scholarly journals A method for evaluating the structural quality of protein models by using higher-order  -  pairs scoring

2006 ◽  
Vol 103 (12) ◽  
pp. 4428-4432 ◽  
Author(s):  
G. E. Sims ◽  
S.-H. Kim
Keyword(s):  
Higher Order ◽  
Structural Quality ◽  
Protein Models

scholarly journals Dockground scoring benchmarks for protein docking

2021 ◽  
Author(s):  
Ian Kotthoff ◽  
Petras J. Kundrotas ◽  
Ilya A. Vakser
Keyword(s):  
Protein Complexes ◽  
Protein Docking ◽  
Structural Quality ◽  
Scoring Functions ◽  
Model Benchmark ◽  
User Friendly ◽  
Development And Validation ◽  
Protein Models ◽  
Docking Benchmark

AbstractProtein docking protocols typically involve global docking scan, followed by re-ranking of the scan predictions by more accurate scoring functions that are either computationally too expensive or algorithmically impossible to include in the global scan. Development and validation of scoring methodologies are often performed on scoring benchmark sets (docking decoys) which offer concise and nonredundant representation of the global docking scan output for a large and diverse set of protein-protein complexes. Two such protein-protein scoring benchmarks were built for the Dockground resource, which contains various datasets for the development and testing of protein docking methodologies. One set was generated based on the Dockground unbound docking benchmark 4, and the other based on protein models from the Dockground model-model benchmark 2. The docking decoys were designed to reflect the reality of the real-case docking applications (e.g., correct docking predictions defined as near-native rather than native structures), and to minimize applicability of approaches not directly related to the development of scoring functions (reducing clustering of predictions in the binding funnel and disparity in structural quality of the near-native and non-native matches). The sets were further characterized by the source organism and the function of the protein-protein complexes. The sets, freely available to the research community on the Dockground webpage, present a unique, user-friendly resource for the developing and testing of protein-protein scoring approaches.

ВЛИЯНИЕ ТВЕРДОФАЗНОЙ РЕКРИСТАЛЛИЗАЦИИ С ДВОЙНОЙ ИМПЛАНТАЦИЕЙ НА ПЛОТНОСТЬ СТРУКТУРНЫХ ДЕФЕКТОВ В УЛЬТРАТОНКИХ СЛОЯХ КРЕМНИЯ НА САПФИРЕ

2020 ◽  
Vol 96 (3s) ◽  
pp. 154-159
Author(s):  
Н.Н. Егоров ◽  
С.А. Голубков ◽  
С.Д. Федотов ◽  
В.Н. Стаценко ◽  
А.А. Романов ◽  
...  
Keyword(s):  
Dislocation Density ◽  
Solid Phase ◽  
Modern Method ◽  
Structural Defects ◽  
Structural Quality ◽  
Mos Transistors ◽  
Ultrathin Layers ◽  
Heteroepitaxial Layers ◽  
Xrd And Tem

Высокая плотность структурных дефектов является основной проблемой при изготовлении электроники на гетероструктурах «кремний на сапфире» (КНС). Современный метод получения ультратонких структур КНС с помощью твердофазной эпитаксиальной рекристаллизации позволяет значительно снизить дефектность в гетероэпитаксиальном слое КНС. В данной работе ультратонкие (100 нм) слои КНС были получены путем рекристаллизации и утонения субмикронных (300 нм) слоев кремния на сапфире, обладающих различным структурным качеством. Плотность структурных дефектов в слоях КНС оценивалась с помощью рентгеноструктурного анализа и просвечивающей электронной микроскопии. Кривые качания от дифракционного отражения Si(400), полученные в ω-геометрии, продемонстрировали максимальную ширину на полувысоте пика не более 0,19-0,20° для ультратонких слоев КНС толщиной 100 нм. Формирование структурно совершенного субмикронного слоя КНС 300 нм на этапе газофазной эпитаксии обеспечивает существенное уменьшение плотности дислокаций в ультратонком кремнии на сапфире до значений ~1 • 104 см-1. Тестовые n-канальные МОП-транзисторы на ультратонких структурах КНС характеризовались подвижностью носителей в канале 725 см2 Вс-1. The high density of structural defects is the main problem on the way to the production of electronics on silicon-on-sapphire (SOS) heteroepitaxial wafers. The modern method of obtaining ultrathin SOS wafers is solid-phase epitaxial recrystallization which can significantly reduce the density of defects in the SOS heteroepitaxial layers. In the current work, ultrathin (100 nm) SOS layers were obtained by recrystallization and thinning of submicron (300 nm) SOS layers, which have various structural quality. The density of structural defects in the layers was estimated by using XRD and TEM. Full width at half maximum of rocking curves (ω-geometry) was no more than 0.19-0.20° for 100 nm ultra-thin SOS layers. The structural quality of 300 nm submicron SOS layers, which were obtained by CVD, depends on dislocation density in 100 nm ultrathin layers. The dislocation density in ultrathin SOS layers was reduced by ~1 • 104 cm-1 due to the utilization of the submicron SOS with good crystal quality. Test n-channel MOS transistors based on ultra-thin SOS wafers were characterized by electron mobility in the channel 725 cm2 V-1 s-1.

The Physical Context of Child Development

2021 ◽  
Vol 30 (1) ◽  
pp. 41-48
Author(s):  
Gary W. Evans
Keyword(s):  
Child Development ◽  
Observational Studies ◽  
Physiological Stress ◽  
Personal Characteristics ◽  
Adverse Outcomes ◽  
Structural Quality ◽  
Physical Context ◽  
Physical Setting ◽  
Physical Features

Child development reflects interactions between personal characteristics and the physical and social environment. Psychology, however, lacks analysis of physical features that influence child development. In this article, I describe a preliminary taxonomy of physical-setting characteristics that can influence child development, focusing on environmental stressors such as noise, crowding, and chaos along with structural quality of housing, day care, and schools. Adverse outcomes associated with suboptimal physical settings during childhood include cognitive and socioemotional difficulties along with chronic physiological stress. Both direct effects on the child as well as indirect effects occurring via significant persons surrounding the child are described. Methodological limitations, particularly reliance on observational studies, are a weakness in the current literature, but increasingly more rigorously obtained findings yield converging evidence of the effects of physical settings on child development.

scholarly journals Kabuli and Apulian black Chickpea Milling By-Products as Innovative Ingredients to Provide High Levels of Dietary Fibre and Bioactive Compounds in Gluten-Free Fresh Pasta

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4442
Author(s):  
Michela Costantini ◽  
Carmine Summo ◽  
Michele Faccia ◽  
Francesco Caponio ◽  
Antonella Pasqualone
Keyword(s):  
Bioactive Compounds ◽  
Dietary Fibre ◽  
Absorption Capacity ◽  
Nutritional Deficiencies ◽  
Structural Quality ◽  
Gluten Free ◽  
Food Industries ◽  
Chickpea Flour ◽  
Fresh Pasta

Gluten-free (GF) products, including pasta, are often characterised by nutritional deficiencies, such as scarce dietary fibre and excess of calories. Chickpea flour is increasingly being used by the food industries. Hulls, rich in dietary fibre and bioactive compounds, are discarded after milling. The aim of this work was to evaluate the quality features of short-cut GF fresh pasta added of hull (8% w/w) derived from kabuli (KH) or Apulian black (ABH) chickpeas, in comparison with control GF pasta prepared without hull. The enriched pasta, which could be labelled as “high fibre”, was characterised by a higher level of bioactive compounds and antioxidant activity than the control. ABH-enriched pasta showed the highest anthocyanins (33.37 ± 1.20 and 20.59 ± 0.11 mg/kg of cyanidin-3-O-glucoside on dry matter in raw and cooked pasta, respectively). Hull addition increased colour intensity and structural quality of GF pasta: ABH-enriched pasta had the lowest cooking loss and the highest water absorption capacity; KH-enriched pasta showed the highest firmness. No significant differences in sensory liking were found among the samples, except for “aftertaste”. Chickpea hull can be used as an innovative ingredient to produce potentially functional GF pasta, meeting the dietary needs of consumers without affecting quality.

On the Structural Quality of Co/Cu Trilayers and Superlattices: The Influence of the Template Layer

1993 ◽  
pp. 439-451
Author(s):  
A. Cebollada ◽  
J. de la Figuera ◽  
A. L. Vázquez de Parga ◽  
C. Ocal ◽  
R. Miranda
Keyword(s):  
Structural Quality

scholarly journals Effect of the turning characteristics of underfloor wheel lathes on the evolution of wheel polygonisation

2018 ◽  
Vol 233 (5) ◽  
pp. 479-488 ◽  
Author(s):  
Dabin Cui ◽  
Boyang An ◽  
Paul Allen ◽  
Ruichen Wang ◽  
Ping Wang ◽  
...  
Keyword(s):  
Fourth Order ◽  
High Speed ◽  
Higher Order ◽  
Ride Quality ◽  
Sustained Use ◽  
High Speed Trains ◽  
Cut Quality ◽  
Multiple Unit ◽  
Component Failures

During both running and wheel cut operations, wheels of railway vehicles and the friction rollers that support and drive the wheelset on a typical wheel cut lathe are subject to wear and hence are likely to develop out-of-round characteristics after sustained use. The resulting out-of-round wheels can significantly affect the ride quality and can potentially increase the incidence of fatigue-related component failures due to the resulting higher intensity loading cycles. Furthermore, the corresponding out-of-round characteristics of the lathe's friction rollers will continue to degrade the subsequent cut quality of wheels. For the analysis of the out-of-round characteristics caused by an underfloor wheel lathe used for the high-speed trains in China, a mathematical model based on a typical electric multiple unit (EMU) vehicle's wheelsets and their interactions with the wheel lathe friction rollers was established. Factors influencing the cut quality of the wheels, including the number of cuts, eccentricity forms of the friction rollers and the longitudinal spacing of the two rollers, have been analysed. The results show that two cuts can effectively remove the higher order polygon on the wheel surface. The eccentricity and phase angle of the friction rollers have no influence on the cut quality of higher order polygons, whereas they are the primary cause for the fourth-order polygons. The severity of the fourth-order polygon depends on the level and the phase of the eccentricity of the friction rollers. The space of the two rollers can also significantly affect the cut quality. Obtaining the theoretical and practical value for the maintenance of polygonised wheels using the underfloor lathe is the main outcome of this study.

scholarly journals Assessing the stochastic error of acoustic scattering matrices using linear methods

2018 ◽  
Vol 10 (4) ◽  
pp. 380-392 ◽  
Author(s):  
Luck Peerlings ◽  
Friedrich Bake ◽  
Susann Boij ◽  
Hans Bodén
Keyword(s):  
Uncertainty Analysis ◽  
Linear Method ◽  
Plane Waves ◽  
Acoustic Scattering ◽  
Higher Order ◽  
Condition Numbers ◽  
Matrix Perturbation ◽  
Stochastic Error ◽  
Scattering Matrices

To be able to compare the measured scattering matrices with model predictions, the quality of the measurements has to be known. Uncertainty analyses are invaluable to assess and improve the quality of measurement results in terms of accuracy and precision. Linear analyses are widespread, computationally fast and give information of the contribution of each error source to the overall measurement uncertainty; however, they cannot be applied in every situation. The purpose of this study is to determine if linear methods can be used to assess the quality of acoustic scattering matrices. The uncertainty in measured scattering matrices is assessed using a linear uncertainty analysis and the results are compared against Monte-Carlo simulations. It is shown that for plane waves, a linear uncertainty analysis, applied to the wave decomposition method, gives correct results when three conditions are satisfied. For higher order mode measurements, the number of conditions that have to be satisfied increases rapidly and the linear analysis becomes an unsuitable choice to determine the uncertainty on the scattering matrix coefficients. As the linear uncertainty analysis is most suitable for the plane wave range, an alternative linear method to assess the quality of the measurements is investigated. This method, based on matrix perturbation theory, gives qualitative information in the form of partial condition numbers and the implementation is straightforward. Using the alternative method, the measurements of higher order modes are analyzed and the observed difference in the measured reflection coefficients for different excitation conditions is explained by the disparity in modal amplitudes.

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