Dynamic framework for large-scale modeling of membranes and peripheral proteins.

In this chapter, we present a novel computational framework to study the dynamic behavior of extensive membrane systems, potentially in interaction with peripheral proteins, as an alternative to conventional simulation methods. The framework effectively describes the complex dynamics in protein-membrane systems in a mesoscopic particle-based setup. Furthermore, leveraging the hydrodynamic coupling between the membrane and its surrounding solvent, the coarse-grained model grounds its dynamics in macroscopic kinetic properties such as viscosity and diffusion coefficients, marrying the advantages of continuum- and particle-based approaches. We introduce the theoretical background and the parameter-space optimization method in a step-by-step fashion, present the hydrodynamic coupling method in detail, and demonstrate the application of the model at each stage through illuminating examples. We believe this modeling framework to hold great potential for simulating membrane and protein systems at biological spatiotemporal scales, and offer substantial flexibility for further development and parametrization.

Acute effects of Nordic hamstring exercise on hip and knee joints proprioception.

BACKGROUND AND OBJECTIVES: Nordic Hamstring Exercise (NHE) is one of the best exercises proposed for injury prevention of hamstring muscles. However, its effects on lower extremity proprioception are unclear. The aim of this study was to investigate the immediate effects of a single bout of NHE on hip and knee joints' proprioception. METHODS: Forty collegiate male soccer players participated in this study with a mean age of 22.85 ± 1.82 years and were randomized into either control (n = 20) or experimental (n = 20) groups. Each subject participated in pre-test measurements in which hip and knee active joints position sense (JPS) were assessed in standing and lying tasks using the image-capturing method. The experimental group then performed three sets of NHE with 10 repetitions in each set, while the control group rested for 10 min. Paired and independent t-tests were used for calculating the differences within and between groups on SPSS software, respectively. The level of significance was P ≤ 0.05. RESULTS: Hip JPS in the lying task and knee JPS in both of the standing and lying tasks were impaired significantly after performing a single bout of NHE (P ≤ 0.05). However, the effects of this exercise on hip JPS in the standing task were not significant (P ≥ 0.05). CONCLUSIONS: NHE performing with three sets of 10 repetitions can significantly impair hip and knee JPS immediately after exercise and reduce the proprioception acuity of the lower limbs. It is recommended to perform this exercise at a time rather than before training or match sessions.

Inferring control objectives in a virtual balancing task in humans and monkeys.

Natural behaviors have redundancy, which implies that humans and animals can achieve their goals with different strategies. Given only observations of behavior, is it possible to infer the control objective that the subject is employing? This challenge is particularly acute in animal behavior because we cannot ask or instruct the subject to use a particular strategy. This study presents a three-pronged approach to infer an animal's control objective from behavior. First, both humans and monkeys performed a virtual balancing task for which different control strategies could be utilized. Under matched experimental conditions, corresponding behaviors were observed in humans and monkeys. Second, a generative model was developed that represented two main control objectives to achieve the task goal. Model simulations were used to identify aspects of behavior that could distinguish which control objective was being used. Third, these behavioral signatures allowed us to infer the control objective used by human subjects who had been instructed to use one control objective or the other. Based on this validation, we could then infer objectives from animal subjects. Being able to positively identify a subject's control objective from observed behavior can provide a powerful tool to neurophysiologists as they seek the neural mechanisms of sensorimotor coordination.

Sub-membrane actin rings compartmentalize the plasma membrane.

The compartmentalization of the plasma membrane (PM) is a fundamental feature of cells. The diffusivity of membrane proteins is significantly lower in biological than in artificial membranes. This is likely due to actin filaments, but assays to prove a direct dependence remain elusive. We recently showed that periodic actin rings in the neuronal axon initial segment (AIS) confine membrane protein motion between them. Still, the local enrichment of ion channels offers an alternative explanation. Here we show, using computational modeling, that in contrast to actin rings, ion channels in the AIS cannot mediate confinement. Furthermore, we show, employing a combinatorial approach of single particle tracking and super-resolution microscopy, that actin rings are close to the PM and that they confine membrane proteins in several neuronal cell types. Finally, we show that actin disruption leads to loss of compartmentalization. Taken together, we here develop a system for the investigation of membrane compartmentalization and show that actin rings compartmentalize the PM.

Protein nanobarcodes enable single-step multiplexed fluorescence imaging.

Multiplexed cellular imaging typically relies on the sequential application of detection probes, as antibodies or DNA barcodes, which is complex and time-consuming. To address this, we developed here protein nanobarcodes, composed of combinations of epitopes recognized by specific sets of nanobodies. The nanobarcodes are read in a single imaging step, relying on nanobodies conjugated to distinct fluorophores, which enables a precise analysis of large numbers of protein combinations. Fluorescence images from nanobarcodes were used as input images for a deep neural network, which was able to identify proteins with high precision. We thus present an efficient and straightforward protein identification method, which is applicable to relatively complex biological assays. We demonstrate this by a multicell competition assay, in which we successfully used our nanobarcoded proteins together with neurexin and neuroligin isoforms, thereby testing the preferred binding combinations of multiple isoforms, in parallel.

To reverse or not to reverse the radial artery in coronary artery bypass graft surgery? Histopathologic concerns and media thickness.

Background and aims: Radial artery (RA) is a popular coronary artery bypass grafting (CABG) conduit. The challenging issue is vasospasm. A few studies are available on histopathological differences between RA's proximal and distal ends. This study aims to compare histopathological features of the proximal and distal end of RA to find the best technique for anastomosis. Methods: In this matched case-control study, 80 patients were included who underwent CABG and used RA as a graft. Ten subjects were excluded. RA was harvested by open technique, and a cocktail of Papaverine, Verapamil, and Nitroglycerine was frequently applied topically. One centimeter of proximal and distal ends of the RA was evaluated considering its Histopathology. Clinical signs of RA graft vasospasm were monitored from harvesting until the post-operative period. Intima, media, and intima-media thickness (IMT) index were compared between the two cohorts. Results: Vasospasm occurred in 1.41% of patients. The mean intimal thickness in the proximal and distal ends were, respectively, 0.20 (standard deviation [SD] 0.17 mm) vs. 0.31 (SD 0.18 mm) (p < 0.001). The mean media thickness in the distal end was higher than the proximal end (0.98 [SD 0.36] vs. 1.09 [SD 0.37], p = 0.004). IMT index of the proximal and distal ends showed a statistically significant difference (0.22 [SD 0.17] vs. 0.31 [SD 0.19]) (p < 0.001). Conclusion: The overall incidence rate of vasospasm in our study is comparable with other studies using the same cocktail. Proximal RA has a relatively lower medial thickness compared to the distal part, which may induce less vasospasm in CABG patients.

Could various angulated implant depths affect the positional accuracy of digital impressions? An in vitro study.

PURPOSE: The purpose of this in vitro investigation was to assess how implant depth could affect the three-dimensional positional accuracy of digital impressions made from angulated implants. MATERIALS AND METHODS: Four modified maxillary models were printed and divided into four study groups. In each model, two angulated implant analogs were placed at the sites of the first premolar and first molar at four different depths of 1 (G1), 2 (G2), 3 (G3), and 4 (G4) mm from the models' edentate area. Scan bodies were connected to the analogs, and one operator made 10 full-arch scans for each master model using an intraoral scanner. Afterward, the marginal gingival part of all models was removed, and digital scans were performed for each model using a laboratory scanner to achieve a reference STL file as the control group. One-way ANOVA and Leven's tests were used to measure and compare the 3D distance deviations across research groups after the superimposing test and control scans. RESULTS: A significant difference between research groups was revealed by trueness and precision analysis (p < 0.001). The trueness and precision results obtained for G1 and G4 were significantly better than those for G2 and G3 (p < 0.05). CONCLUSION: This study demonstrated that implant depth could affect the digital implant impressions' 3D positional accuracy.

Para-Cardiac Inflammatory Mass Compressing the Heart: A possible association with COVID-19.

Infection with the SARS-CoV-2 virus causes coronavirus disease 2019 (COVID-19). COVID-19 usually affects the lungs but may also involve other organs such as the heart. We report a case of a para-cardiac mass in a previously healthy 45-year-old male who developed persistent dyspnea following SARS-CoV-2 infection. The patient underwent cardiac surgery since the mass was attached to the pericardium and was causing constrictive pericarditis. The pathology report indicated an inflammatory pattern for the mass. Based on the authors' knowledge there has been no previous report of developing a para-cardiac inflammatory mass after SARS-CoV-2 infection. This report aimed to increase awareness regarding the possibility of developing a para-cardiac inflammatory mass following COVID-19.

Spatially resolved protein map of intact human cytomegalovirus virions.

Herpesviruses assemble large enveloped particles that are difficult to characterize structurally due to their size, fragility and complex multilayered proteome with partially amorphous nature. Here we used crosslinking mass spectrometry and quantitative proteomics to derive a spatially resolved interactome map of intact human cytomegalovirus virions. This enabled the de novo allocation of 32 viral proteins into four spatially resolved virion layers, each organized by a dominant viral scaffold protein. The viral protein UL32 engages with all layers in an N-to-C-terminal radial orientation, bridging nucleocapsid to viral envelope. We observed the layer-specific incorporation of 82 host proteins, of which 39 are selectively recruited. We uncovered how UL32, by recruitment of PP-1 phosphatase, antagonizes binding to 14-3-3 proteins. This mechanism assures effective viral biogenesis, suggesting a perturbing role of UL32-14-3-3 interaction. Finally, we integrated these data into a coarse-grained model to provide global insights into the native configuration of virus and host protein interactions inside herpesvirions.

Vanillin crosslinked 3D porous chitosan hydrogel for biomedicine applications: Preparation and characterization.

Crosslinked chitosan (CS) is one of the most useable hydrogels in biomedicine and tissue engineering. Unlike most chitosan crosslinkers that are toxic, such as glutaraldehyde, vanillin is a natural, biocompatible, and antimicrobial alternative. The crosslinking of chitosan and vanillin consists of Schiff base bonds between the amines of chitosan and the aldehydes of vanillin, in addition to hydrogen bonds formed across the network. In most studies, the combination of chitosan and vanillin has been investigated in small sizes (micro/nanoscale and biofilms). In this study, a chitosan-vanillin (CV) hydrogel was studied on a macroscale with a three-dimensional porous structure, and it was compared with chitosan crosslinked with glutaraldehyde (CG) on the same scale. Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (FE-SEM) used to identify the bonds formed and examine the morphology of the hydrogels. The gel content, swelling, porosity, mechanical properties, cell viability (on L929 and mesenchymal cells), and antibacterial activity (against Escherichia coli and Staphylococcus aureus) of the samples were investigated. The results showed that the CV had both gel content and high porosity (>90%), with an interconnected porous network of uniform pore size. The CV hydrogel exhibited good antibacterial activity and cell viability. In terms of mechanical properties, CV has weaker mechanical properties compared to CG in the dry state, while the mechanical properties of CV have more improved in the swollen state compared to CG.

3D surface reconstruction of cellular cryo-soft X-ray microscopy tomograms using semisupervised deep learning.

Cryo-soft X-ray tomography (cryo-SXT) is a powerful method to investigate the ultrastructure of cells, offering resolution in the tens of nanometer range and strong contrast for membranous structures without requiring labeling or chemical fixation. The short acquisition time and the relatively large field of view leads to fast acquisition of large amounts of tomographic image data. Segmentation of these data into accessible features is a necessary step in gaining biologically relevant information from cryo-soft X-ray tomograms. However, manual image segmentation still requires several orders of magnitude more time than data acquisition. To address this challenge, we have here developed an end-to-end automated 3D segmentation pipeline based on semisupervised deep learning. Our approach is suitable for high-throughput analysis of large amounts of tomographic data, while being robust when faced with limited manual annotations and variations in the tomographic conditions. We validate our approach by extracting three-dimensional information on cellular ultrastructure and by quantifying nanoscopic morphological parameters of filopodia in mammalian cells.

Inferring control objectives in a virtual balancing task in humans and monkeys.

Natural behaviors have redundancy, which implies that humans and animals can achieve their goals with different control objectives. Given only observations of behavior, is it possible to infer the control strategy that the subject is employing? This challenge is particularly acute in animal behavior because we cannot ask or instruct the subject to use a particular control strategy. This study presents a threepronged approach to infer an animal's control strategy from behavior. First, both humans and monkeys performed a virtual balancing task for which different control objectives could be utilized. Under matched experimental conditions, corresponding behaviors were observed in humans and monkeys. Second, a generative model was developed that represented two main control strategies to achieve the task goal. Model simulations were used to identify aspects of behavior that could distinguish which control objective was being used. Third, these behavioral signatures allowed us to infer the control objective used by human subjects who had been instructed to use one control objective or the other. Based on this validation, we could then infer strategies from animal subjects. Being able to positively identify a subject's control objective from behavior can provide a powerful tool to neurophysiologists as they seek the neural mechanisms of sensorimotor coordination.

Body Mechanics, Optimality, and Sensory Feedback in the Human Control of Complex Objects.

Humans are adept at a wide variety of motor skills, including the handling of complex objects and using tools. Advances to understand the control of voluntary goal-directed movements have focused on simple behaviors such as reaching, uncoupled to any additional object dynamics. Under these simplified conditions, basic elements of motor control, such as the roles of body mechanics, objective functions, and sensory feedback, have been characterized. However, these elements have mostly been examined in isolation, and the interactions between these elements have received less attention. This study examined a task with internal dynamics, inspired by the daily skill of transporting a cup of coffee, with additional expected or unexpected perturbations to probe the structure of the controller. Using optimal feedback control (OFC) as the basis, it proved necessary to endow the model of the body with mechanical impedance to generate the kinematic features observed in the human experimental data. The addition of mechanical impedance revealed that simulated movements were no longer sensitively dependent on the objective function, a highly debated cornerstone of optimal control. Further, feedforward replay of the control inputs was similarly successful in coping with perturbations as when feedback, or sensory information, was included. These findings suggest that when the control model incorporates a representation of the mechanical properties of the limb, that is, embodies its dynamics, the specific objective function and sensory feedback become less critical, and complex interactions with dynamic objects can be successfully managed.

Stochastic Approximation to MBAR and TRAM: Batchwise Free Energy Estimation.

The dynamics of molecules are governed by rare event transitions between long-lived (metastable) states. To explore these transitions efficiently, many enhanced sampling protocols have been introduced that involve using simulations with biases or changed temperatures. Two established statistically optimal estimators for obtaining unbiased equilibrium properties from such simulations are the multistate Bennett acceptance ratio (MBAR) and the transition-based reweighting analysis method (TRAM). Both MBAR and TRAM are solved iteratively and can suffer from long convergence times. Here, we introduce stochastic approximators (SA) for both estimators, resulting in SAMBAR and SATRAM, which are shown to converge faster than their deterministic counterparts, without significant accuracy loss. Both methods are demonstrated on different molecular systems.

One-year prevalence and the association between SARS-CoV-2 cycle threshold, comorbidity and outcomes in population of Babol, North of Iran (2020-2021).

Background: The present study aimed to investigate the one-year prevalence of SARS-CoV-2, common comorbidities and demographic information among negative- and positive rRT-PCR in health care workers (HCW), hospitalized and outpatients. Also, the association between SARS-CoV-2 cycle threshold (Ct) and the outcomes of patients were analyzed in Babol, northern Iran. Methods: This large retrospective cross-sectional study was performed between March 2020 and March 2021. The records of 19232 hospitalized, outpatients and HCW suspected to COVID-19 were collected from teaching hospitals in the North of Iran. Results: Out of the 19232 suspected to COVID-19 patients, 7251 (37.7%) had a positive rRT-PCR result; 652 (9%), 4599 (63.4%) and 2000 (27.6%) of those were categorized as HCW, hospitalized and outpatients, respectively. Moreover, between the hospitalized and the outpatient group, 10.2 and 0.8% cases died, whereas no death cases were reported in the HCW. Furthermore, it seems that death rate was significantly different between the three groups of Ct value, the highest mortality in those with Ct between 21 and 30 (group B=7.6%) and the lowest in the group with the highest Ct (between 31 and 40 = 5.5%) (p<0.001). Conclusion: In summary, 37.7% of cases were positive for SARS-CoV-2; of which, 63.4, 27.6 and 9% were hospitalized, outpatients and HCW, respectively. With regard to the mortality rate in hospitalized patients and the significant association with Ct under 20 and 30, it seems that the early detection and the initial quantification of SARS-CoV-2 in the first week of the conflict and therapeutic considerations to reduce the relative load can reduce the mortality rate.

Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins.

Peripheral membrane-associated proteins are known to accumulate on the surface of biomembranes as a result of membrane-mediated interactions. For a pair of rotationally-symmetric curvature-inducing proteins, membrane mechanics at the low-temperature limit predicts pure repulsion. On the other hand, temperature-dependent entropic forces arise between pairs of stiff-binding proteins suppressing membrane fluctuations. These Casimir-like interactions have thus been suggested as candidates for attractive forces leading to aggregation. With dense assemblies of peripheral proteins on the membrane, both these abstractions encounter short-range and multi-body complications. Here, we make use of a particle-based membrane model augmented with flexible peripheral proteins to quantify purely membrane-mediated interactions and investigate their underlying nature. We introduce a continuous reaction coordinate corresponding to the progression of protein aggregation. We obtain free energy and entropy landscapes for different surface concentrations along this reaction coordinate. In parallel, we investigate time-dependent estimates of membrane entropy corresponding to membrane undulations and coarse-grained director field and how they change dynamically with protein aggregation. Congruent outcomes of the two approaches point to the conclusion that for low surface concentrations, interactions with an entropic nature may drive the aggregation. But at high concentrations, enthalpic contributions due to concerted membrane deformation by protein clusters are dominant.

Decreased serum levels of angiotensin converting enzyme (ACE)2 and enhanced cytokine levels with severity of COVID-19: normalisation upon disease recovery.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). Circulating soluble angiotensin-converting enzyme (sACE2)2, the main receptor for SARS-CoV-2, together with components of the renin-angiotensin system promote infection and disease severity. OBJECTIVE: This pilot study followed the time-course of sACE2 levels in relation to systemic cytokines in severe and moderate COVID-19 patients treated with remdesivir/dexamethasone in combination. METHODS: Peripheral blood was obtained upon admission from 30 patients (12 with moderate disease and 18 with severe disease) and 14 patients with PCR-confirmed mild COVID-19. Severe and moderate patients were treated with remdesivir (200mg/first day and 100mg/day for the remaining days) and dexamethasone (100mg/day). 6 healthy control subjects (HC) were also enrolled. Serum interleukin (IL)-6 and IL-8 and sACE2 levels were measured by ELISA at baseline and during treatment in severe and moderate patients and at baseline in mild and HCs. RESULTS: Baseline sACE2 levels were lower in severe (p = 0.0005) and moderate (p = 0.0022) patients than in patients with mild COVID-19 and in HC (p = 0.0023 and p = 0.0012 respectively). Treatment significantly increased sACE2 levels in patients with moderate disease (p = 0.0156) but only 50% of patients with severe disease showed enhanced levels compared to baseline. Systemic IL-6 and IL-8 levels were higher in all patient groups compared with HC and were not significantly affected over time or by remdesivir/dexamethasone treatment for 5 days. CONCLUSION: Serum sACE2 levels increase in severe COVID-19 patients as they recover over time whilst circulating cytokines are unaffected. Future studies should link these results to clinical outcomes.

Preparing to move: Setting initial conditions to simplify interactions with complex objects.

Humans dexterously interact with a variety of objects, including those with complex internal dynamics. Even in the simple action of carrying a cup of coffee, the hand not only applies a force to the cup, but also indirectly to the liquid, which elicits complex reaction forces back on the hand. Due to underactuation and nonlinearity, the object's dynamic response to an action sensitively depends on its initial state and can display unpredictable, even chaotic behavior. With the overarching hypothesis that subjects strive for predictable object-hand interactions, this study examined how subjects explored and prepared the dynamics of an object for subsequent execution of the target task. We specifically hypothesized that subjects find initial conditions that shorten the transients prior to reaching a stable and predictable steady state. Reaching a predictable steady state is desirable as it may reduce the need for online error corrections and facilitate feed forward control. Alternative hypotheses were that subjects seek to reduce effort, increase smoothness, and reduce risk of failure. Motivated by the task of 'carrying a cup of coffee', a simplified cup-and-ball model was implemented in a virtual environment. Human subjects interacted with this virtual object via a robotic manipulandum that provided force feedback. Subjects were encouraged to first explore and prepare the cup-and-ball before initiating a rhythmic movement at a specified frequency between two targets without losing the ball. Consistent with the hypotheses, subjects increased the predictability of interaction forces between hand and object and converged to a set of initial conditions followed by significantly decreased transients. The three alternative hypotheses were not supported. Surprisingly, the subjects' strategy was more effortful and less smooth, unlike the observed behavior in simple reaching movements. Inverse dynamics of the cup-and-ball system and forward simulations with an impedance controller successfully described subjects' behavior. The initial conditions chosen by the subjects in the experiment matched those that produced the most predictable interactions in simulation. These results present first support for the hypothesis that humans prepare the object to minimize transients and increase stability and, overall, the predictability of hand-object interactions.

ß-Thalassemia minor & renal tubular dysfunction: is there any association?

OBJECTIVE: Beta(ß)-thalassemia is one of the most common hereditary hematologic disorders. Patients with thalassemia minor (TM) are often asymptomatic and the rate of renal dysfunction is unknown in these patients. Due to the high prevalence of renal dysfunction in Iran, the current study aimed to determine renal tubular dysfunction in patients with beta-TM. METHODS: In this case-control study, 40 patients with TM and 20 healthy subjects were enrolled and urinary and blood biochemical analysis was done on their samples. Renal tubular function indices were determined and compared in both groups. Data was analyzed by SPSS software, version 20.0. RESULTS: The fraction excretion (FE) of uric acid was 8.31 ± 3.98% in the case and 6.2 ± 34.71% in the control group (p = 0.048). Also, FE of potassium was significantly higher in patients with TM (3.22 ± 3.13 vs. 1.91 ± 0.81; p = 0.036). The mean Plasma NGAL level was 133.78 ± 120.28 ng/mL in patients with thalassemia and 84.55 ± 45.50 ng/mL in the control group (p = 0.083). At least one parameter of tubular dysfunction was found in 45% of patients with thalassemia. CONCLUSION: Based on the results of this study, the prevalence of tubular dysfunction in beta-thalassemia minor patients is high. Due to the lack of knowledge of patients about this disorder, periodic evaluation of renal function in TM patients can prevent renal failure by early diagnosis.

A case of cardiac angiosarcoma and pulmonary tuberculosis; diagnostic challenges and review of literature.

BACKGROUND: Patient symptoms and primary investigational methods may be misleading at some points in patient management and can consume a lot of time. Sarcomas are rare malignancies and contribute 1% of all cancers of adult. CASE PRESENTATION: A rare case of primary cardiac angiosarcoma is presented, who was first treated because of lung tuberculosis and then with only slight improvement in symptoms, further investigations were done showing right ventricular enlargement and pericardial effusion. Eventually, after ruling out pulmonary embolism and constrictive pericarditis, investigations lead to the diagnosis of primary cardiac angiosarcoma. The patient went under surgery to remove the tumor but he still had residual mass left, leading to chemotherapy and then radiotherapy. Although the tumor has a poor prognosis, our patient has managed to survive a year by now and is doing good for 6 months after radiotherapy. CONCLUSION: The case describes the importance of having in mind different differential diagnosis in managing patients and the role of multi-modality imaging in guiding diagnosis and treatment.