Reproduction ratio and growth rates: Measures for an unfolding pandemic

The initial exponential growth rate of an epidemic is an important measure that follows directly from data at hand, commonly used to infer the basic reproduction number. As the growth rates λ(t) of tested positive COVID-19 cases have crossed the threshold in many countries, with negative numbers as surrogate for disease transmission deceleration, lock- downs lifting are linked to the behavior of the momentary reproduction numbers r(t), often called R0. Important to note that this concept alone can be easily misinterpreted as it is bound to many internal assumptions of the underlying model and significantly affected by the assumed recovery period. Here we present our experience, as part of the Basque Coun- try Modeling Task Force (BMTF), in monitoring the development of the COVID-19 epidemic, by considering not only the behaviour of r(t) estimated for the new tested positive cases— significantly affected by the increased testing capacities, but also the momentary growth rates for hospitalizations, ICU admissions, deceased and recovered cases, in assisting the Basque Health Managers and the Basque Government during the lockdown lifting mea- sures. Two different data sets, collected and then refined during the COVID-19 responses, are used as an exercise to estimate the momentary growth rates and reproduction numbers over time in the Basque Country, and the implications of using those concepts to make deci- sions about easing lockdown and relaxing social distancing measures are discussed. These results are potentially helpful for task forces around the globe which are now struggling to provide real scientific advice for health managers and governments while the lockdown measures are relaxed.Marie Skłodowska-Curie grant agreement No 79249

Modelling COVID 19 in the Basque Country from introduction to control measure response

In March 2020, a multidisciplinary task force (so‐called Basque Modelling Task Force, BMTF) was created to assist the Basque health managers and Government during the COVID‐19 responses. BMTF is a modelling team, working on different approaches, including stochastic processes, statistical methods and artificial intelligence. Here we describe the efforts and challenges to develop a flexible modeling framework able to describe the dynamics observed for the tested positive cases, including the modelling development steps. The results obtained by a new stochastic SHARUCD model framework are presented. Our models differentiate mild and asymptomatic from severe infections prone to be hospitalized and were able to predict the course of the epidemic, providing important projections on the national health system’s necessities during the increased population demand on hospital admissions. Short and longer‐term predictions were tested with good results adjusted to the available epidemiological data. We have shown that the partial lockdown measures were effective and enough to slow down disease transmission in the Basque Country. The growth rate was calculated from the model and from the data and the implications for the reproduction ratio r are shown. The analysis of the growth rates from the data led to improved model versions describing after the exponential phase also the new information obtained during the phase of response to the control measures. This framework is now being used to monitor disease transmission while the country lockdown was gradually lifted, with insights to specific programs for a general policy of “social distancing” and home quarantining.Marie Skłodowska-Curie Grant Agreement No. 79249

The role of mild and asymptomatic infections on COVID-19 vaccines performance: A modeling study

Introduction: Different COVID-19 vaccine efficacies are reported, with remarkable effectiveness against severe disease. The so called sterilizing immunity, occurring when vaccinated individuals cannot transmit the virus, is still being evaluated. It is also unclear to what extent people with no symptoms or mild infection transmit the disease, and estimating their contribution to outbreaks is challenging. Objective: With an uneven roll out of vaccination, the purpose of this study is to investigate the role of mild and asymptomatic infections on COVID-19 vaccine performance as vaccine efficacy and vaccine coverage vary. Methods: We use an epidemiological SHAR (Susceptible-Hospitalized-Asymptomatic-Recovered) model framework to evaluate the effects of vaccination in different epidemiological scenarios of coverage and efficacy. Two vaccination models, the vaccine V1 protecting against severe disease, and the vaccine V2, protecting against infection as well as severe disease, are compared to evaluate the reduction of overall infections and hospitalizations. Results: Vaccine performance is driven by the ability of asymptomatic or mild disease cases transmitting the virus. Vaccines protecting against severe disease but failing to block transmission might not be able to reduce significantly the severe disease burden during the initial stage of a vaccination roll out programme, with an eventual increase on the number of overall infections in a population. Conclusion: The different COVID-19 vaccines currently in use have features placing them closer to one or the other of these two extreme cases, V1 and V2, and insights on the importance of asymptomatic infection in a vaccinated population are of a major importance for the future planning of vaccination programmes. Our results give insights on how to best combine the use of the available COVID-19 vaccines, optimizing the reduction of hospitalizations

The effect of mixed vaccination rollout strategy: A modelling study

Vaccines have measurable efficacy obtained first from vaccine trials. However, vaccine efficacy (VE) is not a static measure and long-term population studies are needed to evaluate its performance and impact. COVID-19 vaccines have been developed in record time and the currently licensed vaccines are extremely effective against severe disease with higher VE after the full immunization schedule. To assess the impact of the initial phase of the COVID-19 vaccination rollout programmes, we used an extended Susceptible - Hospitalized - Asymptomatic/mild - Recovered ($SHAR$) model. Vaccination models were proposed to evaluate different vaccine types: vaccine type 1 which protects against severe disease only but fails to block disease transmission, and vaccine type 2 which protects against both severe disease and infection. VE was assumed as reported by the vaccine trials incorporating the difference in efficacy between one and two doses of vaccine administration. We described the performance of the vaccine in reducing hospitalizations during a momentary scenario in the Basque Country, Spain. With a population in a mixed vaccination setting, our results have shown that reductions in hospitalized COVID-19 cases were observed five months after the vaccination rollout started, from May to June 2021. Specifically in June, a good agreement between modelling simulation and empirical data was well pronounced.BERC 2022-2025 Marie Curie No~792494 Severo Ochoa CEX2021-001142-S/ MICIN / AEI / 10.13039/501100011033 EITB Marathon 2021 call BIO21/COV/00

Changes in Social and Clinical Determinants of COVID-19 Outcomes Achieved by the Vaccination Program: A Nationwide Cohort Study

Background: The objective of this study was to assess changes in social and clinical determinants of COVID-19 outcomes associated with the first year of COVID-19 vaccination rollout in the Basque population. Methods: A retrospective study was performed using the complete database of the Basque Health Service (n = 2,343,858). We analyzed data on age, sex, socioeconomic status, the Charlson comorbidity index (CCI), hospitalization and intensive care unit (ICU) admission, and COVID-19 infection by Cox regression models and Kaplan–Meier curves. Results: Women had a higher hazard ratio (HR) of infection (1.1) and a much lower rate of hospitalization (0.7). With older age, the risk of infection fell, but the risks of hospitalization and ICU admission increased. The higher the CCI, the higher the risks of infection and hospitalization. The risk of infection was higher in high-income individuals in all periods (HR = 1.2–1.4) while their risk of hospitalization was lower in the post-vaccination period (HR = 0.451). Conclusion: Despite the lifting of many control measures during the second half of 2021, restoring human mobility patterns, the situation could not be defined as syndemic, clinical determinants seeming to have more influence than social ones on COVID-19 outcomes, both before and after vaccination program implementation

Características físicas y antropométricas, y análisis de juego en jugadores de pádel de elite

The goals of the present study were, on the one hand, to determine the anthropometric,strength (measured by jump and hand-grip tests) compared to other racquet sports,and on the other hand, to analyze the time-motion characteristics during the under-23Spanish Paddle championships. Thus, 14 men (20,38 ± 1,92 yr) and 12 women(19.73 ± 2,37 yr) participated in this study. Firstly, participants were assessed foranthropometric measurements; secondly, strength was measured by jump andhand-grip tests before and immediately after the match; finally, the time-motion ofmatches were quantified during the under-23 Spanish Championship in 2012. Theanthropometric characteristics of paddle players were slightly different in comparisonto players of other racket sports. In respect of strength parameters, there were notsignificant differences between pre-match and post-match measurements, indicatingno fatigue component after competition. In respect to time motion analyses, restingperiods were significantly longer compared to the effective playing time. Paddle seemsto have less time active than table-tennis and badminton, but more time active thantennis.      Los objetivos de este estudio son, por un lado, determinar las características antropométricas y de fuerza (medida mediante test de hand-grip y salto vertical con brazos libres) comprándolo con otros deportes de raqueta, y por otro, analizar las características propias del juego durante el Campeonato de España de Pádel sub-23. Para ello 14 hombres (20,38 ± 1,92 años) y 12 mujeres (19,73 ± 2,37 años) participaron en este estudio. A todos ellos se les realizó unas mediciones antropométricas, y unos tests de fuerza de miembro superior (hand-grip) y de miembro inferior (salto vertical con brazos libres) antes y después de los partidos. Por último, se registraron los datos de analisis de juego durante dicho evento. Los resultados muestran que las características antropométricas de los jugadores de pádel difieren ligeramente de las de los jugadores de otros deportes de raqueta. Los valores de fuerza, no disminuyeron después del partido, no observándose ningún indicio de fatiga. Respecto al análisis de las características del juego, el pádel se caracteriza por tener menos tiempo activo que el tenis de mesa y el badminton, pero más tiempo activo que el tenis

NewsMeSH: a new classifier designed to annotate health news with MeSH headings

Motivation In the age of big data, the amount of scientific information available online dwarfs the ability of current tools to support researchers in locating and securing access to the necessary materials. Well-structured open data and the smart systems that make the appropriate use of it are invaluable and can help health researchers and professionals to find the appropriate information by, e.g., configuring the monitoring of information or refining a specific query on a disease. Methods We present an automated text classifier approach based on the MEDLINE/MeSH thesaurus, trained on the manual annotation of more than 26 million expert-annotated scientific abstracts. The classifier was developed tailor-fit to the public health and health research domain experts, in the light of their specific challenges and needs. We have applied the proposed methodology on three specific health domains: the Coronavirus, Mental Health and Diabetes, considering the pertinence of the first, and the known relations with the other two health topics. Results A classifier is trained on the MEDLINE dataset that can automatically annotate text, such as scientific articles, news articles or medical reports with relevant concepts from the MeSH thesaurus. Conclusions The proposed text classifier shows promising results in the evaluation of health-related news. The application of the developed classifier enables the exploration of news and extraction of health-related insights, based on the MeSH thesaurus, through a similar workflow as in the usage of PubMed, with which most health researchers are familiar

Effect of resveratrol on alcohol-induced mortality and liver lesions in mice

BACKGROUND: Resveratrol is a polyphenol with important antiinflammatory and antioxidant properties. We investigated the effect of resveratrol on alcohol-induced mortality and liver lesions in mice. METHODS: Mice were randomly distributed into four groups (control, resveratrol-treated control, alcohol and resveratrol-treated alcohol). Chronic alcohol intoxication was induced by progressively administering alcohol in drinking water up to 40% v/v. The mice administered resveratrol received 10 mg/ml in drinking water. The animals had free access to standard diet. Blood levels were determined for transaminases, IL-1 and TNF-α. A histological evaluation was made of liver damage, and survival among the animals was recorded. RESULTS: Transaminase concentration was significantly higher in the alcohol group than in the rest of the groups (p < 0.05). IL-1 levels were significantly reduced in the alcohol plus resveratrol group compared with the alcohol group (p < 0.05). TNF-α was not detected in any group. Histologically, the liver lesions were more severe in the alcohol group, though no significant differences between groups were observed. Mortality in the alcohol group was 78% in the seventh week, versus 22% in the alcohol plus resveratrol group (p < 0.001). All mice in the alcohol group died before the ninth week. CONCLUSION: The results obtained suggest that resveratrol reduces mortality and liver damage in mice

The histology of ovarian cancer: worldwide distribution and implications for international survival comparisons (CONCORD-2)

Objective Ovarian cancers comprise several histologically distinct tumour groups with widely different prognosis. We aimed to describe the worldwide distribution of ovarian cancer histology and to understand what role this may play in international variation in survival. Methods The CONCORD programme is the largest population-based study of global trends in cancer survival. Data on 681,759 women diagnosed during 1995â\u80\u932009 with cancer of the ovary, fallopian tube, peritoneum and retroperitonum in 51 countries were included. We categorised ovarian tumours into six histological groups, and explored the worldwide distribution of histology. Results During 2005â\u80\u932009, type II epithelial tumours were the most common. The proportion was much higher in Oceania (73.1%), North America (73.0%) and Europe (72.6%) than in Central and South America (65.7%) and Asia (56.1%). By contrast, type I epithelial tumours were more common in Asia (32.5%), compared with only 19.4% in North America. From 1995 to 2009, the proportion of type II epithelial tumours increased from 68.6% to 71.1%, while the proportion of type I epithelial tumours fell from 23.8% to 21.2%. The proportions of germ cell tumours, sex cord-stromal tumours, other specific non-epithelial tumours and tumours of non-specific morphology all remained stable over time. Conclusions The distribution of ovarian cancer histology varies widely worldwide. Type I epithelial, germ cell and sex cord-stromal tumours are generally associated with higher survival than type II tumours, so the proportion of these tumours may influence survival estimates for all ovarian cancers combined. The distribution of histological groups should be considered when comparing survival between countries and regions

Global surveillance of cancer survival 1995-2009: analysis of individual data for 25,676,887 patients from 279 population-based registries in 67 countries (CONCORD-2)

BACKGROUND: Worldwide data for cancer survival are scarce. We aimed to initiate worldwide surveillance of cancer survival by central analysis of population-based registry data, as a metric of the effectiveness of health systems, and to inform global policy on cancer control. METHODS: Individual tumour records were submitted by 279 population-based cancer registries in 67 countries for 25·7 million adults (age 15-99 years) and 75,000 children (age 0-14 years) diagnosed with cancer during 1995-2009 and followed up to Dec 31, 2009, or later. We looked at cancers of the stomach, colon, rectum, liver, lung, breast (women), cervix, ovary, and prostate in adults, and adult and childhood leukaemia. Standardised quality control procedures were applied; errors were corrected by the registry concerned. We estimated 5-year net survival, adjusted for background mortality in every country or region by age (single year), sex, and calendar year, and by race or ethnic origin in some countries. Estimates were age-standardised with the International Cancer Survival Standard weights. FINDINGS: 5-year survival from colon, rectal, and breast cancers has increased steadily in most developed countries. For patients diagnosed during 2005-09, survival for colon and rectal cancer reached 60% or more in 22 countries around the world; for breast cancer, 5-year survival rose to 85% or higher in 17 countries worldwide. Liver and lung cancer remain lethal in all nations: for both cancers, 5-year survival is below 20% everywhere in Europe, in the range 15-19% in North America, and as low as 7-9% in Mongolia and Thailand. Striking rises in 5-year survival from prostate cancer have occurred in many countries: survival rose by 10-20% between 1995-99 and 2005-09 in 22 countries in South America, Asia, and Europe, but survival still varies widely around the world, from less than 60% in Bulgaria and Thailand to 95% or more in Brazil, Puerto Rico, and the USA. For cervical cancer, national estimates of 5-year survival range from less than 50% to more than 70%; regional variations are much wider, and improvements between 1995-99 and 2005-09 have generally been slight. For women diagnosed with ovarian cancer in 2005-09, 5-year survival was 40% or higher only in Ecuador, the USA, and 17 countries in Asia and Europe. 5-year survival for stomach cancer in 2005-09 was high (54-58%) in Japan and South Korea, compared with less than 40% in other countries. By contrast, 5-year survival from adult leukaemia in Japan and South Korea (18-23%) is lower than in most other countries. 5-year survival from childhood acute lymphoblastic leukaemia is less than 60% in several countries, but as high as 90% in Canada and four European countries, which suggests major deficiencies in the management of a largely curable disease. INTERPRETATION: International comparison of survival trends reveals very wide differences that are likely to be attributable to differences in access to early diagnosis and optimum treatment. Continuous worldwide surveillance of cancer survival should become an indispensable source of information for cancer patients and researchers and a stimulus for politicians to improve health policy and health-care systems