GDS: A Genomic Database for Strawberries (Fragaria spp.)

Strawberry species (Fragaria spp.) are known as the “queen of fruits” and are cultivated around the world. Over the past few years, eight strawberry genome sequences have been released. The reuse of these large amount of genomic data, and the more large-scale comparative analyses are very challenging to both plant biologists and strawberry breeders. To promote the reuse and exploration of strawberry genomic data and enable extensive analyses using various bioinformatics tools, we have developed the Genome Database for Strawberry (GDS). This platform integrates the genome collection, storage, integration, analysis, and dissemination of large amounts of data for researchers engaged in the study of strawberry. We collected and formatted the eight published strawberry genomes. We constructed the GDS based on Linux, Apache, PHP and MySQL. Different bioinformatic software were integrated. The GDS contains data from eight strawberry species, as well as multiple tools such as BLAST, JBrowse, synteny analysis, and gene search. It has a designed interface and user-friendly tools that perform a variety of query tasks with a few simple operations. In the future, we hope that the GDS will serve as a community resource for the study of strawberries.

Cognition in Primary Care Community Resource Directory for Individuals, Caregivers, and Providers

A KAER Model recommendation is to refer individuals diagnosed with dementia to resources that help them prepare for the future and services that provide ongoing support. The purpose of this project was to locate local quality services and develop a resource directory for persons with cognitive impairment for use by providers, staff, individuals, families, and caregivers. We worked with a Community Advisory Board and interviewed individuals and caregivers to understand what resources are useful and important to include in the resource directory. We built a web-based resource directory that allows users to query resources based on specific needs. We integrated the resource directory within the electronic health record for providers to include after visit summaries. A resource directory was deployed for community use, with goals of sustainability and longevity after this project is completed.

Meet Caregivers Where They Are: A Remote Intervention Connecting Caregivers to Community Resources

Informal caregivers of people with Alzheimer’s disease and related dementias (ADRD) are a vulnerable, often isolated population with high rates of financial strain and need for community resource supports. Little is known about how best to connect these caregivers to resources, especially during the COVID-19 pandemic. CommunityRx-Caregiver is an evidence-based intervention that connects caregivers to community resources for basic needs, wellness, and caregiving. Using preliminary data from a randomized trial of CommunityRx-Caregiver (N=344), we examined caregivers’ baseline confidence in finding community resources and their engagement in the CommunityRx-Caregiver intervention. Caregivers enrolled December 2020-February 2021 (n=26) received (1) personalized lists of community resources via text message (HealtheRx), (2) access to an online resource portal (FindRx) and (3) automated texts offering support for finding resources. Most caregivers were female (65%), Black (92%), >60 years old (64%) and 44% reported very good or excellent health. Nearly half of caregivers (46%) were completely confident in finding community resources. Overall, 81% of caregivers engaged with a text message or the FindRx. Nearly two-thirds (65%) of caregivers responded to at least one text message. More than a quarter (27%) used the FindRx tool; 5/7 of those shared FindRx resources with others. Caregivers sought resources including in-home personal care, exercise classes and support groups. Caregivers of people with ADRD, many of whom had low confidence in finding resources, engaged with a multi-modal information technology-based intervention to obtain community resource support. These preliminary findings suggest caregivers were receptive to a remotely-delivered community referral intervention during the COVID-19 pandemic.

Women's Perception of their Forest Resources in Espiritu Santo (Vanuatu)

<p>Women's perceptions of their environment in two remote communities (Monxhill and Butmas, in Espiritu Santo, Vanuatu) were explored, as their perception is though to guide their involvement in environmental education. Qualitative insights from participatory fieldwork, using ranking exercise, community resource mapping and perception activities, showed that women of Monxhill see the forest as a place to live, to know and to learn about, to plan for and to take care of. In turn, women of Butmas see it as a resource, which has to be managed in order to provide the communities with food, materials and medicines; however, they also see it as a problem, which has to be solved. Furthermore, this research showed that these women are a key actors in community environmental education.</p>

Women's Perception of their Forest Resources in Espiritu Santo (Vanuatu)

<p>Women's perceptions of their environment in two remote communities (Monxhill and Butmas, in Espiritu Santo, Vanuatu) were explored, as their perception is though to guide their involvement in environmental education. Qualitative insights from participatory fieldwork, using ranking exercise, community resource mapping and perception activities, showed that women of Monxhill see the forest as a place to live, to know and to learn about, to plan for and to take care of. In turn, women of Butmas see it as a resource, which has to be managed in order to provide the communities with food, materials and medicines; however, they also see it as a problem, which has to be solved. Furthermore, this research showed that these women are a key actors in community environmental education.</p>

Building and experimenting with an agent-based model to study the population-level impact of CommunityRx, a clinic-based community resource referral intervention

CommunityRx (CRx), an information technology intervention, provides patients with a personalized list of healthful community resources (HealtheRx). In repeated clinical studies, nearly half of those who received clinical “doses” of the HealtheRx shared their information with others (“social doses”). Clinical trial design cannot fully capture the impact of information diffusion, which can act as a force multiplier for the intervention. Furthermore, experimentation is needed to understand how intervention delivery can optimize social spread under varying circumstances. To study information diffusion from CRx under varying conditions, we built an agent-based model (ABM). This study describes the model building process and illustrates how an ABM provides insight about information diffusion through in silico experimentation. To build the ABM, we constructed a synthetic population (“agents”) using publicly-available data sources. Using clinical trial data, we developed empirically-informed processes simulating agent activities, resource knowledge evolution and information sharing. Using RepastHPC and chiSIM software, we replicated the intervention in silico, simulated information diffusion processes, and generated emergent information diffusion networks. The CRx ABM was calibrated using empirical data to replicate the CRx intervention in silico. We used the ABM to quantify information spread via social versus clinical dosing then conducted information diffusion experiments, comparing the social dosing effect of the intervention when delivered by physicians, nurses or clinical clerks. The synthetic population (N = 802,191) exhibited diverse behavioral characteristics, including activity and knowledge evolution patterns. In silico delivery of the intervention was replicated with high fidelity. Large-scale information diffusion networks emerged among agents exchanging resource information. Varying the propensity for information exchange resulted in networks with different topological characteristics. Community resource information spread via social dosing was nearly 4 fold that from clinical dosing alone and did not vary by delivery mode. This study, using CRx as an example, demonstrates the process of building and experimenting with an ABM to study information diffusion from, and the population-level impact of, a clinical information-based intervention. While the focus of the CRx ABM is to recreate the CRx intervention in silico, the general process of model building, and computational experimentation presented is generalizable to other large-scale ABMs of information diffusion.

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. In order to guide forthcoming genome generation efforts and promote efficient prioritisation of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Here we present an automated analysis workflow that surveys genome assemblies from the United States National Center for Biotechnology Information (NCBI), assesses their completeness using the relevant Benchmarking Universal Single-Copy Orthologue (BUSCO) datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, we examine how key assembly metrics relate to gene content completeness, and we compare results from using different BUSCO lineage datasets. These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritisations for ongoing and future sampling, sequencing, and genome generation initiatives.