Protein-Protein Interaction Network Analysis Using NetworkX.

In recent years, extracting information from biological data has become a particularly valuable way of gaining knowledge. Molecular interaction networks provide a framework for visualizing cellular processes, but their complexity frequently makes their interpretation difficult. Proteins are one of the primary determinants of biological function. Indeed, most biological activities in the living cells are functionally regulated by protein-protein interactions (PPIs). Thus, studying protein interactions is critical for understanding their roles within the cell. Exploring the PPI networks can open new avenues for future experimental studies and offer interspecies predictions for effective interaction mapping. In this chapter we will demonstrate how to construct, visualize, and analyze a protein-protein interaction network using NetworkX.

Energetics of cytoskeletal gel contraction.

Cytoskeletal gels are prototyped to reproduce the mechanical contraction of the cytoskeleton in vitro. They are composed of a polymer network (backbone), swollen by the presence of a liquid solvent, and active molecules (molecular motors, MMs) that transduce chemical energy into the mechanical work of contraction. These motors attach to the polymer chains to shorten them and/or act as dynamic crosslinks, thereby constraining the thermal fluctuations of the chains. We describe both mechanisms thermodynamically as a microstructural reconfiguration, where the backbone stiffens to motivate solvent (out)flow and accommodate contraction. Via simple steady-state energetic analysis, under the simplest case of isotropic deformation, we quantify the mechanical energy required to achieve contraction as a function of polymer chain density and molecular motor density. We identify two limit regimes, namely, fast MM activation (FM), and slow MM activation (SM). FM assumes that MMs provide all the available mechanical energy 'instantaneously' and leave the polymer in a stiffened state, i.e. the MM activity occurs at a time scale that is much smaller than that of solvent diffusion. SM assumes that the timescale for MM activation is much longer than that of solvent diffusion. To achieve the same final contracted state, FM requires the largest amount of work per unit reference volume, while SM requires the least. For all intermediate cases where the timescale of MM activation is comparable with that of solvent diffusion, the required work ranges between these two limits. We provide all these quantities as a function of chain density and MM density. Finally, we compare our results on contraction energetics with experiments and observe good agreement.

Prevalence and correlates of knowledge and practices regarding infection prevention and control, and triage in primary healthcare settings: A cross-sectional study in Bangladesh.

Background: Despite the high prevalence of healthcare-acquired infection in resource-limited settings, healthcare workers' (HCWs') knowledge and practices of infection prevention and control (IPC) and triage are not well-researched. We examined thisin Bangladesh's primary healthcare facilities (HCFs) during the COVID-19 pandemic. Methods: We surveyed 312 HCWs in 94 community clinics (CCs) and 90 family welfare centres (FWCs) in six districts from February to April 2021. We assessed HCWs' self-reported knowledge and observed practices in four domains: personal hygiene, medical instrument processing, waste management, and triage. We constructed a weighted composite knowledge score and estimated the association between knowledge and background characteristics using a generalised linear mixed effects model. Practices were described through univariate analysis. Findings: On a scale of 100, the mean composite knowledge score was 38.3 (SD: 13.3) overall and 44.0 (SD: 13.1) and 33.8 (SD: 11.6) for FWCs and CCs, respectively. The HCWs of FWCs were more aged, experienced, and educated than those of CCs. Knowledge score was the highest in personal hygiene and the lowest in medical waste segregation. Knowledge was significantly associated with HCWs' designation and education. Concerning practices, not more than one-third of the HCWs or HCFs, on average, followed the recommended protocols, except for wearing face masks while on duty (87.1%) and referring potential COVID-19 patients to higher-level facilities (68.3%). Conclusions: HCWs' capacity in instrument processing, waste management, and triage needs to be improved through formal education and training initiatives. Our study can contribute to the under-researched IPC and triage domains in resource-limited settings.