probability the user has COVID19 and the GPS location.
Standardization of Trypanosoma cruzi DNA extraction and purification protocol from samples collected on Whatman 903 filter paper to Chagas disease diagnosis
Authors: Medina LS Jurado , Ballering G , Bisio M , Ojeda RM , Altcheh J 
Published: July 2020

AbstractChagas disease (CD) caused by the parasite Trypanosoma cruzi, belongs to the so-called neglected diseases group. In Argentina about 1,500 children are born with congenital Chagas disease per year. The diagnosis of CD in the newborn relies on the ability to detect parasites in the blood by microscopic observation, as the serological tests are ruled out because of the presence of maternal antibodies. CD treatment is more effective during the acute phase of infection. Early diagnosis and treatment of the disease is thus very important. The Argentinian National Program for early detection of metabolic diseases uses Whatman903 filter paper for blood sampling. This type of sample collection presents many advantages as the use of low blood volumes, minimal biological risk, and easy storage and transportation. The objective of the study was to evaluate the conservation efficiency of blood samples on filter paper in order to access good sensitivity on qPCR results for the detection of T. cruzi. To standardize the procedure, negative samples of blood were infected artificially with serial dilutions of trypomastigotes forms of T. cruzi from the TcVI strain obtained by cell culture in Vero cells. Concentrations between 50000 and 5 parasites/mL were prepared and loaded in filter paper for analysis. DNA extraction was conducted by the QIAamp DNA Mini Kit from QIAGEN. For qPCR, a method based on TaqMan technology was used, with a multiplex reaction for quantification of T. cruzi satellite DNA and an internal amplification control (IAC). The detection limit found from our results was 400 parasites/mL, demonstrating that this method could be a reliable option for the diagnosis of congenital CD by the detection of T. cruzi in blood collected in filter paper.
Gender and trust in government modify the association between mental health and stringency of social distancing related public health measures to reduce COVID-19: a global online survey
Authors: O’Hara Lily , Abdul Rahim Hanan F , Shi Zumin 
Published: July 2020

AbstractObjectivesTo investigate the associations between stringency of COVID-19 social distancing policies and mental health outcomes, and the moderating effect of trust in government and gender.Design and settingCross sectional study involving secondary analysis of publicly available data from a global online COVID-19 survey and the Oxford COVID-19 Government Response Tracker.Participants106,497 participants from 58 countries.Main outcome measuresOutcomes were a worries index and a depression index. Predictors were stringency of policies, trust in government, and gender. Multivariable regression was conducted to determine the three-way interaction between the predictor variables for mental health outcomes, adjusting for age, income and education.ResultsThe median age of participants (56.4% women) was 37 years (interquartile range 29 to 48 years). Women had higher worries and depression scores than men. 45.4% distrusted the government and 43.8% trusted the government to take care of its citizens. Among those who strongly trusted the government, an increase in the stringency of policies was associated with a significant increase in the worries index. Among men who distrusted the government, an increase in policy stringency was associated with an increase in the depression index but not the worries index. In women that strongly distrusted the government, there was an inversed U-shaped association between policy stringency and both the worries and depression indices.ConclusionAs the stringency of public health measures increases, so too do depression and worries. The association is moderated by gender and trust in government. For safe and effective public health measures, governments should develop strategies to increase trust in their actions.
Comparative analysis of the molecular mechanism of resistance to vapendavir across a panel of picornavirus species
Authors: Lanko Kristina , Sun Liang , Froeyen Mathy , Leyssen Pieter , Delang Leen , Mirabelli Carmen , Neyts Johan 
Published: July 2020

AbstractVapendavir is a rhino/enterovirus inhibitor that targets a hydrophobic pocket in the viral capsid. Drug-resistant variants were selectedin vitro. Mutations in the drug-binding pocket in VP1 (C199R/Y in hRV14; I194F in PV1; M252L and A156T in EV-D68), typical for this class of compounds, were identified. We also observed mutations that are located outside the pocket (K167E in EV-D68 and G149C in hRV2) and that contribute to the resistant phenotype. Remarkably, the G149C substitution made the replication of human rhinovirus 2 dependent on the presence of vapendavir. Our data suggest that vapendavir binding to the capsid of the dependent isolate may be required to stabilize the viral particle and to allow efficient dissemination of the virus. Our results demonstrate that vapendavir-resistant pheno- and genotypes of clinically relevant picornavirus species are more complex than generally believed.
Personalized Input-Output Hidden Markov Models for Disease Progression Modeling
Authors: Severson Kristen A. , Chahine Lana M. , Smolensky Luba , Ng Kenney , Hu Jianying , Ghosh Soumya 
Published: July 2020

AbstractDisease progression models are important computational tools in healthcare and are used for tasks such as improving disease understanding, informing drug discovery, and aiding in patient management. Although many algorithms for time series modeling exist, healthcare applications face particular challenges such as small datasets, medication effects, disease heterogeneity, and a desire for personalized predictions. In this work, we present a disease progression model that addresses these needs by proposing a probabilistic time-series model that captures individualized disease states, personalized medication effects, disease-state medication effects, or any combination thereof. The model builds on the framework of an input-output hidden Markov model where the parameters are learned using a structured variational approximation. To demonstrate the utility of the algorithm, we apply it to both synthetic and real-world datasets. In the synthetic case, we demonstrate the benefits afforded by the proposed model as compared to standard techniques. In the real-world cases, we use two Parkinson’s disease datasets to show improved predictive performance when ground truth is available and clinically relevant insights that are not revealed via classic Markov models when ground truth is not available.
RISK FACTORS FOR THE DEVELOPMENT OF HOSPITAL-ACQUIRED PEDIATRIC VENOUS THROMBOEMBOLISM: DEALING WITH POTENTIALLY CAUSAL AND CONFOUNDING RISK FACTORS USING DIRECTED ACYCLIC GRAPH (DAG) ANALYSIS
Authors: Campos Leonardo R. , Petroli Maurício , Sztajnzbok Flavio R. , Costa Elaine S. , Brandão Leonardo R. , Land Marcelo G. P. 
Published: July 2020

AbstractIntroductionHospital-acquired venous thromboembolism (HA-VTE) in children comprises multiple risk factors that should not be evaluated separately due to collinearity and multiple cause and effect relationships. This is one of the first case-control study of pediatric HA-VTE risk factors using Directed Acyclic Graph (DAG) analysis.Material and MethodsRetrospective, case-control study with 22 cases of radiologically proved HA-VTE and 76 controls matched by age, sex, unit of admission, and period of hospitalization. Descriptive statistics was used to define distributions of continuous variables, frequencies, and proportions of categorical variables, with a comparison between cases and controls. Due to many potential risk factors of HA-VTE, a directed acyclic graph (DAG) model was created to identify confounding, reduce bias, and increase precision on the analysis. The final model consisted of a DAG-based conditional logistic regression. The study was approved by the Institutional Review Board (CAAE 58056516.0.0000.5264).ResultsIn the initial univariable model, the following variables were selected as potential risk factors for HA-VTE: length of stay (LOS, days), ICU admission in the last 30 days, LOS in ICU, infection, central venous catheter (CVC), L-asparaginase, heart failure, liver failure and nephrotic syndrome. The final model (table 1) revealed LOS (OR=1.108, 95%CI=1.024-1.199, p=0.011), L-asparaginase (OR=27.184, 95%CI=1.639-450.982, p=0.021), and nephrotic syndrome (OR=31.481, 95%CI=1.182-838.706, p=0.039) as independent risk factors for HA-VTE.ConclusionThe DAG-based approach was useful to clarify the influence of confounders and multiple causalities of HA-VTE. Interestingly, CVC placement - a known thrombotic risk factor highlighted in several studies - was considered a confounder, while LOS, L-asparaginase use and nephrotic syndrome were confirmed as risk factors to HA-VTE. Large confidence intervals are related to the sample size, however the results were significant.HighlightsHA-VTE comprises multiple risk factors that should not be evaluated separately due to collinearity and confoundingDirected Acyclic Graph (DAG) helps to clarify collinearity and confounding related to multiple cause and effect relationships that exist in HA-VTE risk factorsThis is a novel study using DAG-based logistic regression to evaluate risk factors for HA-VTE in childrenWe reported the importance of medical conditions on the genesis of HA-VTE using a DAG-based approach, which makes it possible to clarify the influence of confounders and multiple causalities, such as catheter, a significant risk factor highlighted in several studies
Genetic inhibition of interleukin-6 receptor signaling and Covid-19
Authors: Bovijn Jonas , Lindgren Cecilia M , Holmes Michael V 
Published: July 2020

AbstractThere are few effective therapeutic options for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Early evidence has suggested that IL-6R blockers may confer benefit, particularly in severe coronavirus disease 2019 (Covid-19).We leveraged large-scale human genetic data to investigate whether IL6-R blockade may confer therapeutic benefit in Covid-19. A genetic instrument consisting of seven genetic variants in or close to IL6R was recently shown to be linked to altered levels of c-reactive protein (CRP), fibrinogen, circulating IL-6 and soluble IL-6R, concordant to known effects of pharmacological IL- 6R blockade. We investigated the effect of these IL6R variants on risk of hospitalization for Covid- 19 and other SARS-CoV-2-related outcomes using data from The Covid-19 Host Genetics Initiative.The IL6R variants were strongly associated with serum CRP levels in UK Biobank. Meta-analysis of scaled estimates revealed a lower risk of rheumatoid arthritis (OR 0.93 per 0.1 SD lower CRP, 95% CI, 0.90-0.96, P = 9.5 × 10−7), recapitulating this established indication for IL-6R blockers (e.g. tocilizumab and sarilumab). The IL-6R instrument was associated with lower risk of hospitalization for Covid-19 (OR 0.88 per 0.1 SD lower CRP, 95% CI, 0.78-0.99, P = 0.03). We found a consistent association when using a population-based control group (i.e. all non-cases; OR 0.91 per 0.1 SD lower CRP, 95% CI, 0.87-0.96, P = 4.9 × 10−4). Evaluation of further SARS- CoV-2-related outcomes suggested association with risk of SARS-CoV-2 infection, with no evidence of association with Covid-19 complicated by death or requiring respiratory support. We performed several sensitivity analyses to evaluate the robustness of our findings.Our results serve as genetic evidence for the potential efficacy of IL-6R blockade in Covid-19. Ongoing large-scale RCTs of IL-6R blockers will be instrumental in identifying the settings, including stage of disease, in which these agents may be effective.
SARS-CoV-2 viral load in the upper respiratory tract of children and adults with early acute COVID-19
Authors: Baggio Stéphanie , L’Huillier Arnaud G. , Yerly Sabine , Bellon Mathilde , Wagner Noémie , Rohr Marie , Huttner Angela , Blanchard-Rohner Géraldine , Loevy Natasha , Kaiser Laurent , Jacquerioz Frédérique , Eckerle Isabella 
Published: July 2020

AbstractThe role of children in the transmission of SARS-CoV-2 is unclear. We analysed viral load at the time of diagnosis in 53 children vs. 352 adults with COVID-19 in the first 5 days post symptom onset. No significant differences in SARS-CoV-2 RNA loads were seen between children and adults.
Self-Collected Anterior Nasal and Saliva Specimens versus Healthcare Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2
Authors: Hanson KE , Barker AP , Hillyard DR , Gilmore N , Barrett JW , Orlandi RR , Shakir SM 
Published: July 2020

AbstractWe prospectively compared healthcare worker-collected nasopharyngeal swabs (NPS) to self-collected anterior nasal swabs (ANS) and straight saliva for the diagnosis of COVID-19 in 354 patients. The positive percent agreement between NPS and ANS or saliva was 86.3% (95% CI: 76.7-92.9) and 93.8% (95% CI: 86.0-97.9), respectively. Negative percent agreement was 99.6% (95% CI: 98-100) for NPS vs. ANS and 97.8% (95% CI: 95.3 – 99.2) for NPS vs. saliva. NPS (n=80) and saliva (n=81) detected more cases than ANS (n=70), but no single specimen type detected all SARS-CoV2 infections.
Regional COVID-19 spread despite expected declines: how mitigation is hindered by spatio-temporal variation in local control measures
Authors: Kortessis Nicholas , Simon Margaret W. , Barfield Michael , Glass Gregory , Singer Burton H. , Holt Robert D. 
Published: July 2020

AbstractSuccessful public health regimes for COVID-19 push below unity long-term global Rt –the average number of secondary cases caused by an infectious individual. Most assessments use local information. Populations differ in Rt, amongst themselves and over time. We use a SIR model for two populations to make the conceptual point that even if each locality averages Rt < 1, the overall epidemic can still grow, provided these populations have asynchronous variation in transmission, and are coupled by movement of infectious individuals. This emergent effect in pandemic dynamics instantiates “Parrondo’s Paradox,” -- an entity comprised of distinct but interacting units can behave qualitatively differently than each part on its own. For effective COVID-19 disease mitigation strategies, it is critical that infectious individuals moving among locations be identified and quarantined. This does not warrant indiscriminate prevention of movement, but rather rational, targeted testing and national coordination.
Medical Costs of Keeping the US Economy Open During COVID-19
Authors: Chen Jiangzhuo , Vullikanti Anil , Hoops Stefan , Mortveit Henning , Lewis Bryan , Venkatramanan Srinivasan , You Wen , Eubank Stephen , Marathe Madhav , Barrett Chris , Marathe Achla 
Published: July 2020

ABSTRACTWe use an individual based model and national level epidemic simulations to estimate the medical costs of keeping the US economy open during COVID-19 pandemic under different counterfactual scenarios. We model an unmitigated scenario and 12 mitigation scenarios which differ in compliance behavior to social distancing strategies and to the duration of the stay-home order. Under each scenario we estimate the number of people who are likely to get infected and require medical attention, hospitalization, and ventilators. Given the per capita medical cost for each of these health states, we compute the total medical costs for each scenario and show the tradeoffs between deaths, costs, infections, compliance and the duration of stay-home order. We also consider the hospital bed capacity of each Hospital Referral Region (HRR) in the US to estimate the deficit in beds each HRR will likely encounter given the demand for hospital beds. We consider a case where HRRs share hospital beds among the neighboring HRRs during a surge in demand beyond the available beds and the impact it has in controlling additional deaths.
Rapid and sensitive detection of SARS-CoV-2 antibodies by biolayer interferometry
Authors: Dzimianski John V. , Lorig-Roach Nicholas , O’Rourke Sara M. , Alexander David L. , Kimmey Jacqueline M. , DuBois Rebecca M. 
Published: July 2020

AbstractSerological testing to evaluate antigen-specific antibodies in plasma is generally performed by rapid lateral flow test strips that lack quantitative results or by high complexity immunoassays that are time- and labor-intensive but provide quantitative results. Here, we describe a novel application of biolayer interferometry for the rapid detection of antigen-specific antibody levels in plasma samples, and demonstrate its utility for quantification of SARS-CoV-2 antibodies. Our biolayer interferometry immunosorbent assay (BLI-ISA) utilizes single-use biosensors in an automated “dip-and-read” format, providing real-time optical measurements of antigen loading, plasma antibody binding, and antibody isotype detection. Complete quantitative results are obtained in less than 20 minutes. BLI-ISA meets or exceeds the performance of high complexity methods such as Enzyme-Linked Immunosorbent Assay (ELISA) and Chemiluminescent Immunoassay. Importantly, our method can be immediately implemented on existing BLI platforms for urgent COVID-19 studies, such as serosurveillance and the evaluation of vaccine candidates. In a broader sense, BLI-ISA can be developed as a novel diagnostic platform to evaluate antibodies and other biomolecules in clinical specimens.