Influence of model resolution on geometric simulations of antibody aggregation

Robotica ◽  
2016 ◽  
Vol 34 (8) ◽  
pp. 1754-1776 ◽  
Author(s):  
Kasra Manavi ◽  
Bruna Jacobson ◽  
Brittany Hoard ◽  
Lydia Tapia

SUMMARYIt is estimated that allergies afflict up to 40% of the world's population. A primary mediator for allergies is the aggregation of antigens and IgE antibodies bound to cell-surface receptors, FcεRI. Antibody/antigen aggregate formation causes stimulation of mast cells and basophils, initiating cellular degranulation and releasing immune mediators which produce an allergic or anaphylactic response. Understanding the shape and structure of these aggregates can provide critical insights into the allergic response. We have previously developed methods to geometrically model, simulate and analyze antibody aggregation inspired by rigid body robotic motion simulations. Our technique handles the large size and number of molecules involved in aggregation, providing an advantage over traditional simulations such as molecular dynamics (MD) and coarse-grained energetic models. In this paper, we study the impact of model resolution on simulations of geometric structures using both our previously developed Monte Carlo simulation and a novel application of rule-based modeling. These methods complement each other, the former providing explicit geometric detail and the latter providing a generic representation where multiple resolutions can be captured. Our exploration is focused on two antigens, a man-made antigen with three binding sites, DF3, and a common shrimp allergen (antigen), Pen a 1. We find that impact of resolution is minimal for DF3, a small globular antigen, but has a larger impact on Pen a 1, a rod-shaped molecule. The volume reduction caused by the loss in resolution allows more binding site accessibility, which can be quantified using a rule-based model with implicit geometric input. Clustering analysis of our simulation shows good correlation when compared with available experimental results. Moreover, collisions in all-atom reconstructions are negligible, at around 0.2% at 90% reduction.

Author(s):  
Belay Tesfamariam

Neonatal megakaryopoiesis and platelet turnover form a developmentally unique pattern by generating a pool of newly released reticulated platelets from the bone marrow into the circulation. Reticulated platelets are more reactive and hyperaggregable compared to mature platelets, due to their high residual mRNA content, large size, increased expression of platelet surface receptors, and degranulation. The proportion of reticulated platelets in neonates is higher compared to that in adults. Due to the emergence of an uninhibited platelet subpopulation, the newly formed reticulated platelet pool is inherently hyporesponsive to antiplatelets. An elevated population of reticulated platelets is often associated with increased platelet reactivity and is inversely related to high on-treatment platelet reactivity, which can contribute to ischemia. Measurements of the reticulated platelet subpopulation could be a useful indicator of increased tendency for platelet aggregation. Future research is anticipated to define the distinct functional properties of newly formed reticulated or immature platelets in neonates, as well as determine the impact of enhanced platelet turnover and high residual platelet reactivity on the response to antiplatelet agents.


2021 ◽  
Vol 80 (3) ◽  
pp. 1963-1980
Author(s):  
Solomon Adomako ◽  
Christian John Engelsen ◽  
Rein Terje Thorstensen ◽  
Diego Maria Barbieri

AbstractRock aggregates constitute the enormous volume of inert construction material used around the globe. The petrologic description as igneous, sedimentary, and metamorphic types establishes the intrinsic formation pattern of the parent rock. The engineering properties of these rocks vary due to the differences in the transformation process (e.g. hydrothermal deposits) and weathering effect. The two most common mechanical tests used to investigate the performance of aggregates are the Los Angeles (LA) and micro-Deval (MD) tests. This study reviewed the geological parameters (including mineralogy, grain and crystal size, grain shape, and porosity) and the relationship to Los Angeles and micro-Deval tests. It was found that high content of primary minerals in rocks (e.g. quartz and feldspar) is a significant parameter for performance evaluation. Traces of secondary and accessory minerals also affect the performance of rocks, although in many cases it is based on the percentage. Furthermore, some studies showed that the effect of mineralogic composition on mechanical strength is not sufficient to draw final conclusions of mechanical performance; therefore, the impact of other textural characteristics should be considered. The disposition of grain size and crystal size (e.g. as result of lithification) showed that rocks composed of fine-grain textural composition of ≤ 1 mm enhanced fragmentation and wear resistance than medium and coarse grained (≥ 1 mm). The effect of grain shape was based on convex and concave shapes and flat and elongated apexes of tested samples. The equidimensional form descriptor of rocks somehow improved resistance to impact from LA than highly flat and elongated particles. Lastly, the distribution of pore space investigated by means of the saturation method mostly showed moderate (R = 0.50) to strong (R = 0.90) and positive correlations to LA and MD tests.


2017 ◽  
Vol 9 (3) ◽  
pp. 133 ◽  
Author(s):  
Bashar K. Abu Khalaf

The different capital structure theories propose the possible asymmetric behavior of capital structure. Thus, this paper empirically investigates whether non-financial Jordanian firms follow symmetrical or asymmetrical adjustment model. Then, an interaction model with the size and profitability (firm characteristics) investigated the impact of low/high profit and small/large size on the adjustment of leverage towards the target leverage ratio. This paper covered the period of 14 years (2002-2015) for a total of 110 companies listed on Amman Stock Exchange (75 industrial and 35 services). Results indicate that although Jordanian firms seek a target leverage ratio, their adjustment towards that target is Asymmetrical and high profitable and large companies tend to adjust faster than low profitable and small size companies.


2018 ◽  
Vol 937 ◽  
pp. 61-67
Author(s):  
Yu Jie Li ◽  
Jin Wei Lei ◽  
Xuan Wei Lei ◽  
Oleksandr Hress ◽  
Kai Ming Wu

Utilizing submerged arc welding under heat input 50 kJ/cm on 60 mm thick marine engineering structure plate F550, the effect of preheating and post welding heat treatment on the microstructure and impact toughness of coarse-grained heat-affected zone (CGHAZ) has been investigated. The original microstructure of the steel plate is tempered martensite. The yield and tensile strength is 610 and 660 MPa, respectively. The impact absorbed energy at low temperature (-60 °C) at transverse direction reaches about 230~270 J. Welding results show that the preheating at 100 °C did not have obvious influence on the microstructure and toughness; whereas the tempering at 600 °C for 2.5 h after welding could significantly reduce the amount of M-A components in the coarse-grained heat-affected zone and thus improved the low temperature impact toughness.


2021 ◽  
Vol 297 ◽  
pp. 01072
Author(s):  
Rajae Bensoltane ◽  
Taher Zaki

Aspect category detection (ACD) is a task of aspect-based sentiment analysis (ABSA) that aims to identify the discussed category in a given review or sentence from a predefined list of categories. ABSA tasks were widely studied in English; however, studies in other low-resource languages such as Arabic are still limited. Moreover, most of the existing Arabic ABSA work is based on rule-based or feature-based machine learning models, which require a tedious task of feature-engineering and the use of external resources like lexicons. Therefore, the aim of this paper is to overcome these shortcomings by handling the ACD task using a deep learning method based on a bidirectional gated recurrent unit model. Additionally, we examine the impact of using different vector representation models on the performance of the proposed model. The experimental results show that our model outperforms the baseline and related work models significantly by achieving an enhanced F1-score of more than 7%.


2011 ◽  
Vol 1 (32) ◽  
pp. 53
Author(s):  
Ian Ball ◽  
Edgar Mendoza-Baldwin ◽  
David Simmonds ◽  
Adrián Pedrozo-Acuña ◽  
Dominic E Reeve

In this paper we present laboratory observations of plunging wave breaker impact pressure responses on a steep coarse-grained beach, extending previous work conducted by Pedrozo-Acuña et al. (2008). Scale laboratory measurements of plunging breaker impact events are reported and compared with the previous full-scale tests. These tests extend the previous relationships to a wider range of surf-similarity parameters and indicate a continued reduction in impact pressure as the transition from plunging impacts to surging impacts is approached. Additional results from scale tests conducted on a smooth impermeable slope also indicate the presence of a maximum impact pressure within the plunging breaker region; however also suggest it may be necessary to include roughness and permeability in the parameterization of the impact pressure.


2011 ◽  
Vol 1 ◽  
pp. 85
Author(s):  
Tim Pelton ◽  
Leslee Francis Pelton ◽  
Mary Sanseverino

This project began in response to a perceived need to assess students’ perceptions with respect to the emerging use of audience response systems (clickers) in several mid- to large-size undergraduate courses at the University of Victoria. We developed and validated a “Clicker Use Survey” to gather students’ opinions with respect to clicker utility and the impact of clicker use on their learning. With the collected data we generated a set of baseline distributions to support assessment of various clicker use protocols and created a self-evaluation tool to share with instructors to support teacher reflection on the efficacy of their clicker practices. We also provided a sample self-evaluation to model the use of the tool. Links to the survey instrument, baseline data and self-evaluation tool, and sample self-evaluation are provided.


2014 ◽  
Vol 59 (4) ◽  
pp. 1559-1563 ◽  
Author(s):  
M. Ciesla ◽  
M. Manka ◽  
P. Gradon ◽  
F. Binczyk

Abstract The study assesses the impact of surface and bulk modification and filtration during pouring on a durability under accelerated creep conditions of casts made of IN-713C and MAR-247 nickel superalloys scrap used for manufacturing of aircraft engine parts. The impact of solutionizing (1185°C/2 h) with subsequent ageing (870°C/20 h) on the creep resistance of a casting made from MAR-247 coarse-grained superalloy was also examined. Morphological structure parameters were determined with the use of Met-Ilo software. Macrostructure analysis of casts showed very significant impact of surface modification treatment. Creep test results clearly showed that coarse grained samples of IN-713C and MAR-247 superalloys have higher creep resistance. Moreover alloy MAR-247 had higher creep durability after heat treatment compared to as-cast state.


2006 ◽  
Vol 361 (1467) ◽  
pp. 477-482 ◽  
Author(s):  
Stephen G Oliver

Metabolic Control Analysis (MCA) is a conceptual and mathematical formalism that models the relative contributions of individual effectors in a pathway to both the flux through the pathway and the concentrations of individual intermediates within it. To exploit MCA in an initial Systems Biology analysis of the eukaryotic cell, two categories of experiments are required. In category 1 experiments, flux is changed and the impact on the levels of the direct and indirect products of gene action is measured. We have measured the impact of changing the flux on the transcriptome, proteome and metabolome of Saccharomyces cerevisiae . In this whole-cell analysis, flux equates to growth rate. In category 2 experiments, the levels of individual gene products are altered, and the impact on the flux is measured. We have used competition analyses between the complete set of heterozygous yeast deletion mutants to reveal genes encoding proteins with high flux control coefficients. These genes may be exploited, in a top-down analysis, to build a coarse-grained model of the eukaryotic cell, as exemplified by yeast. More detailed modelling requires that ‘natural’ biological systems be identified. The combination of flux balance analysis with both genetics and metabolomics in the definition of metabolic systems is discussed.


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