Search

BackgroundThe COVID-19 pandemic has shined a harsh light on a critical deficiency in our health care system: our inability to access important information about patients’ values, goals, and preferences in the electronic health record (EHR). At Memorial Sloan Kettering Cancer Center (MSK), we have integrated and systematized health-related values discussions led by oncology nurses for newly diagnosed cancer patients as part of routine comprehensive cancer care. Such conversations include not only the patient’s wishes for care at the end of life but also more holistic personal values, including sources of strength, concerns, hopes, and their definition of an acceptable quality of life. In addition, health care providers use a structured template to document their discussions of patient goals of care. ObjectiveTo provide ready access to key information about the patient as a person with individual values, goals, and preferences, we undertook the creation of the Patient Values Tab in our center’s EHR to display this information in a single, central location. Here, we describe the interprofessional, interdisciplinary, iterative process and user-centered design methodology that we applied to build this novel functionality as well as our initial implementation experience and plans for evaluation. MethodsWe first convened a working group of experts from multiple departments, including medical oncology, health informatics, information systems, nursing informatics, nursing education, and supportive care, and a user experience designer. We conducted in-depth, semistructured, audiorecorded interviews of over 100 key stakeholders. The working group sought consensus on the tab’s main content, homing in on high-priority areas identified by the stakeholders. The core content was mapped to various EHR data sources. We established a set of high-level design principles to guide our process. Our user experience designer then created wireframes of the tab design. The designer conducted usability testing with physicians, nurses, and other health professionals. Data validation testing was conducted. ResultsWe have already deployed the Patient Values Tab to a pilot sample of users in the MSK Gastrointestinal Medical Oncology Service, including physicians, advanced practice providers, nurses, and administrative staff. We have early evidence of the positive impact of this EHR innovation. Audit logs show increasing use. Many of the initial user comments have been enthusiastically positive, while others have provided constructive suggestions for additional tab refinements with respect to format and content. ConclusionsIt is our challenge and obligation to enrich the EHR with information about the patient as a person. Realization of this capability is a pressing public health need requiring the collaboration of technological experts with a broad range of clinical leaders, users, patients, and families to achieve solutions that are both principled and practical. Our new Patient Values Tab represents a step forward in this important direction.

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.

Environmental or genomic changes during evolution can relax negative selection pressure on specific loci, permitting high frequency polymorphisms at previously conserved sites. Here, we jointly analyze population genomic and comparative genomic data to search for functional processes showing relaxed negative selection specifically in the human lineage, whereas remaining evolutionarily conserved in other mammals. Consistent with previous studies, we find that olfactory receptor genes display such a signature of relaxation in humans. Intriguingly, proteasome genes also show a prominent signal of human-specific relaxation: multiple proteasome subunits, including four members of the catalytic core particle, contain high frequency nonsynonymous polymorphisms at sites conserved across mammals. Chimpanzee proteasome genes do not display a similar trend. Human proteasome genes also bear no evidence of recent positive or balancing selection. These results suggest human-specific relaxation of negative selection in proteasome subunits; the exact biological causes, however, remain unknown.

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.

Revegetation of exposed wastes at historically abandoned mines is frequently constrained by inherent characteristics of poorly developed and contaminated soils. We tested whether the establishment of seedlings on 85-year-old arsenic rich tailings deposits at an abandoned tin mine in north-east Tasmania was limited by toxicity, nutrient limitation or structural factors. We conducted soil analyses, and tested growth of six native species in pot studies utilising both fertiliser treatments and a replacement series involving tailings and potting medium. An in situ three-year field trial was also conducted to assess the effects of adding sand, compost and biochar on plant growth and water infiltration. Analyses of the tailings identified a finely laminated structure and potential manganese, magnesium and potassium deficiencies. There was no evidence of microbial inhibition or adverse metals toxicity, pH or salinity effects. The pot trial indicated nutrient limitation acting on each of the species tested. Physical amendment within the field trial resulted in a highly significant and sustained improvement in infiltration rate, as well as improved growth in three of the six species tested. We conclude that the correction of nutritional and physical deficiencies in surface soils should overcome limitations to the early establishment of native seedlings at this site. This study shows that systematic site assessment and targeted trials is a valuable first step in the revegetation of previously recalcitrant sites. Additional keywords: amelioration, mine wastes, nutrient limitation, phytoremediation, phytostabilisation, plant establishment, restoration., Introduction Direct revegetation has been proposed as a financially attractive and environmentally sound means of rehabilitating historically abandoned mine wastes. These un-rehabilitated wastes represent a problem of global significance, in [...]