Role of diffusion and reaction of the constituents in spreading of histone modification marks.

Cells switch genes ON or OFF by altering the state of chromatin via histone modifications at specific regulatory locations along the chromatin polymer. These gene regulation processes are carried out by a network of reactions in which the histone marks spread to neighboring regions with the help of enzymes. In the literature, this spreading has been studied as a purely kinetic, non-diffusive process considering the interactions between neighboring nucleosomes. In this work, we go beyond this framework and study the spreading of modifications using a reaction-diffusion (RD) model accounting for the diffusion of the constituents. We quantitatively segregate the modification profiles generated from kinetic and RD models. The diffusion and degradation of enzymes set a natural length scale for limiting the domain size of modification spreading, and the resulting enzyme limitation is inherent in our model. We also demonstrate the emergence of confined modification domains without the explicit requirement of a nucleation site. We explore polymer compaction effects on spreading and show that single-cell domains may differ from averaged profiles. We find that the modification profiles from our model are comparable with existing H3K9me3 data of S. pombe.

A before-after study to evaluate the effect of pharmacy workflow redesign to improve pharmacy waiting time and reduce medication near misses in Malaysia.

OBJECTIVES: This study aimed to evaluate the effectiveness of workflow redesign (eaST system) on pharmacy waiting time and near-missed events. We also investigated other factors that may potentially affect these study outcomes. METHODS: A quasi-experimental (before-after) study design was adopted. Pre-intervention data were collected over 7 months (January-July 2017). Subsequently, the workflow redesign (eaST system) was implemented and the effect of the intervention (August 2017-February 2018) was evaluated. Univariate analysis was used to compare the differences between pre-intervention and post-intervention of pharmacy waiting time and near-missed events. Significant factors affecting study outcomes were analysed using linear regression analysis. KEY FINDINGS: A total of 210,530 prescriptions were analysed. The eaST system significantly increases the percentage of prescriptions dispensed within 30 min per day (median = 68 (interquartile range (IQR) = 41) vs. median = 93 (IQR = 33), P < 0.001) and reduced the mean percentage of near-missed events (mean = 50.71 (standard deviation (SD) = 23.95) vs. mean = 27.87 (SD = 12.23), P < 0.001). However, the eaST system's effects on related outcomes were conditional on a three-way interaction effect. The eaST system's effects on pharmacy waiting time were influenced by the number of prescriptions received and the number of PhIS server disruptions. Conversely, the eaST system's effects on near-missed events were influenced by the number of pharmacy personnel and number of controlled medications. CONCLUSIONS: Overall, the eaST system improved the pharmacy waiting time and reduced near-missed events.

Predicting scale-dependent chromatin polymer properties from systematic coarse-graining.

Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.