The explicit bonding reaction ensemble Monte Carlo method.

We present the explicit bonding Reaction ensemble Monte Carlo (eb-RxMC) method, designed to sample reversible bonding reactions in macromolecular systems in thermodynamic equilibrium. Our eb-RxMC method is based on the reaction ensemble method; however, its implementation differs from the latter by the representation of the reaction. In the eb-RxMC implementation, we are adding or deleting bonds between existing particles, instead of inserting or deleting particles with different chemical identities. This new implementation makes the eb-RxMC method suitable for simulating the formation of reversible linkages between macromolecules, which would not be feasible with the original implementation. To enable coupling of our eb-RxMC algorithm with molecular dynamics algorithm for the sampling of the configuration space, we biased the sampling of reactions only within a certain inclusion radius. We validated our algorithm using a set of ideally behaving systems undergoing dimerization and polycondensation reactions, for which analytical results are available. For dimerization reactions with various equilibrium constants and initial compositions, the degree of conversion measured in our simulations perfectly matched the reference values given by the analytical equations. We also showed that this agreement is not affected by the arbitrary choice of the inclusion radius or the stiffness of the harmonic bond potential. Next, we showed that our simulations can correctly match the analytical results for the distribution of the degree of polymerization and end-to-end distance of ideal chains in polycondensation reactions. Altogether, we demonstrated that our eb-RxMC simulations correctly sample both reaction and configuration spaces of these reference systems, opening the door to future simulations of more complex interacting macromolecular systems.

pyMBE: The Python-based molecule builder for ESPResSo.

We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software application to design custom coarse-grained (CG) models, as well as pre-defined models of polyelectrolytes, peptides, and globular proteins in the Extensible Simulation Package for Research on Soft Matter (ESPResSo). The Python interface of ESPResSo offers a flexible framework, capable of building custom CG models from scratch. As a downside, building CG models from scratch is prone to mistakes, especially for newcomers in the field of CG modeling, or for molecules with complex architectures. The pyMBE module builds CG models in ESPResSo using a hierarchical bottom-up approach, providing a robust tool to automate the setup of CG models and helping new users prevent common mistakes. ESPResSo features the constant pH (cpH) and grand-reaction (G-RxMC) methods, which have been designed to study chemical reaction equilibria in macromolecular systems with many reactive species. However, setting up these methods for systems, which contain several types of reactive groups, is an error-prone task, especially for beginners. The pyMBE module enables the automatic setup of cpH and G-RxMC simulations in ESPResSo, lowering the barrier for newcomers and opening the door to investigate complex systems not studied with these methods yet. To demonstrate some of the applications of pyMBE, we showcase several case studies where we successfully reproduce previously published simulations of charge-regulating peptides and globular proteins in bulk solution and weak polyelectrolytes in dialysis. The pyMBE module is publicly available as a GitHub repository (https://github.com/pyMBE-dev/pyMBE), which includes its source code and various sample and test scripts, including the ones that we used to generate the data presented in this article.

Application of Machine Learning Techniques to Assess Alpha-Fetoprotein at Diagnosis of Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) is the most common primary liver tumor and is associated with high mortality rates. Approximately 80% of cases occur in cirrhotic livers, posing a significant challenge for appropriate therapeutic management. Adequate screening programs in high-risk groups are essential for early-stage detection. The extent of extrahepatic tumor spread and hepatic functional reserve are recognized as two of the most influential prognostic factors. In this retrospective multicenter study, we utilized machine learning (ML) methods to analyze predictors of mortality at the time of diagnosis in a total of 208 patients. The eXtreme gradient boosting (XGB) method achieved the highest values in identifying key prognostic factors for HCC at diagnosis. The etiology of HCC was found to be the variable most strongly associated with a poorer prognosis. The widely used Barcelona Clinic Liver Cancer (BCLC) classification in our setting demonstrated superiority over the TNM classification. Although alpha-fetoprotein (AFP) remains the most commonly used biological marker, elevated levels did not correlate with reduced survival. Our findings suggest the need to explore new prognostic biomarkers for individualized management of these patients.

Quantitative coronary three-dimensional geometry and its association with atherosclerotic disease burden and composition.

BACKGROUND: Isolate features of the coronary anatomy have been associated with the pathophysiology of atherosclerotic disease. Computational methods have been described to allow precise quantification of the complex three-dimensional (3D) coronary geometry. The present study tested whether quantitative parameters that describe the spatial 3D coronary geometry is associated with the extension and composition of the underlying coronary artery disease (CAD). METHODS: Patients with CAD scheduled for percutaneous intervention were investigated with coronary computed tomography angiography (CCTA), and invasive coronary angiography, and virtual histology intravascular ultrasound (IVUS-VH). For all target vessels, 3D centerlines were extracted from CCTA images and processed to quantify 23 geometric indexes, grouped into 3 main categories as follows: (i) length-based; (ii) curvature-based, torsion-based, and curvature/torsion-combined; (iii) vessel path-based. The geometric variables were compared with IVUS-VH parameters assessing the extent and composition of coronary atherosclerosis. RESULTS: A total of 36 coronary patients (99 vessels) comprised the study population. From the 23 geometric indexes, 18 parameters were significantly (p < 0.05) associated with at least 1 IVUS-VH parameter at a univariate analysis. All three main geometric categories provided parameters significantly related with atherosclerosis variables. The 3D geometric indexes were associated with the degree of atherosclerotic extension, as well as with plaque composition. Geometric features remained significantly associated with all IVUS-VH parameters even after multivariate adjustment for clinical characteristics. CONCLUSIONS: Quantitative 3D vessel morphology emerges as a relevant factor associated with atherosclerosis in patients with established CAD.

Reply to the 'Comment on "Simulations of ionization equilibria in weak polyelectrolyte solutions and gels"' by J. Landsgesell, L. Nová, O. Rud, F. Uhlík, D. Sean, P. Hebbeker, C. Holm and P. Kosovan, Soft Matter, 2019, 15, 1155-1185.

Levin and Bakhshandeh suggested in their comment that (1), we stated in our recent review that pH-pKA is a universal parameter for titrating systems, that (2), we omitted to mention in our review the broken symmetry of the constant pH algorithm, and that (3), a constant pH simulation must include a grand-canonical exchange of ions with the reservoir. As a reply to (1), we point out that Levin and Bakhshandeh misquoted and hence invalidated our original statement. We therefore explain in detail under which circumstances pH-pKA can be a universal parameter, and also demonstrate why their numerical example is not in contradiction to our statement. Moreover, the fact that pH-pKA is not a universal parameter for titrating systems is well known in the pertinent literature. Regarding (2), we admit that the symmetry-breaking feature of the constant pH algorithm has escaped our attention at the time of writing the review. We added some clarifying remarks to this behavior. Concerning (3), we point out that the grand-canonical coupling and the resultant Donnan potential are not features of single-phase systems, but are essential for two-phase systems, as was shown in a recent paper by some of us, see J. Landsgesell et al., Macromolecules, 2020, 53, 3007-3020.

Anionically Functionalized Glycogen Encapsulates Melittin by Multivalent Interaction.

We developed acid-functionalized glycogen conjugates as supramolecular carriers for efficient encapsulation and inhibition of a model cationic peptide melittin─the main component of honeybee venom. For this purpose, we synthesized and characterized a set of glycogens, functionalized to various degrees by several different acid groups. These conjugates encapsulate melittin up to a certain threshold amount, beyond which they precipitate. Computer simulations showed that sufficiently functionalized conjugates electrostatically attract melittin, resulting in its efficient encapsulation in a broad pH range around the physiological pH. Hemolytic assays confirmed in vitro that the effective inhibition of melittin's hemolytic activity occurs for highly functionalized samples, whereas no inhibition is observed when using low-functionalized conjugates. It can be concluded that functional glycogens are promising carriers for cationic molecular cargos or antidotes against animal venoms under conditions, in which suitable properties such as biodegradability and biocompatibility are crucial.

The electrostatic potential inside and around α-lactalbumin: Fluctuations and mean-field models.

The electrostatic potential (EP) generated by the protein α-lactoalbumin in the presence of added salt is computed as a thermal average at a given point in space. With this aim, constant pH Monte Carlo (MC) simulations are performed within the primitive model, namely, the solvent is treated as a continuum dielectric. The study of the thermal and spatial fluctuations of the EP reveals that they are remarkably high inside the protein. The calculations indicate that fluctuations inside the protein are mainly due to the asymmetric distribution of the charge groups, while the charge fluctuations of the titratable groups play a minor role. The computed EP matches very well with the one obtained from the Poisson equation for the average charge density in spherical symmetry. The Tanford-Kirkwood multipole expansion reproduces the simulated angular-averaged potential rather accurately. Surprisingly, two of the simplest mean-field models, the linear Poisson-Boltzmann (PB) equation and Donnan potential, provide good estimations of the average EP in the effective protein surface (surface EP). The linear PB equation predicts a linear relationship between charge and surface EP, which is numerically reproduced only if the small ions within the protein are taken into account. On the other hand, the partition coefficients of the small ions inside and outside the protein predicted by Donnan theory reproduce reasonably well the simulation results.

A rare complication of jejunal extension of a percutaneous endoscopic gastrostomy tube for levodopa-carbidopa intestinal gel administration.

Direct intestinal administration of levodopa-carbidopa gel has shown good results in selected patients with Parkinson's disease (1, 2). We want to present a complication related to the device necessary for the administration of this drug. A 58-year-old man, diagnosed with Parkinson's disease, treated for six months with levodopa-carbidopa intestinal gel, administered through a percutaneous endoscopic gastrostomy (PEG) tube with jejunal extension, presented at the emergency department for abdominal pain. The patient complained abdominal discomfort that lasted two months. It was described as pain around the umbilical area that radiated to the left lumbar region, worsened after ingestion, and did not subside with conventional analgesia.

Influence of macromolecular crowding on the charge regulation of intrinsically disordered proteins.

In this work we study the coupling between ionization and conformational properties of two IDPs, histatin-5 and ß-amyloid 42, in the presence of neutral and charged crowders. The latter is modeled to resemble bovine serum albumin (BSA). With this aim, semi-grand canonical Monte Carlo simulations are performed, so that the IDP charge is a dynamic property, undergoing protonation/deprotonation processes. Both ionization properties (global and specific amino acid charge and binding capacitance) and radius of gyration are analyzed in a large range of pH values and salt concentrations. Without crowder agents, the titration curve of histatin-5, a polycation, is salt-dependent while that of ß-amyloid 42, a polyampholyte, is almost unaffected. The salt concentration is found to be particularly relevant at pH values where the protein binding capacitance (directly linked with charge fluctuation) is larger. Upon addition of neutral crowders, charge regulation is observed in histatin-5, while for ß-amyloid 42 this effect is very small. The main mechanism for charge regulation is found to be the effective increase in the ionic strength due to the excluded volume. In the presence of charged crowders, a significant increase in the charge of both IDPs is observed in almost all the pH range. In this case, the IDP charge is altered not only by the increase in the effective ionic strength but also by its direct electrostatic interaction with the charged crowders.

Multi-organ point-of-care ultrasound for COVID-19 (PoCUS4COVID): international expert consensus.

COVID-19 has caused great devastation in the past year. Multi-organ point-of-care ultrasound (PoCUS) including lung ultrasound (LUS) and focused cardiac ultrasound (FoCUS) as a clinical adjunct has played a significant role in triaging, diagnosis and medical management of COVID-19 patients. The expert panel from 27 countries and 6 continents with considerable experience of direct application of PoCUS on COVID-19 patients presents evidence-based consensus using GRADE methodology for the quality of evidence and an expedited, modified-Delphi process for the strength of expert consensus. The use of ultrasound is suggested in many clinical situations related to respiratory, cardiovascular and thromboembolic aspects of COVID-19, comparing well with other imaging modalities. The limitations due to insufficient data are highlighted as opportunities for future research.

Superior vena cava obstruction and mediastinal mass detected by point-of-care ultrasonography.

Superior vena cava syndrome (SVCS) often relates to malignant causes such as lung tumors, metastatic cancer, or lymphomas. While the diagnosis relies nowadays on the use of contrast-enhanced thoracic computed tomography, ultrasonography may have an important value as a first-line imaging technique, particularly when used in point-of-care office-based settings. Here, we report the case of a 67-year-old male presenting with SVCS in whom ultrasound contributed to diagnosis.

The role of clonal communication and heterogeneity in breast cancer.

BACKGROUND: Cancer is a rapidly evolving, multifactorial disease that accumulates numerous genetic and epigenetic alterations. This results in molecular and phenotypic heterogeneity within the tumor, the complexity of which is further amplified through specific interactions between cancer cells. We aimed to dissect the molecular mechanisms underlying the cooperation between different clones. METHODS: We produced clonal cell lines derived from the MDA-MB-231 breast cancer cell line, using the UbC-StarTrack system, which allowed tracking of multiple clones by color: GFP C3, mKO E10 and Sapphire D7. Characterization of these clones was performed by growth rate, cell metabolic activity, wound healing, invasion assays and genetic and epigenetic arrays. Tumorigenicity was tested by orthotopic and intravenous injections. Clonal cooperation was evaluated by medium complementation, co-culture and co-injection assays. RESULTS: Characterization of these clones in vitro revealed clear genetic and epigenetic differences that affected growth rate, cell metabolic activity, morphology and cytokine expression among cell lines. In vivo, all clonal cell lines were able to form tumors; however, injection of an equal mix of the different clones led to tumors with very few mKO E10 cells. Additionally, the mKO E10 clonal cell line showed a significant inability to form lung metastases. These results confirm that even in stable cell lines heterogeneity is present. In vitro, the complementation of growth medium with medium or exosomes from parental or clonal cell lines increased the growth rate of the other clones. Complementation assays, co-growth and co-injection of mKO E10 and GFP C3 clonal cell lines increased the efficiency of invasion and migration. CONCLUSIONS: These findings support a model where interplay between clones confers aggressiveness, and which may allow identification of the factors involved in cellular communication that could play a role in clonal cooperation and thus represent new targets for preventing tumor progression.

Coronary fractional flow reserve derived from intravascular ultrasound imaging: Validation of a new computational method of fusion between anatomy and physiology.

OBJECTIVES: To evaluate the diagnostic performance of a novel computational algorithm based on three-dimensional intravascular ultrasound (IVUS) imaging in estimating fractional flow reserve (IVUSFR ), compared to gold-standard invasive measurements (FFRINVAS ). BACKGROUND: IVUS provides accurate anatomical evaluation of the lumen and vessel wall and has been validated as a useful tool to guide percutaneous coronary intervention. However, IVUS poorly represents the functional status (i.e., flow-related information) of the imaged vessel. METHODS: Patients with known or suspected stable coronary disease scheduled for elective cardiac catheterization underwent FFRINVAS measurement and IVUS imaging in the same procedure to evaluate intermediate lesions. A processing methodology was applied on IVUS to generate a computational mesh condensing the geometric characteristics of the vessel. Computation of IVUSFR was obtained from patient-level morphological definition of arterial districts and from territory-specific boundary conditions. FFRINVAS measurements were dichotomized at the 0.80 threshold to define hemodynamically significant lesions. RESULTS: A total of 24 patients with 34 vessels were analyzed. IVUSFR significantly correlated (r = 0.79; P < 0.001) and showed good agreement with FFRINVAS , with a mean difference of -0.008 ± 0.067 (P = 0.47). IVUSFR presented an overall accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of 91%, 89%, 92%, 80%, and 96%, respectively, to detect significant stenosis. CONCLUSION: The computational processing of IVUSFR is a new method that allows the evaluation of the functional significance of coronary stenosis in an accurate way, enriching the anatomical information of grayscale IVUS.

Lung Ultrasonography for Assessing Lung Aeration in Acute Respiratory Distress Syndrome: A Narrative Review.

Acute respiratory distress syndrome (ARDS) constitutes a high burden for intensive care units. Although several methods are proposed to monitor aeration in ARDS, availability, costs, simplicity, and hazards (eg, ionizing radiation) limit the use of many of them at patients' bedsides. Given the widespread use of lung ultrasonography (US) in intensive care units, research is growing regarding its use to monitor aeration in patients with ARDS. We reviewed the actual role of lung US in ARDS and its potential impact in practice. Lung US can be readily used for assessing aeration, although, as a main limitation, a normal lung cannot be distinguished from hyperinflation. Additionally, an improvement in aeration by lung US does not always correlate with an increase in oxygenation. Lung US can be considered the main imaging method for monitoring aeration in ARDS, but in view of its limitations, it should not be used in isolation. Further studies are needed to validate lung US in large ARDS populations.

Macromolecular diffusion in crowded media beyond the hard-sphere model.

The effect of macromolecular crowding on diffusion beyond the hard-core sphere model is studied. A new coarse-grained model is presented, the Chain Entanglement Softened Potential (CESP) model, which takes into account the macromolecular flexibility and chain entanglement. The CESP model uses a shoulder-shaped interaction potential that is implemented in the Brownian Dynamics (BD) computations. The interaction potential contains only one parameter associated with the chain entanglement energetic cost (Ur). The hydrodynamic interactions are included in the BD computations via Tokuyama mean-field equations. The model is used to analyze the diffusion of a streptavidin protein among different sized dextran obstacles. For this system, Ur is obtained by fitting the streptavidin experimental long-time diffusion coefficient Dlongversus the macromolecular concentration for D50 (indicating their molecular weight in kg mol-1) dextran obstacles. The obtained Dlong values show better quantitative agreement with experiments than those obtained with hard-core spheres. Moreover, once parametrized, the CESP model is also able to quantitatively predict Dlong and the anomalous exponent (α) for streptavidin diffusion among D10, D400 and D700 dextran obstacles. Dlong, the short-time diffusion coefficient (Dshort) and α are obtained from the BD simulations by using a new empirical expression, able to describe the full temporal evolution of the diffusion coefficient.

Practical Use of Robot Manipulators as Intelligent Manufacturing Systems.

This paper presents features and advanced settings for a robot manipulator controller in a fully interconnected intelligent manufacturing system. Every system is made up of different agents. As also occurs in the Internet of Things and smart cities, the big issue here is to ensure not only that implementation is key, but also that there is better common understanding among the main players. The commitment of all agents is still required to translate that understanding into practice in Industry 4.0. Mutual interactions such as machine-to-machine and man-to-machine are solved in real time with cyber physical capabilities. This paper explores intelligent manufacturing through the context of industrial robot manipulators within a Smart Factory. An online communication algorithm with proven intelligent manufacturing abilities is proposed to solve real-time interactions. The algorithm is developed to manage and control all robot parameters in real-time. The proposed tool in conjunction with the intelligent manufacturing core incorporates data from the robot manipulators into the industrial big data to manage the factory. The novelty is a communication tool that implements the Industry 4.0 standards to allow communications among the required entities in the complete system. It is achieved by the developed tool and implemented in a real robot and simulation.

Computer-aided quantification of microvascular networks: Application to alterations due to pathological angiogenesis in the hamster.

Angiogenesis is both a physiological and a pathological process of great complexity, which is difficult to measure objectively and automatically. The hamster cheek pouch (HCP) prepared for intravital-microscopy (IVM) has been used to characterize microvascular functions in many studies and was chosen to investigate microvascular characteristics observed in normal non-infected hamsters as compared to those HCPs parasitized by Trypanosoma cruzi. Images of HCPs captured at IVM were subjected to computer based measurements of angiogenesis and histamine-induced macromolecular (FITC-dextran) leakage with an image segmentation approach that has the capacity to discriminate between fluorescence emitted by macromolecular tracers inside the vasculature and in the extravascular space. We present such an automatic segmentation methodology using known tools from image processing field that, to our knowledge, have not been tested in IVM images. We have compared this methodology with a recently published segmentation strategy based on image intensity thresholding. Our method renders an accurate and robust segmentation of blood vessels for different microvascular scenarios, normal and pathological. Application of the proposed strategy for objective and automatic measurement of angiogenesis detection was explored in detail.

Applications of Transcranial Color-Coded Sonography in the Emergency Department.

Transcranial color-coded Doppler sonography is a noninvasive bedside ultrasound application that combines both imaging of parenchymal structures and Doppler assessment of intracranial vessels. It may aid in rapid diagnoses and treatment decision making of patients with intracranial emergencies in point-of-care settings. This pictorial essay illustrates the technical aspects and emergency department applications of transcranial color-coded Doppler sonography, and provides some rationale for implementation of this technique into the emergency department practice.

Roadmap for cardiovascular circulation model.

Computational models of many aspects of the mammalian cardiovascular circulation have been developed. Indeed, along with orthopaedics, this area of physiology is one that has attracted much interest from engineers, presumably because the equations governing blood flow in the vascular system are well understood and can be solved with well-established numerical techniques. Unfortunately, there have been only a few attempts to create a comprehensive public domain resource for cardiovascular researchers. In this paper we propose a roadmap for developing an open source cardiovascular circulation model. The model should be registered to the musculo-skeletal system. The computational infrastructure for the cardiovascular model should provide for near real-time computation of blood flow and pressure in all parts of the body. The model should deal with vascular beds in all tissues, and the computational infrastructure for the model should provide links into CellML models of cell function and tissue function. In this work we review the literature associated with 1D blood flow modelling in the cardiovascular system, discuss model encoding standards, software and a model repository. We then describe the coordinate systems used to define the vascular geometry, derive the equations and discuss the implementation of these coupled equations in the open source computational software OpenCMISS. Finally, some preliminary results are presented and plans outlined for the next steps in the development of the model, the computational software and the graphical user interface for accessing the model.