The Role of Solvent in the Protein Dynamical Transition

Experimental and computer simulation studies have revealed the presence of a transition in the dynamics of hydrated proteins around 220 K. This transition has been compared with that of a glass phase transition. It manifests itself by a nonlinear behavior in the temperature dependence of the average atomic mean-square displacements and involves an increase of the amplitude of protein dynamics. This increase in flexibility has been correlated with the onset of protein activity. In this thesis, the mechanisms behind the protein dynamical transition are explored using molecular dynamics simulations and neutron scattering experiments

Searching for the Genus Epidemicus in Chinese Patients: Findings from the Clificol COVID-19 Clinical Case Registry.

BACKGROUND  The Clificol COVID-19 Support Project is an innovative international data collection project aimed at tackling some of the core questions in homeopathy. This paper reports on the further investigation of the genus epidemicus concept during the first wave of the pandemic in the Chinese population. METHODS  The design is an observational clinical case registry study of Chinese patients with confirmed or suspected coronavirus disease 2019 (COVID-19). The symptoms were prospectively collected via a 150-item questionnaire. The concept of genus epidemicus, including the role of treatment individualization, was investigated by analyzing whether presenting symptoms clustered into distinct groups. Two standard statistical analysis techniques were utilized: principal component analysis for extracting the most meaningful symptoms of the dataset; the k-means clustering algorithm for automatically assigning groups based on similarity between presenting symptoms. RESULTS  20 Chinese practitioners collected 359 cases in the first half of 2020 (766 consultations, 363 prescriptions). The cluster analysis found two to be the optimum number of clusters. These two symptomatic clusters had a high overlap with the two most commonly prescribed remedies in these sub-populations: in cluster 1 there were 297 prescriptions, 95.6% of which were Gelsemium sempervirens; in cluster 2 there were 61 prescriptions, 95.1% of which were Bryonia alba. CONCLUSION  This is the first study to investigate the notion of genus epidemicus by using modern statistical techniques. These analyses identified at least two distinct symptom pictures. The notion of a single COVID-19 genus epidemicus did not apply in the studied population

Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

<p>Abstract</p> <p>Background</p> <p>Automatic protein modelling pipelines are becoming ever more accurate; this has come hand in hand with an increasingly complicated interplay between all components involved. Nevertheless, there are still potential improvements to be made in template selection, refinement and protein model selection.</p> <p>Results</p> <p>In the context of an automatic modelling pipeline, we analysed each step separately, revealing several non-intuitive trends and explored a new strategy for protein conformation sampling using Genetic Algorithms (GA). We apply the concept of alternating evolutionary pressure (AEP), i.e. intermediate rounds within the GA runs where unrestrained, linear growth of the model populations is allowed.</p> <p>Conclusion</p> <p>This approach improves the overall performance of the GA by allowing models to overcome local energy barriers. AEP enabled the selection of the best models in 40% of all targets; compared to 25% for a normal GA.</p

EpiTools : an open-source image analysis toolkit for quantifying epithelial growth dynamics

Epithelia grow and undergo extensive rearrangements to achieve their final size and shape. Imaging the dynamics of tissue growth and morphogenesis is now possible with advances in time-lapse microscopy, but a true understanding of their complexities is limited by automated image analysis tools to extract quantitative data. To overcome such limitations, we have designed a new open-source image analysis toolkit called EpiTools. It provides user-friendly graphical user interfaces for accurately segmenting and tracking the contours of cell membrane signals obtained from 4D confocal imaging. It is designed for a broad audience, especially biologists with no computer-science background. Quantitative data extraction is integrated into a larger bioimaging platform, Icy, to increase the visibility and usability of our tools. We demonstrate the usefulness of EpiTools by analyzing Drosophila wing imaginal disc growth, revealing previously overlooked properties of this dynamic tissue, such as the patterns of cellular rearrangements

Intercomparison of stratospheric gravity wave observations with AIRS and IASI

Gravity waves are an important driver for the atmospheric circulation and have substantial impact on weather and climate. Satellite instruments offer excellent opportunities to study gravity waves on a global scale. This study focuses on observations from the Atmospheric Infrared Sounder (AIRS) onboard the National Aeronautics and Space Administration's Aqua satellite and the Infrared Atmospheric Sounding Interferometer (IASI) onboard the European MetOp satellites. The main aim of this study is an intercomparison of stratospheric gravity wave observations of both instruments. In particular, we analyzed AIRS and IASI 4.3 μm brightness temperature measurements, which directly relate to stratospheric temperature. Three case studies showed that AIRS and IASI provide a clear and consistent picture of the temporal development of individual gravity wave events. Statistical comparisons based on a five-year period of measurements (2008-2012) showed similar spatial and temporal patterns of gravity wave activity. However, the statistical comparisons also revealed systematic differences of variances between AIRS and IASI (about 45%) that we attribute to the different spatial measurement characteristics of both instruments. We also found differences between day- and nighttime data (about 30%) that are partly due to the local time variations of the gravity wave sources. While AIRS has been used successfully in many previous gravity wave studies, IASI data are applied here for the first time for that purpose. Our study shows that gravity wave observations from different hyperspectral infrared sounders such as AIRS and IASI can be directly related to each other, if instrument-specific characteristics such as different noise levels and spatial resolution and sampling are carefully considered. The ability to combine observations from different satellites provides an opportunity to create a long-term record, which is an exciting prospect for future climatological studies of stratospheric gravity wave activity

Time-efficient and flexible design of optimized multishell HARDI diffusion

Purpose: Advanced diffusion magnetic resonance imaging benefits from collecting as much data as is feasible but is highly sensitive to subject motion and the risk of data loss increases with longer acquisition times. Our purpose was to create a maximally time-efficient and flexible diffusion acquisition capability with built-in robustness to partially acquired or interrupted scans. Our framework has been developed for the developing Human Connectome Project, but different application domains are equally possible. Methods: Complete flexibility in the sampling of diffusion space combined with free choice of phase-encode-direction and the temporal ordering of the sampling scheme was developed taking into account motion robustness, internal consistency, and hardware limits. A split-diffusion-gradient preparation, multiband acceleration, and a restart capacity were added. Results: The framework was used to explore different parameters choices for the desired high angular resolution diffusion imaging diffusion sampling. For the developing Human Connectome Project, a high-angular resolution, maximally time-efficient (20 min) multishell protocol with 300 diffusion-weighted volumes was acquired in >400 neonates. An optimal design of a high-resolution (1.2 × 1.2 mm2) two-shell acquisition with 54 diffusion weighted volumes was obtained using a split-gradient design. Conclusion: The presented framework provides flexibility to generate time-efficient and motion-robust diffusion magnetic resonance imaging acquisitions taking into account hardware constraints that might otherwise result in sub-optimal choices. Magn Reson Med, 2017. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes

Diffusion magnetic resonance imaging assessment of regional white matter maturation in preterm neonates

PURPOSE: Diffusion magnetic resonance imaging (dMRI) studies report altered white matter (WM) development in preterm infants. Neurite orientation dispersion and density imaging (NODDI) metrics provide more realistic estimations of neurite architecture in vivo compared with standard diffusion tensor imaging (DTI) metrics. This study investigated microstructural maturation of WM in preterm neonates scanned between 25 and 45 weeks postmenstrual age (PMA) with normal neurodevelopmental outcomes at 2 years using DTI and NODDI metrics. METHODS: Thirty-one neonates (n = 17 male) with median (range) gestational age (GA) 32+1 weeks (24+2-36+4) underwent 3 T brain MRI at median (range) post menstrual age (PMA) 35+2 weeks (25+3-43+1). WM tracts (cingulum, fornix, corticospinal tract (CST), inferior longitudinal fasciculus (ILF), optic radiations) were delineated using constrained spherical deconvolution and probabilistic tractography in MRtrix3. DTI and NODDI metrics were extracted for the whole tract and cross-sections along each tract to assess regional development. RESULTS: PMA at scan positively correlated with fractional anisotropy (FA) in the CST, fornix and optic radiations and neurite density index (NDI) in the cingulum, CST and fornix and negatively correlated with mean diffusivity (MD) in all tracts. A multilinear regression model demonstrated PMA at scan influenced all diffusion measures, GA and GAxPMA at scan influenced FA, MD and NDI and gender affected NDI. Cross-sectional analyses revealed asynchronous WM maturation within and between WM tracts.). CONCLUSION: We describe normal WM maturation in preterm neonates with normal neurodevelopmental outcomes. NODDI can enhance our understanding of WM maturation compared with standard DTI metrics alone

Model-based analysis of multishell diffusion MR data for tractography: how to get over fitting problems

In this article, we highlight an issue that arises when using multiple b‐values in a model‐based analysis of diffusion MR data for tractography. The non‐monoexponential decay, commonly observed in experimental data, is shown to induce overfitting in the distribution of fiber orientations when not considered in the model. Extra fiber orientations perpendicular to the main orientation arise to compensate for the slower apparent signal decay at higher b‐values. We propose a simple extension to the ball and stick model based on a continuous gamma distribution of diffusivities, which significantly improves the fitting and reduces the overfitting. Using in vivo experimental data, we show that this model outperforms a simpler, noise floor model, especially at the interfaces between brain tissues, suggesting that partial volume effects are a major cause of the observed non‐monoexponential decay. This model may be helpful for future data acquisition strategies that may attempt to combine multiple shells to improve estimates of fiber orientations in white matter and near the cortex

Early development of structural networks and the impact of prematurity on brain connectivity

Preterm infants are at high risk of neurodevelopmental impairment, which may be due to altered development of brain connectivity. We aimed to (i) assess structural brain development from 25 to 45 weeks gestational age (GA) using graph theoretical approaches and (ii) test the hypothesis that preterm birth results in altered white matter network topology. Sixty-five infants underwent MRI between 25(+3) and 45(+6) weeks GA. Structural networks were constructed using constrained spherical deconvolution tractography and were weighted by measures of white matter microstructure (fractional anisotropy, neurite density and orientation dispersion index). We observed regional differences in brain maturation, with connections to and from deep grey matter showing most rapid developmental changes during this period. Intra-frontal, frontal to cingulate, frontal to caudate and inter-hemispheric connections matured more slowly. We demonstrated a core of key connections that was not affected by GA at birth. However, local connectivity involving thalamus, cerebellum, superior frontal lobe, cingulate gyrus and short range cortico-cortical connections was related to the degree of prematurity and contributed to altered global topology of the structural brain network. The relative preservation of core connections at the expense of local connections may support more effective use of impaired white matter reserve following preterm birth