Small Local Changes Research Articles

Vibration‐based structural state identification by a 1‐dimensional convolutional neural network

AbstractDeep learning has ushered in many breakthroughs in vision‐based detection via convolutional neural networks (CNNs), but the vibration‐based structural damage detection by CNN remains being refined. Thus, this study proposes a simple one‐dimensional CNN that detects tiny local structural stiffness and mass changes, and validates the proposed CNN on actual structures. Three independent acceleration databases are established based on a T‐shaped steel beam, a short steel girder bridge (in test field), and a long steel girder bridge (in service). The raw acceleration data are not pre‐processed and are directly used as the training and validation data. The well‐trained CNN almost perfectly identifies the locations of small local changes in the structural mass and stiffness, demonstrating the high sensitivity of the proposed simple CNN to tiny structural state changes in actual structures. The convolutional kernels and outputs of the convolutional and max pooling layers are visualized and discussed as well.

Quantitative cross-linking/mass spectrometry to elucidate structural changes in proteins and their complexes.

Quantitative cross-linking/mass spectrometry (QCLMS/QXL-MS) probes structural changes of proteins in solution. This method has revealed induced conformational changes, composition shifts in conformational ensembles and changes in protein interactions. It illuminates different structural states of proteins or protein complexes by comparing which residue pairs can be cross-linked in these states. Cross-links provide information about structural changes that may be inaccessible by alternative technologies. Small local conformational changes affect relative abundances of nearby cross-links, whereas larger conformational changes cause new cross-links to be formed. Distinguishing between minor and major changes requires a robust analysis based on carefully selected replicates and, when using isotope-labeled cross-linkers, replicated analysis with a permutated isotope-labeling scheme. A label-free workflow allows for application of a wide range of cross-linking chemistries and enables parallel comparison of multiple conformations. In this protocol, we demonstrate both label-free and isotope-labeled cross-linker-based workflows using the cross-linker bis(sulfosuccinimidyl)suberate (BS3). The software XiSearch, developed by our group, is used to identify cross-linked residue pairs, although the workflow is not limited to this search software. The open-access software Skyline is used for automated quantitation. Note that additional manual correction greatly enhances quantitation accuracy. The protocol has been applied to purified multi-protein complexes but is not necessarily limited to that level of sample complexity. Optimizing the cross-linker/protein ratio and fractionating peptides increase the data density of quantified cross-links, and thus the resolution of QCLMS. The entire procedure takes ~1-3 weeks.

Influence of the Real Geometry of the Laser Cut Front on the Absorbed Intensity and the Gas Flow

The numerical investigations on experimentally determined cut front geometries presented in this paper show that the absorbed intensity reacts more sensitively to small local changes of the angle of the cut front than the gas velocity and the pressure. It is also found that the absorbed intensities near the top and the bottom of the cut front increase significantly when the initially regular process at high cutting speeds turns into the regime with interrupted striation patterns on the surface of the cutting edge.

Simulations of a birdcage coil B1+ field on a human body model for designing a 3T multichannel TMS/MRI head coil array.

This article considers a new type of integrated multichannel Transcranial Magnetic Stimulator and Magnetic Resonance Imaging (TMS/MRI) system at 3T that is currently being designed. The system will enable unprecedented spatiotemporal control of the TMS-induced electric fields (Efields) with simultaneous rapid whole-head MRI acquisition to record the brain activity. A critical design question is how TMS coil elements interact with the transmit field (${\mathrm B}_{1}^{+}$) of the volume coil integrated in 3T MRI systems. In general, the TMS coils are not designed to have any resonant characteristics at the MRI frequency, they may potentially disturb the RF field due to the eddy currents induced. This is especially a concern with a multichannel TMS setup where the subject's head will be largely covered with the stimulation coils. Therefore, we investigated this problem by computational simulations with realistic TMS coil geometries and a birdcage transmit coil in conjunction with a human body model. We compared the ${\mathrm B}_{1}^{+}$ interaction effects of a commercially available MR-compatible TMS coil with our coil prototype. In both cases, the results show small local changes in the transmit field ${\mathrm B}_{1}^{+}$of the birdcage coil. Maximal Average Specific Absorption Rate (SAR) values over 1g tissue were found to be slightly lower when the TMS elements were present. We conclude that it should be feasible and safe to use the conventional body transmit coil even when an array of TMS coils is used.

A model to interpret driftwood transport in the Arctic

Driftwood is frequently used to estimate past changes of sea ice extent and circulation in the Arctic. Nevertheless, driftwood observations are difficult to interpret because of the potentially complex relation with climate change. In order to determine the origin of the observed changes, we built a driftwood transport model (DTM) simulating the driftwood trajectories from the boreal forest to Arctic coasts. The model is driven by three main variables, which are the sea ice velocity, concentration and the sea surface current velocity that can be derived from observations or climate model outputs (e.g. from a General Climate Model – GCM). Overall, the DTM model agrees with the observations, although this comparison needs to be taken with caution because of the sparse data and the uncertainties of driftwood provenance. Through simulations performed with the DTM model, we confirm the strong influence of the variability of the atmospheric circulation on the spatial driftwood distribution. Model simulations of the Mid-Holocene period driven by six GCMs show that small local changes in sea ice circulation – a westward shift in the Transpolar Drift and a reduced Beaufort Gyre during the Mid-Holocene compared to the present period – suffice to explain the driftwood landing change during the Mid-Holocene, with a non-negligible contribution from reduced sea ice concentration. Consequently, a change in driftwood deposit should not be directly interpreted as large modifications in atmospheric circulation and the complexity of the response of driftwood trajectories to past climate changes clearly highlights the interest of using a model to interpret driftwood records.

The JAVA Based Computational Tool for Pairwise Comparison of Protein Backbone Folds in Liganded and Apo 3D Structures of the alpha/beta Hydrolase Fold Proteins

Cholinesterases, carboxylesterases and lipases are some of prominent catalytically active proteins with specifically similar, globular tertiary structure fold termed “alpha/beta hydrolase fold”. Ligand binding, both reversible and covalent, frequently results in small, yet systematic and potentially functionally important changes in the conformation of their alpha carbon backbones that can be easily overseen by commonly used overlays based on overall minimization of backbone atom RMSD analysis. In particular, backbone conformations of cholinesterases ‐ acetylcholinesterase and butyrylcholinesterase ‐ show only small conformational changes. This is revealed in more than 200 PDB deposited cholinesterase X‐ray structures in complexes with structurally diverse ligands that affect their function.We developed a novel, reference point based principle for overlay‐independent pairwise comparison of liganded and non‐liganded alpha carbon backbone conformations from respective PDB (Protein Data Bank) deposited 3D structure entries and encoded it in JAVA based computer algorithm for quick analysis. Comparisons are based on differences in distances between each alpha carbon and chosen reference point in each pair of compared structures, as well as on differences in the angle between center of mass, reference point and each of alpha carbons in the comparison. Combination of the two comparison criteria reveals subset of backbone alpha carbons in two structures that maintains best their relative positions in the 3D space and that can be used as tethering points for overlay of compared structures. Created overlay has capacity to reveal small but systematic local changes in the backbone conformation frequently masked by the overall RMSD minimization approach.Our systematic analysis of a number of PDB deposited alpha/beta hydrolase fold structures revealed small, yet functionally important conformational changes in their backbone consistent with experimental observations and instrumental in revealing molecular mechanisms in respective catalytic reactions. These findings are important for complete molecular target template characterization in the structure based development of novel antidotes of exposure to organophosphates which covalently inhibit this family of enzymes.Support or Funding InformationThis work was supported by the CounterACT Program, National Institutes of Health Office of the Director, Grant R21 NS098998 from NINDS.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Allostery and Conformational Dynamics in Protein Evolution

The critical role of protein dynamics has become well recognized in various biological functions, including allosteric signaling and protein ligand recognition electron transfer. Likewise, in protein evolution, the classical view of the one sequence-one structure-one function paradigm is now being extended to a new view: an ensemble of conformations in equilibrium that can evolve new functions. Therefore, understanding inherent structural dynamics are crucial to obtain a more complete picture of protein evolution. A small local structural change due to a single mutation can lead to a large difference in conformational dynamics, even at quite distant residues due to allostery. We have recently analyzed evolution of different protein families including GFP proteins, beta-lactamase inhibitors, and nuclear receptors and observed that alteration of conformational dynamics through allosteric regulations leads to functional changes. Moreover, our site-specific dynamics-based metric reveals that enzymatic function is regulated by dynamically-coupled residues, which forms an allosteric communication network with the active sites. Disease causing mutations trigger a global loss in dynamic coupling, which disrupts the communication network ultimately inhibiting function. Analysis of over 200 missense mutations also shows that Gaucher disease (GD) mutations are abundant at dynamic allosteric residue coupling sites which we call DARC spots. Further tests using 75 human enzymes revealed that diseases emerging from DARC spot mutations are not isolated to GD; indeed, this phenomenon is observed across the proteome.

Regional analysis of age-related local bone loss in the spine of a healthy population using 3D voxel-based modeling

Local variations in bone loss may be of great importance to individually predict osteoporotic fractures but are neglected by current densitometry techniques. The purpose of this study was to evaluate regional variations of normal bone loss at the spine among different age groups using voxel-based morphometry. Non-contrast MDCT scans of 16 patients under the age of 40 (mean age 26years) without spinal pathology were identified as a reference cohort, where each thoracolumbar vertebra was assessed individually. For comparison, 38 patients >40years were grouped by decades in 4 cohorts of 10 patients each, except the youngest, including 8 patients only. All spines were automatically detected, segmented and non-rigidly registered for spatially normalized vertebral bodies. Afterwards, statistical and T-score mapping was performed to highlight local density differences in comparison to the reference cohort. The calculated statistical maps of significantly affected density regions (ADR) started to highlight small local changes of volumetric bone mineral density (vBMD) distribution within the vertebra of L5 (ADR: 7.9%) in the fifties cohort. Regions near the endplates were most affected. The effect dramatically increased in the sixties cohort, where bone loss was most prominent from T12 to L2. In the seventies cohort, around 50% of voxels in T10 to L5 showed significantly decreased vBMD. In conclusion, ADR and local T-score maps of the spine showed age-related local variations in a healthy population, corresponding to known areas of fracture origination and increased fracture incidence. It thus might provide a powerful tool in diagnosis of osteoporosis.

Complex network analysis of thermostable mutants of Bacillus subtilis Lipase A

Three-dimensional structures of proteins that regulate their functions can be modelled using complex network based approaches for understanding the structure-function relationship. The six mutants of the protein Lipase A from Bacillus subtilis, harbouring 2 to 12 mutations, retain their function at higher temperatures with negligible variation in their overall three-dimensional crystallographic structures. This enhanced thermostability of the mutants questions the structure-function paradigm. In this paper, a coarse-grained complex network approach is used to elucidate the structural basis of enhanced thermostability in the mutant proteins, by uncovering small but significant local changes distributed throughout the structure, rendering stability to the mutants at higher temperatures. Community structure analysis of the six mutant protein networks uncovers the specific reorganisations among the nodes/residues that occur, in absence of overall structural variations, which induce enhanced rigidity underlying the increased thermostability. This study offers a novel and significant application of complex network analysis that proposes to be useful in the understanding and designing of thermostable proteins.

Surface chemistry and morphology in single particle optical imaging

AbstractBiological nanoparticles such as viruses and exosomes are important biomarkers for a range of medical conditions, from infectious diseases to cancer. Biological sensors that detect whole viruses and exosomes with high specificity, yet without additional labeling, are promising because they reduce the complexity of sample preparation and may improve measurement quality by retaining information about nanoscale physical structure of the bio-nanoparticle (BNP). Towards this end, a variety of BNP biosensor technologies have been developed, several of which are capable of enumerating the precise number of detected viruses or exosomes and analyzing physical properties of each individual particle. Optical imaging techniques are promising candidates among broad range of label-free nanoparticle detectors. These imaging BNP sensors detect the binding of single nanoparticles on a flat surface functionalized with a specific capture molecule or an array of multiplexed capture probes. The functionalization step confers all molecular specificity for the sensor’s target but can introduce an unforeseen problem; a rough and inhomogeneous surface coating can be a source of noise, as these sensors detect small local changes in optical refractive index. In this paper, we review several optical technologies for label-free BNP detectors with a focus on imaging systems. We compare the surface-imaging methods including dark-field, surface plasmon resonance imaging and interference reflectance imaging. We discuss the importance of ensuring consistently uniform and smooth surface coatings of capture molecules for these types of biosensors and finally summarize several methods that have been developed towards addressing this challenge.

Structural insights into the mechanism of the drastic changes in enzymatic activity of the cytochrome P450 vitamin D3 hydroxylase (CYP107BR1) caused by a mutation distant from the active site.

Cytochromes P450 (P450s) are haem-containing enzymes that catalyze medically and industrially important oxidative reactions, and many P450s have been subjected to directed evolution and site-directed mutagenesis to improve their activity and substrate specificity. Nonetheless, in most cases the mechanism that leads to drastic changes in specific activity after the introduction of an amino-acid substitution distant from the active-site pocket is unclear. Here, two crystal structures of inactive mutants of the P450 vitamin D3 hydroxylase (Vdh), Vdh-F106V and Vdh-L348M, which were obtained in the course of protein-engineering experiments on Vdh, are reported. The overall structures of these mutants show an open conformation similar to that of wild-type Vdh (Vdh-WT), whereas a rearrangement of the common main-chain hydrogen bonds is observed in the CD-loop (residues 102-106), resulting in a more compactly folded CD-loop relative to that of Vdh-WT. The previously reported structures of Vdh-WT and of the highly active Vdh-T107A and Vdh-K1 mutants have a more stretched CD-loop, with partial formation of 310-helix-type hydrogen bonds, both in the open and closed states. Molecular-dynamics simulations also showed that the frequency of the 310-helix is significantly reduced in Vdh-F106V and Vdh-L348M. The closed conformation is crucial for substrate and ferredoxin binding to initiate the catalytic reaction of Vdh. Therefore, it is implied that the small local structural changes observed in this study might disrupt the conformational transition from the open to the closed state, thereby leading to a complete loss of vitamin D3 hydroxylase activity.

On the effects of tip deflection in flapping propulsion

The research described in this paper is inspired by the fact that nature’s flyers and swimmers use a wide variety of control mechanisms in order to produce the impulse and the thrust required in each situation they are involved in. This control is made through complex passive and active mechanisms that are used to impose the desired momentum transfer in their wake.Experiments have been performed with a flapping system that allows to set different inclinations to the tip of a robotic fin. Direct force measurements and Digital Particle Image Velocimetry (DPIV) have been used to study the propulsive performance for the different tip configurations investigated. The effects of the geometry of the tip and the kinematics imposed to the fin on the impulse generated, are discussed in detail. We show how the capacity of the system to produce impulse can be altered by imposing certain tip geometries that imply small local changes of the trailing edge. The modified tip geometries are closely related to the way vortices evolve in the near wake region and therefore how momentum is transferred to the wake. We have found that the configurations that produce the highest impulses have the tip deflected to the suction side of the system while flapping. The dynamic control of the tip allows changes in the impulse generated.

Patch Reordering: A NovelWay to Achieve Rotation and Translation Invariance in Convolutional Neural Networks

Convolutional Neural Networks (CNNs) have demonstrated state-of-the-art performance on many visual recognition tasks. However, the combination of convolution and pooling operations only shows invariance to small local location changes in meaningful objects in input. Sometimes, such networks are trained using data augmentation to encode this invariance into the parameters, which restricts the capacity of the model to learn the content of these objects. A more efficient use of the parameter budget is to encode rotation or translation invariance into the model architecture, which relieves the model from the need to learn them. To enable the model to focus on learning the content of objects other than their locations, we propose to conduct patch ranking of the feature maps before feeding them into the next layer. When patch ranking is combined with convolution and pooling operations, we obtain consistent representations despite the location of meaningful objects in input. We show that the patch ranking module improves the performance of the CNN on many benchmark tasks, including MNIST digit recognition, large-scale image recognition, and image retrieval.

Local microstructural analysis for Y2O3/Eu3+/Mg2+ nanorods by Raman and photoluminescence spectra under high pressure**Project supported by the National Natural Science Foundation of China (Grant Nos. 11304380, 11404241, 11275138, 11604240, and 51320105007) and the Program for Changjiang Scholars and Innovative Research Team in University, China (Grant No. IRT1132).

In this paper, we investigate the Raman and photoluminescence spectra of Y2O3/Eu3+ and Y2O3/Eu3+/Mg2+ nanorods under high pressures using 514-nm and 532-nm laser light excitation. We observe transitions from the initial cubic phase to amorphous at pressures higher than 24 GPa for both Y2O3/Eu3+ and Y2O3/Eu3+/Mg2+ nanorods. In addition, Y2O3/Eu3+ and Y2O3/Eu3+/Mg2+ nanorods exhibit different distorted states after the pressure has been raised to 8 GPa. The analyses of intensity ratios, I0−2/I0−1 from 5D0–7F2 to 5D0–7F1 and I0−2A/B of 5D0–7F2 transitions indicate that Y2O3/Eu3+/Mg2+ nanorods exhibit stronger local micro-surrounding characteristics for Eu3+ ions in a pressure-modulated crystal field. The doped Mg2+ ion results in reducing the crystal ionicity in the distorted lattice state under high pressures. The use of doped ions as an ion modifier can be applied to the study of small local microstructural changes through Eu3+ luminescence.

Quantitative cross-linking/mass spectrometry reveals subtle protein conformational changes.

Quantitative cross-linking/mass spectrometry (QCLMS) probes protein structural dynamics in solution by quantitatively comparing the yields of cross-links between different conformational statuses. We have used QCLMS to understand the final maturation step of the proteasome lid and also to elucidate the structure of complement C3(H2O). Here we benchmark our workflow using a structurally well-described reference system, the human complement protein C3 and its activated cleavage product C3b. We found that small local conformational changes affect the yields of cross-linking residues that are near in space while larger conformational changes affect the detectability of cross-links. Distinguishing between minor and major changes required robust analysis based on replica analysis and a label-swapping procedure. By providing workflow, code of practice and a framework for semi-automated data processing, we lay the foundation for QCLMS as a tool to monitor the domain choreography that drives binary switching in many protein-protein interaction networks.

Development of cortical shape in the human brain from 6 to 24 months of age via a novel measure of shape complexity

The quantification of local surface morphology in the human cortex is important for examining population differences as well as developmental changes in neurodegenerative or neurodevelopmental disorders. We propose a novel cortical shape measure, referred to as the ‘shape complexity index’ (SCI), that represents localized shape complexity as the difference between the observed distributions of local surface topology, as quantified by the shape index (SI) measure, to its best fitting simple topological model within a given neighborhood. We apply a relatively small, adaptive geodesic kernel to calculate the SCI. Due to the small size of the kernel, the proposed SCI measure captures fine differences of cortical shape. With this novel cortical feature, we aim to capture comparatively small local surface changes that capture a) the widening versus deepening of sulcal and gyral regions, as well as b) the emergence and development of secondary and tertiary sulci. Current cortical shape measures, such as the gyrification index (GI) or intrinsic curvature measures, investigate the cortical surface at a different scale and are less well suited to capture these particular cortical surface changes. In our experiments, the proposed SCI demonstrates higher complexity in the gyral/sulcal wall regions, lower complexity in wider gyral ridges and lowest complexity in wider sulcal fundus regions. In early postnatal brain development, our experiments show that SCI reveals a pattern of increased cortical shape complexity with age, as well as sexual dimorphisms in the insula, middle cingulate, parieto-occipital sulcal and Broca's regions. Overall, sex differences were greatest at 6months of age and were reduced at 24months, with the difference pattern switching from higher complexity in males at 6months to higher complexity in females at 24months. This is the first study of longitudinal, cortical complexity maturation and sex differences, in the early postnatal period from 6 to 24months of age with fine scale, cortical shape measures. These results provide information that complement previous studies of gyrification index in early brain development.

Effect of Angle of Incidence on Anterior Chamber Angle Metrics From Optical Coherence Tomography.

To evaluate the local variability of anterior chamber angle (ACA) metrics obtained by time domain (TD) and spectral domain (SD) optical coherence tomography (OCT). Anterior-segment OCT imaging was performed on 30 normal eyes using Visante TD-OCT and 40 normal eyes using Cirrus SD-OCT. For Visante OCT, a single 16-mm line scan of the inferior angle with 3 slightly different rotations of 265, 270, and 275 degrees was performed. For Cirrus OCT, a 5-line raster of the inferior angle was performed, centering the third scan line at the 6 o'clock position, with 0.25 mm between lines. ACA measurements were taken for angle-opening distance (AOD) and trabecular iris space area (TISA) at 500/750 μm from the scleral spur for Visante OCT and at Schwalbe's line (SL) for Cirrus OCT. For Visante OCT, AOD500 was 0.406 mm (SD=0.143 mm) and TISA500 was 0.139 mm (0.054 mm). There was no difference in AOD500, AOD750, TISA500, or TISA750 between the 3 scan orientations (P>0.1 for all comparisons). For Cirrus OCT, AOD500 was 0.850±0.318 mm and TISA500 was 0.325±0.145 mm. No difference was found in SL-AOD and SL-TISA between the 3 scan positions. These findings suggest that small local changes in the position of the OCT line scan spaced up to 1.0 mm apart on Cirrus, or 10-degree apart on Visante, did not significantly alter the inferior ACA metrics in achieving reliable measurements in young healthy eyes. Given the absence of tracking and registration for current anterior-segment OCT instruments, this observation is of relevance for longitudinal and dynamic studies of angle geometry.

Using ferrule-top opto-mechanical probes as a new tool in VCSEL reliability experiments.

Today, vertical cavity surface emitting lasers (VCSELs) are used in many high-end applications, for which the laser lifetime is a critical parameter. Changes in the spatial distribution of the various emission modes of the VCSEL can be used as an early sign of device degradation, enhancing the speed and detail of failure mode analysis. We have developed a ferrule-top combined atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM) probe that can be used to analyze the transverse mode pattern of the 850 nm radiation at a <200 nm spatial resolution. During accelerated lifetime testing, the newly developed method shows that small local changes in the optical output can already be detected before any sign of device degradation is observed with conventional methods.

Deuterium ordering found in new ferroelectric compound Co2(OD)3Cl

A detailed temperature-dependent Raman spectroscopic study revealed a new type of deuterium-order ferroelectrics in a geometrically frustrated magnet Co2(OD)3Cl at Tϵ = 229 K. Significant changes in the parameters of the Raman vibration modes were observed near Tϵ, suggesting a strong phonon-charge coupling. Additional asymmetric phonon bands appeared below around Tϵ, which are consistently interpreted by phonon folding processes due to a small local structural change resulting from the ordering of deuterium. The wavenumber and intensity changes of the Raman-active modes, as well as the normalized intensities of the additional bands, all follow a power-law fit Δω, ΔI, I ∝ (1 − T/TC)2β, wherein TC = 230 K ∼ Tϵ and β = 0.35(2), clearly demonstrating an ordering process below Tϵ. The critical exponent is reminiscent of a second order transition. Our study presents a rare and new type of multiferroic material with ferroelectricity arising from the deuterium ordering in geometrically frustrated magnets.

Monitoring Effects of Excipients, Formulation Parameters and Mutations on the High Order Structure of Filgrastim by NMR.

Filgrastim is the generic name for recombinant methionyl human granulocyte colony-stimulating factor (r-metHuG-CSF). It is marketed under the brand name Neupogen® by Amgen. Since this product has lost patent protection, many biosimilar versions have been approved or are in the process of filing for market authorization throughout the world. Here we show that NMR spectroscopy can be used to assess the three-dimensional structure of the active ingredient in the formulated approved product Neupogen®. Recombinant metHuG-CSF was prepared in E. coli and isotopically enriched with (13)C and (15) N isotopes. NMR spectroscopy was used to study the effects of excipients on the conformation. The effects of pH variation on the amide chemical shifts suggest the presence of cation-pi interactions between His-79 and Trp-118, and His-156-Trp-58-His-52 that stabilizes the conformation at low pH. This may be associated with a small local conformational change. The NMR data showed that polysorbate does not interact significantly with filgrastim thus allowing the collection of spectra in the presence of 20 times the formulation concentration in the sample. However, at higher detergent concentrations a reduction of signal intensity is observed. Conclusions The NMR fingerprint assay applied to filgrastim (Neupogen® and a CRS from the European Pharmacopeia (EP)) provided residue specific information of the structure of the drug substance. In addition to current methods, the ability to assess the conformation with a high degree of resolution can greatly facilitate comparability exercises.