bluuebunny/crossref_metadata_2025 huggingface dataset:
Warning ‘Don't spread’ versus ‘Don't be a spreader’ to prevent the COVID-19 pandemic
Authors: Yonemitsu Fumiya , Ikeda Ayumi , Yoshimura Naoto , Takashima Kaito , Mori Yuki , Sasaki Kyoshiro , Qian Kun , Yamada Yuki
Published: September 2020

The coronavirus disease 2019 (COVID-19) outbreak is threatening not only health but also life worldwide. It is important to encourage citizens to voluntarily practise infection-prevention (IP) behaviours such as social distancing and self-restraint. Previous research on social cognition suggested that emphasizing self-identity is key to changing a person's behaviour. The present study investigated whether reminders that highlight self-identity would be effective in changing intention and behaviour related to the COVID-19 outbreak, and hypothesized that those who read reminders highlighting self-identity (Don't be a spreader) would change IP intention and behaviour better than those who read ‘Don't spread’ or no reminder. We conducted a two-wave survey of the same participants with a one-week interval, during which we assigned one of three reminder conditions to the participants: ‘Don't spread’ (spreading condition), ‘Don't be a spreader’ (spreader condition) and no reminder (control condition). Participants marked their responses to IP intentions and actual behaviours each week based on the Japanese Ministry of Health, Labour and Welfare guidelines. While the results did not show significant differences between the conditions, the
post hoc
analyses showed significant equivalence in either IP intentions or behavioural scores. We discussed the results from the perspective of the effect size, ceiling effects and ways of manipulation checks as future methods with more effective persuasive messaging. Following in-principle acceptance, the approved Stage 1 version of this manuscript was pre-registered on the OSF at https://doi.org/10.17605/OSF.IO/KZ5Y4. This pre-registration was performed prior to data collection and analysis.
Possible fates of the spread of SARS-CoV-2 in the Mexican context
Authors: Santamaría-Holek I. , Castaño V.
Published: September 2020

The determination of the adequate time for house confinement and when social distancing restrictions should end are now two of the main challenges that any country has to face in an ongoing battle against SARS-CoV-2. The possibility of a new outbreak of the pandemic and how to avoid it is, nowadays, one of the primary objectives of epidemiological research. In this work, we present an innovative compartmental model that explicitly introduces the number of active cases, and employ it as a conceptual tool to explore the possible fates of the spread of SARS-CoV-2 in the Mexican context. We incorporated the impact of starting, inattention and end of restrictive social policies on the pandemic’s time evolution via time-dependent corrections to the infection rates. The magnitude and impact on the epidemic due to post-social restrictive policies are also studied. The scenarios generated by the model could help authorities determine an adequate time and population load that may be allowed to reassume normal activities.
The increasing diversity and complexity of the RNA-binding protein repertoire in plants
Authors: Marondedze C.
Published: September 2020

Post-transcriptional regulation has far-reaching implications on the fate of RNAs. It is gaining increasing momentum as a critical component in adjusting global cellular transcript levels during development and in response to environmental stresses. In this process, RNA-binding proteins (RBPs) are indispensable chaperones that naturally bind RNA via one or multiple globular RNA-binding domains (RBDs) changing the function or fate of the bound RNAs. Despite the technical challenges faced in plants in large-scale studies, several hundreds of these RBPs have been discovered and elucidated globally over the past few years. Recent discoveries have more than doubled the number of proteins implicated in RNA interaction, including identification of RBPs lacking classical RBDs. This review will discuss these new emerging classes of RBPs, focusing on the current state of the RBP repertoire inArabidopsis thaliana, including the diverse functional roles derived from quantitative studies implicating RBPs in abiotic stress responses. Notably, this review highlights that 836 RBPs are enriched asArabidopsisRBPs while 1865 can be classified as candidate RBPs. The review will also outline outstanding areas within this field that require addressing to advance our understanding and potential biotechnological applications of RBPs.
Mate-searching context of prey influences the predator–prey space race
Authors: Torsekar Viraj R. , Thaker Maria
Published: September 2020

Predation risk is a strong driver of prey distribution and movement. However, fitness-influencing behaviours, such as mating, can alter risk and influence predator–prey space-use dynamics. In tree crickets,Oecanthus henryi, mate searching involves acoustic signalling by immobile males and phonotactic movement by females. Space-use patterns in tree crickets relative to their primary predators, green lynx spiders (Peucetia viridans), should therefore depend on their current mate-searching state; whether males are calling or non-calling and whether females are phonotactic or non-phonotactic. We first measured the degree of spatial anchoring of crickets to specific bushes in the field and determined whether that influenced the probability of broad-scale spatial overlap with spiders. In the absence of spiders, all crickets, independent of sex or male calling status, were found to be spatially anchored to specific types of bushes and not uniformly distributed on the landscape. At the broad spatial scale, spiders were more likely to be found on bushes with female crickets and, to a lesser degree, calling male crickets. At a finer spatial scale within a bush, movement strategies of crickets not only varied depending on the presence or absence of a spider, but also on their current mate-searching state. Phonotactic females showed clear predator avoidance, whereas calling and non-calling males moved towards the spider instead of away, similar to predator inspection behaviour seen in many taxa. As the strongly selected sex, males are more likely to undertake risky mate-searching activities, which includes inspection of predator positions. Overall, we found that all crickets were predictably anchored at the landscape scale, but their sex and mate-seeking behaviour influenced the degree of overlap with predators and their antipredator movement strategies. Reproductive strategies within a prey species, therefore, can alter predator–prey space race at multiple spatial scales.
The evolution of coloration and opsins in tarantulas
Authors: Foley Saoirse , Saranathan Vinodkumar , Piel William H.
Published: September 2020

Tarantulas paradoxically exhibit a diverse palette of vivid coloration despite their crepuscular to nocturnal habits. The evolutionary origin and maintenance of these colours remains mysterious. In this study, we reconstructed the ancestral states of both blue and green coloration in tarantula setae, and tested how these colours correlate with presence of stridulation, urtication and arboreality. Green coloration has probably evolved at least eight times, and blue coloration is probably an ancestral condition that appears to be lost more frequently than gained. While our results indicate that neither colour correlates with the presence of stridulation or urtication, the evolution of green coloration appears to depend upon the presence of arboreality, suggesting that it ptobably originated for and functions in crypsis through substrate matching among leaves. We also constructed a network of opsin homologues across tarantula transcriptomes. Despite their crepuscular tendencies, tarantulas express a considerable diversity of opsin genes—a finding that contradicts current consensus that tarantulas have poor colour vision on the basis of low opsin diversity. Overall, our findings raise the possibility that blue coloration could have ultimately evolved via sexual selection and perhaps proximately be used in mate choice or predation avoidance due to possible sex differences in mate-searching.
Seasonal niche tracking of climate emerges at the population level in a migratory bird
Authors: Fandos Guillermo , Rotics Shay , Sapir Nir , Fiedler Wolfgang , Kaatz Michael , Wikelski Martin , Nathan Ran , Zurell Damaris
Published: September 2020

Seasonal animal migration is a widespread phenomenon. At the species level, it has been shown that many migratory animal species track similar climatic conditions throughout the year. However, it remains unclear whether such a niche tracking pattern is a direct consequence of individual behaviour or emerges at the population or species level through behavioural variability. Here, we estimated seasonal niche overlap and seasonal niche tracking at the individual and population level of central European white storks (Ciconia ciconia). We quantified niche tracking for both weather and climate conditions to control for the different spatio-temporal scales over which ecological processes may operate. Our results indicate that niche tracking is a bottom-up process. Individuals mainly track weather conditions while climatic niche tracking mainly emerges at the population level. This result may be partially explained by a high degree of intra- and inter-individual variation in niche overlap between seasons. Understanding how migratory individuals, populations and species respond to seasonal environments is key for anticipating the impacts of global environmental changes.
Health Heatmap of India: An Open Data Platform
Authors: Dinesh Akshay S , Mathur Varnita , Ansil B. R. , Chandru Vijay , Chellam Ravi , Vanak Abi Tamim , Ramakrishnan Uma , Rajagopal Prabhakar
Published: September 2020

Health Heatmap of India is an open data platform built for bringing together data from diverse sources and facilitating visualization, analysis, and insight building from such data. In this paper, we describe the context and need for such an open data platform and describe the technical aspects of building it. The beta site of the portal is available at http://healthheatmapindia.org
Prolonged SARS-CoV-2 replication in an immunocompromised patient
Authors: Baang Ji Hoon , Smith Christopher , Mirabelli Carmen , Valesano Andrew L. , Manthei David M. , Bachman Michael , Wobus Christiane E. , Adams Michael , Washer Laraine , Martin Emily T. , Lauring Adam S.
Published: September 2020

We describe a case of chronic COVID-19 in a patient with lymphoma and associated B-cell immunodeficiency. Viral cultures and sequence analysis demonstrate ongoing replication of infectious SARS-CoV-2 virus for at least 119 days. The patient had three admissions related to COVID-19 over a four-month period and was treated twice with remdesivir and convalescent plasma with resolution of symptoms. The patient’s lack of seroconversion and prolonged course illustrate the importance of humoral immunity in resolving SARS-CoV-2 infection. This case highlights challenges in managing immunocompromised hosts, who may act as persistent shedders and sources of transmission.
Modelling the risk of SARS-CoV-2 infection through PPE doffing in a hospital environment
Authors: King Marco-Felipe , Wilson Amanda M , Weir Mark H. , López-García Martín , Proctor Jessica , Hiwar Waseem , Khan Amirul , Fletcher Louise A. , Sleigh P. Andrew , Clifton Ian , Dancer Stephanie J. , Wilcox Mark , Reynolds Kelly A. , Noakes Catherine J.
Published: September 2020

Self-contamination during doffing of personal protective equipment (PPE) is a concern for healthcare workers (HCW) following SARS-CoV-2 positive patient care. Staff may subconsciously become contaminated through improper glove removal, so quantifying this risk is critical for safe working procedures. HCW surface contact sequences on a respiratory ward were modelled using a discrete-time Markov chin for: IV-drip care, blood pressure monitoring and doctors’ rounds. Accretion of viral RNA on gloves during care was modelled using a stochastic recurrence relation. The HCW then doffed PPE and contaminated themselves in a fraction of cases based on increasing case load. The risk of infection from this exposure was quantified using a dose-response methodology. A parametric study was conducted to analyse the effect of: 1a) increasing patient numbers on the ward, 1b) the proportion of COVID-19 cases, 2) the length of a shift and 3) the probability of touching contaminated PPE. The driving factors for infection risk were surface contamination and number of surface contacts. HCWs on a 100% COVID-19 ward were less than 2-fold more at risk than on a 50% COVID ward (1.6% vs 1%), whilst on a 5% COVID-19 ward, the risk dropped to 0.1% per shift (sd=0.6%). IV-drip care resulted in higher risk than blood pressure monitoring (1.1% vs 1% p<0.0001), whilst doctors’ rounds produced a 0.6% risk (sd=0.8%). Recommendations include supervised PPE doffing procedures such as the “doffing buddy” scheme, maximising hand hygiene compliance post-doffing and targeted surface cleaning for surfaces away from the patient vicinity.

Importance

Infection risk from self-contamination during doffing PPE is an important concern in healthcare settings, especially on a COVID-19 ward. Fatigue during high workload shifts may result in increased frequency of mistakes and hence risk of exposure. Length of staff shift and number of COVID-19 patients on a ward correlate positively with the risk to staff through self-contamination after doffing. Cleaning of far-patient surfaces is equally important as cleaning traditional “high-touch surfaces”, given that there is an additional risk from bioaerosol deposition outside the patient zone(1).
At home and online during the early months of the COVID-19 pandemic and the relationship to alcohol consumption in a national sample of U.S. adults
Authors: Chartier Karen G. , Guidry Jeanine P.D. , Lee Catherine A.
Published: September 2020

Objective

The current study seeks to understand the links between social media use and alcohol consumption during the early months of the COVID-19 pandemic.

Method

Data were from the national Understanding American Study, a probability-based Internet panel weighted to represent the U.S. population. Subjects (N=5874; 51% female) were adults, 18 years and older, who completed a March survey (wave 1) and a follow-up survey one month later (wave 3). Analyses assessed the relationship of social media use at wave 1 with wave 3 alcohol use, accounting for wave 1 alcohol use and the sociodemographic characteristics of the sample. We examined the effect of working or studying from home as a moderator.

Results

Twitter and Instagram users, but not Facebook users, drank more frequently at wave 3 than non-users. For Instagram users, more frequent alcohol use at wave 3 was at least partially attributed to the frequency of drinking at wave 1. The interaction between Twitter use and working or studying from home was statistically significant. The combination of being on Twitter and working or studying from home was associated with drinking more days a week.

Conclusions

Exposure to content about COVID-19 and increased alcohol consumption during the pandemic may contribute to more frequent alcohol use for some social media users, especially those sheltering at home. The study of public health messaging via social media to change alcohol use behaviors during traumatic events is warranted.
Establishment of National DRL for CT in Hybrid Imaging Studies (The Second Phase of the National NM CT (PET) Dose Audit for Kuwait Population -2019)
Authors: Masoomi Michael , Al-Shammeri Iman , Al-Kandari Latifah , Elrahman Hany , Al-Shammari Jehan
Published: September 2020

DRLs for CT part used in PET/CT examinations are limited. The aim was to execute the second phase of the national DRL for CT part of PET/CT imaging operating in KW, in support of optimisation and dose reduction as imaging technology is advancing. In this multicentre collaborative PET centers (No:8) audit, data collection was restricted to the adult oncology patients due to a limited number of the other studies and also due to the National MOH Ethical Committee recommendation. The CTDIvol, DLP and SL were recorded and the Median, Mean, SD, 75th, 25th percentiles as well as WB effective dose (ED) were calculated. Dose and scan length statistics for HB and WB scans (65% and 35% of total: 309) and the WB+HB presented together with the proposed NDRLs and the Achievable doses. Third quartile DLP (mGy x cm) and CTDIvol (mGy) values for the HB were (537, 5) which were higher than the UK NDRL (400, 4.3) but were lower than the Swiss NDRL (620, 6) and the France NDRL (762, 7.7). Comparatively, the Proposed NDRLs for (WB) were (684, 4.1) which were lower than Swiss National Data (720, 5.0). It is worth noted that, the Swiss had about 5000 (HB) & 706 (WB), the UK had 370 (HB) and France had 1000 (HB) entries. Calculated ED varied from 4.1 to 10.2 mSv, (mean values=6.9 mSv) for HB and from 2.6 to 7 mSv (mean value=4.6 mSv) for WB scans which were lower than the first phase (2018). Although, there was 9.1% improvement in NDRL, but the outcome suggested there is a continuous need for monitoring NDRL.
COVID-19 dynamics across the US: A deep learning study of human mobility and social behavior
Authors: Bhouri Mohamed Aziz , Costabal Francisco Sahli , Wang Hanwen , Linka Kevin , Peirlinck Mathias , Kuhl Ellen , Perdikaris Paris
Published: September 2020

Abstract

This paper presents a deep learning framework for epidemiology system identification from noisy and sparse observations with quantified uncertainty. The proposed approach employs an ensemble of deep neural networks to infer the time-dependent reproduction number of an infectious disease by formulating a tensor-based multi-step loss function that allows us to efficiently calibrate the model on multiple observed trajectories. The method is applied to a mobility and social behavior-based SEIR model of COVID-19 spread. The model is trained on Google and Unacast mobility data spanning a period of 66 days, and is able to yield accurate future forecasts of COVID-19 spread in 203 US counties within a time-window of 15 days. Strikingly, a sensitivity analysis that assesses the importance of different mobility and social behavior parameters reveals that attendance of close places, including workplaces, residential, and retail and recreational locations, has the largest impact on the basic reproduction number. The model enables us to rapidly probe and quantify the effects of government interventions, such as lock-down and re-opening strategies. Taken together, the pro-posed framework provides a robust workflow for data-driven epidemiology model discovery under uncertainty and produces probabilistic forecasts for the evolution of a pandemic that can judiciously inform policy and decision making. All codes and data accompanying this manuscript are available at https://github.com/PredictiveIntelligenceLab/DeepCOVID19.
An expert judgment model to predict early stages of the COVID-19 outbreak in the United States
Authors: McAndrew Thomas , Reich Nicholas G.
Published: September 2020

During early stages of the COVID-19 pandemic, forecasts provided actionable information about disease transmission to public health decision-makers. Between February and May 2020, experts in infectious disease modeling made weekly predictions about the impact of the pandemic in the U.S. We aggregated these predictions into consensus predictions. In March and April 2020, experts predicted that the number of COVID-19 related deaths in the U.S. by the end of 2020 would be in the range of 150,000 to 250,000, with scenarios of near 1m deaths considered plausible. The wide range of possible future outcomes underscored the uncertainty surrounding the outbreak’s trajectory. Experts’ predictions of measurable short-term outcomes had varying levels of accuracy over the surveys but showed appropriate levels of uncertainty when aggregated. An expert consensus model can provide important insight early on in an emerging global catastrophe.

One Sentence Summary

Expert predictions provided valuable insight of future societal burden during the early stages of the COVID-19 pandemic in the US.
A simplified approach to monitoring the COVID-19 epidemiologic situation using waste water analysis and its application in Russia
Authors: Kuryntseva Polina Alexandrovna , Karamova Kamalya Oktay , Fomin Valentin Petrovich , Selivanovskaya Svetlana Yurevna , Galitskaya Polina Yurevna
Published: September 2020

The number of registered cases of COVID-19 is increasing in the world, and some countries are reporting a second wave of the pandemic. Accurate and real time information about epidemiological situation is therefore urgently needed for managing decisions in the countries, regions and municipalities which are affected. Massive testing of viral presence in people’s saliva, a smear from the nose, nasopharynx and / or oropharynx, bronchial lavage water obtained by fibrobronchoscopy (bronchoalveolar lavage), as well as from (endo) tracheal, nasopharyngeal aspirate, sputum, biopsy or autopsy material of the lungs, whole blood, serum or antibodies presence in blood cannot give relevant information about the COVID-19 infection rate in the community since simultaneous testing of the whole community is not technically possible, the information obtained in testing of specific groups is retarded and, in addition, such testing is expensive. The alternative to mass testing of the population is the testing of wastewater that could contain SARS-CoV-2 particles originating from excreta. Such testing has several limitations connected with the particularities of the testing procedure.

In the present study, a modified approach for detection of COVID-19 infection rate using wastewater analysis has been developed. The approach includes i) the creation of a calibration curve on the basis of the serial dilution of excreta collected from people who are infected with COVID-19 and ii) the analysis of the wastewater samples and their serial dilutions, the approach excludes usage of concentrating techniques before wastewater sample analysis as well as usage of external control in RT-PCR reactions for calculation of numbers of viral particles. The minimum infection rate that can be detected using this approach is 10-2%. The approach developed was used to investigate wastewater from eleven sewage inspection chambers in the city of Kazan (Russia). It was demonstrated that the average infection rate of people using these sewers was over 0.4% in July 2020.
Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients
Authors: Hashem Anwar M , Algaissi Abdullah , Almahboub Sarah A , Alfaleh Mohamed A , Abujamel Turki S , Alamri Sawsan S , Alluhaybi Khalid A , Hobani Haya I , AlHarbi Rahaf H , Alsulaiman Reem M , ElAssouli M-Zaki , Hala Sharif , Alharbi Naif K , Alhabbab Rowa Y , AlSaieedi Ahdab A , Abdulaal Wesam H , Bukhari Abdullah , AL-Somali Afrah A , Alofi Fadwa S , Khogeer Asim A , Pain Arnab , Alkayyal Almohanad A , Almontashiri Naif AM , Mahmoud Ahmad Bakur , Li Xuguang
Published: September 2020

The Coronavirus Disease 2019 (COVID-19), caused by the novel SARS-CoV-2, continues to spread globally with significantly high morbidity and mortality rates. Immunological surrogate markers, in particular antigen-specific responses, are of unquestionable value for clinical management of patients with COVID-19. Here, we investigated the kinetics of IgM, IgG against the spike (S) and nucleoproteins (N) proteins and their neutralizing capabilities in hospitalized patients with RT-PCR confirmed COVID-19 infection. Our data show that SARS-CoV-2 specific IgG, IgM and neutralizing antibodies (nAbs) were readily detectable in almost all COVID-19 patients with various clinical presentations. Notably, anti-S and -N IgG, peaked 20-40 day after disease onset, and were still detectable for at least up to 70 days, with nAbs observed during the same time period. Moreover, nAbs titers were strongly correlated with IgG antibodies. Significantly higher levels of nAbs as well as anti-S1 and N IgG and IgM antibodies were found in patients with more severe clinical presentations, patients requiring admission to intensive care units (ICU) or those with fatal outcomes. Interestingly, lower levels of antibodies, particularly anti-N IgG and IgM in the first 15 days after symptoms onset, were found in survivors and those with mild clinical presentations. Collectively, these findings provide new insights into the characteristics and kinetics of antibody responses in COVID-19 patients with different disease severity.
Prevalences and healthcare expenditures related to 58 health conditions from 2012 to 2017 in France: diseases and healthcare expenditure mapping, a national population-based study
Authors: Rachas Antoine , Gastaldi-Ménager Christelle , Denis Pierre , Lesuffleur Thomas , Nicolas Muriel , Pestel Laurence , Mette Corinne , Drouin Jérôme , Rivière Sébastien , Tajahmady Ayden , Gissot Claude , Fagot-Campagna Anne
Published: September 2020

Background

Description of the prevalence of diseases and resources mobilized for the management of each disease is essential to identify public health priorities. We described the prevalences of 58 health conditions and all reimbursed healthcare expenditure by health condition in France between 2012 and 2017.

Methods and Findings

All national health insurance general scheme beneficiaries (87% of the French population) with at least one reimbursed healthcare expenditure were included from the French national health database. We identified health conditions (diseases, episodes of care, chronic treatments) by algorithms using ICD-10 codes for long-term diseases or hospitalisations, medications or medical procedures. We reported crude and age and sex-standardized annual prevalences between 2012 and 2017, and total and mean (per patient) reimbursed expenditure attributed to each condition without double counting, and according to the type of expenditure.

In 2017, in a population of 57.6 million people (54% of women, median age: 40 years), the most prevalent diseases were diabetes (standardized prevalence: 5.8%), chronic respiratory diseases (5.5%) and chronic coronary heart disease (2.9%). Diseases concentrating the highest expenditures were active cancers (10% of total expenditure of €140.1 billion), mental illness (10%; neurotic and mood disorders: 4%; psychotic disorders: 3%), and chronic cardiovascular diseases (8%). Between 2012 and 2017, the most marked increase in total expenditure concerned liver and pancreatic diseases (+9.3%), related to the increased drug expenditure in 2014. Conversely, the increase in the number of patients (and the prevalence) explained the majority of the increase of total expenditures for cardiovascular disease, diabetes and mental illness.

Conclusions

These results showed a regular increase of the prevalence and expenditure of certain chronic diseases, probably related to ageing of the population, and increased expenditures related to major therapeutic innovations. The Diseases and Healthcare Expenditure Mapping therefore enlightens decision-makers in charge of public health and health accounts.
LOW PSYCHOLOGICAL WELL-BEING IN MEN WHO HAVE SEX WITH MEN (MSM) DURING THE SHELTER-IN-PLACE ORDERS TO PREVENT THE COVID-19 SPREAD: RESULTS FROM A NATIONWIDE STUDY
Authors: Silva Camargo Emerson Lucas , de Oliveira Bruna Isabela Adolpho , Siffoni Igor Fessina , de Sousa Anderson Reis , Teixeira Jules Ramon Brito , Amélia Costa Mendes Isabel , de Sousa Álvaro Francisco Lopes
Published: September 2020

Introduction

Little is known about how sheltering in place to contain the spread of COVID-19 over extended periods affects individuals’ psychological well-being. This study’s objective was to analyze the factors associated with MSM’s low psychological well-being in the COVID-19 pandemic context.

Method

This cross-sectional study was conducted online in the entire Brazilian territory (26 states and federal district) in April and May 2020. The participants were recruited using an adapted version of Respondent-Driven Sampling (RDS). Data were collected using social media and MSM dating apps. We estimated the prevalence, crude prevalence ratio (PR), and respective confidence intervals (CI95%).

Results

Only 44.4% of the sample presented high levels of well-being. Low psychological well-being appeared associated with the youngest age group (PR: 2.76; CI95%: 1.90-4.01), polyamorous relationships (PR: 2.78; CI95%: 1.51-5.11), not complying with social isolation measures (PR: 6.27; CI95%: 4.42-8.87), not using the social media to find partners (PR: 1.63; CI95%: 1.06-2.53), having multiple sexual partners (PR: 1.80; CI95%: 1.04-3.11), having reduced the number of partners (PR: 2.67; CI95%: 1.44-4.95), and group sex (PR: 1.82; CI95%: 1.23-2.69)

Conclusion

The well-being of MSM living in Brazil was negatively affected during the social distancing measures intended to control the spread of COVID-19.

Policy Implications

Planning and implementing public policies and actions to promote psychological well-being are needed to improve MSM’s resilience through the adoption of safe strategies and behavior.
Treatment of Moderate to Severe Respiratory COVID-19—A Cost-Utility Analysis
Authors: Congly Stephen E. , Varughese Rhea A. , Brown Crystal E. , Clement Fiona M. , Saxinger Lynora
Published: September 2020

Background

Due to COVID-19’s significant morbidity and mortality, identifying the most cost-effective pharmacologic treatment strategy is critical. As such, we determined the most cost-effective strategy for moderate to severe COVID-19 respiratory infections using the United States health care system as a representative model.

Methods

A decision analytic model modelled a base case scenario of a 60-year-old patient admitted to hospital with COVID-19. Patients requiring oxygen were considered moderate severity, and patients with severe COVID-19 required intubation with intensive care. Strategies modelled included giving remdesivir to all patients, remdesivir in severe infections, remdesivir in moderate infections, dexamethasone to all patients, dexamethasone in severe infections, remdesivir in moderate/dexamethasone in severe infections, and best supportive care. Data for the model came from the published literature. The time horizon was 1 year; no discounting was performed due to the short duration. The perspective was of the payer in the United States health care system.

Results

Supportive care for moderate/severe COVID-19 cost $11,112.98/0.8256 QALY. Remdesivir in moderate/dexamethasone in severe infections was the most cost-effective with an incremental cost-effectiveness ratio of $19,764.56/QALY gained compared to supportive care. Probabilistic sensitivity analyses showed remdesivir for moderate/dexamethasone for severe COVID-19 infection was most cost-effective in 88.6% of scenarios and dexamethasone in moderate-severe infections in 11.4% of scenarios. With lower willingness to pay thresholds ($250-$37,500), dexamethasone for severe infections was favoured.

Conclusions

Remdesivir for moderate/dexamethasone for severe COVID-19 infections was the0020most cost-effective strategy. Further data is required for remdesivir to better assess its cost effectiveness in treatment of COVID-19.
The N300: An Index For Predictive Coding Of Complex Visual Objects and Scenes
Authors: Kumar Manoj , Federmeier Kara D. , Beck Diane M.
Published: September 2020

Predictive coding models can simulate known perceptual or neuronal phenomena, but there have been fewer attempts to identify a reliable neural signature of predictive coding for complex stimuli. In a pair of studies, we test whether the N300 component of the event-related potential, occurring 250-350 ms post-stimulus-onset, has the response properties expected for such a signature of perceptual hypothesis testing at the level of whole objects and scenes. We show that N300 amplitudes are smaller to representative (“good exemplars”) compared to less representative (“bad exemplars”) items from natural scene categories. Integrating these results with patterns observed for objects, we establish that, across a variety of visual stimuli, the N300 is responsive to statistical regularity, or the degree to which the input is “expected” (either explicitly or implicitly) based on prior knowledge, with statistically regular images evoking a reduced response. Moreover, we show that the measure exhibits context-dependency; that is, we find the N300 sensitivity to category representativeness when stimuli are congruent with, but not when they are incongruent with, a category pre-cue. Thus, we argue that the N300 is the best candidate to date for an index of perceptual hypotheses testing for complex visual objects and scenes.
EPISPOT: an epigenome-driven approach for detecting and interpreting hotspots in molecular QTL studies
Authors: Ruffieux Hélène , Fairfax Benjamin P. , Nassiri Isar , Vigorito Elena , Wallace Chris , Richardson Sylvia , Bottolo Leonardo
Published: September 2020

We present EPISPOT, a fully joint framework which exploits large panels of epigenetic annotations as variant-level information to enhance molecular quantitative trait locus (QTL) mapping. Thanks to a purpose-built Bayesian inferential algorithm, EPISPOT accommodates functional information for bothcisandtransactions, including QTLhotspoteffects. It effectively couples simultaneous QTL analysis of thousands of genetic variants and molecular traits, and hypothesis-free selection of biologically interpretable annotations which directly contribute to the QTL effects. This unified, epigenome-aided learning boosts statistical power and sheds light on the regulatory basis of the uncovered hits; EPISPOT therefore marks an essential step towards improving the challenging detection and functional interpretation oftrans-acting genetic variants and hotspots. We illustrate the advantages of EPISPOT in simulations emulating real-data conditions and in a monocyte expression QTL study, which confirms known hotspots and finds other signals, as well as plausible mechanisms of action. In particular, by highlighting the role of monocyte DNase-I sensitivity sites from > 150 epigenetic annotations, we clarify the mediation effects and cell-type specificity of major hotspots close to the lysozyme gene. Our approach forgoes the daunting and underpowered task of one-annotation-at-a-time enrichment analyses for prioritisingcisandtransQTL hits and is tailored to any transcriptomic, proteomic or metabolomic QTL problem. By enabling principled epigenome-driven QTL mapping transcriptome-wide, EPISPOT helps progress towards a better functional understanding of genetic regulation.
Multi-hops functional connectivity improves individual prediction of fusiform face activation via a graph neural network
Authors: Wu Dongya , Li Xin , Feng Jun
Published: September 2020

Brain connectivity plays an important role in determining the brain region’s function. Previous researchers proposed that the brain region’s function is characterized by that region’s input and output connectivity profiles. Following this proposal, numerous studies have investigated the relationship between connectivity and function. However, based on a preliminary analysis, this proposal is deficient in explaining individual differences in the brain region’s function. To overcome this problem, we proposed that a brain region’s function is characterized by that region’s multi-hops connectivity profile. To test this proposal, we used multi-hops functional connectivity to predict the individual face response of the right fusiform face area (rFFA) via a multi-layers graph neural network and showed that the prediction performance is essentially improved. Results also indicated that the 2-layers graph neural network is the best in characterizing rFFA’s face response and revealed a hierarchical network for the face processing of rFFA.
Large-scale characterization of sex pheromone communication systems inDrosophila
Authors: Khallaf Mohammed A. , Cui Rongfeng , Weißflog Jerrit , Svatoš Aleš , Dweck Hany K.M. , Valenzano Dario Riccardo , Hansson Bill S. , Knaden Markus
Published: September 2020

Insects use sex pheromones as a reproductive isolating mechanism to attract conspecifics and repel heterospecifics. Despite the profound knowledge of sex pheromones, little is known about the coevolutionary mechanisms and constraints on their production and detection. Using whole-genome sequences to infer the kinship among 99 drosophilids, we investigate how phylogenetic and chemical traits have interacted at a wide evolutionary timescale. Through a series of chemical syntheses and electrophysiological recordings, we identify 51 sex-specific compounds, many of which are detected via olfaction. Behavioral analyses reveal that many of the 42 male-specific compounds are transferred to the female during copulation and mediate female receptivity and/or male courtship inhibition. Measurement of phylogenetic signals demonstrates that sex pheromones and their cognate olfactory channels evolve rapidly and independently over evolutionary time to guarantee efficient intra- and inter-specific communication systems. Our results show how sexual isolation barriers between species can be reinforced by species-specific olfactory signals.
Whole Exome Sequencing identifies multiple pathogenic variants in a large south Indian family with Primary Open Angle Glaucoma
Authors: Shah Mohd Hussain , Kumaran Manojkumar , Chermakani Prakash , Kader Mohideen Abdul , Ramakrishnan R. , Krishnadas Subbiah. R. , Devarajan Bharanidharan , Sundaresan Periasamy
Published: September 2020

Purpose

To identify the pathogenic variants associated with POAG by using Whole Exome Sequencing (WES) data of a large South Indian family.

Methods

We recruited a large five generation of South Indian family (n=84) with positive family history of POAG. All study participants had comprehensive ocular evaluation (of the 84, 19 study subjects were diagnosed as POAG). Sanger sequencing of the candidate genes associated with POAG (MYOC, OPTN and TBK1) showed no genetic variation in the POAG affected family members. Therefore, we performed whole exome sequencing (WES) for 16 samples including (9 POAG and 7 unaffected controls) and the data was analysed using an in-house pipeline for prioritizing the pathogenic variants based on its segregation among the POAG individual.

Results

We identified one novel and five low-frequency pathogenic variants with consistent co-segregation in all affected individuals. The variant c.G3719A in RPGR-interacting domain of RPGRIP1 that segregated heterozygously with the six POAG cases is distinct from variants causing photoreceptor dystrophies, reported to affect the RPGR protein complex signaling in primary cilia. The cilia in TM cells has been reported to mediate the intraocular pressure (IOP) sensation. Furthermore, we identified a novel c.A1295G variant in Rho guanine nucleotide exchange factors Gene 40 (ARHGEF40) and likely pathogenic variant in the RPGR gene, suggesting that they may alter the RhoA activity essential for IOP regulation

Conclusion

Our study supports that low-frequency pathogenic variants in multiple genes and pathways probably affect the pathogenesis of Primary Open Angle Glaucoma in the large South Indian family.
Deep learning of gene relationships from single cell time-course expression data
Authors: Yuan Ye , Bar-Joseph Ziv
Published: September 2020

Motivation

Time-course gene expression data has been widely used to infer regulatory and signaling relationships between genes. Most of the widely used methods for such analysis were developed for bulk expression data. Single cell RNA-Seq (scRNA-Seq) data offers several advantages including the large number of expression profiles available and the ability to focus on individual cells rather than averages. However, this data also raises new computational challenges.

Results

Using a novel encoding for scRNA-Seq expression data we develop deep learning methods for interaction prediction from time-course data. Our methods use a supervised framework which represents the data as a 3D tensor and train convolutional and recurrent neural networks (CNN and RNN) for predicting interactions. We tested our Time-course Deep Learning (TDL) models on five different time series scRNA-Seq datasets. As we show, TDL can accurately identify causal and regulatory gene-gene interactions and can also be used to assign new function to genes. TDL improves on prior methods for the above tasks and can be generally applied to new time series scRNA-Seq data.

Availability and Implementation

Freely available athttps://github.com/xiaoyeye/TDL.

Contact

zivbj@cs.cmu.edu

Supplementary information

Supplementary data are available atXXXonline.
Probing Causality of the Brainstem-Hypothalamic Murine Models of Sleep-Wake Regulation
Authors: Bahari Fatemeh , Billard Myles W. , Kimbugwe John , Curay Carlos , Watson Glenn D.R. , Alloway Kevin D. , Gluckman Bruce J.
Published: September 2020

Sleep-wake regulation is thought to be governed by interactions among several nuclei in midbrain, pons, and hypothalamic regions. Determination of the causal role of these nuclei in state transitions requires simultaneous measurements from the nuclei with sufficient spatial and temporal resolution. We obtained long-term experimental single- and multi-unit measurements simultaneously from multiple nuclei of the putative hypothalamic and brainstem sleep-wake regulatory network in freely behaving rats. Cortical and hippocampal activity, along with head acceleration were also acquired to assess behavioral state. Here, we confirm that the general activity profile of the recorded sleep-wake regulatory nuclei is similar to the patterns presented previously in brief recordings of individual nuclei in head-fixed animals. However, we found that these activity profiles when studied with respect to cortical and behavioral signs of state transitions differ significantly from previous reports. Our findings pose fundamental questions about the neural mechanisms that maintain specific states and the neural interactions that lead to the emergence of sleep-wake states.
Towards understanding Afghanistan pea symbiotic phenotype through the molecular modeling of the interaction between LykX-Sym10 receptor heterodimer and Nod factors
Authors: Solovev Ya.V. , Igolkina A.A. , Kuliaev P.O. , Sulima A.S. , Zhukov V.A. , Porozov Yu.B. , Pidko E.A. , Andronov E.E.
Published: September 2020

The difference in symbiotic specificity between peas of Afghanistan and European phenotypes was interrogated using molecular modeling. Considering segregating amino acid polymorphism, we examined interactions of pea LykX-Sym10 receptor heterodimers with four forms of Nod factor (NF) that varied in natural decorations (acetylation and length of the glucosamine chain). First, we showed the stability of the LykX-Sym10 dimer during molecular dynamics (MD) in solvent and in the presence of a membrane. Then, four NFs were separately docked to one European and two Afghanistan dimers, and the results of these interactions were in line with corresponding pea symbiotic phenotypes. The European variant of the LykX-Sym10 dimer effectively interacts with both acetylated and non-acetylated forms of NF, while the Afghanistan variants successfully interact with the acetylated form only. We additionally demonstrated that the length of the NF glucosamine chain contributes to controlling the effectiveness of the symbiotic interaction. The obtained results support a recent hypothesis that the LykX gene is a suitable candidate for the unidentified Sym2 allele, the determinant of pea specificity towardsRhizobium leguminosarum bv. viciaestrains producing NFs with or without an acetylation decoration. The developed modeling methodology demonstrated its power in multiple searches for genetic determinants, when experimental detection of such determinants has proven extremely difficult.
Single-molecule interaction microscopy reveals antibody binding kinetics
Authors: Perera Thilini , Gunasekara Hirushi , Hu Ying S.
Published: September 2020

Single-molecule imaging has provided new insights on weak transient biomolecular interactions with micromolar to millimolar affinity. However, the limited duration of observation has hindered the study of strong and reversible interactions with sub-nanomolar affinity. We report single-molecule interaction microscopy (SMIM), which combines point accumulation for imaging in nanoscale topography (PAINT) with extended imaging durations that enables the study of antibody binding kinetics in the cellular environment. SMIM revealed heterogeneous binding kinetics and the effect of concentration and antibody valency on the association and dissociation rates on antibody-antigen interactions in their cellular environments. We thereby demonstrate SMIM as a versatile single-molecule technique for studying strong, transient biomolecular interactions.
Epigenetic clock and DNA methylation studies of roe deer in the wild
Authors: Lemaître Jean-François , Rey Benjamin , Gaillard Jean-Michel , Régis Corinne , Gilot Emmanuelle , Pellerin Maryline , Haghani Amin , Zoller Joseph A. , Li Caesar Z. , Horvath Steve
Published: September 2020

DNA methylation-based biomarkers of aging (epigenetic clocks) promise to lead to new insights in the evolutionary biology of ageing. Relatively little is known about how the natural environment affects epigenetic aging effects in wild species. In this study, we took advantage of a unique long-term (>40 years) longitudinal monitoring of individual roe deer (Capreolus capreolus) living in two wild populations (Chizé and Trois Fontaines, France) facing different ecological contexts to investigate the relationship between chronological age and levels of DNA methylation (DNAm). We generated novel DNA methylation data from n=90 blood samples using a custom methylation array (HorvathMammalMethylChip40). We present three DNA methylation-based estimators of age (DNAm or epigenetic age), which were trained in males, females, and both sexes combined. We investigated how sex differences influenced the relationship between DNAm age and chronological age through the use of sex-specific epigenetic clocks. Our results highlight that both populations and sex influence the epigenetic age, with the bias toward a stronger male average age acceleration (i.e. differences between epigenetic age and chronological ages) particularly pronounced in the population facing harsh environmental conditions. Further, we identify the main sites of epigenetic alteration that have distinct aging patterns across the two sexes. These findings open the door to promising avenues of research at the crossroad of evolutionary biology and biogerontology.