Stroke Inpatient Rehabilitation Environments: Aligning Building Construction and Clinical Practice Guidelines Through Care Process Mapping.

BACKGROUND: Stroke inpatient rehabilitation is a complex process involving stroke survivors, staff, and family utilizing a common space for a shared purpose: to optimize recovery. This complex pathway is rarely fully described. Stroke care is ideally guided by Clinical Practice Guidelines, and the rehabilitation built environment should serve to optimize care delivery, patient and staff experience. We aimed to articulate the inpatient stroke rehabilitation process of care in a series of process maps, and to understand the degree to which current stroke clinical and building construction (ie, design) guidelines align to support inpatient stroke rehabilitation. METHODS: We used the Value-Focused Process Engineering methodology to create maps describing the events and activities that typically occur in the current stroke inpatient rehabilitation service model. These maps were completed through individual and group session consultations with stroke survivors, architects, policy makers, and clinical experts. We then determined which sections of the Australian Stroke Rehabilitation Guidelines and the Australasian Health Facility Design Guidelines could be aligned and applied to the process maps. RESULTS: We present a summary process map for stroke inpatient rehabilitation, alongside detailed process maps for 4 different phases of rehabilitation (admission, a normal weekday, a weekend day, and discharge) using Value-Focused Process Engineering notation. The integration of design and clinical guidelines with care pathway maps revealed where guidelines lack detail to be readily linked to current stroke inpatient care practice, providing an opportunity to design stroke inpatient rehabilitation spaces based on the activities occurring within them. CONCLUSIONS: Our findings highlight gaps where clinical and design experts should work together to use guidelines to their full potential; and to improve the process of planning for future stroke rehabilitation units.

Application of User-Centered Codesign Principles to Address Barriers in Therapeutic Drug Monitoring.

BACKGROUND: Different software applications have been developed to support health care professionals in individualized drug dosing. However, their translation into clinical practice is limited, partly because of poor usability and integration into workflow, which can be attributed to the limited involvement of health care professionals in the development and implementation of drug dosing software. This study applied codesign principles to inform the design of a drug dosing software to address barriers in therapeutic drug monitoring using vancomycin as an example. METHODS: Three workshops (face-to-face and online) were conducted by design researchers with pharmacists and prescribers. User journey storyboards, user personas, and prototyping tools were used to explore existing barriers to practice and opportunities for innovation through drug dosing software design. A prototype of the software interface was developed for further evaluation. RESULTS: Health care professionals (11 hospital pharmacists and 6 prescribers) with ≥2 years of clinical experience were recruited. Confidence and software usability emerged as the main themes. Participants identified a lack of confidence in vancomycin dosing and pharmacokinetic understanding and difficulty in accessing practice guidelines as key barriers that could be addressed through software implementation. Accessibility to information (eg, guidelines and pharmacokinetic resources) and information presentation (eg, graphical) within the dosing software were dependent on the needs and experience of the user. A software prototype with a speedometer-dial visual to convey optimal doses was well received by participants. CONCLUSIONS: The perspectives of health care professionals highlight the need for drug dosing software to be user centered and adaptable to the needs and workflow of end users. Continuous engagement with stakeholders on tool usability, training, and education is needed to promote the implementation in practice.

Disrupting future discounting: a commentary on an underutilised psychological approach for improving adherence to diet and physical activity interventions.

Non-communicable diseases (NCD) such as CVD and type 2 diabetes mellitus are major contributors to the burden of disease. NCD are largely driven by modifiable lifestyle factors including poor diet and insufficient physical activity, and consequently, prevention is a public health priority. Although diet and physical activity levels can be improved via lifestyle interventions, long-term adherence to such interventions remains low, which limits their effectiveness. Thus, it is critical to identify the underlying mechanisms that challenge uptake and adherence to such interventions. The current commentary discusses an important, but underexplored, psychological driver of poor adherence to lifestyle interventions, namely, future discounting, which describes the tendency to prefer smaller, short-term rewards over larger, long-term rewards. For example, in the nutrition domain, future discounting refers to valuing the immediate reward of excessive intake of energy-dense, nutrient-poor, discretionary foods high in salt, sugar, and saturated fat, and insufficient intake of low-energy, nutrient-dense, whole foods such as vegetables. Prominent theoretical models propose that excessive future discounting is a major contributor to the development of unhealthy lifestyle behaviours. Furthermore, a vast body of evidence suggests that future discounting plays a key role in risk of NCD. Thus, the evidence to date supports the idea that future discounting is an important multi-behaviour target for supporting lifestyle behaviour change; however, this approach has been largely neglected in preventive health efforts. Furthermore, this commentary discusses promising techniques (e.g. Episodic Future Thinking) for disrupting future discounting to promote improved adherence to lifestyle interventions aimed at reducing NCD risk.

Evolutionary determinism and convergence associated with water-column transitions in marine fishes.

Repeatable, convergent outcomes are prima facie evidence for determinism in evolutionary processes. Among fishes, well-known examples include microevolutionary habitat transitions into the water column, where freshwater populations (e.g., sticklebacks, cichlids, and whitefishes) recurrently diverge toward slender-bodied pelagic forms and deep-bodied benthic forms. However, the consequences of such processes at deeper macroevolutionary scales in the marine environment are less clear. We applied a phylogenomics-based integrative, comparative approach to test hypotheses about the scope and strength of convergence in a marine fish clade with a worldwide distribution (snappers and fusiliers, family Lutjanidae) featuring multiple water-column transitions over the past 45 million years. We collected genome-wide exon data for 110 (∼80%) species in the group and aggregated data layers for body shape, habitat occupancy, geographic distribution, and paleontological and geological information. We also implemented approaches using genomic subsets to account for phylogenetic uncertainty in comparative analyses. Our results show independent incursions into the water column by ancestral benthic lineages in all major oceanic basins. These evolutionary transitions are persistently associated with convergent phenotypes, where deep-bodied benthic forms with truncate caudal fins repeatedly evolve into slender midwater species with furcate caudal fins. Lineage diversification and transition dynamics vary asymmetrically between habitats, with benthic lineages diversifying faster and colonizing midwater habitats more often than the reverse. Convergent ecological and functional phenotypes along the benthic-pelagic axis are pervasive among different lineages and across vastly different evolutionary scales, achieving predictable high-fitness solutions for similar environmental challenges, ultimately demonstrating strong determinism in fish body-shape evolution.

Potential beverage quality of three wild coffee species (Coffea brevipes, C. congensis and C. stenophylla) and consideration of their agronomic use.

BACKGROUND: Of the 130 known coffee (Coffea) species, very few have been properly evaluated for their beverage quality. The diversity of wild coffee species is considered critical to the long-term sustainability of the coffee sector, particularly under climate change. The challenge is finding coffee crops that satisfy agronomic criteria, now and under the altered climatic conditions of the future, as well as consumer requirements for flavour. We evaluated the sensory characteristics of three wild coffee species with four independent sensory panels, and the key environmental/agronomic requirements of these wild species based on a literature review. RESULTS: Coffea congensis and C. stenophylla have a lower unroasted seed weight compared to C. arabica and C. canephora, while C. brevipes has the largest. Sensory analysis showed that the main differences between species was for the fruitiness attribute. Coffea stenophylla was the fruitiest wild species, and was considered an Arabica-like coffee. The flavour profile range of C. stenophylla covers herb-like, vegetal, floral and fruit; C. brevipes resembles C. stenophylla in some respects. Opinions concerning C. congensis were contradictory and several judges considered the industry-standard coffee flavour wheel not suitable for the beverage produced from this species. CONCLUSION: The three wild species have the required sensory qualities for commercialization. According to published data, C. stenophylla has agronomic potential, especially in warmer climates than Arabica areas. Coffea brevipes and C. congensis have the potential to be easily crossed with C. canephora to form interspecific hybrids capable of adapting to different climatic and agronomic conditions. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes.

PREMISE: Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. METHODS: Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. RESULTS: We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). CONCLUSIONS: The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.

Structural Features of a Family of Coumarin-Enamine Fluorescent Chemodosimeters for Ion Pairs.

A family of coumarin-enamine chemodosimeters is evaluated for their potential use as fluorescent molecular probes for multiple analytes [cadmium(II), cobalt(II), copper(II), iron(II), nickel(II), lead(II), and zinc(II)], as their chloride and acetate salts. These fluorophores displayed excellent optical spectroscopic modulation when exposed to ion pairs with different Lewis acidic and basic properties in dimethyl sulfoxide (DMSO). The chemodosimeters were designed to undergo excited-state intramolecular proton transfer (ESIPT), which leads to significant Stokes shifts (ca. 225 nm) and lower-energy fluorescence emission (ca. 575 nm). A more basic anion, e.g., acetate, inhibited the ESIPT mechanism by deprotonation of the enol, producing a binding pocket (N^O- chelate) that can coordinate to an appropriate metal ion. Coordination of the metal ions enhances the fluorescent intensity via the chelation-enhanced fluorescence emission mechanism. Subjecting the spectroscopic data to linear discriminant analysis provided insights into the source of these systems' markedly different behavior toward ion pairs, despite the subtle structural differences in the organic framework. These compounds are examples of versatile, low-molecular-weight, dual-channel fluorescent sensors for ion-pair recognition. This study paves the way for using these probes as practical components of a sensing array for different metal ions and their respective anions.

Co-design of a digital dietary intervention for adults at risk of type 2 diabetes.

BACKGROUND: Co-design has the potential to create interventions that lead to sustainable health behaviour change. Evidence suggests application of co-design in various health domains has been growing; however, few public-facing digital interventions have been co-designed to specifically address the needs of adults at risk of Type 2 diabetes (T2D). This study aims to: (1) co-design, with key stakeholders, a digital dietary intervention to promote health behaviour change among adults at risk of T2D, and (2) evaluate the co-design process involved in developing the intervention prototype. METHODS: The co-design study was based on a partnership between nutrition researchers and designers experienced in co-design for health. Potential end-users (patients and health professionals) were recruited from an earlier stage of the study. Three online workshops were conducted to develop and review prototypes of an app for people at risk of T2D. Themes were inductively defined and aligned with persuasive design (PD) principles used to inform ideal app features and characteristics. RESULTS: Participants were predominantly female (range 58-100%), aged 38 to 63 years (median age = 59 years), consisting of a total of 20 end-users and four experts. Participants expressed the need for information from credible sources and to provide effective strategies to overcome social and environmental influences on eating behaviours. Preferred app features included tailoring to the individual's unique characteristics, ability to track and monitor dietary behaviour, and tools to facilitate controlled social connectivity. Relevant persuasive design principles included social support, reduction (reducing effort needed to reach target behaviour), tunnelling (guiding users through a process that leads to target behaviour), praise, rewards, and self-monitoring. The most preferred prototype was the Choices concept, which focusses on the users' journey of health behaviour change and recognises progress, successes, and failures in a supportive and encouraging manner. The workshops were rated successful, and feedback was positive. CONCLUSIONS: The study's co-design methods were successful in developing a functionally appealing and relevant digital health promotion intervention. Continuous engagement with stakeholders such as designers and end-users is needed to further develop a working prototype for testing.

A conserved asparagine in a ubiquitin-conjugating enzyme positions the substrate for nucleophilic attack.

The mechanism used by the ubiquitin-conjugating enzyme, Ubc13, to catalyze ubiquitination is probed with three computational techniques: Born-Oppenheimer molecular dynamics, single point quantum mechanics/molecular mechanics energies, and classical molecular dynamics. These simulations support a long-held hypothesis and show that Ubc13-catalyzed ubiquitination uses a stepwise, nucleophilic attack mechanism. Furthermore, they show that the first step-the formation of a tetrahedral, zwitterionic intermediate-is rate limiting. However, these simulations contradict another popular hypothesis that supposes that the negative charge on the intermediate is stabilized by a highly conserved asparagine (Asn79 in Ubc13). Instead, calculated reaction profiles of the N79A mutant illustrate how charge stabilization actually increases the barrier to product formation. Finally, an alternate role for Asn79 is suggested by simulations of wild-type, N79A, N79D, and H77A Ubc13: it stabilizes the motion of the electrophile prior to the reaction, positioning it for nucleophilic attack. © 2019 Wiley Periodicals, Inc.

Least concern to endangered: Applying climate change projections profoundly influences the extinction risk assessment for wild Arabica coffee.

Arabica coffee (Coffea arabica) is a key crop in many tropical countries and globally provides an export value of over US$13 billion per year. Wild Arabica coffee is of fundamental importance for the global coffee sector and of direct importance within Ethiopia, as a source of harvestable income and planting stock. Published studies show that climate change is projected to have a substantial negative influence on the current suitable growing areas for indigenous Arabica in Ethiopia and South Sudan. Here we use all available future projections for the species based on multiple general circulation models (GCMs), emission scenarios, and migration scenarios, to predict changes in Extent of Occurrence (EOO), Area of Occupancy (AOO), and population numbers for wild Arabica coffee. Under climate change our results show that population numbers could reduce by 50% or more (with a few models showing over 80%) by 2088. EOO and AOO are projected to decline by around 30% in many cases. Furthermore, present-day models compared to the near future (2038), show a reduction for EOO of over 40% (with a few cases over 50%), although EOO should be treated with caution due to its sensitivity to outlying occurrences. When applying these metrics to extinction risk, we show that the determination of generation length is critical. When applying the International Union for Conservation of Nature's Red list of Threatened Species (IUCN Red List) criteria, even with a very conservative generation length of 21 years, wild Arabica coffee is assessed as Threatened with extinction (placed in the Endangered category) under a broad range of climate change projections, if no interventions are made. Importantly, if we do not include climate change in our assessment, Arabica coffee is assessed as Least Concern (not threatened) when applying the IUCN Red List criteria.

Enset in Ethiopia: a poorly characterized but resilient starch staple.

BACKGROUND: Enset (Ensete ventricosum, Musaceae) is an African crop that currently provides the staple food for approx. 20 million Ethiopians. Whilst wild enset grows over much of East and Southern Africa and the genus extends across Asia to China, it has only ever been domesticated in the Ethiopian Highlands. Here, smallholder farmers cultivate hundreds of landraces across diverse climatic and agroecological systems. SCOPE: Enset has several important food security traits. It grows over a relatively wide range of conditions, is somewhat drought-tolerant, and can be harvested at any time of the year, over several years. It provides an important dietary starch source, as well as fibres, medicines, animal fodder, roofing and packaging. It stabilizes soils and microclimates and has significant cultural importance. In contrast to the other cultivated species in the family Musaceae (banana), enset has received relatively little research attention. Here, we review and critically evaluate existing research, outline available genomic and germplasm resources, aspects of pathology, and explore avenues for crop development. CONCLUSION: Enset is an underexploited starch crop with significant potential in Ethiopia and beyond. Research is lacking in several key areas: empirical studies on the efficacy of current agronomic practices, the genetic diversity of landraces, approaches to systematic breeding, characterization of existing and emerging diseases, adaptability to new ranges and land-use change, the projected impact of climate change, conservation of crop wild relatives, by-products or co-products or non-starch uses, and the enset microbiome. We also highlight the limited availability of enset germplasm in living collections and seedbanks, and the lack of knowledge of reproductive and germination biology needed to underpin future breeding. By reviewing the current state of the art in enset research and identifying gaps and opportunities, we hope to catalyse the development and sustainable exploitation of this neglected starch crop.

Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes.

Ecological opportunity arising in the aftermath of mass extinction events is thought to be a powerful driver of evolutionary radiations. Here, we assessed how the wake of the Cretaceous-Palaeogene (K-Pg) mass extinction shaped diversification dynamics in a clade of mostly marine fishes (Carangaria), which comprises a disparate array of benthic and pelagic dwellers including some of the most astonishing fish forms (e.g. flatfishes, billfishes, remoras, archerfishes). Analyses of lineage diversification show time-heterogeneous rates of lineage diversification in carangarians, with highest rates reached during the Palaeocene. Likewise, a remarkable proportion of Carangaria's morphological variation originated early in the history of the group and in tandem with a marked incidence of habitat shifts. Taken together, these results suggest that all major lineages and body plans in Carangaria originated in an early burst shortly after the K-Pg mass extinction, which ultimately allowed the occupation of newly released niches along the benthic-pelagic habitat axis.

Widespread ecomorphological convergence in multiple fish families spanning the marine-freshwater interface.

The theoretical definition and quantification of convergence is an increasingly topical focus in evolutionary research, with particular growing interest on study scales spanning deep phylogenetic divergences and broad geographical areas. While much progress has recently been made in understanding the role of convergence in driving terrestrial (e.g. anole lizards) and aquatic (e.g. cichlids) radiations, little is known about its macroevolutionary effects across environmental gradients. This study uses a suite of recently developed comparative approaches integrating diverse aspects of morphology, dietary data, habitat affiliation and phylogeny to assess convergence across several well-known tropical-temperate fish families in the percomorph suborder Terapontoidei, a clade with considerable phenotypic and ecological diversity radiating in both marine and freshwater environments. We demonstrate significant widespread convergence across many lineages occupying equivalent trophic niches, particularly feeding habits such as herbivory and biting of attached prey off hard substrates. These include several examples of convergent morphotypes evolving independently in marine and freshwater clades, separated by deep evolutionary divergences (tens of millions of years). The Terapontoidei present a new example of the macroevolutionary dynamics of morphological and ecological coevolution in relation to habitat and trophic preferences, at a greater phylogenetic and habitat scale than most well-studied adaptive radiations.

Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content.

A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.

Herbivory Promotes Dental Disparification and Macroevolutionary Dynamics in Grunters (Teleostei: Terapontidae), a Freshwater Adaptive Radiation.

Trophic shifts into new adaptive zones have played major (although often conflicting) roles in reshaping the evolutionary trajectories of many lineages. We analyze data on diet, tooth, and oral morphology and relate these traits to phenotypic disparification and lineage diversification rates across the ecologically diverse Terapontidae, a family of Australasian fishes. In contrast to carnivores and most omnivores, which have retained relatively simple, ancestral caniniform tooth shapes, herbivorous terapontids appear to have evolved a variety of novel tooth shapes at significantly faster rates to meet the demands of plant-based diets. The evolution of herbivory prompted major disparification, significantly expanding the terapontid adaptive phenotypic continuum into an entirely novel functional morphospace. There was minimal support for our hypothesis of faster overall rates of integrated tooth shape, spacing, and jaw biomechanical evolution in herbivorous terapontids in their entirety, compared with other trophic strategies. There was, however, considerable support for accelerated disparification within a diverse freshwater clade containing a range of specialized freshwater herbivores. While the evolutionary transition to herbivorous diets has played a central role in terapontid phenotypic diversification by pushing herbivores toward novel fitness peaks, there was little support for herbivory driving significantly higher lineage diversification compared with background rates across the family.

Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species.

The completion of the genome assembly for the economically important coffee plant Coffea canephora (Rubiaceae) has allowed the use of bioinformatic tools to identify and characterize a diverse array of transposable elements (TEs), which can be used in evolutionary studies of the genus. An overview of the copy number and location within the C. canephora genome of four TEs is presented. These are tested for their use as molecular markers to unravel the evolutionary history of the Millotii Complex, a group of six wild coffee (Coffea) species native to Madagascar. Two TEs from the Gypsy superfamily successfully recovered some species boundaries and geographic structure among samples, whereas a TE from the Copia superfamily did not. Notably, species occurring in evergreen moist forests of eastern and southeastern Madagascar were divergent with respect to species in other habitats and regions. Our results suggest that the peak of transpositional activity of the Gypsy and Copia TEs occurred, respectively, before and after the speciation events of the tested Madagascan species. We conclude that the utilization of active TEs has considerable potential to unravel the evolutionary history and delimitation of closely related Coffea species. However, the selection of TE needs to be experimentally tested, since each element has its own evolutionary history. Different TEs with similar copy number in a given species can render different dendrograms; thus copy number is not a good selection criterion to attain phylogenetic resolution.

DNA methylation of the LIN28 pseudogene family.

BACKGROUND: DNA methylation directs the epigenetic silencing of selected regions of DNA, including the regulation of pseudogenes, and is widespread throughout the genome. Pseudogenes are decayed copies of duplicated genes that have spread throughout the genome by transposition. Pseudogenes are transcriptionally silenced by DNA methylation, but little is known about how pseudogenes are targeted for methylation or how methylation levels are maintained in different tissues. RESULTS: We employed bisulfite next generation sequencing to examine the methylation status of the LIN28 gene and four processed pseudogenes derived from LIN28. The objective was to determine whether LIN28 pseudogenes maintain the same pattern of methylation as the parental gene or acquire a methylation pattern independent of the gene of origin. In this study, we determined that the methylation status of LIN28 pseudogenes does not resemble the pattern evident for the LIN28 gene, but rather these pseudogenes appear to acquire methylation patterns independent of the parental gene. Furthermore, we observed that methylation levels of the examined pseudogenes correlate to the location of insertion within the genome. LIN28 pseudogenes inserted into gene bodies were highly methylated in all tissues examined. In contrast, pseudogenes inserted into genomic regions that are not proximal to genes were differentially methylated in various tissue types. CONCLUSIONS: Our analysis suggests that Lin28 pseudogenes do not acquire patterns of tissue-specific methylation as for the parental gene, but rather are methylated in patterns specific to the local genomic environment into which they were inserted.