Specimens as research objects: reconciliation across distributed repositories to enable metadata propagation

Botanical specimens are shared as long-term consultable research objects in a global network of specimen repositories. Multiple specimens are generated from a shared field collection event; generated specimens are then managed individually in separate repositories and independently augmented with research and management metadata which could be propagated to their duplicate peers. Establishing a data-derived network for metadata propagation will enable the reconciliation of closely related specimens which are currently dispersed, unconnected and managed independently. Following a data mining exercise applied to an aggregated dataset of 19,827,998 specimen records from 292 separate specimen repositories, 36% or 7,102,710 specimens are assessed to participate in duplication relationships, allowing the propagation of metadata among the participants in these relationships, totalling: 93,044 type citations, 1,121,865 georeferences, 1,097,168 images and 2,191,179 scientific name determinations. The results enable the creation of networks to identify which repositories could work in collaboration. Some classes of annotation (particularly those regarding scientific name determinations) represent units of scientific work: appropriate management of this data would allow the accumulation of scholarly credit to individual researchers: potential further work in this area is discussed.Comment: 9 pages, 1 table, 3 figure

Targeting malaria parasites inside mosquitoes:Ecoevolutionary consequences

Proof-of-concept studies demonstrate that antimalarial drugs designed for human treatment can also be applied to mosquitoes to interrupt malaria transmission. Deploying a new control tool is ideally undertaken within a stewardship programme that maximises a drug’s lifespan by minimising the risk of resistance evolution and slowing its spread once emerged. We ask: what are the epidemiological and evolutionary consequences of targeting parasites within mosquitoes? Our synthesis argues that targeting parasites inside mosquitoes (i) can be modelled by readily expanding existing epidemiological frameworks; (ii) provides a functionally novel control method that has potential to be more robust to resistance evolution than targeting parasites in humans; and (iii) could extend the lifespan and clinical benefit of antimalarials used exclusively to treat humans

Understanding tsunami warning systems

The eastern Australian coastline faces some 8000km of active tectonic plate boundary that is capable of generating a tsunami thatcould reach Australia in two to four hours. This makes it imperative that coastal communities understand and can respond effectively to the Australian Tsunami Warning System. Activation of this warning system could result in warning times ranging from 90 minutes to three hours. Warning times of these durations could leave insufficient time for people to implement their emergency plan (e.g., to prepare their property, plan an evacuation etc.) on receipt of a warning. This project is researching key aspects of community response capability

Relationship between markers of malnutrition and clinical outcomes in older adults with cancer: systematic review, narrative synthesis and meta-analysis

© 2020, The Author(s). Malnutrition predicts poorer clinical outcomes for people with cancer. Older adults with cancer are a complex, growing population at high risk of weight-losing conditions. A number of malnutrition screening tools exist, however the best screening tool for this group is unknown. The aim was to systematically review the published evidence regarding markers and measures of nutritional status in older adults with cancer (age ≥ 70). A systematic search was performed in Ovid Medline, EMBASE, Web of Science, CINAHL, British Nursing Database and Cochrane CENTRAL; search terms related to malnutrition, cancer, older adults. Titles, abstracts and papers were screened and quality-appraised. Data evaluating ability of markers of nutritional status to predict patient outcomes were subjected to meta-analysis or narrative synthesis. Forty-two studies, describing 15 markers were included. Meta-analysis found decreased food intake was associated with mortality (OR 2.15 [2.03–4.20] p = < 0.00001) in univariate analysis. Prognostic Nutritional Index (PNI) was associated with overall survival (HR 1.89 [1.03–3.48] p = 0.04). PNI markers (albumin, total lymphocyte count) could be seen as markers of inflammation rather than nutrition. There a suggested relationship between very low body mass index (BMI)

Community understanding of tsunami risk and warnings in Australia

The development of the Australian Tsunami Warning System (ATWS) was in recognition of the fact that the Australian coastline faces some 8000 km of active tectonic plate boundary capable of generating a tsunami that could reach Australia in two to four hours. The work reported in this paper complements an earlier questionnaire study (Paton, Frandsen &amp; Johnston 2010) with detailed interview data to inform understanding of respondents' awareness of tsunami risk and their willingness (or lack of) to respond to a rare but possible natural hazard. A belief that no tsunami events had occurred in Australia (at least since colonial times) and that major causes (e.g. seismic and volcanic) were absent, supported the view of participants that tsunami is a non-existent or a very lowprobability hazard for Australia. This view was reinforced by the lack of discussion of tsunami by government or in the media. The ensuing sense of 'risk rejection' resulted in respondents believing that no resources or effort should be directed to tsunami risk reduction. The data raises the possibility that the ATWS may not be fully effective unless action is taken to increase tsunami risk acceptance and readiness. Recommendations for doing so draw on participant discussions of how to localise risk reduction activities. Their suggestions for increasing tsunami readiness in coastal communities included integrating it with community-based, localised discussions around frequent flash floods, coastal storms, bushfires and climate change hazards. These concepts are discussed, as well as the use of local volunteer resources to develop preparedness activities.</p

Influenza Hospitalisations in England during the 2022/23 Season: do different data sources drive divergence in modelled waves? A comparison of surveillance and administrative data

Accurate and representative data is vital for precisely reporting the impact of influenza in healthcare systems. Northern hemisphere winter 2022/23 experienced the most substantial influenza wave since the COVID-19 pandemic began in 2020. Simultaneously, new data streams become available within health services because of the pandemic. Comparing these data, surveillance and administrative, supports the accurate monitoring of population level disease trends. We analysed admissions rates per capita from four different collection mechanisms covering National Health Service hospital Trusts in England over the winter 2022/23 wave. We adjust for difference in reporting and extracted key epidemic characteristics including the maximum admission rate, peak timing, cumulative season admissions and growth rates by fitting generalised additive models at national and regional levels. By modelling the admission rates per capita across surveillance and administrative data systems we show that different data measuring the epidemic produce different estimates of key quantities. Nationally and in most regions the data correspond well for the maximum admission rate, date of peak and growth rate, however, in subnational analysis discrepancies in estimates arose, particularly for the cumulative admission rate. This research shows that the choice of data used to measure seasonal influenza epidemics can influence analysis substantially at sub-national levels. For the admission rate per capita there is comparability in the sentinel surveillance approach (which has other important functions), rapid situational reports, operational databases and time lagged administrative data giving assurance in their combined value. Utilising multiple sources of data aids understanding of the impact of seasonal influenza epidemics in the population

Chapter Plant Name Resources

Plant names are the key to communicating and managing information about plants. This paper considers how providers of high quality technical plant name information can better meet the requirements non-botanical audiences who also rely on plant names for elements of their work. The International Plant Name Index, World Checklist of Selected Plant Families and The Plant List are used as examples to illustrate the strengths and weaknesses of plant name resources from a non-expert user’s perspective. The above resources can be thought of as botanists pushing data at audiences. Without closer engagement with users, however, there is a limit to their relevance and impact. The need to cover common names is a frequent criticism of existing resources. The Medicinal Plant Names Services (MPNS, www.kew.org/mpns) is an example of how plant name resources can be adapted to better address the needs of a non-botanical audience. Some of the major challenges are outlined and solutions suggested

Real-time COVID-19 hospital admissions forecasting with leading indicators and ensemble methods in England

Hospitalisations from COVID-19 with Omicron sub-lineages have put a sustained pressure on the English healthcare system. Understanding the expected healthcare demand enables more effective and timely planning from public health. We collect syndromic surveillance sources, which include online search data, NHS 111 telephonic and online triages. Incorporating this data we explore generalised additive models, generalised linear mixed-models, penalised generalised linear models and model ensemble methods to forecast over a two-week forecast horizon at an NHS Trust level. Furthermore, we showcase how model combinations improve forecast scoring through a mean ensemble, weighted ensemble, and ensemble by regression. Validated over multiple Omicron waves, at different spatial scales, we show that leading indicators can improve performance of forecasting models, particularly at epidemic changepoints. Using a variety of scoring rules, we show that ensemble approaches outperformed all individual models, providing higher performance at a 21-day window than the corresponding individual models at 14-days. We introduce a modelling structure used by public health officials in England in 2022 to inform NHS healthcare strategy and policy decision making. This paper explores the significance of ensemble methods to improve forecasting performance and how novel syndromic surveillance can be practically applied in epidemic forecasting

Identification of signal peptide features for substrate specificity in human Sec62/Sec63-dependent ER protein import

In mammalian cells, one‐third of all polypeptides are integrated into the membrane or translocated into the lumen of the endoplasmic reticulum (ER) via the Sec61 channel. While the Sec61 complex facilitates ER import of most precursor polypeptides, the Sec61‐associated Sec62/Sec63 complex supports ER import in a substrate‐specific manner. So far, mainly posttranslationally imported precursors and the two cotranslationally imported precursors of ERj3 and prion protein were found to depend on the Sec62/Sec63 complex in vitro. Therefore, we determined the rules for engagement of Sec62/Sec63 in ER import in intact human cells using a recently established unbiased proteomics approach. In addition to confirming ERj3, we identified 22 novel Sec62/Sec63 substrates under these in vivo‐like conditions. As a common feature, those previously unknown substrates share signal peptides (SP) with comparatively longer but less hydrophobic hydrophobic region of SP and lower carboxy‐terminal region of SP (C‐region) polarity. Further analyses with four substrates, and ERj3 in particular, revealed the combination of a slowly gating SP and a downstream translocation‐disruptive positively charged cluster of amino acid residues as decisive for the Sec62/Sec63 requirement. In the case of ERj3, these features were found to be responsible for an additional immunoglobulin heavy‐chain binding protein (BiP) requirement and to correlate with sensitivity toward the Sec61‐channel inhibitor CAM741. Thus, the human Sec62/Sec63 complex may support Sec61‐channel opening for precursor polypeptides with slowly gating SPs by direct interaction with the cytosolic amino‐terminal peptide of Sec61α or via recruitment of BiP and its interaction with the ER‐lumenal loop 7 of Sec61α. These novel insights into the mechanism of human ER protein import contribute to our understanding of the etiology of SEC63‐linked polycystic liver disease