99 research outputs found
Reconstructing the Forest of Lineage Trees of Diverse Bacterial Communities Using Bio-inspired Image Analysis
Cell segmentation and tracking allow us to extract a plethora of cell
attributes from bacterial time-lapse cell movies, thus promoting computational
modeling and simulation of biological processes down to the single-cell level.
However, to analyze successfully complex cell movies, imaging multiple
interacting bacterial clones as they grow and merge to generate overcrowded
bacterial communities with thousands of cells in the field of view,
segmentation results should be near perfect to warrant good tracking results.
We introduce here a fully automated closed-loop bio-inspired computational
strategy that exploits prior knowledge about the expected structure of a
colony's lineage tree to locate and correct segmentation errors in analyzed
movie frames. We show that this correction strategy is effective, resulting in
improved cell tracking and consequently trustworthy deep colony lineage trees.
Our image analysis approach has the unique capability to keep tracking cells
even after clonal subpopulations merge in the movie. This enables the
reconstruction of the complete Forest of Lineage Trees (FLT) representation of
evolving multi-clonal bacterial communities. Moreover, the percentage of valid
cell trajectories extracted from the image analysis almost doubles after
segmentation correction. This plethora of trustworthy data extracted from a
complex cell movie analysis enables single-cell analytics as a tool for
addressing compelling questions for human health, such as understanding the
role of single-cell stochasticity in antibiotics resistance without losing site
of the inter-cellular interactions and microenvironment effects that may shape
it
Inflammatory bowel disease [IBD] and physical activity : a study on the impact of diagnosis on the level of exercise amongst patients with IBD
Background and Aims: Inflammatory bowel disease [IBD] can impair patients’ functional capacity
with significant negative effects on their quality of life. Our aim was to determine the impact of IBD
diagnosis on fitness levels and to assess the levels of engagement in physical activity and fatigue
in IBD patient before and after diagnosis.
Methods: A prospective multi-centre cross-sectional study was performed. Patients diagnosed
with IBD in the previous 18 months were recruited. Inclusion criteria included clinical remission
and/or no treatment changes within the previous 6 months. Physical exercise levels were assessed
by the Godin score and fatigue levels was assessed by the functional assessment of chronic illness
therapy [FACIT] score.
Results: In total, 158 patients (100 Crohn’s disease [CD]) were recruited. Mean age was 35.1 years
(95% confidence interval [CI] ± 2.0). Gender distribution was approximately equal [51.3% male]. The
Mean Harvey Bradshaw and Simple Clinical Colitis Activity indices were 2.25 [95% CI ± 0.40] and
1.64 [95% CI ± 0.49], respectively. The mean Godin score difference before and after IBD diagnosis
was 6.94 [p = 0.002]. Patients with ulcerative colitis [UC] [41.8%] were more likely than patients
with CD [23.0%] to reduce their exercise levels [p = 0.04]. FACIT scores were lower in patients who
had experienced relapses [p = 0.012] and had severe disease [p = 0.011]. Approximately one-third
of patients reduced their activity level following IBD diagnosis.
Conclusions: Patients were significantly less physically active after a diagnosis of IBD and this was
more apparent in UC. Identification of the risk factors associated with loss of fitness levels would
help to address the reduced patient quality of life.peer-reviewe
An early history of T cell-mediated cytotoxicity.
After 60 years of intense fundamental research into T cell-mediated cytotoxicity, we have gained a detailed knowledge of the cells involved, specific recognition mechanisms and post-recognition perforin-granzyme-based and FAS-based molecular mechanisms. What could not be anticipated at the outset was how discovery of the mechanisms regulating the activation and function of cytotoxic T cells would lead to new developments in cancer immunotherapy. Given the profound recent interest in therapeutic manipulation of cytotoxic T cell responses, it is an opportune time to look back on the early history of the field. This Timeline describes how the early findings occurred and eventually led to current therapeutic applications
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