Small Local Changes Research Articles

Structure and Internal Dynamics of Short RNA Duplexes Determined by a Combination of Pulsed EPR Methods and MD Simulations.

We used EPR spectroscopy to characterize the structure of RNA duplexes and their internal twist, stretch and bending motions. We prepared eight 20-base-pair-long RNA duplexes containing the rigid spin-label Çm, a cytidine analogue, at two positions and acquired orientation-selective PELDOR/DEER data. By using different frequency bands (X-, Q-, G-band), detailed information about the distance and orientation of the labels was obtained and provided insights into the global conformational dynamics of the RNA duplex. We used 19F Mims ENDOR experiments on three singly Çm- and singly fluorine-labeled RNA duplexes to determine the exact position of the Çm spin label in the helix. In a quantitative comparison to MD simulations of RNA with and without Çm spin labels, we found that state-of-the-art force fields with explicit parameterization of the spin label were able to describe the conformational ensemble present in our experiments. The MD simulations further confirmed that the Çm spin labels are excellent mimics of cytidine inducing only small local changes in the RNA structure. Çm spin labels are thus ideally suited for high-precision EPR experiments to probe the structure and, in conjunction with MD simulations, motions of RNA.

Structure and Internal Dynamics of Short RNA Duplexes Determined by a Combination of Pulsed EPR Methods and MD Simulations

AbstractWe used EPR spectroscopy to characterize the structure of RNA duplexes and their internal twist, stretch and bending motions. We prepared eight 20‐base‐pair‐long RNA duplexes containing the rigid spin‐label Çm, a cytidine analogue, at two positions and acquired orientation‐selective PELDOR/DEER data. By using different frequency bands (X‐, Q‐, G‐band), detailed information about the distance and orientation of the labels was obtained and provided insights into the global conformational dynamics of the RNA duplex. We used 19F Mims ENDOR experiments on three singly Çm‐ and singly fluorine‐labeled RNA duplexes to determine the exact position of the Çm spin label in the helix. In a quantitative comparison to MD simulations of RNA with and without Çm spin labels, we found that state‐of‐the‐art force fields with explicit parameterization of the spin label were able to describe the conformational ensemble present in our experiments. The MD simulations further confirmed that the Çm spin labels are excellent mimics of cytidine inducing only small local changes in the RNA structure. Çm spin labels are thus ideally suited for high‐precision EPR experiments to probe the structure and, in conjunction with MD simulations, motions of RNA.

Mechanistic Insights into the Adsorption of Monoclonal Antibodies at the Water/Vapor Interface.

Monoclonal antibodies (mAbs) are active components of therapeutic formulations that interact with the water-vapor interface during manufacturing, storage, and administration. Surface adsorption has been demonstrated to mediate antibody aggregation, which leads to a loss of therapeutic efficacy. Controlling mAb adsorption at interfaces requires a deep understanding of the microscopic processes that lead to adsorption and identification of the protein regions that drive mAb surface activity. Here, we report all-atom molecular dynamics (MD) simulations of the adsorption behavior of a full IgG1-type antibody at the water/vapor interface. We demonstrate that small local changes in the protein structure play a crucial role in promoting adsorption. Also, interfacial adsorption triggers structural changes in the antibody, potentially contributing to the further enhancement of surface activity. Moreover, we identify key amino acid sequences that determine the adsorption of antibodies at the water-air interface and outline strategies to control the surface activity of these important therapeutic proteins.

A vibration-based 1DCNN-BiLSTM model for structural state recognition of RC beams

The vibration signal analysis-based structural health monitoring (SHM) system has been widely used for bridge condition identification. With the development of artificial intelligence (AI), machine learning (ML) has made numerous breakthroughs in the detection of civil engineering structures. However, conventional data-driven ML methods heavily rely on prior knowledge for their performance. This paper proposes a deep learning (DL) model 1DCNN-BiLSTM for detecting small local structural changes of reinforced concrete (RC) beams, which applies the structure of the Inception module in GoogLeNet to one-dimensional convolution neural networks (1DCNNs) for feature extraction at different scales, and combines the advantages of bidirectional long short-term memory (BiLSTM) modules for processing long time-series data. Firstly, a three-dimensional numerical model of the RC beam was established using finite element software, and the accuracy of the numerical model was verified by comparing it with the test results. Based on the numerical model, tests on RC beams impacted by falling hammers were carried out, and the acceleration signals of the beam in different states were collected as a dataset. The proposed DL model can automatically extract the spatial and temporal domain features in the signals, accurately identify the location of small bridge local variations, the accuracy in the test set is 98.8% compared to 92.6% for a traditional ML model, and has better noise immunity performance and robustness to the missing data than the traditional ML model. Finally, the internal inference process of the model was explored and visualized, illustrating that the model has adaptive learning capabilities.

NMR Signatures and Electronic Structure of Ti Sites in Titanosilicalite-1 from Solid-State 47/49Ti NMR Spectroscopy.

Although titanosilicalite-1 (TS-1) is among the most successful oxidation catalysts used in industry, its active site structure is still debated. Recent efforts have mostly focused on understanding the role of defect sites and extraframework Ti. Here, we report the 47/49Ti signature of TS-1 and molecular analogues [Ti(OTBOS)4] and [Ti(OTBOS)3(OiPr)] using novel MAS CryoProbe to enhance the sensitivity. While the dehydrated TS-1 displays chemical shifts similar to those of molecular homologues, confirming the tetrahedral environment of Ti consistent with X-ray absorption spectroscopy, it is associated with a distribution of larger quadrupolar coupling constants, indicating an asymmetric environment. Detailed computational studies on cluster models highlights the high sensitivity of the NMR signatures (chemical shift and quadrupolar coupling constant) to small local structural changes. These calculations show that, while it will be difficult to distinguish mono- vs dinuclear sites, the sensitivity of the 47/49Ti NMR signature should enable distinguishing the Ti location among specific T site positions.

Airfoil optimization using Design-by-Morphing

Abstract Design-by-Morphing (DbM) is a novel design methodology that creates a search space for topology optimization. Traditional design techniques often impose geometric constraints and, sometimes, the designer’s biases on the design space, which restricts the novelty of the designs and allows for only small local changes. On the contrary, we show in this paper that DbM does not impose such restrictions on the design space, thus allowing for a radical and expansive search space with only a few design parameters. We compare DbM with other methods in the case of design space generation for 2D airfoils and find that DbM can reconstruct the entire UIUC database with >99.5% accuracy. Furthermore, using a bi-objective genetic algorithm, we optimize the airfoil designs created by DbM to maximize both the lift-over-drag ratio, CLDmax, and stall angle tolerance, Δα, which results in a Pareto-front of innovative airfoils that exhibit substantial improvements in both objectives.

Phylogenetic and Evolutionary Analysis of Plant Small RNA 2'-O-Methyltransferase (HEN1) Protein Family.

HUA ENHANCER 1 (HEN1) is a pivotal mediator in protecting sRNAs from 3'-end uridylation and 3' to 5' exonuclease-mediated degradation in plants. Here, we investigated the pattern of the HEN1 protein family evolutionary history and possible relationships in the plant lineages using protein sequence analyses and conserved motifs composition, functional domain identification, architecture, and phylogenetic tree reconstruction and evolutionary history inference. According to our results, HEN1 protein sequences bear several highly conserved motifs in plant species retained during the evolution from their ancestor. However, several motifs are present only in Gymnosperms and Angiosperms. A similar trend showed for their domain architecture. At the same time, phylogenetic analysis revealed the grouping of the HEN1 proteins in the three main super clads. In addition, the Neighbor-net network analysis result provides some nodes have multiple parents indicating a few conflicting signals in the data, which is not the consequence of sampling error, the effect of the selected model, or the estimation method. By reconciling the protein and species tree, we considered the gene duplications in several given species and found 170 duplication events in the evolution of HEN1 in the plant lineages. According to our analysis, the main HEN1 superclass mostly showed orthologous sequences that illustrate the vertically transmitting of HEN1 to the main lines. However, in both orthologous and paralogs, we predicted insignificant structural deviations. Our analysis implies that small local structural changes that occur continuously during the folds can moderate the changes created in the sequence. According to our results, we proposed a hypothetical model and evolutionary trajectory for the HEN1 protein family in the plant kingdom.

Strain Measurement in Single Crystals by 4D-ED

A new method is presented to measure strain over a large area of a single crystal. The 4D-ED data are collected by recording a 2D diffraction pattern at each position in the 2D area of the TEM lamella scanned by the electron beam of STEM. Data processing is completed with a new computer program (available free of charge) that runs under the Windows operating system. Previously published similar methods are either commercial or need special hardware (electron holography) or are based on HRTEM, which involves limitations with respect to the size of the field of view. All these limitations are overcome by our approach. The presence of defects results in small local changes in orientation that change the subset of experimentally available diffraction spots in the individual patterns. Our method is based on a new principle, namely fitting a lattice to (a subset of) measured diffraction spots to improve the precision of the measurement. Although a spot to be measured may be missing in some of the patterns even the missing spot can be precisely measured by the lattice determined from the available spots. Application is exemplified by heavily boron-doped silicon with intended usage as a low-temperature superconductor in qubits.

The barriers and facilitators to hand hygiene practices in Nigeria: A qualitative study: “There are so many barriers ... the barriers are limitless.”

Health care associated infections (HCAIs) are a global challenge and hand hygiene is the primary measure to reduce these. In developing countries, patients are between 2 and 20 times more likely to acquire an HCAI compared with developed countries. Estimates of hand hygiene in Sub-Saharan Africa suggests 21% concordance. There are few studies investigating barriers and facilitators and those published tend to be surveys. This study aimed to understand barriers and facilitators to hand hygiene in a hospital in Nigeria. A theoretically underpinned in-depth qualitative interview study with thematic analysis of nurses and doctors working in surgical wards. There were individual and institutional factors constituting barriers or facilitators: (1) knowledge, skills, and education, (2) perceived risks of infection to self and others, (3) memory, (4) the influence of others and (5) skin irritation. Institutional factors were (1) environment and resources and (2) workload and staffing levels. Our study presents barriers and facilitators not previously reported and offers nuances and detail to those already reported in the literature. Although the primary recommendation is adequate resources, however small local changes such as gentle soap, simple skills and reminder posters and mentorship or support could address many of the barriers listed.

Cooperative Protein Allosteric Transition Mediated by a Fluctuating Transmission Network

Allosteric communication between distant protein sites represents a key mechanism of biomolecular regulation and signal transduction. Compared to other processes such as protein folding, however, the dynamical evolution of allosteric transitions is still not well understood. As an example of allosteric coupling between distant protein regions, we consider the global open-closed motion of the two domains of T4 lysozyme, which is triggered by local motion in the hinge region. Combining extensive molecular dynamics simulations with a correlation analysis of interresidue contacts, we identify a network of interresidue distances that move in a concerted manner. The cooperative process originates from a cogwheel-like motion of the hydrophobic core in the hinge region, which constitutes an evolutionary conserved and flexible transmission network. Through rigid contacts and the protein backbone, the small local changes of the hydrophobic core are passed on to the distant terminal domains and lead to the emergence of a rare global conformational transition. As in an Ising-type model, the cooperativity of the allosteric transition can be explained via the interaction of local fluctuations.

On noise covariance estimation for Kalman filter-based damage localization

In Structural Health Monitoring, Kalman filters can be used as prognosis models, and for damage detection and localization. For a proper functioning, it is necessary to tune these filters with noise covariance matrices for process and measurement noise, which are unknown in practice. Therefore, in the presented work, we apply an autocovariance least-squares method with semidefinite constraints solely based on model parameters. We facilitate this novel approach by formulating the considered innovations covariance function in infinite horizon, which follows inherently from the assumption of linear time-invariant systems. For damage analysis, we adapt a framework based on state-projection estimation errors that was recently established, and yet only applied using H∞ filters. These estimators represent an alternative to Kalman filters, and are considered robust. Because of this property, the necessity of filter tuning is relaxed, and a naive design is often considered. Based on the damage analysis framework, we derive a new damage indicator that features a high sensitivity towards localized damage. We demonstrate the efficacy of the proposed schemes for noise covariance estimation and damage analysis in a series of simulations inspired by a preceding laboratory test. We finally offer experimental validation, based on vibration test data of a cantilever beam featuring damages at multiple positions, where high sensitivity towards small local stiffness changes is achieved. In our investigations, we compare the damage detection and localization performance of Kalman and H∞ filters as well as differences in mode shape curvatures (MSC). In the simulation studies, the proposed Kalman filter-based approach outperforms the alternative strategy using H∞ estimators. The experimental investigations demonstrate a significantly higher sensitivity of the filters towards localized damage compared to differences in MSCs. Considering the totality of investigations, the combined application of both estimators can lead to an increased robustness and sensitivity regarding damage detection and localization.

Structural effects of disease related mutations in actin binding period 3 of tropomyosin

Tropomyosin (Tpm) is an actin-binding coiled-coil protein, which in muscle regulates contraction in troponin/Ca2+-dependent manner and length of the thin filament at the pointed end. Due to its size and multidomain structure, it is difficult to observe small local structural changes in the coiled coil caused by some disease-related mutations. In this study, we designed 97-residue peptides, Tpm3.1265-155 and Tpm1.164-154, focusing on the period-3 region of two Tpm isoforms. Using these peptides, we evaluated the effects of cardiomyopathy mutations located in this region: I92T and V95A in Tpm1.1, and congenital myopathy mutations R91P and R91C in Tpm3.12.

Structural Effects of Disease-Related Mutations in Actin-Binding Period 3 of Tropomyosin.

Tropomyosin (Tpm) is an actin-binding coiled-coil protein. In muscle, it regulates contractions in a troponin/Ca2+-dependent manner and controls the thin filament lengths at the pointed end. Due to its size and periodic structure, it is difficult to observe small local structural changes in the coiled coil caused by disease-related mutations. In this study, we designed 97-residue peptides, Tpm1.164–154 and Tpm3.1265–155, focusing on the actin-binding period 3 of two muscle isoforms. Using these peptides, we evaluated the effects of cardiomyopathy mutations: I92T and V95A in Tpm1.1, and congenital myopathy mutations R91P and R91C in Tpm3.12. We introduced a cysteine at the N-terminus of each fragment to promote the formation of the coiled-coil structure by disulfide bonds. Dimerization of the designed peptides was confirmed by gel electrophoresis in the presence and absence of dithiothreitol. Using circular dichroism, we showed that all mutations decreased coiled coil stability, with Tpm3.1265–155R91P and Tpm1.164–154I92T having the most drastic effects. Our experiments also indicated that adding the N-terminal cysteine increased coiled coil stability demonstrating that our design can serve as an effective tool in studying the coiled-coil fragments of various proteins.

CAMP Compartmentalization in Cerebrovascular Endothelial Cells: New Therapeutic Opportunities in Alzheimer's Disease.

The vascular hypothesis used to explain the pathophysiology of Alzheimer’s disease (AD) suggests that a dysfunction of the cerebral microvasculature could be the beginning of alterations that ultimately leads to neuronal damage, and an abnormal increase of the blood–brain barrier (BBB) permeability plays a prominent role in this process. It is generally accepted that, in physiological conditions, cyclic AMP (cAMP) plays a key role in maintaining BBB permeability by regulating the formation of tight junctions between endothelial cells of the brain microvasculature. It is also known that intracellular cAMP signaling is highly compartmentalized into small nanodomains and localized cAMP changes are sufficient at modifying the permeability of the endothelial barrier. This spatial and temporal distribution is maintained by the enzymes involved in cAMP synthesis and degradation, by the location of its effectors, and by the existence of anchor proteins, as well as by buffers or different cytoplasm viscosities and intracellular structures limiting its diffusion. This review compiles current knowledge on the influence of cAMP compartmentalization on the endothelial barrier and, more specifically, on the BBB, laying the foundation for a new therapeutic approach in the treatment of AD.

Construções sustentáveis: aplicações para a cidade de Uberaba - MG

Objetivo do Estudo: Indicar possíveis adequações para construções sustentáveis na cidade de Uberaba/MG, auxiliando em escolhas de alternativas para uma melhor qualidade ambiental do meio urbano. Foram elencados a percolação, o retardo e infiltração de águas pluviais e telhados com cobertura verde.Metodologia/Abordagem: Tanto as metrópoles quanto as cidades do interior do nosso País estão enfrentando vários problemas ambientais, demonstrando a necessidade de se repensar sua configuração urbana, colocando como desafio ao conjunto do poder público e privado a necessidade de garantir uma cidade sustentável nos aspectos ambiental, social e econômico. Devido a esse desequilíbrio no tripé da sustentabilidade, as instituições públicas e privadas buscaram a criação de planos e ações voltadas ao macro e micro ambiente em que a sociedade está inserida, como, por exemplo, as Agendas Sustentáveis. Além disso, contam com o auxílio de sistemas e dispositivos sustentáveis na redução do consumo de recursos naturais e diminuição dos impactos ambientais.Originalidade/Relevância: Por meio de revisões de literaturas buscamos indicadores como sugestão para a sustentabilidade que possam se enquadrar para a malha urbana de Uberaba, obtendo como resultado algumas análises locais e contrastando com os estudos sobre sustentabilidade.Resultados: Foi observada a presença de ações que auxiliam na sustentabilidade e se mostram como alternativas sustentáveis tanto para o governo quanto para a própria comunidade, como, por exemplo, nas de vias e calçadas: o aumento das áreas permeáveis e da infiltração para diminuição da percolação em período de chuvas.Contribuições teórico-metodológicas: Os resultados deste estudo identificam como pequenas mudanças locais nas residências e na área coletiva urbana podem auxiliar para a minimização de danos causados por catástrofes urbanas, que surgem por meio de uma intervenção humana sem estudo adequado do meio, sugerindo contribuições para o aumento da qualidade ambiental da cidade.Conclusão: O uso do pavimento de blocos de concreto intertravados foi o indicador escolhido para sugestão de sustentabilidade. Apesar da análise econômica não ser totalmente viável, devido ao elevado custo do pavimento de concreto para o passeio, levando-se em conta o critério de desempenho para auxílio da percolação de água pluvial, sua escolha é a mais assertiva. No quesito sustentabilidade, são necessários vários critérios de escolha para cada ação específica.

Modulation of granulocyte colony stimulating factor conformation and receptor binding by methionine oxidation.

Biosimilars offer an avenue for potential cost savings and enhanced patient access to various emerging therapies in a budget neutral way. Biosimilars of the granulocyte colony stimulating factor (GCSF) are an excellent example in this regard with as many as 18 versions of the drug being currently approved across globe for treatment of neutropenia. Here, we identified oxidation of the various methionine residues in GCSF as a key heterogeneity that adversely impact its efficacy. In agreement with earlier studies, it was found that oxidation of Met 122 and Met 127 significantly contributes toward reduction of GCSF efficacy, measured using binding affinity to the GCSF receptor. The combination of molecular dynamics simulation along with structural characterization studies established that oxidation of Met 127 and Met 122 brings about a small local conformational change around the B-C loop in GCSF structure due to slight displacement of Asp113 and Thr117 residues. The simulation studies were validated using fluorescence quenching experiments using acrylamide as quencher and site-directed mutagenesis by replacing Met 122 and Met 127 residues with alanine. The results of this study lead to an enhanced mechanistic understanding of the oxidation in GCSF and should be useful in protein engineering efforts to design stable, safe, and efficacious GCSF product. In addition, the structure-function information can provide targets for protein engineering during early drug development and setting specifications of allowable limits of product variants in biosimilar products.

Using memetic algorithm for robustness testing of contract-based software models

Graph Transformation System (GTS) can formally specify the behavioral aspects of complex systems through graph-based contracts. Test suite generation under normal conditions from GTS specifications is a task well-suited to evolutionary algorithms such as Genetic and Particle Swarm Optimization (PSO) metaheuristics. However, testing the vulnerabilities of a system under unexpected events such as invalid inputs is essential. Furthermore, the mentioned global search algorithms tend to make big jumps in the system’s state-space that are not concentrated on particular test goals. In this paper, we extend the HGAPSO approach into a cost-aware Memetic Algorithm (MA) by making small local changes through a proposed local search operator to optimize coverage score and testing costs. Moreover, we test GTS specifications not only under normal events but also under unexpected situations. So, three coverage-based testing strategies are investigated, including normal testing, robustness testing, and a hybrid strategy. The effectiveness of the proposed test generation algorithm and the testing strategies are evaluated through a type of mutation analysis at the model-level. Our experimental results show that (1) the hybrid testing strategy outperforms normal and robustness testing strategies in terms of fault-detection capability, (2) the robustness testing is the most cost-efficient strategy, and (3) the proposed MA with the hybrid testing strategy outperforms the state-of-the-art global search algorithms.

Depth-selective data analysis for time-domain fNIRS: moments vs. time windows.

Time-domain measurements facilitate the elimination of the influence of extracerebral, systemic effects, a key problem in functional near-infrared spectroscopy (fNIRS) of the adult human brain. The analysis of measured time-of-flight distributions of photons often relies on moments or time windows. However, a systematic and quantitative characterization of the performance of these measurands is still lacking. Based on perturbation simulations for small localized absorption changes, we compared spatial sensitivity profiles and depth selectivity for moments (integral, mean time of flight and variance), photon counts in time windows and their ratios for different time windows. The influence of the instrument response function (IRF) was investigated for all measurands and for various source-detector separations. Variance exhibits the highest depth selectivity among the moments. Ratios of photon counts in different late time windows can achieve even higher selectivity. An advantage of moments is their robustness against the shape of the IRF and instrumental drifts.

Development of a reduced-complexity plant canopy physics surrogate model for use in chemical transport models: a case study with GEOS-Chem v12.3.0

Abstract. Biosphere–atmosphere interactions strongly influence the chemical composition of the atmosphere. Simulating these interactions at a detailed process-based level has traditionally been computationally intensive and resource prohibitive, commonly due to complexities in calculating radiation and light at the leaf level within plant canopies. Here we describe a surrogate canopy physics model based on the MEGAN3 detailed canopy model parameterized using a statistical learning technique. This surrogate canopy model is specifically designed to rapidly calculate leaf-level temperature and photosynthetically active radiative (PAR) for use in large-scale chemical transport models (CTMs). Our surrogate model can reproduce the dominant spatiotemporal variability of the more detailed MEGAN3 canopy model to within 10 % across the globe. Implementation of this surrogate model into the GEOS-Chem CTM leads to small local changes in ozone dry deposition velocities of less than 5 % and larger local changes in isoprene emissions of up to ∼40 %, though annual global isoprene emissions remain largely consistent (within 5 %). These changes to surface–atmosphere exchange lead to small changes in surface ozone concentrations of ±1 ppbv, modestly reducing the northern hemispheric ozone bias, which is common to many CTMs, here from 8 to 7 ppbv. The use of this computationally efficient surrogate canopy model drives emissions of isoprene and concentrations of surface ozone closer to observationally constrained values. Additionally, this surrogate model allows for the further development and implementation of leaf-level emission factors in the calculation of biogenic emissions in the GEOS-Chem CTM. Though not the focus of this work, this ultimately enables a complete implementation of the MEGAN3 emissions framework within GEOS-Chem, which produces 570 Tg yr−1 of isoprene for 2012.

Improvement of Text Segmentation TextTiling Algorithm

Text segmentation has a wide range of applications in the fields of information extraction and abstract generation. The method uses local information to determine a specific segmentation, and cannot fully consider the information of the remaining paragraphs. In response to this problem, this paper improves the segmentation point selection of the algorithm. After the similarity values of the respective interval points are obtained by the similarity calculation, the sliding window is used to slide on the interval points, and the similarity value of the interval points at the center of the window is replaced with the average of all the similarity values in the window. The experimental results show that the text segmentation based on the improved method can suppress small local changes on the curve, thus highlighting the large similarity value changes, and effectively improving the performance of text segmentation.