Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE.

Single-cell RNA-sequencing enables testing for differential expression (DE) between conditions at a cell type level. While powerful, one of the limitations of such approaches is that the sensitivity of DE testing is dictated by the sensitivity of clustering, which is often suboptimal. To overcome this, we present miloDE-a cluster-free framework for DE testing (available as an open-source R package).

Sensitive cluster-free differential expression testing.

Comparing molecular features, including the identification of genes with differential expression (DE) between conditions, is a powerful approach for characterising disease-specific phenotypes. When testing for DE in single-cell RNA sequencing data, current pipelines first assign cells into discrete clusters (or cell types), followed by testing for differences within each cluster. Consequently, the sensitivity and specificity of DE testing are limited and ultimately dictated by the granularity of the cell type annotation, with discrete clustering being especially suboptimal for continuous trajectories.

A reference human induced pluripotent stem cell line for large-scale collaborative studies.

Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.

Narrative trajectories of disaster response: ethical preparedness from Katrina to COVID-19.

While COVID-19 brings unprecedented challenges to the US healthcare system, understanding narratives of historical disasters illuminates ethical complexities shared with COVID-19. In 2005, Hurricane Katrina revealed a lack of disaster preparation and protocol, not dissimilar to the challenges faced by COVID-19 healthcare workers. A case study of Memorial Hospital during Hurricane Katrina reported by journalist-MD Sheri Fink reveals unique ethical challenges at the forefront of health crises.

COVID-19 impacts and adaptations in Asia and Africa's aquatic food value chains.

The COVID-19 pandemic is a shock affecting all areas of the global food system. We tracked the impacts of COVID-19 and associated policy responses on the availability and price of aquatic foods and production inputs during 2020, using a high frequency longitudinal survey of 768 respondents in Bangladesh, Egypt, India, Myanmar, Nigeria. We found the following: (1) Aquatic food value chains were severely disrupted but most effects on the availability and accessibility of aquatic foods and production inputs were short-lived.

Mapping out epistemic justice in the clinical space: using narrative techniques to affirm patients as knowers.

Epistemic injustice sits at the intersection of ethics, epistemology, and social justice. Generally, this philosophical term describes when a person is wrongfully discredited as a knower; and within the clinical space, epistemic injustice is the underlying reason that some patient testimonies are valued above others. The following essay seeks to connect patterns of social prejudice to the clinical realm in the United States: illustrating how factors such as race, gender identity, and socioeconomic status influence epistemic credence and associatively, the quality of healthcare a person receives.

Seasonal changes in diet and chemical defense in the Climbing Mantella frog (Mantella laevigata).

Poison frogs acquire chemical defenses from the environment for protection against potential predators. These defensive chemicals are lipophilic alkaloids that are sequestered by poison frogs from dietary arthropods and stored in skin glands. Despite decades of research focusing on identifying poison frog alkaloids, we know relatively little about how environmental variation and subsequent arthropod availability impacts alkaloid loads in poison frogs.

Food stories: Unraveling the mechanisms underlying healthful eating.

The biomedical model of health (BMH) studies the causes and origins of disease. When applied to nutrition research, eating is studied as a behavior that supports physical health. However, the lack of attention the BMH pays to social and historical circumstances in which health behaviors are constructed has been widely addressed in literature.