Probing iron in Earth's core with molecular-spin dynamics.

Dynamic compression of iron to Earth-core conditions is one of the few ways to gather important elastic and transport properties needed to uncover key mechanisms surrounding the geodynamo effect. Herein, a machine-learned ab initio derived molecular-spin dynamics (MSD) methodology with explicit treatment for longitudinal spin-fluctuations is utilized to probe the dynamic phase-diagram of iron. This framework uniquely enables an accurate resolution of the phase-transition kinetics and Earth-core elastic properties, as highlighted by compressional wave velocity and adiabatic bulk moduli measurements.

Long-living periodic solutions of complex cubic-quintic Ginzburg-Landau equation in the presence of intrapulse Raman scattering: A bifurcation and numerical study.

We have found long-living periodic solutions of the complex cubic-quintic Ginzburg-Landau equation (CCQGLE) perturbed with intrapulse Raman scattering. To achieve this we have applied a model system of ordinary differential equations (SODE). A set of the fixed points of the system has been described.

Platelet heterogeneity enhances blood clot volumetric contraction: An example of asynchrono-mechanical amplification.

Physiological processes such as blood clotting and wound healing as well as pathologies such as fibroses and musculoskeletal contractures, all involve biological materials composed of a contracting cellular population within a fibrous matrix, yet how the microscale interactions among the cells and the matrix lead to the resultant emergent behavior at the macroscale tissue level remains poorly understood. Platelets, the anucleate cell fragments that do not divide nor synthesize extracellular matrix, represent an ideal model to study such systems. During blood clot contraction, microscopic platelets actively pull fibers to shrink the macroscale clot to less than 10% of its initial volume.

Can DNA barcoding be used to identify closely related Clunio Haliday, 1855 species (Diptera: Chironomidae, Orthocladiinae)?

DNA barcoding based on a fragment of mitochondrial Cytochrome C Oxidase subunit 1 gene (COI) was applied to the two chironomids Clunio balticus Heimbach (690 base pairs) and C. ponticus Michailova (691 base pairs). The two species differed by one deletion in the nucleotide sequence Adenine.

Mathematical Modelling in Biomedicine: A Primer for the Curious and the Skeptic.

In most disciplines of natural sciences and engineering, mathematical and computational modelling are mainstay methods which are usefulness beyond doubt. These disciplines would not have reached today's level of sophistication without an intensive use of mathematical and computational models together with quantitative data. This approach has not been followed in much of molecular biology and biomedicine, however, where qualitative descriptions are accepted as a satisfactory replacement for mathematical rigor and the use of computational models is seen by many as a fringe practice rather than as a powerful scientific method.

Absolute Monocyte and Platelet Counts May Provide Additional Prognostic Information in Primary Gastric Diffuse Large B-cell Lymphoma Patients Treated with Rituximab and CHOP.

Introduction: Primary gastric diffuse large B cell lymphoma (PG-DLBCL) is the most common histological subtype of primary gastric lymphoma. The standard of care of PG-DLBCL patients is the combination rituximab-based immunochemotherapy (R-CHOP). Re-cently, different host-related factors have been shown to have significant prognostic significance in non-Hodgkin lymphoma.

Behavior and mechanics of dense microgel suspensions.

Suspensions of soft and highly deformable microgels can be concentrated far more than suspensions of hard colloids, leading to their unusual mechanical properties. Microgels can accommodate compression in suspensions in a variety of ways such as interpenetration, deformation, and shrinking. Previous experiments have offered insightful, but somewhat conflicting, accounts of the behavior of individual microgels in compressed suspensions.

The role of cooperativity in a p53-miR34 dynamical mathematical model.

The objective of this study is to evaluate the role of cooperativity, captured by the Hill coefficient, in a minimal mathematical model describing the interactions between p53 and miR-34a. The model equations are analyzed for negative, none and normal cooperativity using a specific version of bifurcation theory and they are solved numerically. Special attention is paid to the sign of so-called first Lyapunov value.

Hierarchical Levels of Biological Systems and their Integration as a Principal Cause for Tumour Occurrence.

The development of new theories, mathematical methods and models for effective control of complex systems is one of the main problems for modern science. Biological systems are complex and hierarchically organized, with the behaviour of higher levels influencing the dynamics of the lower ones and vice versa. Hierarchical organization can be observed from subcellular to supercellular levels.

Imaging Performance for Two Row-Column Arrays.

This study evaluates the volumetric imaging performance of two prototyped 62 + 62 row-column-addressed (RCA) 2-D array transducer probes using three synthetic aperture imaging (SAI) emission sequences and two different beamformers. The probes are fabricated using capacitive micromachined ultrasonic transducer (CMUT) and piezoelectric transducer (PZT) technology. Both have integrated apodization to reduce ghost echoes and are designed with similar acoustical features, i.

Phagocyte-Inspired Smart Microcapsules.

Phagocytes protect the organism by ingesting harmful foreign particles and cells. We use mesoscale computer simulations to design a phagocyte-inspired active microcapsule that is capable of selectively capturing nanoparticles dispersed in solvent. Our fully synthetic microdevice is actuated by a temperature-sensitive microgel enclosed inside a perforated spherical shell.

Use of a Real-Time Stress Map for Assessment of Applied Stress for Strain Elastography: Utility in Training and Computation of Strain Ratios.

Objectives: There is a significant learning curve in strain elastography. Uniform appropriate levels of stress must be applied for accurate elastograms. If the stress is not applied appropriately, inaccurate results will be obtained, particularly when strain ratios are being estimated.

Extreme thermodynamics with polymer gel tori: Harnessing thermodynamic instabilities to induce large-scale deformations.

When a swollen, thermoresponsive polymer gel is heated in a solvent bath, it expels solvent and deswells. When this heating is slow, deswelling proceeds homogeneously, as observed in a toroid-shaped gel that changes volume while maintaining its toroidal shape. By contrast, if the gel is heated quickly, an impermeable layer of collapsed polymer forms and traps solvent within the gel, arresting the volume change.

Curvilinear 3-D Imaging Using Row-Column-Addressed 2-D Arrays With a Diverging Lens: Phantom Study.

A double-curved diverging lens over the flat row-column-addressed (RCA) 2-D array can extend its inherent rectilinear 3-D imaging field of view (FOV) to a curvilinear volume region, which is necessary for applications such as abdominal and cardiac imaging. Two concave lenses with radii of 12.7 and 25.

Model-Based Phenotypic Signatures Governing the Dynamics of the Stem and Semi-differentiated Cell Populations in Dysplastic Colonic Crypts.

Mathematical modeling of cell differentiated in colonic crypts can contribute to a better understanding of basic mechanisms underlying colonic tissue organization, but also its deregulation during carcinogenesis and tumor progression. Here, we combined bifurcation analysis to assess the effect that time delay has in the complex interplay of stem cells and semi-differentiated cells at the niche of colonic crypts, and systematic model perturbation and simulation to find model-based phenotypes linked to cancer progression. The models suggest that stem cell and semi-differentiated cell population dynamics in colonic crypts can display chaotic behavior.

Macroscopic Strain-Induced Transition from Quasi-infinite Gold Nanoparticle Chains to Defined Plasmonic Oligomers.

We investigate the formation of chains of few plasmonic nanoparticles-so-called plasmonic oligomers-by strain-induced fragmentation of linear particle assemblies. Detailed investigations of the fragmentation process are conducted by in situ atomic force microscopy and UV-vis-NIR spectroscopy. Based on these experimental results and mechanical simulations computed by the lattice spring model, we propose a formation mechanism that explains the observed decrease of chain polydispersity upon increasing strain and provides experimental guidelines for tailoring chain length distribution.

Curvilinear 3-D Imaging Using Row-Column-Addressed 2-D Arrays With a Diverging Lens: Feasibility Study.

Constructing a double-curved row-column-addressed (RCA) 2-D array or applying a diverging lens over the flat RCA 2-D array can extend the imaging field-of-view (FOV) to a curvilinear volume without increasing the aperture size, which is necessary for applications, such as abdominal and cardiac imaging. Extended FOV and low channel count of double-curved RCA 2-D arrays make 3-D imaging possible with equipment in the price range of conventional 2-D imaging. This paper proposes a delay-and-sum beamformation scheme specific to double-curved RCA 2-D arrays and validates its focusing ability based on simulations.

Ultrasound Vector Flow Imaging-Part II: Parallel Systems.

This paper gives a review of the current state-of-the-art in ultrasound parallel acquisition systems for flow imaging using spherical and plane waves emissions. The imaging methods are explained along with the advantages of using these very fast and sensitive velocity estimators. These experimental systems are capable of acquiring thousands of images per second for fast moving flow as well as yielding the estimates of low velocity flow.

Ultrasound Vector Flow Imaging-Part I: Sequential Systems.

This paper gives a review of the most important methods for blood velocity vector flow imaging (VFI) for conventional sequential data acquisition. This includes multibeam methods, speckle tracking, transverse oscillation, color flow mapping derived VFI, directional beamforming, and variants of these. The review covers both 2-D and 3-D velocity estimation and gives a historical perspective on the development along with a summary of various vector flow visualization algorithms.

Functional adaptation of crustacean exoskeletal elements through structural and compositional diversity: a combined experimental and theoretical study.

The crustacean cuticle is a composite material that covers the whole animal and forms the continuous exoskeleton. Nano-fibers composed of chitin and protein molecules form most of the organic matrix of the cuticle that, at the macroscale, is organized in up to eight hierarchical levels. At least two of them, the exo- and endocuticle, contain a mineral phase of mainly Mg-calcite, amorphous calcium carbonate and phosphate.

Bimorph Silk Microsheets with Programmable Actuating Behavior: Experimental Analysis and Computer Simulations.

Microscaled self-rolling construct sheets from silk protein material have been fabricated, containing a silk bimorph composed of silk ionomers as an active layer and cross-linked silk β-sheet as the passive layer. The programmable morphology was experimentally explored along with a computational simulation to understand the mechanism of shape reconfiguration. The neutron reflectivity shows that the active silk ionomers layer undergoes remarkable swelling (eight times increase in thickness) after deprotonation while the passive silk β-sheet retains constant volume under the same conditions and supports the bimorph construct.

Model-based genotype-phenotype mapping used to investigate gene signatures of immune sensitivity and resistance in melanoma micrometastasis.

In this paper, we combine kinetic modelling and patient gene expression data analysis to elucidate biological mechanisms by which melanoma becomes resistant to the immune system and to immunotherapy. To this end, we systematically perturbed the parameters in a kinetic model and performed a mathematical analysis of their impact, thereby obtaining signatures associated with the emergence of phenotypes of melanoma immune sensitivity and resistance. Our phenotypic signatures were compared with published clinical data on pretreatment tumor gene expression in patients subjected to immunotherapy against metastatic melanoma.

Self-(Un)rolling Biopolymer Microstructures: Rings, Tubules, and Helical Tubules from the Same Material.

We have demonstrated the facile formation of reversible and fast self-rolling biopolymer microstructures from sandwiched active-passive, silk-on-silk materials. Both experimental and modeling results confirmed that the shape of individual sheets effectively controls biaxial stresses within these sheets, which can self-roll into distinct 3D structures including microscopic rings, tubules, and helical tubules. This is a unique example of tailoring self-rolled 3D geometries through shape design without changing the inner morphology of active bimorph biomaterials.

Self-Propelled Microswimmer Actuated by Stimuli-Sensitive Bilayered Hydrogel.

Using computational modeling, we design a microscopic swimmer made of a bilayered responsive hydrogel capable of swimming in a viscous fluid when actuated by a periodically applied stimulus. The gel has an X-shaped geometry and two bonded layers, one of which is responsive to environmental changes and the other which is passive. When the stimulus is turned on, the responsive layer swells and causes the swimmer to deform.