1,327 research outputs found
Confined compression of collagen hydrogels
Reconstituted collagen hydrogels are often used for in vitro studies of cell-matrix interaction and as scaffolds for tissue engineering. Understanding the mechanical and transport behaviours of collagen hydrogels is therefore extremely important, albeit difficult due to their very high water content (typically > 99.5%). In the present study the mechanical behaviour of collagen hydrogels in confined compression was investigated using biphasic theory (J. Biomech. Eng. 102 (1980) 73), to ascertain whether the technique is sufficiently sensitive to determine differences in the characteristics of hydrogels of between 0.2% and 0.4% collagen. Peak stress, equilibrium stress, aggregate modulus and hydraulic permeability of the hydrogels exhibited sensitivity to collagen content, demonstrating that the technique is clearly able to discriminate between hydrogels with small differences in collagen content and may also be sensitive to factors that affect matrix remodelling. The results also offer additional insight into the deformation-dependent permeability of collagen hydrogels. This study suggests that confined compression, together with biphasic theory, is a suitable technique for assessing the mechanical properties of collagen hydrogels
A detailed binding free energy study of 2 : 1 ligandâDNA complex formation by experiment and simulation
In 2004, we used NMR to solve the structure of the minor groove binder thiazotropsin A bound in a 2 : 1 complex to the DNA duplex, d(CGACTAGTCG)2. In this current work, we have combined theory and experiment to confirm the binding thermodynamics of this system. Molecular dynamics simulations that use polarizable or non-polarizable force fields with single and separate trajectory approaches have been used to explore complexation at the molecular level. We have shown that the binding process invokes large conformational changes in both the receptor and ligand, which is reflected by large adaptation energies. This is compensated for by the net binding free energy, which is enthalpy driven and entropically opposed. Such a conformational change upon binding directly impacts on how the process must be simulated in order to yield accurate results. Our MM-PBSA binding calculations from snapshots obtained from MD simulations of the polarizable force field using separate trajectories yield an absolute binding free energy (-15.4 kcal mol-1) very close to that determined by isothermal titration calorimetry (-10.2 kcal mol-1). Analysis of the major energy components reveals that favorable non-bonded van der Waals and electrostatic interactions contribute predominantly to the enthalpy term, whilst the unfavorable entropy appears to be driven by stabilization of the complex and the associated loss of conformational freedom. Our results have led to a deeper understanding of the nature of side-by-side minor groove ligand binding, which has significant implications for structure-based ligand development
Structure-activity relationships and molecular modeling of sphingosine kinase inhibitors
The design, synthesis, and evaluation of the potency of new isoform-selective inhibitors of sphingosine kinases 1 and 2 (SK1 and SK2), the enzyme that catalyzes the phosphorylation of d-erythro-sphingosine to produce the key signaling lipid, sphingosine 1-phosphate, are described. Recently, we reported that 1-(4-octylphenethyl)piperidin-4-ol (RB-005) is a selective inhibitor of SK1. Here we report the synthesis of 43 new analogues of RB-005, in which the lipophilic tail, polar headgroup, and linker region were modified to extend the structure-activity relationship profile for this lead compound, which we explain using modeling studies with the recently published crystal structure of SK1. We provide a basis for the key residues targeted by our profiled series and provide further evidence for the ability to discriminate between the two isoforms using pharmacological intervention
Participatory impact pathways analysis : A practical application of program theory in research-for-development
The Challenge Program on Water and Food pursues food security and poverty alleviation through the efforts of some 50 research-for-development projects. These involve almost 200 organizations working in nine river basins around the world. An approach was developed to enhance the developmental impact of the program through better impact assessment, to provide a framework for monitoring and evaluation, to permit stakeholders to derive strategic and programmatic lessons for future initiatives, and to provide information that can be used to inform public awareness efforts. The approach makes explicit a project's program theory by describing its impact pathways in terms of a logic model and network maps. A narrative combines the logic model and the network maps into a single explanatory account and adds to overall plausibility by explaining the steps in the logic model and the key risks and assumptions. Participatory Impact Pathways Analysis is based on concepts related to program theory drawn from the fields of evaluation, organizational learning, and social network analysis
A new class of ratiometric small molecule intracellular pH sensors for Raman microscopy
Intracellular pH (pHi) homeostasis is intertwined with a myriad of normal cellular behaviors as well as pathological processes. As such, small molecule probes for the measurement of pHi are invaluable tools for chemical biology, facilitating the study of the role of pH in cellular function and disease. The field of small molecule pHi sensors has traditionally been dominated with probes based on fluorescent scaffolds. In this study, a series of low molecular weight (<260) oligoyne compounds have been developed which exhibit pH sensitive alkyne stretching frequencies (Îœalkyne) in Raman spectroscopy. The modular design of the compounds enabled tuneability of their pKa(H) through simple structural modification, such that continuous pH sensitivity is achieved over the range 2-10. Alkyne stretching bands reside in the 'cell-silent' region of the Raman spectrum (1800-2600 cm-1) and are readily detectable in a cellular environment with subcellular spatial resolution. This enabled the application of a pH sensitive oligoyne compound to the ratiometric sensing of pHi in prostate cancer (PC3) cells in response to drug treatment. We propose that probes based on Alkyne Tag Raman Imaging offer an entirely new platform for the sensing of pHi, complementary to fluorescence microscopy
Knee joint distraction results in MRI cartilage thickness increase up to 10 years after treatment
OBJECTIVES: Knee joint distraction (KJD) has been shown to result in long-term clinical improvement and short-term cartilage restoration in young OA patients. The objective of the current study was to evaluate MRI cartilage thickness up to 10âyears after KJD treatment, using a 3D surface-based approach. METHODS: Twenty end-stage knee OA patients were treated with KJD. MRI scans (1.5âT) were performed before and at 1, 2, 5, 7, and 10âyears after treatment. Tibia and femur cartilage segmentation and registration to a canonical surface were performed semi-automatically. Statistical parametric mapping with linear mixed models was used to analyse whole-joint changes. The influence of baseline patient characteristics was analysed with statistical parametric mapping using linear regression. Relevant weight-bearing parts of the femur were selected to obtain the average cartilage thickness in the femur and tibia of the most- (MAC) and least-affected compartment. These compartmental changes over time were analysed using repeated measures ANOVA; missing data was imputed. In all cases, P 0.05). Compartmental analyses showed significant short- and long-term thickness increase in the tibia and femur MAC (all P <0.05). CONCLUSION: KJD results in significant short- and long-term cartilage regeneration, up to 10âyears post-treatment. TRIAL REGISTRATION: Netherlands Trial Register, https://www.trialregister.nl, NL419
Bayesian model comparison in cosmology with Population Monte Carlo
We use Bayesian model selection techniques to test extensions of the standard
flat LambdaCDM paradigm. Dark-energy and curvature scenarios, and primordial
perturbation models are considered. To that end, we calculate the Bayesian
evidence in favour of each model using Population Monte Carlo (PMC), a new
adaptive sampling technique which was recently applied in a cosmological
context. The Bayesian evidence is immediately available from the PMC sample
used for parameter estimation without further computational effort, and it
comes with an associated error evaluation. Besides, it provides an unbiased
estimator of the evidence after any fixed number of iterations and it is
naturally parallelizable, in contrast with MCMC and nested sampling methods. By
comparison with analytical predictions for simulated data, we show that our
results obtained with PMC are reliable and robust. The variability in the
evidence evaluation and the stability for various cases are estimated both from
simulations and from data. For the cases we consider, the log-evidence is
calculated with a precision of better than 0.08.
Using a combined set of recent CMB, SNIa and BAO data, we find inconclusive
evidence between flat LambdaCDM and simple dark-energy models. A curved
Universe is moderately to strongly disfavoured with respect to a flat
cosmology. Using physically well-motivated priors within the slow-roll
approximation of inflation, we find a weak preference for a running spectral
index. A Harrison-Zel'dovich spectrum is weakly disfavoured. With the current
data, tensor modes are not detected; the large prior volume on the
tensor-to-scalar ratio r results in moderate evidence in favour of r=0.
[Abridged]Comment: 11 pages, 6 figures. Matches version accepted for publication by
MNRA
Association between APOE e4 and white matter hyperintensity volume, but not total brain volume or white matter integrity
Apolipoprotein (APOE) e4 genotype is an accepted risk factor for accelerated cognitive aging and dementia, though its neurostructural substrates are unclear. The deleterious effects of this genotype on brain structure may increase in magnitude into older age. This study aimed to investigate in UK Biobank the association between APOE e4 allele presence vs. absence and brain imaging variables that have been associated with worse cognitive abilities; and whether this association varies by cross-sectional age. We used brain magnetic resonance imaging (MRI) and genetic data from a general-population cohort: the UK Biobank (Nâ=â8395 after exclusions). We adjusted for the covariates of age in years, sex, Townsend social deprivation scores, smoking history and cardiometabolic diseases. There was a statistically significant association between APOE e4 genotype and increased (i.e. worse) white matter (WM) hyperintensity volumes (standardised betaâ=â0.088, 95% confidence intervalsâ=â0.036 to 0.139, Pâ=â0.001), a marker of poorer cerebrovascular health. There were no associations with left or right hippocampal, total grey matter (GM) or WM volumes, or WM tract integrity indexed by fractional anisotropy (FA) and mean diffusivity (MD). There were no statistically significant interactions with age. Future research in UK Biobank utilising intermediate phenotypes and longitudinal imaging hold significant promise for this area, particularly pertaining to APOE e4âs potential link with cerebrovascular contributions to cognitive aging
Mitokyne : a ratiometric raman probe for mitochondrial pH
Mitochondrial pH (pHmito) is intimately related to mitochondrial function and aberrant values for pHmito are linked to several disease states. We report the design, synthesis and application of mitokyne 1 â the first small molecule pHmito sensor for Stimulated Raman Scattering (SRS) microscopy. This ratiometric probe can determine subtle changes in pHmito in response to external stimuli and the inhibition of both the electron transport chain and ATP synthase with small molecule inhibitors. In addition, 1 was also used to monitor mitochondrial dynamics in a time-resolved manner with subcellular spatial resolution during mitophagy providing a powerful tool for dissecting the molecular and cell biology of this critical organelle
Chaotic systems in complex phase space
This paper examines numerically the complex classical trajectories of the
kicked rotor and the double pendulum. Both of these systems exhibit a
transition to chaos, and this feature is studied in complex phase space.
Additionally, it is shown that the short-time and long-time behaviors of these
two PT-symmetric dynamical models in complex phase space exhibit strong
qualitative similarities.Comment: 22 page, 16 figure
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