Direct visualization of single virus restoration after damage in real time

We use the nano-dissection capabilities of atomic force microscopy to induce structural alterations on individual virus capsids in liquid milieu. We fracture the protein shells either with single nanoindentations or by increasing the tip-sample interaction force in amplitude modulation dynamic mode. The normal behavior is that these cracks persist in time. However, in very rare occasions they self-recuperate to retrieve apparently unaltered virus particles. In this work, we show the topographical evolution of three of these exceptional events occurring in T7 bacteriophage capsids. Our data show that single nanoindentation produces a local recoverable fracture that corresponds to the deepening of a capsomer. In contrast, imaging in dynamic mode induced cracks that separate the virus morphological subunits. In both cases, the breakage patterns follow intratrimeric loci.     

A real time learning algorithm for recurrent analog neural networks

A new learning algorithm is described for a general class of recurrent analog neural networks which ultimately settle down to a steady state. Recently, Pineda (Pineda 1987; Almeida 1987; Ikeda et al. 1988) has introduced a learning rule for the recurrent net in which the connection weights are adjusted so that the distance between the stable outputs of the current system and the desired outputs will be maximally decreased. In this method, many cycles are needed in order to get a target system. In each cycle, the recurrent net is run until it reaches a stable state. After that, the weight change is calculated by using a linearized recurrent net which receives the current error of the system as a bias input. In the new algorithm the weights are changed so that the total error of neuron outputs over the entire trajectory is minimized. The weights are adjusted in real time when the network is running. In this method, the trajectory to the target system can be controlled, whereas Pineda's algorithm only controls the position of the fixed point. The relation to the back propagation method (Hinton et al. 1986) is also discussed.     

Lumbar back muscle activity of helicopter pilots and whole-body vibration

Several studies have attributed the prevalence of low back pain (LBP) in helicopter pilots mainly to poor posture in-flight and whole-body vibration, with the latter hypothesis particularly related to a cyclic response of the erector spine (ES) muscle to vibration. This work aims to determine if helicopter vibration and the pilot's normal posture during flight have significant effects on the electromyogram (EMG) of the ES muscle. The bilateral surface EMG of the ES muscle at the L3 level was collected in 10 young pilots before and during a short flight in UH-50 helicopters. The vibration was monitored by a triaxial accelerometer fixed to the pilots' seat. Prior to the flight, the EMG was recorded for relaxed seated and standing postures with 0 degrees (P0) and 35 degrees (P35) of trunk flexion. The effect of the posture during the flight was tested by comparing left and right EMG (normalized with respect to P35). The in-flight muscle stress was evaluated by histograms of EMG activity, and compared to P0 values. Only one pilot in ten showed significant (p<0.05) correlation between the vibration and the EMG over cycles of vibration, and no consistent causal effect was found. The pilots' posture did not show significant asymmetric muscular activity, and low EMG levels were observed during most of the duration of the flight. The results do not provide evidence that LBP in helicopter pilots is caused by ES muscle stress in the conditions studied.     

Titin visualization in real time reveals an unexpected level of mobility within and between sarcomeres

The giant muscle protein titin is an essential structural component of the sarcomere. It forms a continuous periodic backbone along the myofiber that provides resistance to mechanical strain. Thus, the titin filament has been regarded as a blueprint for sarcomere assembly and a prerequisite for stability. Here, a novel titin-eGFP knockin mouse provided evidence that sarcomeric titin is more dynamic than previously suggested. To study the mobility of titin in embryonic and neonatal cardiomyocytes, we used fluorescence recovery after photobleaching and investigated the contribution of protein synthesis, contractility, and calcium load to titin motility. Overall, the kinetics of lateral and longitudinal movement of titin-eGFP were similar. Whereas protein synthesis and developmental stage did not alter titin dynamics, there was a strong, inhibitory effect of calcium on titin mobility. Our results suggest a model in which the largely unrestricted movement of titin within and between sarcomeres primarily depends on calcium, suggesting that fortification of the titin filament system is activity dependent.     

VisTrails SAHM: visualization and workflow management for species habitat modeling

The Software for Assisted Habitat Modeling (SAHM) has been created to both expedite habitat modeling and help maintain a record of the various input data, pre‐ and post‐processing steps and modeling options incorporated in the construction of a species distribution model through the established workflow management and visualization VisTrails software. This paper provides an overview of the VisTrails:SAHM software including a link to the open source code, a table detailing the current SAHM modules, and a simple example modeling an invasive weed species in Rocky Mountain National Park, USA.     

Biological networks 101: Computational modeling for molecular biologists

Computational modeling of biological networks permits the comprehensive analysis of cells and tissues to define molecular phenotypes and novel hypotheses. Although a large number of software tools have been developed, the versatility of these tools is limited by mathematical complexities that prevent their broad adoption and effective use by molecular biologists. This study clarifies the basic aspects of molecular modeling, how to convert data into useful input, as well as the number of time points and molecular parameters that should be considered for molecular regulatory models with both explanatory and predictive potential. We illustrate the necessary experimental preconditions for converting data into a computational model of network dynamics. This model requires neither a thorough background in mathematics nor precise data on intracellular concentrations, binding affinities or reaction kinetics. Finally, we show how an interactive model of crosstalk between signal transduction pathways in primary human articular chondrocytes allows insight into processes that regulate gene expression.     

Real time visualization of protein kinase activity in living cells.

A library of fluorescently labeled protein kinase C (PKC) peptide substrates was prepared to identify a phosphorylation-induced reporter of protein kinase activity. The lead PKC substrate displays a 2.5-fold change in fluorescence intensity upon phosphorylation. PKC activity is readily sampled in cell lysates containing the activated PKCs. Immunodepletion of conventional PKCs from the cell lysate eliminates the fluorescence response, suggesting that this peptide substrate is selectively phosphorylated by PKCalpha, beta, and gamma. Finally, living cells microinjected with the peptide substrate exhibit a 2-fold increase in fluorescence intensity upon exposure to a PKC activator. These results suggest that peptide-based protein kinase biosensors may be useful in monitoring the temporal and spatial dynamics of PKC activity in living cells.     

The L3 to L4 molt of Brugia malayi: real time visualization by video microscopy

Brugia malayi and other filarial parasites have been studied in great detail, especially in the context of human disease. In common with other nematodes, these organisms molt 4 times in their life cycles, but details of this process have not been described. We have recently developed an in vitro culture system that supports the L3 to L4 molt at high efficiency. This has permitted us to visualize, for the first time, details of this molt using real-time video microscopy. Molting is preceded by a phase of altered motility during which the larva exhibits contractile, coiling movements. The earliest evidence of ecdysis is a clearing at one end, more frequently caudal, caused by the larva retracting from that end. A cleavage develops in the cuticle near the head end, forming a rostral cap, which is continuous with the pharyngeal cuticle. Simultaneously, it retracts out of the cuticle using coiling and writhing movements. This process takes 5 to 10 min. Finally, it retracts out of the cap and extrudes the pharyngeal cuticle. Detachment of the pharyngeal cuticle is the final event in the process and continues up to an hour after the rest of the cuticle has been shed.     

Older adults show higher increases in lower-limb muscle activity during whole-body vibration exercise

The purpose of this study was to compare lower limb muscle activity during whole-body vibration (WBV) exercise between a young and an older study population. Thirty young (25.9±4.3 yrs) and thirty older (64.2±5.3 yrs) individuals stood on a side-alternating WBV platform while surface electromyography (sEMG) was measured for the tibialis anterior (TA), gastrocnemius medialis (GM), soleus (SOL), vastus lateralis (VL), vastus medialis (VM), and biceps femoris (BF). The WBV protocol included nine vibration settings consisting of three frequencies (6, 11, 16 Hz) x three amplitudes (0.9, 2.5, 4.0 mm), and three control trials without vibration (narrow, medium, wide stance). The vertical platform acceleration (peak values of maximal displacement from equilibrium) was quantified during each vibration exercise using an accelerometer. The outcomes of this study showed that WBV significantly increased muscle activity in both groups for most vibration conditions in the TA (averaged absolute increase: young: +3.9%, older: +18.4%), GM (young: +4.1%, older: +9.5%), VL (young: +6.3%, older: +12.6%) and VM (young: +5.4%, older: +8.0%), and for the high frequency-amplitude combinations in the SOL (young: +7.5%, older: +12.6%) and BF (young: +1.9%, older: +7.5%). The increases in sEMG activity were significantly higher in the older than the young adults for all muscles, i.e., TA (absolute difference: 13.8%, P<0.001), GM (4.6%, P=0.034), VL (7.6%, P=0.001), VM (6.7%, P=0.042), BF (6.4%, P<0.001), except for the SOL (0.3%, P=0.248). Finally, the vertical platform acceleration was a significant predictor of the averaged lower limb muscle activity in the young (r=0.917, P<0.001) and older adults (r=0.931, P<0.001). In conclusion, the older population showed greater increases in lower limb muscle activity during WBV exercise than their young counterparts, meaning that they might benefit more from WBV exercises. Additionally, training intensity can be increased by increasing the vertical acceleration load.     

Computational framework to understand the clinical stages of COVID-19 and visualization of time course for various treatment strategies

Coronavirus disease 2019 is known to be regulated by multiple factors such as delayed immune response, impaired T cell activation, and elevated levels of proinflammatory cytokines. Clinical management of the disease remains challenging due to interplay of various factors as drug candidates may elicit different responses depending on the staging of the disease. In this context, we propose a computational framework which provides insights into the interaction between viral infection and immune response in lung epithelial cells, with an aim of predicting optimal treatment strategies based on infection severity. First, we formulate the model for visualizing the nonlinear dynamics during the disease progression considering the role of T cells, macrophages and proinflammatory cytokines. Here, we show that the model is capable of emulating the dynamic and static data trends of viral load, T cell, macrophage levels, interleukin (IL)-6 and TNF-α levels. Second, we demonstrate the ability of the framework to capture the dynamics corresponding to mild, moderate, severe, and critical condition. Our result shows that, at late phase (>15 days), severity of disease is directly proportional to pro-inflammatory cytokine IL6 and tumor necrosis factor (TNF)-α levels and inversely proportional to the number of T cells. Finally, the simulation framework was used to assess the effect of drug administration time as well as efficacy of single or multiple drugs on patients. The major contribution of the proposed framework is to utilize the infection progression model for clinical management and administration of drugs inhibiting virus replication and cytokine levels as well as immunosuppressant drugs at various stages of the disease.     

Acute effects of whole-body vibration on muscle activity, strength, and power

The purpose of this study was to investigate the effects of a single bout of whole-body vibration on isometric squat (IS) and countermovement jump (CMJ) performance. Nine moderately resistance-trained men were tested for peak force (PF) during the IS and jump height (JH) and peak power (PP) during the CMJ. Average integrated electromyography (IEMG) was measured from the vastus medialis, vastus lateralis, and biceps femoris muscles. Subjects performed the 2 treatment conditions, vibration or sham, in a randomized order. Subjects were tested for baseline performance variables in both the IS and CMJ, and were exposed to either a 30-second bout of whole-body vibration or sham intervention. Subjects were tested immediately following the vibration or sham treatment, as well as 5, 15, and 30 minutes posttreatment. Whole-body vibration resulted in a significantly higher (p < or = 0.05) JH during the CMJ immediately following vibration, as compared with the sham condition. No significant differences were observed in CMJ PP; PF during IS or IEMG of the vastus medialis, vastus lateralis, or biceps femoris during the CMJ; or IS between vibration and sham treatments. Whole-body vibration may be a potential warm-up procedure for increasing vertical JH. Future research is warranted addressing the influence of various protocols of whole-body vibration (i.e., duration, amplitude, frequency) on athletic performance.     

Fluorescent monitoring of kinase activity in real time: development of a robust fluorescence-based assay for Abl tyrosine kinase activity

Fluorescent biosensors hold great promise for drug discovery. Using a solid-phase version of protein semi-synthesis, we incorporated two fluorophores at specific sites within a truncated version of the c-Crk-II protein. The resulting fluorescent protein biosensor permits the real-time monitoring of Abl kinase activity and provides a robust and rapid method for assaying Abl kinase inhibitors.     

New software QRS detector algorithm suitable for real time applications with low signal-to-noise ratios

A new algorithm for QRS-detection is presented; it is based on template-comparison, but unlike the cross-corelation algorithm, it involves no multiplications, and is less time-consuming and therefore suitable for real-time applications. It is demonstrated that the new algorithm performs practically as well as cross correlation, and is useful in situations where low signal to noise ratios are common.     

An improved cost function for modeling of muscle activity during running

This paper tries to improve a recently developed mass-spring-damper model of the human body during running. The previous model took the muscle activity into account using a nonlinear controller that tuned the mechanical properties of the soft-tissue package based on two physiological hypotheses, namely "constant-force" and "constant-vibration". Three cost functions were used, out of which one was based on the constant-force hypothesis and two others were based on the constant-vibration hypothesis. The results of the study showed that the proposed cost functions are only partially successful in capturing the experimentally observed trends of the ground reaction force and vibration. The current paper proposes an improved cost function that combines both above-mentioned hypotheses. It is shown that the improved cost function can capture all the trends that were observed in the measurements of the ground reaction force and vibration level. It is therefore advised to use the new cost function in place of the previous ones.     

XmMol: An X11 and motif program for macromolecular visualization and modeling

XmMol is a desktop tool designed to provide both interactive molecular graphics on X11 displays and easy interface with external applications. A kernel provides an interactive wire-frame display of macromolecules. It supports depth cueing, 3D clipping, and stereo. Various representations, coloring, and labeling modes are proposed. Docking and interactive back-bone deformation tools are also supported. Communication protocols allow the user to develop new external features or to use XmMol as a visualization tool for external numerical programs.     

Computational approaches for modeling human intestinal absorption and permeability

Human intestinal absorption (HIA) is an important roadblock in the formulation of new drug substances. Computational models are needed for the rapid estimation of this property. The measurements are determined via in vivo experiments or in vitro permeability studies. We present several computational models that are able to predict the absorption of drugs by the human intestine and the permeability through human Caco-2 cells. The training and prediction sets were derived from literature sources and carefully examined to eliminate compounds that are actively transported. We compare our results to models derived by other methods and find that the statistical quality is similar. We believe that models derived from both sources of experimental data would provide greater consistency in predictions. The performance of several QSPR models that we investigated to predict outside the training set for either experimental property clearly indicates that caution should be exercised while applying any of the models for quantitative predictions. However, we are able to show that the qualitative predictions can be obtained with close to a 70% success rate.Electronic Supplementary Material Supplementary material is available for this article at .Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday.     

Chromosome condensation: DNA compaction in real time

Mitotic chromosomes must be organised into a highly ordered and compacted form to allow proper segregation of DNA during each round of cell division. Two new studies report observations of DNA compaction by eukaryotic and bacterial condensin molecules in real time using magnetic and optical trapping micromanipulation techniques.