A machine learning approach to predict resilience and sickness absence in the healthcare workforce during the COVID-19 pandemic

During the COVID-19 pandemic, healthcare workers (HCWs) have faced unprecedented workloads and personal health risks leading to mental disorders and surges in sickness absence. Previous work has shown that interindividual differences in psychological resilience might explain why only some individuals are vulnerable to these consequences. However, no prognostic tools to predict individual HCW resilience during the pandemic have been developed. We deployed machine learning (ML) to predict psychological resilience during the pandemic. The models were trained in HCWs of the largest Finnish hospital, Helsinki University Hospital (HUS, N = 487), with a six-month follow-up, and prognostic generalizability was evaluated in two independent HCW validation samples (Social and Health Services in Kymenlaakso: Kymsote, N = 77 and the City of Helsinki, N = 322) with similar follow-ups never used for training the models. Using the most predictive items to predict future psychological resilience resulted in a balanced accuracy (BAC) of 72.7-74.3% in the HUS sample. Similar performances (BAC = 67-77%) were observed in the two independent validation samples. The models' predictions translated to a high probability of sickness absence during the pandemic. Our results provide the first evidence that ML techniques could be harnessed for the early detection of COVID-19-related distress among HCWs, thereby providing an avenue for potential targeted interventions.Peer reviewe

Combined systems approaches reveal highly plastic responses to antimicrobial peptide challenge in Escherichia coli

Obtaining an in-depth understanding of the arms races between peptides comprising the innate immune response and bacterial pathogens is of fundamental interest and will inform the development of new antibacterial therapeutics. We investigated whether a whole organism view of antimicrobial peptide (AMP) challenge on Escherichia coli would provide a suitably sophisticated bacterial perspective on AMP mechanism of action. Selecting structurally and physically related AMPs but with expected differences in bactericidal strategy, we monitored changes in bacterial metabolomes, morphological features and gene expression following AMP challenge at sub-lethal concentrations. For each technique, the vast majority of changes were specific to each AMP, with such a plastic response indicating E. coli is highly capable of discriminating between specific antibiotic challenges. Analysis of the ontological profiles generated from the transcriptomic analyses suggests this approach can accurately predict the antibacterial mode of action, providing a fresh, novel perspective for previous functional and biophysical studies

A New Highly Conserved Antibiotic Sensing/Resistance Pathway in Firmicutes Involves an ABC Transporter Interplaying with a Signal Transduction System

Signal transduction systems and ABC transporters often contribute jointly to adaptive bacterial responses to environmental changes. In Bacillus subtilis, three such pairs are involved in responses to antibiotics: BceRSAB, YvcPQRS and YxdJKLM. They are characterized by a histidine kinase belonging to the intramembrane sensing kinase family and by a translocator possessing an unusually large extracytoplasmic loop. It was established here using a phylogenomic approach that systems of this kind are specific but widespread in Firmicutes, where they originated. The present phylogenetic analyses brought to light a highly dynamic evolutionary history involving numerous horizontal gene transfers, duplications and lost events, leading to a great variety of Bce-like repertories in members of this bacterial phylum. Based on these phylogenetic analyses, it was proposed to subdivide the Bce-like modules into six well-defined subfamilies. Functional studies were performed on members of subfamily IV comprising BceRSAB from B. subtilis, the expression of which was found to require the signal transduction system as well as the ABC transporter itself. The present results suggest, for the members of this subfamily, the occurrence of interactions between one component of each partner, the kinase and the corresponding translocator. At functional and/or structural levels, bacitracin dependent expression of bceAB and bacitracin resistance processes require the presence of the BceB translocator loop. Some other members of subfamily IV were also found to participate in bacitracin resistance processes. Taken together our study suggests that this regulatory mechanism might constitute an important common antibiotic resistance mechanism in Firmicutes. [Supplemental material is available online at http://www.genome.org.

The flight feather moult pattern of the bearded vulture (Gypaetus barbatus).

Moult is an extremely time-consuming and energy-demanding task for large birds. In addition, there is a trade-off between the time devoted to moulting and that invested in other activities such as breeding and/or territory exploration. Moreover, it takes a long time to grow a long feather in large birds, and large birds that need to fly while moulting cannot tolerate large gaps in the wing, but only one or two simultaneously growing feathers. As a consequence, large birds take several years to complete a full moult cycle, and they resume the moult process during suboptimal conditions. A clear example of this pattern is the Bearded Vulture (Gypaetus barbatus), which needs 2-3 years for changing all flight feathers. Here we describe the sequence, extent, and timing of moult of 124 Bearded Vultures in detail for the first time. We found that extent and timing of flight feather moult was different between age classes. Subadults (from 3rd to 5th calendar year) started moult, on average, in early March, whereas adults only started moult, on average, in late April, possibly due to breeding requirements. Second calendar year individuals delayed onset of moult until the middle of May. In general, the moult lasted until November, and although adults started to moult later than subadults, they moulted more feathers. Subadults needed 3 years for moulting all flight feathers, whereas adults normally completed it in 2 years

Climate change reshuffles northern species within their niches

Climate change is a pervasive threat to biodiversity. While range shifts are a known consequence of climate warming contributing to regional community change, less is known about how species' positions shift within their climatic niches. Furthermore, whether the relative importance of different climatic variables prompting such shifts varies with changing climate remains unclear. Here we analysed four decades of data for 1,478 species of birds, mammals, butterflies, moths, plants and phytoplankton along a 1,200 km high latitudinal gradient. The relative importance of climatic drivers varied non-uniformly with progressing climate change. While species turnover among decades was limited, the relative position of species within their climatic niche shifted substantially. A greater proportion of species responded to climatic change at higher latitudes, where changes were stronger. These diverging climate imprints restructure a full biome, making it difficult to generalize biodiversity responses and raising concerns about ecosystem integrity in the face of accelerating climate change.The authors analyse four decades of distribution data for various taxonomic groups to understand the shift of species within their climatic niches and the changing influences of different climate factors. The diverse and diverging climate imprints raise concerns about future ecosystem integrity.</p

The effect of climate change on avian offspring production: A global meta-analysis

Climate change affects timing of reproduction in many bird species, but few studies have investigated its influence on annual reproductive output. Here, we assess changes in the annual production of young by female breeders in 201 populations of 104 bird species (N = 745,962 clutches) covering all continents between 1970 and 2019. Overall, average offspring production has declined in recent decades, but considerable differences were found among species and populations. A total of 56.7% of populations showed a declining trend in offspring production (significant in 17.4%), whereas 43.3% exhibited an increase (significant in 10.4%). The results show that climatic changes affect offspring production through compounded effects on ecological and life history traits of species. Migratory and larger-bodied species experienced reduced offspring production with increasing temperatures during the chick-rearing period, whereas smaller-bodied, sedentary species tended to produce more offspring. Likewise, multi-brooded species showed increased breeding success with increasing temperatures, whereas rising temperatures were unrelated to repro- ductive success in single-brooded species. Our study suggests that rapid declines in size of bird populations reported by many studies from different parts of the world are driven only to a small degree by changes in the production of young

Screening out irrelevant cell-based models of disease

The common and persistent failures to translate promising preclinical drug candidates into clinical success highlight the limited effectiveness of disease models currently used in drug discovery. An apparent reluctance to explore and adopt alternative cell-and tissue-based model systems, coupled with a detachment from clinical practice during assay validation, contributes to ineffective translational research. To help address these issues and stimulate debate, here we propose a set of principles to facilitate the definition and development of disease-relevant assays, and we discuss new opportunities for exploiting the latest advances in cell-based assay technologies in drug discovery, including induced pluripotent stem cells, three-dimensional (3D) co-culture and organ-on-a-chip systems, complemented by advances in single-cell imaging and gene editing technologies. Funding to support precompetitive, multidisciplinary collaborations to develop novel preclinical models and cell-based screening technologies could have a key role in improving their clinical relevance, and ultimately increase clinical success rates