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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

Favipiravir Effects on the Control of Clinical Symptoms of Hospitalized COVID-19 Cases: An Experience with Iranian Formulated Dosage Form.

Coronavirus disease -19 (COVID-19) pandemic, caused by SARS-CoV-2, has gradually spread worldwide, becoming a major public health event. This situation requires designing a novel antiviral agent against the SARS-CoV-2; however, this is time-consuming and the use of repurposed medicines may be promising. One such medicine is favipiravir, primarily introduced as an anti-influenza agent in east world.

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.

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.

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

Objective: Beta(β)-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.

Thermodynamics and Kinetics of Aggregation of Flexible Peripheral Membrane Proteins.

Biomembrane remodeling is essential for cellular trafficking, with membrane-binding peripheral proteins playing a key role in it. Significant membrane remodeling as in endo- and exocytosis is often due to aggregates of many proteins with direct or membrane-mediated interactions. Understanding this process via computer simulations is extremely challenging: protein-membrane systems involve time and length scales that make atomistic simulations impractical, while most coarse-grained models fall short in resolving dynamics and physical effects of protein and membrane flexibility.

Hydrodynamic coupling for particle-based solvent-free membrane models.

The great challenge with biological membrane systems is the wide range of scales involved, from nanometers and picoseconds for individual lipids to the micrometers and beyond millisecond for cellular signaling processes. While solvent-free coarse-grained membrane models are convenient for large-scale simulations and promising to provide insight into slow processes involving membranes, these models usually have unrealistic kinetics. One major obstacle is the lack of an equally convenient way of introducing hydrodynamic coupling without significantly increasing the computational cost of the model.

Clinical Manifestations of Patients with Coronavirus Disease 2019 (COVID-19) in a Referral Center in Iran.

Background: Following the recent epidemic of coronavirus disease 2019 (COVID-19) in Wuhan, China, a novel betacoronavirus was isolated from two patients in Iran on February 19, 2020. In this study, we aimed to determine the clinical manifestations and outcomes of the first confirmed cases of COVID-19 infection (n=127).

Materials And Methods: This prospective study was conducted on all COVID-19-suspected cases, admitted to Masih Daneshvari Hospital (a designated hospital for COVID-19), Tehran, Iran, since February 19, 2020.

Promising effects of tocilizumab in COVID-19: A non-controlled, prospective clinical trial.

Background: The clinical presentation of SARS-CoV-2 infection ranges from mild symptoms to severe complications, including acute respiratory distress syndrome. In this syndrome, inflammatory cytokines are released after activation of the inflammatory cascade, with the predominant role of interleukin (IL)-6. The aim of this study was to evaluate the effects of tocilizumab, as an IL-6 antagonist, in patients with severe or critical SARS-CoV-2 infection.

Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models.

Biomembranes are two-dimensional assemblies of phospholipids that are only a few nanometres thick, but form micrometre-sized structures vital to cellular function. Explicit molecular modelling of biologically relevant membrane systems is computationally expensive due to the large number of solvent particles and slow membrane kinetics. Coarse-grained solvent-free membrane models offer efficient sampling but sacrifice realistic kinetics, thereby limiting the ability to predict pathways and mechanisms of membrane processes.

Evaluation of CCR5-Δ32 mutation among individuals with high risk behaviors, neonates born to HIV-1 infected mothers, HIV-1 infected individuals, and healthy people in an Iranian population.

One of the important genetic factors related to resistance to HIV-1 infection is the presence of the C-C chemokine receptor type 5 delta 32 (CCR5-Δ32) homozygous genotype (Δ32/Δ32). The aim of this study was to evaluate the CCR5-Δ32 mutation among individuals with high-risk behaviors, neonates born to HIV-1-infected mothers in the prevention of mother-to-child transmission (PMTCT) project, HIV-1-infected individuals, and healthy people. The frequency of the CCR5-Δ32 genotype was assessed in a cross-sectional survey carried out from March 2014 to March 2019 among four different groups of the Iranian population.