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A detailed ultrastructural examination of lung cryobiopsy samples from a COVID-19 patient case series – Data set 05

We investigated six cryobiopsy samples from six deceased patients (patients C03 to C08 from Barisione et al. 2020 <a href="https://doi.org/10.1007/s00428-020-02934-1">doi.org/10.1007/s00428-020-02934-1</a>) by using thin section electron microscopy (Cortese et al. 2022 <a href="http://doi.org/10.1007/s00428-022-03308-5">doi.org/10.1007/s00428-022-03308-5</a>). A detailed description of the methods and the data set is provided in the download container. Data set 05 contains a stitched image montage of the first and of the last semithin section from the analysis of patient C07, which was acquired by bright-field light microscopy.

A detailed ultrastructural examination of lung cryobiopsy samples from a COVID-19 patient case series – Data set 15

We investigated six cryobiopsy samples from six deceased patients (patients C03 to C08 from Barisione et al. 2020 <a href="https://doi.org/10.1007/s00428-020-02934-1">doi.org/10.1007/s00428-020-02934-1</a>) by using thin section electron microscopy (Cortese et al. 2022 <a href="http://doi.org/10.1007/s00428-022-03308-5">doi.org/10.1007/s00428-022-03308-5</a>). A detailed description of the methods and the data set is provided in the download container. Data set 15 contains stitched image montages of a thin section through the lung of patient C05 which were acquired by scanning electron microscopy. The file “Data_set_15.tif” contains a montage of the entire thin section while the other files contain selected areas of the section recorded at higher resolution.

A detailed ultrastructural examination of lung cryobiopsy samples from a COVID-19 patient case series – Data set 13

We investigated six cryobiopsy samples from six deceased patients (patients C03 to C08 from Barisione et al. 2020 <a href="https://doi.org/10.1007/s00428-020-02934-1">doi.org/10.1007/s00428-020-02934-1</a>) by using thin section electron microscopy (Cortese et al. 2022 <a href="http://doi.org/10.1007/s00428-022-03308-5">doi.org/10.1007/s00428-022-03308-5</a>). A detailed description of the methods and the data set is provided in the download container. Data set 13 contains stitched image montages of a thin section through the lung of patient C03 which were acquired by scanning electron microscopy. The file “Data_set_13.tif” contains a montage of the entire thin section while the other files contain selected areas of the section recorded at higher resolution.

A detailed ultrastructural examination of lung cryobiopsy samples from a COVID-19 patient case series – Data set 01

We investigated six cryobiopsy samples from six deceased patients (patients C03 to C08 from Barisione et al. 2020 <a href="https://doi.org/10.1007/s00428-020-02934-1">doi.org/10.1007/s00428-020-02934-1</a>) by using thin section electron microscopy (Cortese et al. 2022 <a href="http://doi.org/10.1007/s00428-022-03308-5">doi.org/10.1007/s00428-022-03308-5</a>). A detailed description of the methods and the data set is provided in the download container. Data set 01 contains a stitched image montage of the first and of the last semithin section from the analysis of patient C03, which was acquired by bright-field light microscopy.

A detailed ultrastructural examination of lung cryobiopsy samples from a COVID-19 patient case series – Data set 02

We investigated six cryobiopsy samples from six deceased patients (patients C03 to C08 from Barisione et al. 2020 <a href="https://doi.org/10.1007/s00428-020-02934-1">doi.org/10.1007/s00428-020-02934-1</a>) by using thin section electron microscopy (Cortese et al. 2022 <a href="http://doi.org/10.1007/s00428-022-03308-5">doi.org/10.1007/s00428-022-03308-5</a>). A detailed description of the methods and the data set is provided in the download container. Data set 02 contains a stitched image montage of the first and of the last semithin section from the analysis of patient C04, which was acquired by bright-field light microscopy.

A detailed ultrastructural examination of lung cryobiopsy samples from a COVID-19 patient case series – Data set 03

We investigated six cryobiopsy samples from six deceased patients (patients C03 to C08 from Barisione et al. 2020 <a href="https://doi.org/10.1007/s00428-020-02934-1">doi.org/10.1007/s00428-020-02934-1</a>) by using thin section electron microscopy (Cortese et al. 2022 <a href="http://doi.org/10.1007/s00428-022-03308-5">doi.org/10.1007/s00428-022-03308-5</a>). A detailed description of the methods and the data set is provided in the download container. Data set 03 contains a stitched image montage of the first and of the last semithin section from the analysis of patient C05, which was acquired by bright-field light microscopy.

A detailed ultrastructural examination of lung cryobiopsy samples from a COVID-19 patient case series – Data set 18

We investigated six cryobiopsy samples from six deceased patients (patients C03 to C08 from Barisione et al. 2020 <a href="https://doi.org/10.1007/s00428-020-02934-1">doi.org/10.1007/s00428-020-02934-1</a>) by using thin section electron microscopy (Cortese et al. 2022 <a href="http://doi.org/10.1007/s00428-022-03308-5">doi.org/10.1007/s00428-022-03308-5</a>). A detailed description of the methods and the data set is provided in the download container. Data set 18 contains stitched image montages of a thin section through the lung of patient C08 which were acquired by scanning electron microscopy. The file “Data_set_18.tif” contains a montage of the entire thin section while the other files contain selected areas of the section recorded at higher resolution.

A detailed ultrastructural examination of lung cryobiopsy samples from a COVID-19 patient case series – Data set 17

We investigated six cryobiopsy samples from six deceased patients (patients C03 to C08 from Barisione et al. 2020 <a href="https://doi.org/10.1007/s00428-020-02934-1">doi.org/10.1007/s00428-020-02934-1</a>) by using thin section electron microscopy (Cortese et al. 2022 <a href="http://doi.org/10.1007/s00428-022-03308-5">doi.org/10.1007/s00428-022-03308-5</a>). A detailed description of the methods and the data set is provided in the download container. Data set 17 contains stitched image montages of a thin section through the lung of patient C07 which were acquired by scanning electron microscopy. The file “Data_set_17.tif” contains a montage of the entire thin section while the other files contain selected areas of the section recorded at higher resolution.

A Repeated Measures Dataset on Public Responses to the COVID-19 Pandemic: Social Norms, Attitudes, Behaviors, Conspiracy Thinking, and (Mis)Information

We present a quantitative repeated measures dataset from intensive longitudinal research (diary survey) conducted with participants drawn from a nationally representative sample of the German population. This diary survey addresses a wide range of variables relevant to the COVID-19 pandemic, including information seeking, attitudes towards science, public health, and related behaviors.  Respondents were asked about their thoughts, challenges, concerns, and experiences related to the pandemic. Survey responses were requested every two weeks from November 2020 and September 2021 for a total of 18 stages of data collection. The diary survey responses were all matched to the same individual. Using the unique identifier for each individual, the diary survey dataset can be analyzed in concert with a larger representative survey sample that was conducted three times within the same research project over this time period. The diary dataset we present here includes socio-demographic information and other potentially relevant variables, ready for secondary analysis. Initial sample frame: N = 1,480 Initial diary survey sub-sample: N = 133

Impact of Community Masking on COVID-19: A Cluster-Randomized Trial in Bangladesh

We ran a randomized trial of mask promotion in Bangladesh; the intervention increased mask-use and reduced symptomatic SARS-CoV-2 infections.

How did the US and UK markets react to the COVID-19 vaccines' announcements? A preliminary assessment

This data has been used for the preparation of the manuscript: 'How did the US and UK markets react to the COVID-19 vaccines’ announcements? A preliminary assessment'

opencc-zeroNov 2021View details →

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Effects of COVID-19 lockdown restrictions on parents' attitudes towards green space and time spent outside by children in Cambridgeshire and North London, United Kingdom

1. In the United Kingdom, children are spending less time outdoors and are more disconnected from nature than previous generations. However, interaction with nature at a young age can benefit wellbeing and long-term support for conservation. Green space accessibility in the UK varies between rural and urban areas and is lower for children than for adults. It is possible that COVID-19 lockdown restrictions may have influenced these differences. 2. In this study, we assessed parents' attitudes towards green space, as well as whether the COVID-19 lockdown restrictions had affected their attitudes or the amount of time spent outside by their children, via an online survey for parents of primary school-aged children in Cambridgeshire and North London, UK (n = 171). We assessed whether responses were affected by local environment (rural, suburban or urban), school type (state-funded or fee-paying) or garden access (with or without private garden access). 3. Parents' attitudes towards green space were significantly different between local environments: 76.9% of rural parents reported being happy with the amount of green space to which their children had access, in contrast with only 40.5% of urban parents. 4. COVID-19 lockdown restrictions also affected parents' attitudes to the importance of green space, and this differed between local environments: 75.7% of urban parents said their views had changed during lockdown, in contrast with 35.9% of rural parents. The change in amount of time spent outside by children during lockdown was also significantly different between local environments: most urban children spent more time inside during lockdown, whilst most rural children spent more time outside. 5. Neither parents' attitudes towards green space nor the amount of time spent outside by their children varied with school type or garden access. 6. Our results suggest that lockdown restrictions exacerbated pre-existing differences in access to nature between urban and rural children in our sampled population. We suggest that the current increased public and political awareness of the value of green space should be capitalised on to increase provision and access to green space and to reduce inequalities in accessibility and awareness of nature between children from different backgrounds.

Nasopharyngeal virome analysis of COVID-19 patients during three different waves in Campania Region of Italy.

From December 2019, SARS-CoV-2 infection has spread rapidly, leading to a global pandemic. Little is known about possible relationships between SARS-CoV-2 and other viruses in the respiratory system affecting patient prognosis and outcomes. This study aims to characterize respiratory virome profiles in association with SARS-CoV-2 infection and disease severity, through the analysis in 89 nasopharyngeal swabs collected in a patient’s cohort from the Campania region (Southern Italy).We found coinfections with viral species that belonged to Coronaviridae, Retroviridae, Herpesviridae, Poxviridae, Pneumoviridae, Pandoraviridae, and Anelloviridae families and only in 2% of cases (2/89) we identified respiratory viruses.

opencc-zeroDec 2021View details →

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Socioeconomic status affects the incidence of COVID-19 in Chilean multiple sclerosis patients

Objective: To investigate the frequency of coronavirus disease (COVID-19) in patients with multiple sclerosis (pwMSs) living in a high socioeconomic vulnerability area in Chile. Methods: In this prospective cohort study, we compared the frequency of COVID-19 in 52 Chilean pwMSs on disease-modifying treatments (DMTs), living in urban municipalities with low-income/high-poverty levels, with that previously reported in pwMSs living in municipalities with high-income/low-poverty rates in Santiago, Chile. Demographic and clinical features of the pwMSs were obtained from their last consultation between March 3, 2020, and August 29, 2020. Results: In the low-income pwMSs, the mean patient age was 34 years, 69% were women, mean disease duration was 3 years, and mean Expanded Disability Status Scale score was 1.6. Of these, 61.5% pwMSs (32/52) underwent quarantine during the study period. COVID-19 diagnosis was confirmed by reverse transcriptase polymerase chain reaction in five patients (10%): two were on glatiramer acetate, one was on fingolimod, and two were on alemtuzumab. All pwMSs with COVID-19 recovered fully. The previously reported frequency of confirmed COVID-19 in middle‒upper income pwMSs living in Santiago was 1%. The frequency of COVID-19 among pwMSs in the low- and middle‒high income inhabitants of Santiago differed significantly (z = -4.3235, p < 0.00001; one-tailed Fisher exact test, p < 0.01). Conclusion: The frequency of COVID-19 in the low-income/high-poverty cohort in Santiago, Chile, was markedly high. Accordingly, high socioeconomic vulnerability should be considered as an important risk factor for COVID-19 in pwMSs.

Prueba depósito términos más usados durante la Pandemia Covid-19 en España y Francia

Búsqueda y comparación entre Francia y España de los términos más usados sobre el Covid-19.

History of daily forecast of cumulative COVID-19 mortality in multiple geographic entities across the world

Forecasts are available from 2020-04-01 to 2021-10-20 for dozens to more than 200 geographic entities (GE) across the world (from 46 GE on 2020-04-01 to 246 GE on 2021-10-20).  Each forecast of cumulative mortality is grounded on a probabilistic mixture of mortality trajectories of ahead-of-time geographic entities playing the role of real-life predictors eventually complemented by a parametric model based on a SIR representation. The methodology is presented in Soubeyrand, Ribaud et al. (2020, https://doi.org/10.1371/journal.pone.0238410) and Soubeyrand, Demongeot et al. (2020, https://doi.org/10.1016/j.onehlt.2020.100187).  The forecast are daily implemented by a web application entitled "COVID-19 Visualization" available at https://shiny.biosp.inrae.fr/app_direct/mapCovid19/ The original code is available here: https://gitlab.paca.inrae.fr/biosp/shinyMapCovid19 Raw data for drawing the forecast are provided by the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE; https://systems.jhu.edu/) available at https://github.com/CSSEGISandData/COVID-19/ (Dong et al., 2020, https://doi.org/10.1016/S1473-3099(20)30120-1).  Information about the data set and the code are provided in the readme.txt file. Data are provided in the forecast_data.rds file produced originally with the saveRDS() function of the R Statistical Software (https://cran.r-project.org/).  A code for loading the data set and extracting some data corresponding to specific dates and geographic entities with the R Statistical Software is provided in the read_data.R file.

Nordic comparative study on green space use during COVID-19 – Case Helsinki (NCS-Helsinki)

This dataset includes the data used in the Helsinki case study of an original research paper “Pandemic urban resilience in the Nordic context - a cross-city analysis on associations between outdoor recreation and green infrastructure” (Fagerholm et al., upcoming). The data were collected in the PLAN-Health (PLAN-H) research project (<a href="https://participatorymapping.org/project/health-promoting-urban-environment-plan-h/">https://participatorymapping.org/project/health-promoting-urban-environment-plan-h/</a>) and include point data of respondent-mapped outdoor locations visited in leisure time.

Dataset- Self-reported periodontal disease, dental presence and COVID-19, in older adults of the Playa municipality

Esta base de datos fue creada con el objetivo de determinar la relación existente entre la enfermedad periodontal autoinformada, la perdida dentaria y el comportamiento de la covid-19. ---------------------------------------------------------------------------------ENG This database was created with the objective of determining the relationship between self-reported periodontal disease, tooth loss and the behavior of covid-19.

opencc-zeroDec 2021View details →

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Modeling to determine when to re-open HIV services during COVID-19 pandemic

The Risks and Benefits of Providing HIV Services during the COVID-19 Pandemic Introduction The COVID-19 pandemic has caused widespread disruptions including to health services. In the early response to the pandemic many countries restricted population movements and some health services were suspended or limited. In late 2020 and early 2021 some countries re-imposed restrictions. Health authorities need to balance the potential harms of additional SARS-CoV-2 transmission due to contacts associated with health services against the benefits of those services, including fewer new HIV infections and deaths. This paper examines these trade-offs for select HIV services. Methods We used four HIV simulation models (Goals, HIV Synthesis, Optima HIV and EMOD) to estimate the benefits of continuing HIV services in terms of fewer new HIV infections and deaths. We used three COVID-19 transmission models (Covasim, Cooper/Smith and a simple contact model) to estimate the additional deaths due to SARS-CoV-2 transmission among health workers and clients. We examined four HIV services: voluntary medical male circumcision, HIV diagnostic testing, viral load testing and programs to prevent mother-to-child transmission. We compared COVID-19 deaths in 2020 and 2021 with HIV deaths occurring now and over the next 50 years discounted to present value. The models were applied to countries with a range of HIV and COVID-19 epidemics. Results Maintaining these HIV services could lead to additional COVID-19 deaths of 0.002 to 0.15 per 10,000 clients. HIV-related deaths averted are estimated to be much larger, 19 - 146 discounted deaths per 10,000 clients. Discussion While there is some additional short-term risk of SARS-CoV-2 transmission associated with providing HIV services, the risk of additional COVID-19 deaths is at least 100 times less than the HIV deaths averted by those services. Ministries of Health need to take into account many factors in deciding when and how to offer essential health services during the COVID-19 pandemic. This work shows that the benefits of continuing key HIV services are far larger than the risks of additional SARS-CoV-2 transmission.

Impairment of aversive episodic memories during Covid-19 pandemic: The impact of emotional context on memory processes

The threatening context of the COVID-19 pandemic provided a unique setting to study the effects of negative psychological symptoms on memory processes. Episodic memory is an essential function of the human being related to the ability to store and remember experiences and anticipate possible events in the future. Studying this function in this context is crucial to understand what effects the pandemic will have on the formation of episodic memories. To study this, the formation of episodic memories was evaluated by free recall, recognition, and episode order tasks for an aversive and neutral content. The results indicated that aversive episodic memory is impaired both in the free recall task and in the recognition task. Even the beneficial effect that emotional memory usually has for the episodic order was undermined as there were no differences between the neutral and aversive condition. The present work adds to the evidence that indicates that the level of activation does not modify memory processes in a linear way, which also depends on the type of recall and the characteristics of the content to be encoded.