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. We discovered that platelets utilize a new emergent behavior, asynchrono-mechanical amplification, to enhanced volumetric material contraction and to magnify contractile forces. This behavior is triggered by the heterogeneity in the timing of a population of actuators. This result indicates that cell heterogeneity, often attributed to stochastic cell-to-cell variability, can carry an essential biophysical function, thereby highlighting the importance of considering 4 dimensions (space + time) in cell-matrix biomaterials. This concept of amplification via heterogeneity can be harnessed to increase mechanical efficiency in diverse systems including implantable biomaterials, swarm robotics, and active polymer composites.

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. However, the 658-nucleotide long sequences of DNA from the mitochondrial Cytochrome C Oxidase subunit 1 gene (COI) of C. balticus and C. ponticus were identical upon comparison. Further, they compared with homologous sequences for C. marinus Holiday and C. tsushimensis Tokunaga from the Barcode of Life (BOLD) database and the results plotted as a weighted graph, where C. tsushimensis, C. marinus and C. balticus C. ponticus formed three almost equidistant groups. From this, we established that the genetic distance between the respective COI sequences of C. balticus and C. ponticus is minimal, indicating a close relationship between the species indicative of recent common origin. However, the comparative analysis between C. tsushimensis, C. marinus, C. balticus and C. ponticus showed a wider divergence in their respective nucleotide sequences. Overall, our results emphasized that the COI region does not work well as a DNA barcode to identify species within the Clunio genus. Either longer sequences or a multifaceted methodological approach, including morphology, cytogenetic and ecology is needed to distinguish some members of Clunio genus.

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. This position disregards mathematical thinking as having contributed key discoveries in biology for more than a century, e.g., in the connection between genes, inheritance, and evolution or in the mechanisms of enzymatic catalysis. Here, we discuss the role of computational modelling in the arsenal of modern scientific methods in biomedicine. We list frequent misconceptions about mathematical modelling found among biomedical experimentalists and suggest some good practices that can help bridge the cognitive gap between modelers and experimental researchers in biomedicine. This manuscript was written with two readers in mind. Firstly, it is intended for mathematical modelers with a background in physics, mathematics, or engineering who want to jump into biomedicine. We provide them with ideas to motivate the use of mathematical modelling when discussing with experimental partners. Secondly, this is a text for biomedical researchers intrigued with utilizing mathematical modelling to investigate the pathophysiology of human diseases to improve their diagnostics and treatment.

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. We develop a mesoscale computational model to probe the behavior of compressed suspensions consisting of microgels with different architectures at a variety of packing fractions and solvent conditions. We find that microgels predominantly change shape and mildly shrink above random close packing. Interpenetration is only appreciable above space filling, remaining small relative to the mean distance between cross-links. At even higher packing fractions, microgels solely shrink. Remarkably, irrespective of the single-microgel properties, and whether the suspension concentration is changed via changing the particle number density or the swelling state of the particles, which can even result in colloidal gelation, the mechanics of the suspension can be quantified in terms of the single-microgel bulk modulus, which thus emerges as the correct mechanical measure for these type of soft-colloidal suspensions. Our results rationalize the many and varied experimental results, providing insights into the relative importance of effects defining the mechanics of suspensions comprising soft particles.

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. Interpretations of the results are given, both according to dynamic theory and in biological terms. In terms of cell signaling, we propose the hypothesis that when the outgoing signal of a system spends a physiologically significant amount of time outside of its equilibrium state, then the value of that signal can be sampled at any point along the trajectory towards that equilibrium and indeed, at multiple points. Coupled with non-linear behavior, such as that caused by cooperativity, this feature can account for a complex and varied response, which p53 is known for. From dynamical point of view, we found that when cooperativity is negative, the system has only one stable equilibrium point. In the absence of cooperativity, there is a single unstable equilibrium point with a critical boundary of stability. In the case with normal cooperativity, the system can have one, two, or three steady states with both, bi-stability and bi-instability occurring.

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. However, data regarding their prognostic contribution to PG-DLBCL are limited. AIM: To assess the prognostic impact of a panel of simple, cost-effective laboratory variables which are easy to apply in routine labora-tory use for R-CHOP-treated PG-DLBCL patients in an attempt to identify those among them that are high-risk category. MATERIALS AND METHODS: We retrospectively assessed the possible prognostic impact of different laboratory markers in 42 R-CHOP treated PG-DLBCL patients treated between 2004 and 2014 and followed at a single institution. RESULTS: The estimated 5-year overall (OS) and progression-free survival (PFS) of the whole group were 80.9% and 78%, respectively. The absolute monocyte and platelet counts in univariate analysis predicted PFS and OS when analyzed as continuous and dichotomized variables. On multivariate analysis performed with factors included in the stage-modified International Prognostic Index (m-IPI), the absolute monocyte and platelet counts remained independent predictors of PFS and OS. Therefore, the absolute monocyte and platelet counts were combined to generate a prognostic index that identified patients with an especially poor overall survival. CONCLUSIONS: This prognostic index was independent of the m-IPI and could provide additional prognostic information for better stratification of these patients.

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. When biological systems are far from their steady states, then nonlinear dependences take place, and a slight external impact can cause unexpected and unpredictable (chaotic, irregular) behaviour in these systems, resulting in fractal hierarchical structures. By examining tumours as strange (chaotic) attractors, we define in this article the hypothesis that the cause of their occurrence, development and spread (metastasis) is due to disorders in the hierarchical structure and integration of cell signalling pathways in tumour cells. An essential point in this article is the thesis (contrary to the view that the only causality in hierarchical systems is physical causality, i.e. there is no "top-down,' "holistic causality,' "intelligent causality,' etc.) that hierarchical systems are built on the principle of communication. Intelligent systems (in particular biological) that do not interact as mechanical objects, but on the basis of different meanings of biochemical signals obtained after their interpretation, participate in this communication.

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.e., 3-MHz center frequency, λ /2 pitch, and [Formula: see text] active footprint. Raw RF data are obtained using an experimental research ultrasound scanner, SARUS. The SAI sequences are designed for imaging down to 14 cm at a volume rate of 88 Hz. Two beamforming methods, spatial matched filtering and row-column adapted delay-and-sum, are used for beamforming the RF data. The imaging quality is investigated through simulations and phantom measurements. Both probes on average have similar lateral full-width at half-maximum (FWHM) values, but the PZT probe has 20% smaller cystic resolution values and 70% larger contrast-to-noise ratio (CNR) compared to the capacitive micromachined ultrasonic transducer (CMUT) probe. The CMUT probe can penetrate down to 15 cm, and the PZT probe down to 30 cm. The CMUT probe has 17% smaller axial FWHM values. The matched filter focusing shows an improved B-mode image for measurements on a cyst phantom with an improved speckle pattern and better visualization of deeper lying cysts. The results of this study demonstrate the potentials of RCA 2-D arrays against fully addressed 2-D arrays, which are low channel count (e.g., 124 instead of 3844), low acoustic intensity mechanical index (MI ≤ 0.88 and spatial-peak-temporal-average intensity [Formula: see text]), and high penetration depth (down to 30 cm), which makes 3-D imaging at high volume rates possible with equipment in the price range of conventional 2-D imaging.

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. This paper describes a new technique which allows the real-time visualization of the applied stress with a color-coded stress map. The potential use of this map is discussed. METHODS: Ten patients (5 breast, 5 thyroid) and phantoms were scanned using the stress map. The stress applied was varied and the resultant change in the strain image evaluated. RESULTS: The stress map was able to document if appropriate stress was applied when performing strain elastography. When inappropriate stress was applied or physiological process effected the strain image the stress map demonstrated the areas of inaccurate measurements in the stress map. CONCLUSIONS: The display of a stress map that depicts the degree and uniformity of applied stress would be helpful both for training of the appropriate technique, for confirming that the elastogram is appropriate for evaluation, and that strain ratio estimates are accurate.

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. The shell pores are decorated with a copolymer brush that regulates the transport of solutes into the capsule interior. When exposed to an external stimulus, the microgel swells, expanding through the shell pores to make contact with the nanoparticle-rich solution surrounding the capsule. Upon removal of the external stimulus, the gel retracts back into the shell, bringing along with it captured nanoparticles. We probe how periodic application of the stimulus combined with nanoparticle-microgel adhesion enable selectivity and enhance capturing efficiency of our nature-inspired microdevice.

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. The ensuing evolution of the gel then happens at fixed volume, leading to phase separation and the development of inhomogeneous stress that deforms the toroidal shape. We observe that this stress can cause the torus to buckle out of the plane, via a mechanism analogous to the bending of bimetallic strips upon heating. Our results demonstrate that thermodynamic instabilities, i.e., phase transitions, can be used to actuate mechanical deformation in an extreme thermodynamics of materials.

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 25.4 mm were manufactured using RTV664 silicone. The diverging properties of the lenses were evaluated based on simulations and measurements on several phantoms. The measured FOV for both lenses in contact with tissue mimicking phantom was less than 15% different from the theoretical predictions, i.e., a curvilinear FOV of and for the 12.7- and 25.4-mm radii lenses. A synthetic aperture imaging sequence with single-element transmissions was designed for imaging down to 140 mm at a volume rate of 88 Hz. The performance was evaluated in terms of signal-to-noise ratio, FOV, and full-width at half-maximum (FWHM) of a focused beam. The penetration depths in a tissue mimicking phantom with 0.5-dB/(cm MHz) attenuation were 100 and 125 mm for the lenses with radii of 12.7 and 25.4 mm. The azimuth, elevation, and radial FWHM at 43-mm depth were (5.8, 5.8, 1) and (6, 6, 1) . The results of this study confirm that the proposed lens approach is an effective method for increasing the FOV, when imaging with RCA 2-D arrays.

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. In addition, we found that clinical profiling of colorectal cancer correlates with the in silico phenotypes proposed by the mathematical model. Further, potential therapeutic targets for chemotherapy resistant phenotypes are proposed, which in any case will require experimental validation.

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. By evaluation of the strain-dependent optical properties, we find a reversible, nonlinear shift of the dominant plasmonic resonance. We could quantitatively explain this feature based on simulations using generalized multiparticle Mie theory (GMMT). Both optical and morphological characterization show that the unstrained sample is dominated by chains with a length above the so-called infinite chain limit-above which optical properties show no dependency on chain length-while during deformation, the average chain length decrease below this limit and chain length distribution becomes more narrow. Since the formation mechanism results in a well-defined, parallel orientation of the oligomers on macroscopic areas, the effect of finite chain length can be studied even using conventional UV-vis-NIR spectroscopy. The scalable fabrication of oriented, linear plasmonic oligomers opens up additional opportunities for strain-dependent optical devices and mechanoplasmonic sensing.

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. A synthetic aperture imaging sequence with single element transmissions is designed for imaging down to 14 cm at a volume rate of 88 Hz. Using a diverging lens with an f-number of -1 circumscribing the underlying RCA array, the imaging quality of a double-curved λ/2 -pitch 3-MHz 62 + 62 RCA 2-D array is investigated as a function of depth within a curvilinear FOV of 60 °×60° . The simulated double-curved 2-D array exhibits the same full-width-at-half-maximum values for a point scatterer within its curvilinear FOV at a fixed radial distance compared with a flat 2-D array within its rectilinear FOV. The results of this paper demonstrate that the proposed beamforming approach is accurate for achieving correct time-of-flight calculations, and hence avoids geometrical distortions.

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. The current state of the art is explained along with an overview of clinical studies conducted and methods for presenting and using VFI. A number of examples of VFI images are presented, and the current limitations and potential solutions are discussed.

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. These emerging techniques allow the vector flow systems to assess highly complex flow with transitory vortices and moving tissue, and they can also be used in functional ultrasound imaging for studying brain function in animals. This paper explains the underlying acquisition and estimation methods for fast 2-D and 3-D velocity imaging and gives a number of examples. Future challenges and the potentials of parallel acquisition systems for flow imaging are also discussed.

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. The high number of hierarchical levels and the compositional diversity provide a high degree of freedom for varying the physical, in particular mechanical, properties of the material. This makes the cuticle a versatile material ideally suited to form a variety of skeletal elements that are adapted to different functions and the eco-physiological strains of individual species. This review presents our recent analytical, experimental and theoretical studies on the cuticle, summarising at which hierarchical levels structure and composition are modified to achieve the required physical properties. We describe our multi-scale hierarchical modeling approach based on the results from these studies, aiming at systematically predicting the structure-composition-property relations of cuticle composites from the molecular level to the macro-scale. This modeling approach provides a tool to facilitate the development of optimized biomimetic materials within a knowledge-based design approach.

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 ß-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 ß-sheet retains constant volume under the same conditions and supports the bimorph construct. This selective swelling within the silk-on-silk bimorph microsheets generates strong interfacial stress between layers and out-of-plane forces, which trigger autonomous self-rolling into various 3D constructs such as cylindrical and helical tubules. The experimental observations and computational modeling confirmed the role of interfacial stresses and allow programming the morphology of the 3D constructs with particular design. We demonstrated that the biaxial stress distribution over the 2D planar films depends upon the lateral dimensions, thickness and the aspect ratio of the microsheets. The results allow the fine-tuning of autonomous shape transformations for the further design of complex micro-origami constructs and the silk based rolling/unrolling structures provide a promising platform for polymer-based biomimetic devices for implant applications.

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. To this end, the differentially expressed genes were annotated with standard gene ontology terms and aggregated into metagenes. Our method sheds light on putative mechanisms by which melanoma may develop immunoresistance. Precisely, our results and the clinical data point to the existence of a signature of intermediate expression levels for genes related to antigen presentation that constitutes an intriguing resistance mechanism, whereby micrometastases are able to minimize the combined anti-tumor activity of complementary responses mediated by cytotoxic T cells and natural killer cells, respectively. Finally, we computationally explored the efficacy of cytokines used as low-dose co-adjuvants for the therapeutic anticancer vaccine to overcome tumor immunoresistance.