Structural identifiability of compartmental models for infectious disease transmission is influenced by data type

If model identifiability is not confirmed, inferences from infectious disease transmission models may not be reliable, so they might result in misleading recommendations. Structural identifiability analysis characterises whether it is possible to obtain unique solutions for all unknown model parameters, given the model structure. In this work, we studied the structural identifiability of some typical deterministic compartmental models for infectious disease transmission, focusing on the influence of the data type considered as model output on the identifiability of unknown model parameters, including initial conditions. We defined 26 model versions, each having a unique combination of underlying compartmental structure and data type(s) considered as model output(s). Four compartmental model structures and three common data types in disease surveillance (incidence, prevalence and detected vector counts) were studied. The structural identifiability of some parameters varied depending on the type of model output. In general, models with multiple data types as outputs had more structurally identifiable parameters, than did models with a single data type as output. This study highlights the importance of a careful consideration of data types as an integral part of the inference process with compartmental infectious disease transmission models

Engaging local communities in aquatic resources research and activities: a technical manual

This document is part of a series of 5 technical manuals produced by the Challenge Program Project CP34 “Improved fisheries productivity and management in tropical reservoirs”. The objective of this technical manual is to relay the field experience of a group of scientists who have worked extensively in small fisheries in sub-Sahara Africa and Asia and lay out a series of simple and pragmatic pointers on how to establish and run initiatives for community catch assessment. The manual relies in particular on practical experience gained implementing Project 34 of the Challenge Programme on Water and Food: Improved Fisheries Productivity and Management in Tropical Reservoirs. (PDF contains 26 pages

Engaging local communities in aquatic resources research and activities: a technical manual

This document is part of a series of 5 technical manuals produced by the Challenge Program Project CP34 ôImproved fisheries productivity and management in tropical reservoirsö. The objective of this technical manual is to relay the field experience of a group of scientists who have worked extensively in small fisheries in sub-Sahara Africa and Asia and lay out a series of simple and pragmatic pointers on how to establish and run initiatives for community catch assessment. The manual relies in particular on practical experience gained implementing Project 34 of the Challenge Programme on Water and Food: Improved Fisheries Productivity and Management in Tropical Reservoirs.Research, Fishery data

Changes in resource partitioning between and within organs support growth adjustment to neighbor proximity in <i>Brassicaceae</i> seedlings.

In shade-intolerant plants, the perception of proximate neighbors rapidly induces architectural changes resulting in elongated stems and reduced leaf size. Sensing and signaling steps triggering this modified growth program have been identified. However, the underlying changes in resource allocation that fuel stem growth remain poorly understood. Through &lt;sup&gt;14&lt;/sup&gt; CO &lt;sub&gt;2&lt;/sub&gt; pulse labeling of &lt;i&gt;Brassica rapa&lt;/i&gt; seedlings, we show that perception of the neighbor detection signal, low ratio of red to far-red light (R:FR), leads to increased carbon allocation from the major site of photosynthesis (cotyledons) to the elongating hypocotyl. While carbon fixation and metabolite levels remain similar in low R:FR, partitioning to all downstream carbon pools within the hypocotyl is increased. Genetic analyses using &lt;i&gt;Arabidopsis thaliana&lt;/i&gt; mutants indicate that low-R:FR-induced hypocotyl elongation requires sucrose transport from the cotyledons and is regulated by a PIF7-dependent metabolic response. Moreover, our data suggest that starch metabolism in the hypocotyl has a growth-regulatory function. The results reveal a key mechanism by which metabolic adjustments can support rapid growth adaptation to a changing environment

Ten months of temporal variation in the clinical journey of hospitalised patients with COVID-19: an observational cohort

Background: There is potentially considerable variation in the nature and duration of the care provided to hospitalised patients during an infectious disease epidemic or pandemic. Improvements in care and clinician confidence may shorten the time spent as an inpatient, or the need for admission to an intensive care unit (ICU) or high density unit (HDU). On the other hand, limited resources at times of high demand may lead to rationing. Nevertheless, these variables may be used as static proxies for disease severity, as outcome measures for trials, and to inform planning and logistics. Methods: We investigate these time trends in an extremely large international cohort of 142,540 patients hospitalised with COVID-19. Investigated are: time from symptom onset to hospital admission, probability of ICU/HDU admission, time from hospital admission to ICU/HDU admission, hospital case fatality ratio (hCFR) and total length of hospital stay. Results: Time from onset to admission showed a rapid decline during the first months of the pandemic followed by peaks during August/September and December 2020. ICU/HDU admission was more frequent from June to August. The hCFR was lowest from June to August. Raw numbers for overall hospital stay showed little variation, but there is clear decline in time to discharge for ICU/HDU survivors. Conclusions: Our results establish that variables of these kinds have limitations when used as outcome measures in a rapidly-evolving situation. Funding: This work was supported by the UK Foreign, Commonwealth and Development Office and Wellcome [215091/Z/18/Z] and the Bill and Melinda Gates Foundation [OPP1209135]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Ten months of temporal variation in the clinical journey of hospitalised patients with COVID-19: an observational cohort

Background: There is potentially considerable variation in the nature and duration of the care provided to hospitalised patients during an infectious disease epidemic or pandemic. Improvements in care and clinician confidence may shorten the time spent as an inpatient, or the need for admission to an intensive care unit (ICU) or high density unit (HDU). On the other hand, limited resources at times of high demand may lead to rationing. Nevertheless, these variables may be used as static proxies for disease severity, as outcome measures for trials, and to inform planning and logistics. Methods: We investigate these time trends in an extremely large international cohort of 142,540 patients hospitalised with COVID-19. Investigated are: time from symptom onset to hospital admission, probability of ICU/HDU admission, time from hospital admission to ICU/HDU admission, hospital case fatality ratio (hCFR) and total length of hospital stay. Results: Time from onset to admission showed a rapid decline during the first months of the pandemic followed by peaks during August/September and December 2020. ICU/HDU admission was more frequent from June to August. The hCFR was lowest from June to August. Raw numbers for overall hospital stay showed little variation, but there is clear decline in time to discharge for ICU/HDU survivors. Conclusions: Our results establish that variables of these kinds have limitations when used as outcome measures in a rapidly-evolving situation. Funding: This work was supported by the UK Foreign, Commonwealth and Development Office and Wellcome [215091/Z/18/Z] and the Bill and Melinda Gates Foundation [OPP1209135]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

StopCOVID cohort : An observational study of 3,480 patients admitted to the Sechenov University hospital network in Moscow city for suspected COVID-19 infection

© 2020 Oxford University Press. This is a pre-copyedited, author-produced PDF of an article accepted for publication in Clinical Infectious Diseases following peer review. The version of record is available online at: https://doi.org/10.1093/cid/ciaa1535.BACKGROUND: The epidemiology, clinical course, and outcomes of COVID-19 patients in the Russian population are unknown. Information on the differences between laboratory-confirmed and clinically-diagnosed COVID-19 in real-life settings is lacking. METHODS: We extracted data from the medical records of adult patients who were consecutively admitted for suspected COVID-19 infection in Moscow, between April 8 and May 28, 2020. RESULTS: Of the 4261 patients hospitalised for suspected COVID-19, outcomes were available for 3480 patients (median age 56 years (interquartile range 45-66). The commonest comorbidities were hypertension, obesity, chronic cardiac disease and diabetes. Half of the patients (n=1728) had a positive RT-PCR while 1748 were negative on RT-PCR but had clinical symptoms and characteristic CT signs suggestive of COVID-19 infection.No significant differences in frequency of symptoms, laboratory test results and risk factors for in-hospital mortality were found between those exclusively clinically diagnosed or with positive SARS-CoV-2 RT-PCR.In a multivariable logistic regression model the following were associated with in-hospital mortality; older age (per 1 year increase) odds ratio [OR] 1.05 (95% confidence interval (CI) 1.03 - 1.06); male sex (OR 1.71, 1.24 - 2.37); chronic kidney disease (OR 2.99, 1.89 - 4.64); diabetes (OR 2.1, 1.46 - 2.99); chronic cardiac disease (OR 1.78, 1.24 - 2.57) and dementia (OR 2.73, 1.34 - 5.47). CONCLUSIONS: Age, male sex, and chronic comorbidities were risk factors for in-hospital mortality. The combination of clinical features were sufficient to diagnoseCOVID-19 infection indicating that laboratory testing is not critical in real-life clinical practice.Peer reviewe

Improved fisheries productivity and management in tropical reservoirs

The main objective of this 3.5 year project was to increase the productivity of reservoir fisheries and provide sustainable livelihoods to the rural poor through a series of interventions in tropical reservoirs. The main project activities focused on two reservoirs in the Indo-Gangetic basin (Dahob in Madhya Pradesh, and Pahuj in Uttar Pradesh, both in India), the Lake Nasser in Egypt as part as the Nile basin, and the Volta Lake in Ghana as part as the Volta basin. The project also encompassed an initial data inventory from a wide variety of tropical reservoirs within the three basins, and the detailed assessment of the selected reservoirs, including market evaluation and post-capture improvements. (PDF contains 117 pages

Author Correction: Adaptation of Plasmodium falciparum to humans involved the loss of an ape-specific erythrocyte invasion ligand.

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-21491-y</jats:p

Adaptation of Plasmodium falciparum to humans involved the loss of an ape-specific erythrocyte invasion ligand

Abstract: Plasmodium species are frequently host-specific, but little is currently known about the molecular factors restricting host switching. This is particularly relevant for P. falciparum, the only known human-infective species of the Laverania sub-genus, all other members of which infect African apes. Here we show that all tested P. falciparum isolates contain an inactivating mutation in an erythrocyte invasion associated gene, PfEBA165, the homologues of which are intact in all ape-infective Laverania species. Recombinant EBA165 proteins only bind ape, not human, erythrocytes, and this specificity is due to differences in erythrocyte surface sialic acids. Correction of PfEBA165 inactivating mutations by genome editing yields viable parasites, but is associated with down regulation of both PfEBA165 and an adjacent invasion ligand, which suggests that PfEBA165 expression is incompatible with parasite growth in human erythrocytes. Pseudogenization of PfEBA165 may represent a key step in the emergence and evolution of P. falciparum