Clinical reasoning in pragmatic trial randomization: a qualitative interview study.

BACKGROUND: Pragmatic trials, because they study widely used treatments in settings of routine practice, require intensive participation from clinicians who determine whether patients can be enrolled. Clinicians are often conflicted between their therapeutic obligation to patients and their willingness to enroll them in trials in which treatments are randomly determined and thus potentially suboptimal. Refusal to enroll eligible patients can hinder trial completion and damage generalizability. In order to help evaluate and mitigate clinician refusal, this qualitative study examined how clinicians reason about whether to randomize eligible patients. METHODS: We performed interviews with 29 anesthesiologists who participated in REGAIN, a multicenter pragmatic randomized trial comparing spinal and general anesthesia in hip fracture. Interviews included a chart-stimulated section in which physicians described their reasoning pertaining to specific eligible patients as well as a general semi-structured section about their views on clinical research. Guided by a constructivist grounded theory approach, we analyzed data via coding, synthesized thematic patterns using focused coding, and developed an explanation using abduction. RESULTS: Anesthesiologists perceived their main clinical function as preventing peri- and intraoperative complications. In some cases, they used prototype-based reasoning to determine whether patients with contraindications should be randomized; in others, they used probabilistic reasoning. These modes of reasoning involved different types of uncertainty. In contrast, anesthesiologists expressed confidence about anesthetic options when they accepted patients for randomization. Anesthesiologists saw themselves as having a fiduciary responsibility to patients and thus did not hesitate to communicate their inclinations, even when this complicated trial recruitment. Nevertheless, they voiced strong support for clinical research, stating that their involvement was mainly hindered by production pressure and workflow disruptions. CONCLUSIONS: Our findings suggest that prominent ways of assessing clinician decisions about trial randomization are based on questionable assumptions about clinical reasoning. Close examination of routine clinical practice, attuned to the features of clinical reasoning we reveal here, will help both in evaluating clinicians' enrollment determinations in specific trials and in anticipating and responding to them. TRIAL REGISTRATION: Regional Versus General Anesthesia for Promoting Independence After Hip Fracture (REGAIN). CLINICALTRIALS: gov NCT02507505. Prospectively registered on July 24, 2015.

A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion.

A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean-field approach. Extensive BD simulations were performed to calculate the diffusion coefficients of three different proteins in the cellular environment. The results are in close agreement with experimental or previously simulated values, where available. Control simulations without HI showed that use of HI is essential to obtain accurate diffusion coefficients. Anomalous diffusion inside the crowded cellular medium was investigated with Fractional Brownian motion analysis, and found to be present in this model. By running a series of control simulations in which various forces were removed systematically, it was found that repulsive interactions (volume exclusion) are the main cause for anomalous diffusion, with a secondary contribution from HI.

The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery.

αß-tubulin dimers need to convert between a 'bent' conformation observed for free dimers in solution and a 'straight' conformation required for incorporation into the microtubule lattice. Here, we investigate the free energy landscape of αß-tubulin using molecular dynamics simulations, emphasizing implications for models of assembly, and modulation of the conformational landscape by colchicine, a tubulin-binding drug that inhibits microtubule polymerization. Specifically, we performed molecular dynamics, potential-of-mean force simulations to obtain the free energy profile for unpolymerized GDP-bound tubulin as a function of the ∼12° intradimer rotation differentiating the straight and bent conformers. Our results predict that the unassembled GDP-tubulin heterodimer exists in a continuum of conformations ranging between straight and bent, but, in agreement with existing structural data, suggests that an intermediate bent state has a lower free energy (by ∼1 kcal/mol) and thus dominates in solution. In agreement with predictions of the lattice model of microtubule assembly, lateral binding of two αß-tubulins strongly shifts the conformational equilibrium towards the straight state, which is then ∼1 kcal/mol lower in free energy than the bent state. Finally, calculations of colchicine binding to a single αß-tubulin dimer strongly shifts the equilibrium toward the bent states, and disfavors the straight state to the extent that it is no longer thermodynamically populated.

Angiotensin-I converting enzyme inhibitory activity of hydrolysates from oat (Avena sativa) proteins by in silico and in vitro analyses.

The potential for producing antihypertensive peptides from oat proteins through enzymatic hydrolysis was assessed in silico and confirmed in vitro. Thermolysin (EC 3.4.24.27) was predicted using BIOPEP database as the enzyme that would theoretically produce the most angiotensin I converting enzyme (ACE) inhibitory peptides from oat. Experimental evidence confirmed that strong ACE-inhibitory activity was produced under various hydrolysis conditions. Hydrolysates produced under high enzyme-to-substrate ratio (3%) short time (20 min) (HEST) and low enzyme-to-substrate ratio (0.1%) long time (120 min) (LELT) conditions had IC(50) values of 30 and 50 microg/mL, respectively. After simulated gastrointestinal digestion, the IC(50) of the HEST hydrolysate was 35 microg/mL whereas the IC(50) of the LELT hydrolysate was higher at 85 microg/mL. Ultrafiltration revealed that potent ACE-inhibitory peptides had molecular weights below 3 kDa. This study demonstrates the usefulness of in silico analysis to select enzymes for hydrolysis of proteins not previously examined as sources of bioactive peptides.