bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protocol for a retrospective, comparative effectiveness study of the association between transesophageal echocardiography (TEE) monitoring used in coronary artery bypass graft (CABG) surgery and clinical outcomes
Authors: Mackay Emily J. , Zhang Bo , Heng Siyu , Ye Ting 
Published: May 2020

AbstractBackgroundCoronary artery bypass graft (CABG) surgery is the most widely performed adult cardiac surgery in the US. Transesophageal echocardiography (TEE) is an ultrasound-based cardiac imaging modality used in CABG surgery for hemodynamic monitoring and management of complications related to cardiopulmonary bypass. However, there are no comparative effectiveness studies (randomized or non-randomized) that have investigated the relationship between TEE monitoring and clinical outcomes among patients undergoing CABG surgery. Because of this lack of evidence, recommendations for TEE in CABG surgery remain indeterminate (Class II). We aim to compare the clinical outcomes of patients undergoing CABG surgery with vs without TEE monitoring. This protocol will detail how we plan to investigate the hypothesis that TEE monitoring in CABG surgery will be associated with improved clinical outcomes.Methods and AnalysisThis investigation will be an observational retrospective, comparative effectiveness, cohort study using Centers for Medicare and Medicaid Services (CMS) claims data from January 1, 2013 to October 15, 2015. The aim is to determine if TEE monitoring during CABG surgery is associated with improved 30-day survival, lower incidence of stroke, shorter length of hospitalization, and incidence of esophageal perforation. To alleviate the potential bias from unmeasured confounding, we propose leveraging hospitals’ (or surgeons’) preference for TEE in CABG surgery as an instrumental variable (IV). We will combine this IV technique with statistical-matching-based methods by pairing hospitals (or surgeons) with similar observed confounding variables but considerably different preference for TEE monitoring in CABG surgery. Our research design is meant to emulate a cluster-randomized encouragement experiment. The following a priori protocol will detail how we plan to execute this analysis.
Verification of two Alternative Do-it-yourself Equipment Respirators Seal as COVID-19 Protection (VADERS-CoV): a quality assessment pilot study
Authors: Pettinger Marco , Momeni Mona , Michaud Clemence , Van Dyck Michel , Kahn David , Lemaire Guillaume 
Published: May 2020

AbstractBackgroundDuring the ongoing COVID-19 pandemic, healthcare workers are facing shortage in personal protective equipment, especially adequate respirators. Alternative do-it-yourself respirators (ADR) emerge, without any proof of protection.ObjectiveVerify seal potential of two ADR compared to a common FFP2 respirator.DesignQuality assessment pilot study.SettingTertiary Care Hospital.ParticipantsTen anaesthesiology residents.InterventionsParticipants performed quantitative face-fit tests (QNFT) with three respirators to evaluate seal. A common FFP2 respirator was used as baseline (control group). ADR tested in this study are an Anaesthesia Face Mask (AFM) and a full-face Modified Snorkelling Mask (MSM) with a 3D-printed connector, both in conjunction with a breathing system filter.Main outcome measuresNon-inferior seal performance of ADR over FFP2, assessed by calculated QNFT based on measured individual fit factors, as defined by the Occupational Safety and Health Administration.ResultsFor each respirator a total of 90 individual fit factor measurements were taken. Within the control group, seal failed in 37 (41%) measurements but only in 10 (11%) within the AFM group and in 6 (7%) within the MSM group (P < 0.001 respectively). However, when calculating the final, mean QNFT results, no statistically significant difference was found between respirators. Successful QNFT were determined for 5 out of 10 participants in the control group, for 8 in the AFM group (P = 0.25) and for 7 in the MSM group (P = 0.69).ConclusionBoth ADR do have the potential to provide non inferior seal compared to a common FFP2 respirator. While AFM respirators are easily assembled, snorkelling masks must undergo significant but feasible modifications. Our results suggest that those ADR masks might be further investigated as they seem to be viable alternatives for situations when certified respirators are not available.Trial registrationClinicaltrials.gov identifier: NCT04375774
Do Face Masks Create a False Sense of Security? A COVID-19 Dilemma
Authors: Yan Youpei , Bayham Jude , Fenichel Eli P. , Richter Aaron 
Published: May 2020

AbstractFace masks have become an emblem of the public response to COVID-19, with many governments mandating their use in public spaces. The logic is that face masks are low cost and might help prevent some transmission. However, from the start, the assumption that face masks are “low cost” was questioned. Early on, there were warnings of the opportunity cost of public use of medical masks given shortages of personal protective equipment for healthcare providers. This led to recommendations for cloth masks and other face coverings, with little evidence of their ability to prevent transmission. However, there may also be a high cost to these recommendations if people rely on face masks in place of other more effective ways to break transmission, such as staying home. We use SafeGraph smart device location data to show that the representative American in states that have face mask mandates spent 20-30 minutes less time at home, and increase visits to a number of commercial locations, following the mandate. Since the reproductive rate of SAR-COV2, the pathogen that causes COVID-19 is hovering right around one, such substitution behavior could be the difference between controlling the epidemic and a resurgence of cases.HighlightsWe use smart device location data to show the behavioral response to face mask mandates during the 2020 COVID-19 epidemic.We find face mask mandates lead people to spend 20-30 minutes less time at home per day.We find face mask mandates increase trip taking to a variety of locations, chief among them are restaurants.This substitution behavior is concerning given the limited information on the protective value of casual face coverings.
No evidence for allelic association between Covid-19 and ACE2 genetic variants by direct exome sequencing in 99 SARS-CoV-2 positive patients
Authors: Novelli Antonio , Biancolella Michela , Borgiani Paola , Cocciadiferro Dario , Colona Vito Luigi , D’Apice Maria Rosaria , Rogliani Paola , Zaffina Salvatore , Leonardis Francesca , Campana Andrea , Raponi Massimiliano , Andreoni Massimo , Grelli Sandro , Novelli Giuseppe 
Published: May 2020

AbstractBackgroundCoronaviruses (CoV) are a large family of viruses that are common in people and many animal species. Animal coronaviruses rarely infect humans with the exceptions of the Middle East Respiratory Syndrome (MERS-CoV), the Severe acute respiratory syndrome coronavirus (SARS-CoV), and now SARS-CoV-2, which is the cause of the ongoing pandemic of coronavirus disease 2019 (COVID-19). Many studies suggested that genetic variants in ACE2 gene may influence the host susceptibility/resistance to SARS-CoV-2 virus according to the functional role of ACE2 in human pathophysiology. However, all these studies have been conducted in silico based on epidemiological and population data. We therefore investigated the occurrence of ACE2 variants in a cohort of 99 Italian unrelated individuals clinically diagnosed with coronavirus disease 19 (COVID-19) to experimental demonstrate allelic association with disease severity.MethodsBy whole-exome sequencing we analysed 99 DNA samples of severely and extremely severely COVID-19 patients hospitalized at the University Hospital of Rome “Tor Vergata” and Bambino Gesù Hospital in Rome.ResultsWe identified three different germline variants, one intronic (c.439+4G>A) and two missense (c.2158A>G, p.Asn720Asp; c.1888G>C, p.Asp630His), in 26 patients with a similar frequency between male and female and a not statistically different frequency, except for c.1888G>C, (p.Asp630His) with the ethnically matched populations (EUR).ConclusionsOur results suggest that there is not any ACE2 exonic allelic association with disease severity. It is possible that rare susceptibility alleles are located in the non-coding region of the gene able to control ACE2 gene activity. It is therefore of interest, to explore the existence of ACE2 susceptibility alleles to SARS-Co-V2 in these regulatory regions. In addition, we found no significant evidence that ACE2 alleles is associated with disease severity/sex bias in the Italian population.
Visualizing the invisible: The effect of asymptomatic transmission on the outbreak dynamics of COVID-19
Authors: Peirlinck Mathias , Linka Kevin , Costabal Francisco Sahli , Bhattacharya Jay , Bendavid Eran , Ioannidis John P.A. , Kuhl Ellen 
Published: May 2020

AbstractUnderstanding the outbreak dynamics of the COVID-19 pandemic has important implications for successful containment and mitigation strategies. Recent studies suggest that the population prevalence of SARS-CoV-2 antibodies, a proxy for the number of asymptomatic cases, could be an order of magnitude larger than expected from the number of reported symptomatic cases. Knowing the precise prevalence and contagiousness of asymptomatic transmission is critical to estimate the overall dimension and pandemic potential of COVID-19. However, at this stage, the effect of the asymptomatic population, its size, and its outbreak dynamics remain largely unknown. Here we use reported symptomatic case data in conjunction with antibody seroprevalence studies, a mathematical epidemiology model, and a Bayesian framework to infer the epidemiological characteristics of COVID-19. Our model computes, in real time, the time-varying contact rate of the outbreak, and projects the temporal evolution and credible intervals of the effective reproduction number and the symptomatic, asymptomatic, and recovered populations. Our study quantifies the sensitivity of the outbreak dynamics of COVID-19 to three parameters: the effective reproduction number, the ratio between the symptomatic and asymptomatic populations, and the infectious periods of both groups. For nine distinct locations, our model estimates the fraction of the population that has been infected and recovered by Jun 15, 2020 to 24.15% (95% CI: 20.48%-28.14%) for Heinsberg (NRW, Germany), 2.40% (95% CI: 2.09%-2.76%) for Ada County (ID, USA), 46.19% (95% CI: 45.81%-46.60%) for New York City (NY, USA), 11.26% (95% CI: 7.21%-16.03%) for Santa Clara County (CA, USA), 3.09% (95% CI: 2.27%-4.03%) for Denmark, 12.35% (95% CI: 10.03%-15.18%) for Geneva Canton (Switzerland), 5.24% (95% CI: 4.84%-5.70%) for the Netherlands, 1.53% (95% CI: 0.76%-2.62%) for Rio Grande do Sul (Brazil), and 5.32% (95% CI: 4.77%-5.93%) for Belgium. Our method traces the initial outbreak date in Santa Clara County back to January 20, 2020 (95% CI: December 29, 2019 - February 13, 2020). Our results could significantly change our understanding and management of the COVID-19 pandemic: A large asymptomatic population will make isolation, containment, and tracing of individual cases challenging. Instead, managing community transmission through increasing population awareness, promoting physical distancing, and encouraging behavioral changes could become more relevant.
COVID-19 in Latin America: Contrasting phylodynamic inference with epidemiological surveillance. (Molecular epidemiology of COVID-19 in Latin America)
Authors: Rojas-Gallardo Diana M. , Garzón-Castaño Sandra C. , Millán Natalia , Jiménez-Posada Erika V. , Martínez-Gutiérrez Marlen , Ruiz-Saenz Julian , Cardona-Ospina Jaime A. 
Published: May 2020

AbstractBackgroundSARS-CoV-2 revealed important gaps in infectious disease surveillance. Molecular epidemiology can help monitoring and adapting traditional surveillance to surpass those limitations. This work aims to contrast data driven from traditional surveillance with parameters inferred from molecular epidemiology in Latin America (LATAM)MethodsWe obtained epidemiological data up to 4th June, 2020. We estimated Effective Reproductive Number (Re) and epidemic curves using maximum likelihood (ML). SARS-CoV-2 genomes were obtained from GISAID up to June 4th 2020. We aligned sequences, generated a ML phylogenetic tree, and ran a coalescent model Birth Death SIR. Phylodynamic analysis was performed for inferring Re, number of infections and date of introduction.FindingsA total of 1,144,077 cases were reported up to 4th June 2020. Countries with the largest cumulative cases were Chile, Peru and Panama. We found at least 18 different lineages circulating, with a predominance of B.1 and B.1.1. We inferred an underestimation of the daily incident cases. When contrasting observed and inferred Re, we did not find statistically significant differences except for Chile and Mexico. Temporal analysis of the introduction of SARS-CoV-2 suggested a detection lag of at least 21 days.InterpretationOur results support that epidemiological and genomic surveillance are two complementary approaches. Even with a low number of genomes proper estimations of Re could be performed. We suggest that countries, especially developing countries, should consider to add genomic surveillance to their systems for monitoring and adapting epidemiological control of SARS-CoV-2.
Estimation of the case fatality rate based on stratification for the COVID-19 outbreak
Authors: Kim Byungwon , Kim Seonghong , Jang Woncheol , Jung Sungkyu , Lim Johan 
Published: May 2020

AbstractThis work is motivated by the recent worldwide pandemic of the novel coronavirus disease (COVID-19). When an epidemiological disease is prevalent, estimating the case fatality rate, the proportion of deaths out of the total cases, accurately and quickly is important as the case fatality rate is one of the crucial indicators of the risk of a disease. In this work, we propose an alternative estimator of the case fatality rate that provides more accurate estimate during an outbreak by reducing the downward bias (underestimation) of the naive CFR, the proportion of deaths out of confirmed cases at each time point, which is the most commonly used estimator due to the simplicity. The proposed estimator is designed to achieve the availability of real-time update by using the commonly reported quantities, the numbers of confirmed, cured, deceased cases, in the computation. To enhance the accuracy, the proposed estimator adapts a stratification, that allows the estimator to use information from heterogeneous strata separately. With the COVID-19 cases of China, South Korea and the United States, we numerically show the proposed stratification-based estimator plays a role of providing an early warning about the severity of a epidemiological disease that estimates the final case fatality rate accurately and shows faster convergence to the final case fatality rate.
Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater
Authors: Mehrshad Maliheh , Lopez-Fernandez Margarita , Sundh John , Bell Emma , Simone Domenico , Buck Moritz , Bernier-Latmani Rizlan , Bertilsson Stefan , Dopson Mark 
Published: May 2020

AbstractExtremely oligotrophic deep groundwaters host organisms attuned to the low-end of the bioenergetics spectrum. While all domains of life along with viruses are active in this habitat, the evolutionary and ecological constraints on colonization and niche shifts and their consequences for the microbiome convergence are unknown. Here we provide a comparative genome-resolved analysis of the prokaryotic community in disconnected fracture fluids of the Fennoscandian Shield. The data show that the oligotrophic deep groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common deep groundwater core microbiome. Based on this high resolution “multi-omics” enabled understanding of the underlying mechanisms via functional expression analysis, we conclude that deep groundwater ecosystems foster highly diverse, yet cooperative microbial communities adapted to this setting. The fitness of primary energy producers is increased by ecological traits such as aggregate or biofilm formation. This also facilitates reciprocal promiscuous partnerships with diverse and prevalent epi-bionts, alleviating the “tragedy of common goods”. Hence, instead of a lifestyle where microbes predominantly invest in functions related to maintenance and survival, an episodic and cooperative lifestyle ensures the subsistence of the deep groundwater microbiome. We suggest the name “halt and catch fire” for this way of life.
Learning is shaped by abrupt changes in neural engagement
Authors: Hennig Jay A. , Oby Emily R. , Golub Matthew D. , Bahureksa Lindsay A. , Sadtler Patrick T. , Quick Kristin M. , Ryu Stephen I. , Tyler-Kabara Elizabeth C. , Batista Aaron P. , Chase Steven M. , Yu Byron M. 
Published: May 2020

AbstractInternal states such as arousal, attention, and motivation are known to modulate brain-wide neural activity, but how these processes interact with learning is not well understood. During learning, the brain must modify the neural activity it produces to improve behavioral performance. How do internal states affect the evolution of this learning process? Using a brain-computer interface (BCI) learning paradigm in non-human primates, we identified large fluctuations in neural population activity in motor cortex (M1) indicative of arousal-like internal state changes. These fluctuations drove population activity along dimensions we term neural engagement axes. Neural engagement increased abruptly at the start of learning, and then gradually retreated. In a BCI, the causal relationship between neural activity and behavior is known. This allowed us to understand how these changes impacted behavioral performance for different task goals. We found that neural engagement interacted with learning, helping to explain why animals learned some task goals more quickly than others.
Regenerating motor neurons prime muscle stem cells for myogenesis by enhancing protein synthesis and mitochondrial bioenergetics
Authors: Choi Jeongmoon J. , Shin Eun Jung , Han Woojin M. , Anderson Shannon E. , Mohiuddin Mahir , Lee Nan Hee , Tran Thu , Nakhai Shadi , Jeong Hyeonsoo , Shcherbina Anna , Jeong Gunjae , Oh Dong Gun , Weinstock Laura D. , Sankar Sitara B. , Ogle Molly E. , Katsimpardi Lida , Rao Tata Nageswara , Wood Levi , Aguilar Carlos A. , Wagers Amy J. , Jang Young C. 
Published: May 2020

SUMMARYThroughout life, skeletal muscle, the arbiter of voluntary movements, is maintained by a population of skeletal muscle-dedicated stem cells, called muscle satellite cells (MuSCs). Similar to other adult stem cells, the function of MuSCs is tightly coordinated by the cellular and acellular components of their microenvironment, or the niche. While the processes that control the coupling of neurotransmission and muscle contraction have been well characterized, little is known on the reciprocal crosstalk between neural cells and MuSCs within the muscle microenvironment. Here, we report that mild peripheral nerve injury enhances MuSC myogenic function and muscle regeneration by synergistically augmenting MuSC mitochondrial bioenergetics and upregulating anabolic protein synthesis pathways. We also demonstrate that chronic disruption or degeneration of neuromuscular synapses, such as in muscular dystrophy and biological aging, abolishes MuSC and motor neuron interactions, causing significant deficits in muscle regeneration following injury. These results underscore the importance of neuromuscular junction and neural network as an essential niche of MuSCs. Determining the significance of MuSC-nerve interactions and their functional outcomes, as well as the possibility of modulating these connections, have important implications for our understanding of neuromuscular disease pathology and development of therapeutic interventions.HighlightsMild peripheral nerve injury increases muscle stem cell bioavailability of healthy muscle.Nerve perturbation stimulates myogenesis by enhancing protein synthesis and mitochondrial metabolism in young, healthy muscle.Synergistic crosstalk within neuromuscular niche boosts muscle regeneration in young, healthy muscle.Positive influences from the neural network on muscle stem cells are abolished in pathological denervation manifested in dystrophic and aging muscle.
The visual ecology of Holocentridae, a nocturnal coral reef fish family with a deep-sea-like multibank retina
Authors: de Busserolles Fanny , Cortesi Fabio , Fogg Lily , Stieb Sara M. , Luerhmann Martin , Marshall N. Justin 
Published: May 2020

AbstractThe visual systems of teleost fishes usually match their habitats and lifestyles. Since coral reefs are bright and colourful environments, the visual systems of their diurnal inhabitants have been more extensively studied than those of nocturnal species. In order to fill this knowledge gap, we conducted a detailed investigation of the visual systems of the coral reef fish family Holocentridae (squirrelfish and soldierfish). In addition to their nocturnality, this family is particularly interesting for dim-light vision studies due to its ecological and evolutionary connection to deeper habitats. Results showed that the visual system of holocentrids is well adapted to their nocturnal lifestyle with a rod-dominated retina. Surprisingly, rods in all species were arranged into 6-17 well-defined banks, a feature most commonly found in deep-sea fishes, that may increase the light sensitivity of the eye and/or allow colour discrimination in dim-light. Holocentrids also have the potential for dichromatic colour vision during the day with the presence of at least two spectrally different cone types: single cones expressing the blue-sensitiveSWS2Agene, and double cones expressing one or two green-sensitiveRH2genes. Some differences were observed between the two subfamilies, with Holocentrinae having a slightly more developed photopic visual system than Myripristinae. Moreover, retinal topography of both ganglion cells and cone photoreceptors showed specific patterns for each cell type, likely highlighting different visual demands at different times of the day, such as feeding. Overall, their well-developed scotopic visual systems and the ease of catching and maintaining holocentrids in aquaria, make them ideal models to investigate teleost dim-light vision and more particularly shed light on the function of multibank retina and its potential for dim-light colour vision.
Inferring the effective start dates of non-pharmaceutical interventions during COVID-19 outbreaks
Authors: Kohanovski Ilia , Obolski Uri , Ram Yoav 
Published: May 2020

AbstractDuring Feb-Apr 2020, many countries implemented non-pharmaceutical interventions, such as school closures and lockdowns, with variable schedules, to control the COVID-19 pandemic caused by the SARS-CoV-2 virus. Overall, these interventions seem to have successfully reduced the spread of the pandemic. We hypothesise that the official and effective start date of such interventions can significantly differ, for example due to slow adoption by the population, or because the authorities and the public are unprepared. We fit an SEIR model to case data from 12 countries to infer the effective start dates of interventions and contrast them with the official dates. We find mostly late, but also early effects of interventions. For example, Italy implemented a nationwide lockdown on Mar 11, but we infer the effective date on Mar 17 (±2.99 days 95% CI). In contrast, Germany announced a lockdown on Mar 22, but we infer an effective start date on Mar 19 (± 1.05 days 95% CI). We demonstrate that differences between the official and effective start of NPIs can distort conclusions about their impact, and discuss potential causes and consequences of our results.