Generalized cell phenotyping for spatial proteomics with language-informed vision models.

We present a novel approach to cell phenotyping for spatial proteomics that addresses the challenge of generalization across diverse datasets with varying marker panels. Our approach utilizes a transformer with channel-wise attention to create a language-informed vision model; this model's semantic understanding of the underlying marker panel enables it to learn from and adapt to heterogeneous datasets. Leveraging a curated, diverse dataset with cell type labels spanning the literature and the NIH Human BioMolecular Atlas Program (HuBMAP) consortium, our model demonstrates robust performance across various cell types, tissues, and imaging modalities.

"The leadership shown by nurses gave me such a boost": health resources used by nurses who experienced COVID-19 pandemic stressors.

Purpose: To thoroughly describe 1) the stressors experienced by nurses during the first waves of the COVID-19 pandemic, 2) the extent to which experiencing these stressors affected nurses' psychological and physical health and 3) the health resources nurses used to protect and maintain their psychological and physical health during this period.

Method: We used a theory-driven descriptive qualitative design and conducted seven focus groups of 2-5 nurses (total = 23 nurses) distinguished by their degree of contact with COVID-19 patients hospitalized in Switzerland.

Results: A thematic analysis identified three main themes and their respective sub-themes: 1) Lived experiences and stressors (Living in a strange world; Hard work alone behind closed doors; Contaminating or being contaminated; Living at home behind closed doors; A war of attrition after the first wave); 2) Health (Everything is fine; Multiple traumas; Stress; Long-term exhaustion); 3) Resources (Societal and institutional resources; Direct relational resources; Resources specific to individuals).

COVID-19's Impact in Long-Term Care Facilities: The Health and Coping Strategies of Older Adults and Their Families.

Aim: Describe the stressors that long-term care facility (LTCF) residents and their family members were exposed to during the COVID-19 pandemic, the resources they mobilised to cope with them, and the strategies used by professionals to support them.

Design: A descriptive qualitative design study.

Method: Between March 2021 and February 2022, we carried out semi-structured interviews with 8 LTCF residents, 11 family members, and 6 focus groups made up of healthcare and support staff from 8 LTCFs.

Monoclonal antibody-mediated neutralization of Clostridioides difficile toxin does not diminish induction of the protective innate immune response to infection.

Clostridioides difficile infection causes pathology that ranges in severity from diarrhea to pseudomembranous colitis. Toxin A and Toxin B are the two primary virulence factors secreted by C. difficile that drive disease severity.

Identification and characterization of a potent and selective HUNK inhibitor for treatment of HER2+ breast cancer.

Human epidermal growth factor receptor 2 (HER2)-targeted agents have proven to be effective, however, the development of resistance to these agents has become an obstacle in treating HER2+ breast cancer. Evidence implicates HUNK as an anti-cancer target for primary and resistant HER2+ breast cancers. In this study, a selective inhibitor of HUNK is characterized alongside a phosphorylation event in a downstream substrate of HUNK as a marker for HUNK activity in HER2+ breast cancer.

Starvation helps transition to abundance - a ferrosome story.

Iron is an essential nutrient for bacterial pathogenesis. In their study, Skaar and colleagues (Pi et al.) discovered and determined the detailed structure of ferrosomes within Clostridioides difficile, the iron-storage organelles that form under iron-limited conditions in anticipation of future iron overload.

Mapping the Anti-Cancer Activity of α-Connexin Carboxyl-Terminal (aCT1) Peptide in Resistant HER2+ Breast Cancer.

Connexin 43 (Cx43) is a protein encoded by the gene and is a component of cell membrane structures called gap junctions, which facilitate intercellular communication. Prior evidence indicates that elevated expression in the HER2-positive (HER2+) subtype of breast cancer is associated with poor prognosis. Prior evidence also suggests that HER2+ breast cancers that have become refractory to HER2-targeted agents have a loss of Cx43 gap junction intercellular communication (GJIC).

MFP1 defines the subchloroplast location of starch granule initiation.

Starch is one of the major carbohydrate storage compounds in plants. The biogenesis of starch granules starts with the formation of initials, which subsequently expand into granules. Several coiled-coil domain-containing proteins have been previously implicated with the initiation process, but the mechanisms by which they act remain largely elusive.

A Foundation Model for Cell Segmentation.

Cells are a fundamental unit of biological organization, and identifying them in imaging data - cell segmentation - is a critical task for various cellular imaging experiments. While deep learning methods have led to substantial progress on this problem, most models in use are specialist models that work well for specific domains. Methods that have learned the general notion of "what is a cell" and can identify them across different domains of cellular imaging data have proven elusive.

The impact of protective measures against COVID-19 on the wellbeing of residents in nursing homes and their relatives: a rapid review.

During the COVID-19 pandemic and compared to other population groups, older people were at a heightened risk of developing lethal disease symptoms. Thus, many countries put in place protective measures to protect this "at-risk" population, especially in nursing homes, to limit the number of infections. These measures consisted mostly in the absence of social gatherings, the impossibility for relatives to enter the nursing homes, limitations in group activities, and the ban of group-eating.

Opportunities and challenges with decentralized trials in Neuroscience.

Decentralized clinical trials (DCTs), that is, studies integrating elements of telemedicine and mobile/local healthcare providers allowing for home-based assessments, are an important concept to make studies more resilient and more patient-centric by taking into consideration participant's views and shifting trial activities to better meet the needs of trial participants. There are however, not only advantages but also challenges associated with DCTs. An area to be addressed by appropriate statistical methodology is the integration of data resulting from a possible mix of home and clinic assessments at different visits for the same variable, especially in adjusting for sources of possible systematic differences.

LIKE EARLY STARVATION 1 and EARLY STARVATION 1 promote and stabilize amylopectin phase transition in starch biosynthesis.

Starch, the most abundant carbohydrate reserve in plants, primarily consists of the branched glucan amylopectin, which forms semi-crystalline granules. Phase transition from a soluble to an insoluble form depends on amylopectin architecture, requiring a compatible distribution of glucan chain lengths and a branch-point distribution. Here, we show that two starch-bound proteins, LIKE EARLY STARVATION 1 (LESV) and EARLY STARVATION 1 (ESV1), which have unusual carbohydrate-binding surfaces, promote the phase transition of amylopectin-like glucans, both in a heterologous yeast system expressing the starch biosynthetic machinery and in plants.

Single-cell segmentation in bacterial biofilms with an optimized deep learning method enables tracking of cell lineages and measurements of growth rates.

Bacteria often grow into matrix-encased three-dimensional (3D) biofilm communities, which can be imaged at cellular resolution using confocal microscopy. From these 3D images, measurements of single-cell properties with high spatiotemporal resolution are required to investigate cellular heterogeneity and dynamical processes inside biofilms. However, the required measurements rely on the automated segmentation of bacterial cells in 3D images, which is a technical challenge.

Characterizing metabolic drivers of infection with activity-based hydrazine probes.

Many enzymes require post-translational modifications or cofactor machinery for primary function. As these catalytically essential moieties are highly regulated, they act as dual sensors and chemical handles for context-dependent metabolic activity. is a major nosocomial pathogen that infects the colon.

Antigen-specific memory Th17 cells promote cross-protection against nontypeable Haemophilus influenzae after mild influenza A virus infection.

Secondary bacterial pneumonia after influenza A virus (IAV) infection is the leading cause of hospitalization and death associated with IAV infection worldwide. Nontypeable Haemophilus influenzae (NTHi) is one of the most common causes of secondary bacterial pneumonia. Current efforts to develop vaccines against NTHi infection focus on inducing antibodies but are hindered by antigenic diversity among NTHi strains.

Immunological consequences of microbiome-based therapeutics.

The complex network of microscopic organisms living on and within humans, collectively referred to as the microbiome, produce wide array of biologically active molecules that shape our health. Disruption of the microbiome is associated with susceptibility to a range of diseases such as cancer, diabetes, allergy, obesity, and infection. A new series of next-generation microbiome-based therapies are being developed to treat these diseases by transplanting bacteria or bacterial-derived byproducts into a diseased individual to reset the recipient's microbiome and restore health.

The PRK/Rubisco shunt strongly influences Arabidopsis seed metabolism and oil accumulation, affecting more than carbon recycling.

The carbon efficiency of storage lipid biosynthesis from imported sucrose in green Brassicaceae seeds is proposed to be enhanced by the PRK/Rubisco shunt, in which ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) acts outside the context of the Calvin-Benson-Bassham cycle to recycle CO2 molecules released during fatty acid synthesis. This pathway utilizes metabolites generated by the nonoxidative steps of the pentose phosphate pathway. Photosynthesis provides energy for reactions such as the phosphorylation of ribulose 5-phosphate by phosphoribulokinase (PRK).

Tuning heterologous glucan biosynthesis in yeast to understand and exploit plant starch diversity.

Background: Starch, a vital plant-derived polysaccharide comprised of branched glucans, is essential in nutrition and many industrial applications. Starch is often modified post-extraction to alter its structure and enhance its functionality. Targeted metabolic engineering of crops to produce valuable and versatile starches requires knowledge of the relationships between starch biosynthesis, structure, and properties, but systematic studies to obtain this knowledge are difficult to conduct in plants.

Determining Protein-Protein Interaction with GFP-Trap Beads.

Protein-protein interactions play a vital role in the cellular physiology of living organisms. Among several available approaches, co-immunoprecipitation (co-IP) has emerged as a reliable method to investigate such interactions. The underlying principle is to retrieve a bait protein from a protein extract using bait-specific antibodies and thereby indirectly capture the interacting partner proteins.

Health and coping strategies of nursing home residents and their relatives during the COVID-19 pandemic: a mixed-methods study protocol.

Introduction: The COVID-19 pandemic hit older adults particularly hard, especially those living in nursing homes. The present study's primary aim is to quantify the states of physical and mental health of nursing home residents and their relatives following the implementation of the exceptional confinement measures. The secondary aim is to explore the lived experiences of the stressors perceived by older adults and their relatives, as well as the support strategies implemented by health professionals and their results.

BETA-AMYLASE9 is a plastidial nonenzymatic regulator of leaf starch degradation.

β-Amylases (BAMs) are key enzymes of transitory starch degradation in chloroplasts, a process that buffers the availability of photosynthetically fixed carbon over the diel cycle to maintain energy levels and plant growth at night. However, during vascular plant evolution, the BAM gene family diversified, giving rise to isoforms with different compartmentation and biological activities. Here, we characterized BETA-AMYLASE 9 (BAM9) of Arabidopsis (Arabidopsis thaliana).

Circulating Biomarkers of Inflammation and Endothelial Activation in Diabetic Retinopathy.

Inflammation and endothelial activation play a pivotal role in development and progression of diabetic retinopathy (DR), a vision-threatening complication of diabetes mellitus (DM) and the leading cause of blindness in the working age population. Easily accessible and validated biomarkers for DR early diagnosis and progression are required for use in clinical trials: here, we reviewed the available literature to understand the association of circulating levels of selected markers of inflammation and endothelial activation with the presence of nonproliferative and proliferative DR (NPDR and PDR) and investigate the relationship between their systemic and ocular levels. We additionally provide data synthesis and perform statistical analysis for interpretation of the collected evidence.

Monocyte Reconstitution and Gut Microbiota Composition after Hematopoietic Stem Cell Transplantation.

Background: Monocytes are an essential cellular component of the innate immune system that support the host's effectiveness to combat a range of infectious pathogens. Hemopoietic cell transplantation (HCT) results in transient monocyte depletion, but the factors that regulate recovery of monocyte populations are not fully understood. In this study, we investigated whether the composition of the gastrointestinal microbiota is associated with the recovery of monocyte homeostasis after HCT.