Rate constants for proteins binding to substrates with multiple binding sites using a generalized forward flux sampling expression

To predict the response of a biochemical system, knowledge of the intrinsic and effective rate constants of proteins is crucial. The experimentally accessible effective rate constant for association can be decomposed in a diffusion-limited rate at which proteins come into contact and an intrinsic association rate at which the proteins in contact truly bind. Reversely, when dissociating, bound proteins first separate into a contact pair with an intrinsic dissociation rate, before moving away by diffusion. While microscopic expressions exist that enable the calculation of the intrinsic and effective rate constants by conducting a single rare event simulation of the protein dissociation reaction, these expressions are only valid when the substrate has just one binding site. If the substrate has multiple binding sites, a bound enzyme can, besides dissociating into the bulk, also hop to another binding site. Calculating transition rate constants between multiple states with forward flux sampling requires a generalized rate expression. We present this expression here and use it to derive explicit expressions for all intrinsic and effective rate constants involving binding to multiple states, including rebinding. We illustrate our approach by computing the intrinsic and effective association, dissociation, and hopping rate constants for a system in which a patchy particle model enzyme binds to a substrate with two binding sites. We find that these rate constants increase as a function of the rotational diffusion constant of the particles. The hopping rate constant decreases as a function of the distance between the binding sites. Finally, we find that blocking one of the binding sites enhances both association and dissociation rate constants. Our approach and results are important for understanding and modeling association reactions in enzyme-substrate systems and other patchy particle systems and open the way for large multiscale simulations of such systems

The magnitude of the intrinsic rate constant: How deep can association reactions be in the diffusion limited regime?

Intrinsic and effective rate constants have an important role in the theory of diffusion-limited reactions. In a previous paper, we provide detailed microscopic expressions for these intrinsic rates [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, Faraday Discuss. 195, 421 (2016)], which are usually considered as abstract quantities and assumed to be implicitly known. Using these microscopic expressions, we investigate how the rate of association depends on the strength and the range of the isotropic potential and the strength of the non- specific attraction in case of the anisotropic potential. In addition, we determine the location of the interface where these expressions become valid for anisotropic potentials. In particular, by investigating the particles' orientational distributions, we verify whether the interface at which these distributions become isotropic agrees with the interface predicted by the effective association rate constant. Finally, we discuss how large the intrinsic association rate can become, and what are the consequences for the existence of the diffusion limited regime. Published by AIP Publishing

Support for the global feasibility of the Ages and Stages Questionnaire as developmental screener

Objective: To investigate the psychometric properties of the Dutch version of the 48 months Ages and Stages Questionnaire (D_ASQ_48). Design: Prospective cohort study of a community-based sample of children born in 2002 and 2003 whose parents filled out the D_ASQ_48 and a questionnaire on school status at 60 months. The ASQ was translated into Dutch and back-translated into English by three independent translators. Setting: Well Child Centers covering 25% of the Netherlands. Participants: Parents of 1510 preterm and 562 term children born in 2002-2003 attending routine Well Child visits at age 45-50 months. Main outcome measures: Reliability, validity and mean population scores for D_ASQ_48 compared to other countries. Results: Mean population scores for the D_ASQ_48 were mostly similar to those in the USA, Norway and Korea. Exceptions (effect sizes of difference >0.5) were problem solving (USA) and fine motor (Korea). Reliability was good for the total score (Cronbach alpha 0.79) and acceptable for all domains (0.61-0.74). As expected, infants born at gestational age Conclusions: The good psychometric properties of the Dutch ASQ_48 and the small differences when compared to other countries support its usefulness in the early detection of developmental problems amongst children worldwide. (C) 2009 Elsevier Ireland Ltd. All rights reserved

Thinner Regions of Intracranial Aneurysm Wall Correlate with Regions of Higher Wall Shear Stress: A 7T MRI Study

BACKGROUND AND PURPOSE: Both hemodynamics and aneurysm wall thickness are important parameters in aneurysm pathophysiology. Our aim was to develop a method for semi-quantitative wall thickness assessment on in vivo 7T MR images of intracranial aneurysms for studying the relation between apparent aneurysm wall thickness and wall shear stress. MATERIALS AND METHODS: Wall thickness was analyzed in 11 unruptured aneurysms in 9 patients who underwent 7T MR imaging with a TSE-based vessel wall sequence (0.8-mm isotropic resolution). A custom analysis program determined the in vivo aneurysm wall intensities, which were normalized to the signal of nearby brain tissue and were used as measures of apparent wall thickness. Spatial wall thickness variation was determined as the interquartile range in apparent wall thickness (the middle 50% of the apparent wall thickness range). Wall shear stress was determined by using phase-contrast MR imaging (0.5-mm isotropic resolution). We performed visual and statistical comparisons (Pearson correlation) to study the relation between wall thickness and wall shear stress. RESULTS: 3D colored apparent wall thickness maps of the aneurysms showed spatial apparent wall thickness variation, which ranged from 0.07 to 0.53, with a mean variation of 0.22 (a variation of 1.0 roughly means a wall thickness variation of 1 voxel [0.8 mm]). In all aneurysms, apparent wall thickness was inversely related to wall shear stress (mean correlation coefficient, −0.35; P < .05). CONCLUSIONS: A method was developed to measure the wall thickness semi-quantitatively, by using 7T MR imaging. An inverse correlation between wall shear stress and apparent wall thickness was determined. In future studies, this noninvasive method can be used to assess spatial wall thickness variation in relation to pathophysiologic processes such as aneurysm growth and rupture

Brain Pro-TCT:Quality improvement of delirium detection on a cardiothoracic surgical ward

1) Please declare any conflicts of interest below: The authors declare a potential conflict of interest but not a personal conflict of interest. Part of the costs for this study are covered by Heartcentre Twente Foundation. Prolira provided training and the DeltaScans during the study period free of charge and applied a discount to the disposable patch costs. 2) Ethics Approval: Ethical approval was waived by the Advisory committee Medisch Spectrum Twente at Enschede. The Institutional Review Board of Medisch Spectrum Twente has concluded that this study does not fall under the remit of the Medical Research Involving Human Subjects. 3) Context: The study was done on the cardiothoracic surgery ward at Thoraxcentrum Twente (Medisch Spectrum Twente, Enschede, the Netherlands), a tertiary teaching hospital. Patients 70 years or older who underwent cardiac surgery were included. The quality improvement team included nurse practitioners in cardiac surgery and psychiatry, a cardiac surgeon, nurses, a technical physician, and an epidemiologist. 4) Problem: Delirium is a common syndrome of acute brain failure, which often occurs in hospitalized older patients following cardiac surgery. Delirium after cardiac surgery is related to adverse long-term outcomes, more readmissions to hospital, and decreased cognitive and functional outcomes. Early detection of delirium allows early treatment of underlying causes. In standard care, we use a delirium observation scale score (DOSS). Recently, a single-channel electroencephalography (EEG) medical device was developed to screen delirium based on detection of delta waves (DeltaScan). Using DeltaScan in routine care may improve delirium detection and clinical outcomes. 5) Assessment of problem and analysis of its causes: Previous delirium studies in Thoraxcentrum Twente using DOSS as standard care reported an incidence of delirium of 13 to 17% in elective patients aged ≥45 years. Published and unpublished research data for cardiothoracic surgery wards show an increase of delirium detection by &gt;15% (absolute percentage growth), when DeltaScan was used in clinical studies. Nurses, nurse practitioners, and medical doctors were informed  about the aims of the study and importance of delirium screening. A nurse improvement project, including a workgroup, was started, where the importance of screening was emphasized. Before the implementation of the DeltaScan, nurses on the surgical ward received education and training. Medical doctors, residents, and nurse practitioners were trained on how to interpret the DeltaScan scores. 6) Intervention: First, we continued the DOSS as regular care for delirium screening; three measurements a day for the first three postoperative days. Second, DeltaScan was implemented as new regular care. DeltaScan measurements took place twice a day for at least three consecutive days. 7) Strategy for change: In February 2021 additional training of the DOSS for delirium screening began, and from April 2021 onwards, prospective data collection of the first group continued till May 2022. Training with DeltaScan started in March/April 2022. The DeltaScan data collection started in May 2022, and is still ongoing. 8) Measurement of improvement: The primary endpoints to measure improvement were incidence of delirium, and length of hospital stay. Secondary endpoints included delirium duration, adherence to delirium protocol, and costs related to the innovation. The innovation was deemed successful with an incidence increase from 15 to 30%, and a length of stay reduction with at least 1.5 days. This abstract is based on preliminary data until October 2022. 9) Effects of changes: In total 612 patients were included, with 450 patients in the DOSS group and 162 patients (interim results) in the DeltaScan group. Incidence of finding delirium increased from 15% to 25% (p = 0.008). Median length of hospital stay for delirium patients was reduced from 9 hospital nights to 5.5 nights (p = 0.002). Median duration of delirium decreased (not significantly) from 77 hours to 65 hours (p = 0.12). 10) Lessons learned: Involving all stakeholders early in the project helped to gain commitment to the innovation. The change was measured in a scientific study, as no formal results on effectivity are known at the moment. Introducing a new device for delirium screening arouses resistance. Reducing or removing this resistance remains difficult. 11) Messages for others: Involving all stakeholders in a working group for delirium screening helped to start an innovation, monitor benefits, and motivated colleagues to actually commit to the innovation. Screening for delirium with DeltaScan in our study leads to an increase of finding delirium, and reduced hospital stay (interim results) for patients after cardiothoracic surgery. It is unknown yet, whether this is cost-effective. We hypothesize that these results are expected to be similar for other patient groups such as geriatric or general surgical patients. 12) Please describe how you have involved patients, carers, or family members in the project: Patients and their relatives are informed about the risk of delirium and the impact of delirium before hospital admission. Relatives and patients are often informed during measurements on the importance of adequate delirium screening, where positive responses are often heard. No formal co-creation by patients was done, but informal feedback will be collected in the near future. </p

Homogeneous nucleation of a non-critical phase near a continuous phase transition

Homogeneous nucleation of a new phase near a second, continuous, transition, is considered. The continuous transition is in the metastable region associated with the first-order phase transition, one of whose coexisting phases is nucleating. Mean-field calculations show that as the continuous transition is approached, the size of the nucleus varies as the response function of the order parameter of the continuous transition. This response function diverges at the continuous transition, as does the temperature derivative of the free energy barrier to nucleation. This rapid drop of the barrier as the continuous transition is approached means that the continuous transition acts to reduce the barrier to nucleation at the first-order transition. This may be useful in the crystallisation of globular proteins.Comment: 6 pages, 1 figur

Effect of Ordering on Spinodal Decomposition of Liquid-Crystal/Polymer Mixtures

Partially phase-separated liquid-crystal/polymer dispersions display highly fibrillar domain morphologies that are dramatically different from the typical structures found in isotropic mixtures. To explain this, we numerically explore the coupling between phase ordering and phase separation kinetics in model two-dimensional fluid mixtures phase separating into a nematic phase, rich in liquid crystal, coexisting with an isotropic phase, rich in polymer. We find that phase ordering can lead to fibrillar networks of the minority polymer-rich phase