Decoys Reveal Multiple Basins of Attraction for Cryo-Electron-Microscopy Flexible Fitting.

Total ion current chromatograms (TICCs) generated by liquid chromatography-mass spectrometry (LC-MS) are prone to noise from chemical and electronic sources. This noise can severely impact the detection of analytes in a mixture. Recently, we introduced a new variable selection tool based on Pattern Recognition Entropy (PRE) that selects good quality (high signal-to-noise ratio) mass chromatograms from an LC-MS dataset and thereby creates a reduced TICC with low noise and a flat background (J. Chrom. A.2018, 1558, 21–28). PRE, which is based on Shannon’s entropy, was shown to be a straightforward and powerful shape recognition tool for this problem. However, while the chromatographic signals in the reduced TICC from PRE were well resolved, some noise remained in the TICC, which suggested that the algorithm had selected some false positives, i.e., poor quality mass chromatograms. In this paper, we report an improved version of the PRE algorithm that utilizes a second variable selection filter based on cross-correlation (CC). As a check on the ability of PRE and CC to select high quality mass chromatograms, every mass chromatogram in our data set (1451 in total) was individually inspected and rated as either high quality (green), intermediate quality (yellow), or poor quality (red). A color-coded plot of the CC value vs. the PRE value for the mass chromatograms was created, which shows that, as expected, the higher quality mass chromatograms are localized in its upper left quadrant, which corresponds to lower PRE values and higher CC values. In our original paper on this topic, we recommended a threshold of 0.5 σ for PRE, which caused the algorithm to select 151 mass chromatograms out of 1451. Of these, 98 were of high quality, 6 were of intermediate quality, and 47 were of poor quality. Using a second threshold for CC, the algorithm retains all the high and intermediate quality mass chromatograms, while removing all 47 of the poor quality ones. The resulting TICC from the PRE-CC algorithm shows less noise compared to the TICC generated from the PRE approach alone. The PRE-CC algorithm is arguably a faster, simpler and more intuitive approach as compared to the widely used CODA_DW algorithm.

An association between maternal and fetal heart rate (HR) has been reported but, so far, little is known about its physiological implication and importance relative to fetal development. Associations between both HRs were investigated previously by performing beat-by-beat coupling analysis and correlation analysis between average maternal and fetal HRs. However, studies reporting on the presence of similarities between maternal and fetal HRs or RR intervals (RRIs) over the short term (e.g., 5-min) at different gestational ages (GAs) are scarce. Here, we demonstrate the presence of similarities in the variations exhibited by maternal and fetal RRl tachograms (RRITs). To quantify the same similarities, a cross-correlation (CC) analysis between resampled maternal and fetal RRITs was conducted; RRITs were obtained from non-invasive electrocardiogram (ECG). The degree of similarity between maternal and fetal RRITs (bmfRRITs) was quantified by calculating four CC coefficients. CC analysis was performed for a total of 330 segments (two 5-min segments from 158 subjects and one 5-min from 14 subjects). To investigate the association of the similarity bmfRRITs with fetal development, the linear correlation between the calculated CC coefficients and GA was calculated. The results from the latter analysis showed that similarities bmfRRITs are common occurrences, they can be negative or positive, and they increase with GA suggesting the presence of a regulation that is associated with proper fetal development. To get an insight into the physiological mechanisms involved in the similarity bmfRRITs, the association of the same similarity with maternal and fetal HR variability (HRV) was investigated by comparing the means of two groups in which one of them had higher CC values compared to the other. The two groups were created by using the data from the 158 subjects where fetal RRI (fRRI) calculation from two 5-min ECG segments was feasible. The results of the comparison showed that the maternal very low frequency (VLF) HRV parameter is potentially associated with the similarity bmfRRITs implying that maternal hormones could be linked to the regulations involved in the similarity bmfRRITs. Our findings in this study reinforce the role of the maternal intrauterine environment on fetal development.

Introduction: Electrograms during atrial fibrillation (AF) are complex and seemingly chaotic. It is still unknown how to best analyze and utilize AF electrograms. Hypothesis: We hypothesize that the frequency and patterns of AF electrogram morphology recurrence determined by a modified recurrence plot (RP) analysis will show differences based on region in this pilot study. Methods: AF electrograms (>16 s) recorded from documented left atrial (LA) and right atrial (RA) sites in 13 patients (10 male, 59±10 years old) prior to AF ablation were analyzed. A 100 ms window for each automatically detected activation was extracted and cross-correlated with every other activation in a 30-sec recording. The result was a set of NxN cross-correlation (CC) values, where N is the number of detected activations. These values were displayed in a two-dimensional RP. A recurrence index (RI), the percentage of the most common morphology, was also computed. A high RI likely indicates consistent activation directions at the site of bipolar electrogram recording. Results: Figure A is a RP example. The checker board pattern of alternating high and low CC values indicates periodic recurrences in morphologies (RI=70% for this example). The mean RI for all sites and all patients was 38±25%. The highest RI was found in the left superior LA in all 4 paroxysmal AF patients (85±18%, see Figure B). For 9 persistent AF patients, the highest RI was found in the RA (91±10%) in 5 patients and in the left superior LA (95±6%) in 4 patients. The persistent AF patients had higher maximum RIs in the RA than the paroxysmal AF patients (87±16 vs. 51±15%, p=0.01). Conclusion: Electrogram morphology with highest recurrence rates were most frequently found in the left superior LA, a common location for AF triggers. Further work is needed to determine whether high electrogram repeatability reflects AF driver activity and whether RPs could be used as part of an ablation strategy.

<p>At the northern Chilean subduction zone, where the IPOC network has been monitoring seismicity since 2007, we have identified multiple families of repeating earthquakes. High data quality and long observation time allow analyzing these sequences in detail. <br>Often repeaters are searched to be used as creep proxies and their spatio-temporal cumulative displacement is compared with the tectonic plate convergence rate or GPS based slip rate estimates for smaller fault patches. Repeaters can be classified into periodic, pseudo-periodic or aperiodic types. Put into relation with large earthquakes such as the 2014 M<sub>W</sub>8.1 Iquique earthquake, repeaters may be described as continuous or burst type families. A precondition for such an analysis is that events are collocated and show highly similar mechanism. This is usually ensured via high cross correlation values between waveforms or by catalog location, or both. Errors in grouping would heavily bias the analysis for individual groups. <br>Therefore, we not only use cross correlation values, but we analyze the intra-family relations in detail. Events are relocated relative to each other based on phase based cross correlation refined s-p travel time differences. Rupture sizes are estimated and intra-family rupture histories are resolved. Having confirmed the characteristics of true repeating earthquake families in this way, we make the classifications and compute the slip rates mentioned above. <br>This study shows that the concept of repeating earthquakes holds beautifully in the case of the northern Chilean subduction zone. Repeater families repeatedly rupture the same patches, and they are observed to respond different to the 2014 Iquique with a strong dependence on their location. Particularly, the time around the Iquique megathrust event shows very interesting patterns in several families. We observe clear precursor patterns, burst reactions and unresponsive families simultaneously.</p>

Modeling Tricks and Fitting Techniques for Multiresolution Structures

Cryo-electron microscopy has become an important tool for protein structure determination in recent decades. Since proteins may exist in multiple conformational states, combining high resolution X-ray or NMR structures with cryo-electron microscopy maps is a useful approach to obtain proteins in different functional states. Flexible fitting methods used in cryo-electron microscopy aim to obtain an unknown protein conformation from a high resolution structure and a cryo-electron microscopy map. Since all-atom flexible fitting is computationally expensive, many efficient flexible fitting algorithms that utilize coarse-grained elastic network models have been proposed. In this study, we investigated performance of three coarse-grained elastic network model-based flexible fitting methods (EMFF, iModFit, NMFF) using 25 protein pairs at four resolutions. This study shows that the application of coarse-grained elastic network models to flexible fitting of cryo-electron microscopy maps can provide fast and fruitful models of various conformational states of proteins.

To study the connections between bilateral mesial frontal (MF) regions. We evaluated synchrony of spikes, recorded by subdural electrodes, arising from bilateral MF regions using cross correlation in MF epilepsy. A seven-year-old boy with intractable daily bilateral asymmetric tonic seizures and a normal MRI was investigated. To confirm the lateralization of epileptogenicity, subdural electrodes were implanted bilaterally. Only spikes of an amplitude of 400 μV or more were analyzed. Of 92.4% (194/210) of the left MF spikes recorded for 30 minutes, an approximately synchronous spike was also detected in the right MF region. Cross correlation analysis demonstrated that for 88.7% of the bilateral MF spikes (172/194, 88.7%) the left MF spike led the contralateral spikes with relative fixed peak-to-peak intervals (18.9 ± 11.1 ms) and high cross correlation values (0.81 ± 0.10). An estimated conduction velocity of 7.2 ± 9.8 m/sec was calculated (assuming no synaptic delay). After a second period of more extended invasive EEG monitoring, a left partial frontal lobectomy was performed and the patient immediately had a few brief seizures before remaining seizure-free for a follow-up period of 14 months. We conclude that the propagation of spikes between bilateral MF regions most likely occurs mainly through myelinated callosal fibres. In addition, this cross correlation method showed that the left MF spikes, most of the time, preceded the right MF spikes suggesting that the epileptogenic zone was localized in the left MF region.

Plasma lipoprotein levels are predictors of risk for coronary artery disease. Lipoprotein structure-function relationships provide important clues that help identify the role of lipoproteins in cardiovascular disease. The compositional and conformational heterogeneity of lipoproteins are major barriers to the identification of their structures, as discovered using traditional approaches. Although electron microscopy (EM) is an alternative approach, conventional negative staining (NS) produces rouleau artifacts. In a previous study of apolipoprotein (apo)E4-containing reconstituted HDL (rHDL) particles, we optimized the NS method in a way that eliminated rouleaux. Here we report that phosphotungstic acid at high buffer salt concentrations plays a key role in rouleau formation. We also validate our protocol for analyzing the major plasma lipoprotein classes HDL, LDL, IDL, and VLDL, as well as homogeneously prepared apoA-I-containing rHDL. High-contrast EM images revealed morphology and detailed structures of lipoproteins, especially apoA-I-containing rHDL, that are amenable to three-dimensional reconstruction by single-particle analysis and electron tomography.

Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning

Objective: The aim of this study was to monitor the physiological changes and cytotoxic effects of exogenous contrast agents during photoacoustic imaging (PAI) and photothermal therapy (PTT). In this paper, a low-power telemetric device for mouse vital signs monitoring was designed and demonstrated. Approach: The power consumption was optimized through hardware and software co-design with a 17% increased operating time compared with typical operation. To demonstrate the feasibility of the monitoring device, PAI and PTT experiments with chitosan-polypyrrole nanocomposites (CS-PPy NCs) as exogenous contrast agents were conducted. Herein, the physiological variation in groups of mice with different CS-PPy NC concentrations was observed and analyzed. Main results: The experimental results indicated the influence of CS-PPy NCs and anesthesia on mouse vital signs in PAI and PTT. Additionally, the association between core temperature, heart rate, and saturation of peripheral oxygen (SpO2) during PAI and PTT was shown. The strong near-infrared absorbance of exogenous contrast agents could account for the increase in mouse core temperature and tumor temperature in this study. Furthermore, high cross-correlation values between core temperature, heart rate, and SpO2 were demonstrated to explain the fluctuation of mouse vital signs during PAI and PTT. Significance: A design of a vital signs monitoring device, with low power consumption, was introduced in this study. A high cross correlation coefficient of mouse vital signs and the effects of CS-PPy NCs were observed, which explained the mouse physiological variation during the PAI and PTT experiments.

Waveform clipping due to instrumental limitation is a common problem in seismic data recorded by local and regional networks. With high-amplitude data missing, clipped waveforms, which usually have short epicentral distances and high signal-to-noise ratios, have to be removed from the estimation of magnitudes and other earthquake properties. An efficient automatic algorithm for detecting clipped waveforms can help eliminate artifacts associated with analysis of clipped seismograms. In addition, a reliable algorithm for correcting some clipped waveforms can increase the availability of data closer to the source locations and data for larger magnitude events. The severity of waveform clipping at a given station is expected to increase with the earthquake size. Since the frequency of earthquakes generally decreases with size, following the Gutenberg-Richter relation, a large number of clipped waveforms are likely to have only a small number of clipped points. In such cases, it may be possible to provide reasonably accurate corrections for the clipped waveforms. Interpolation methods are often used to reconstruct missing data. By using a spline interpolation method, Karabulut and Bouchon (2007) corrected the peak values of clipped waveforms recorded by strong motion accelerometers during the 1999 Mw 7.1 Duzce earthquake in Turkey. Subsets of earthquakes recorded by local or regional networks often have very similar waveforms with high cross-correlation coefficient (CCC) values ( e.g. , Aster and Scott 1993; Nadeau et al. 1994). Another possible way of correcting clipped waveforms may be by scaling up portions of unclipped similar waveforms with sufficiently high CCC values. Here we analyze statistical features of clipped waveforms in a large data set of 26,080 aftershocks, recorded with sampling frequency of 100 Hz by a ten-station near-fault seismic network in the six months following the 1999 Mw 7.4, Izmit mainshock (Figure 1). Based on the response of instruments to amplitude saturation, …

BackgroundBiofeedback of body motion can serve as a balance aid and rehabilitation tool. To date, mathematical models considering the integration of biofeedback into postural control have represented this integration as a sensory addition and limited their application to a single degree-of-freedom representation of the body. This study has two objectives: 1) to develop a scalable method for incorporating biofeedback into postural control that is independent of the model’s degrees of freedom, how it handles sensory integration, and the modeling of its postural controller; and 2) to validate this new model using multidirectional perturbation experimental results.MethodsBiofeedback was modeled as an additional torque to the postural controller torque. For validation, this biofeedback modeling approach was applied to a vibrotactile biofeedback device and incorporated into a two-link multibody model with full-state-feedback control that represents the dynamics of bipedal stance. Average response trajectories of body sway and center of pressure (COP) to multidirectional surface perturbations of subjects with vestibular deficits were used for model parameterization and validation in multiple perturbation directions and for multiple display resolutions. The quality of fit was quantified using average error and cross-correlation values.ResultsThe mean of the average errors across all tactor configurations and perturbations was 0.24° for body sway and 0.39 cm for COP. The mean of the cross-correlation value was 0.97 for both body sway and COP.ConclusionsThe biofeedback model developed in this study is capable of capturing experimental response trajectory shapes with low average errors and high cross-correlation values in both the anterior-posterior and medial-lateral directions for all perturbation directions and spatial resolution display configurations considered. The results validate that biofeedback can be modeled as an additional torque to the postural controller without a need for sensory reweighting. This novel approach is scalable and applicable to a wide range of movement conditions within the fields of balance and balance rehabilitation. The model confirms experimental results that increased display resolution does not necessarily lead to reduced body sway. To our knowledge, this is the first theoretical confirmation that a spatial display resolution of 180° can be as effective as a spatial resolution of 22.5°.

OBJECTIVETo compare the EMG activity between the recti abdominii muscles and between the lumbar erector spinae muscles in hemiparetic and hemiplegic patients during functional symmetric trunk movements and to compare...

Maturation of dsDNA bacteriophages involves assembling the virus prohead from a limited set of structural components followed by rearrangements required for the stability that is necessary for infecting a host under challenging environmental conditions. Here, we determine the mature capsid structure of T7 at 1 nm resolution by cryo-electron microscopy and compare it with the prohead to reveal the molecular basis of T7 shell maturation. The mature capsid presents an expanded and thinner shell, with a drastic rearrangement of the major protein monomers that increases in their interacting surfaces, in turn resulting in a new bonding lattice. The rearrangements include tilting, in-plane rotation, and radial expansion of the subunits, as well as a relative bending of the A- and P-domains of each subunit. The unique features of this shell transformation, which does not employ the accessory proteins, inserted domains, or molecular interactions observed in other phages, suggest a simple capsid assembling strategy that may have appeared early in the evolution of these viruses.

High-resolution modeling of protein structures based on flexible fitting of low-resolution structural data.