Parametric t-Distributed Stochastic Exemplar-centered Embedding

Parametric embedding methods such as parametric t-SNE (pt-SNE) have been widely adopted for data visualization and out-of-sample data embedding without further computationally expensive optimization or approximation. However, the performance of pt-SNE is highly sensitive to the hyper-parameter batch size due to conflicting optimization goals, and often produces dramatically different embeddings with different choices of user-defined perplexities. To effectively solve these issues, we present parametric t-distributed stochastic exemplar-centered embedding methods. Our strategy learns embedding parameters by comparing given data only with precomputed exemplars, resulting in a cost function with linear computational and memory complexity, which is further reduced by noise contrastive samples. Moreover, we propose a shallow embedding network with high-order feature interactions for data visualization, which is much easier to tune but produces comparable performance in contrast to a deep neural network employed by pt-SNE. We empirically demonstrate, using several benchmark datasets, that our proposed methods significantly outperform pt-SNE in terms of robustness, visual effects, and quantitative evaluations.Comment: fixed typo

Computer Mediated Communication in Negotiations: The Effect of Intragroup Faultlines on Intergroup Communication and Outcomes

This work examines the effect of faultlines in virtual computer mediated communications of two collocated negotiation teams. We expand upon prior diversity literature by considering the effect of both surface and deep-level faultlines on the intergroup computer mediated communications in virtual negotiations. Faultlines are hypothetical lines that divide teams into multiple subgroups based on diversity attributes. We confirm that the effect of team diversity on intergroup computer mediated communications can be better captured through faultlines. Our results suggest that faultlines mediate the effect of diversity on teams’ computer mediated intergroup communication and that deep-level faultlines significantly lower the frequency and quality of intergroup communication of virtual negotiations

Proteome phenotypes discriminate the growing location and malting traits in field-grown barley

Barley is one of the key cereal grains for malting and brewing industries. However, climate variability and unprecedented weather events can impact barley yield and end-product quality. The genetic background and environmental conditions are key factors in defining the barley proteome content and malting characteristics. Here, we measure the barley proteome and malting characteristics of three barley lines grown in Western Australia, differing in genetic background and growing location, by applying liquid chromatography-mass spectrometry (LC-MS). Using data-dependent acquisition LC-MS, 1571 proteins were detected with high confidence. Quantitative data acquired using sequential window acquisition of all theoretical (SWATH) MS on barley samples resulted in quantitation of 920 proteins. Multivariate analyses revealed that the barley lines\u27 genetics and their growing locations are strongly correlated between proteins and desired traits such as the malt yield. Linking meteorological data with proteomic measurements revealed how high-temperature stress in northern regions affects seed temperature tolerance during malting, resulting in a higher malt yield. Our results show the impact of environmental conditions on the barley proteome and malt characteristics; these findings have the potential to expedite breeding programs and malt quality prediction

From grain to malt: Tracking changes of ultra-low-gluten barley storage proteins after malting

Barley (Hordeum vulgare L.) is a major cereal crop produced globally. Hordeins, the major storage proteins in barley, can trigger immune responses leading to celiac disease or symptoms associated with food allergy. Here, proteomics approaches were employed to investigate the proteome level changes of grain and malt from the malting barley cultivar, Sloop, and single-, double- and triple hordein-reduced lines. The triple hordein-reduced line is an ultra-low gluten barley cultivar, Kebari®. Using discovery proteomics, 2,688 and 3,034 proteins in the barley and malt samples were detected respectively. Through the application of targeted proteomics, a significant reduction in the quantity of B-, D-, and γ-hordeins, as well as avenin-like proteins, was observed in the ultra-low gluten malt sample. A compensation mechanism was observed evidenced by increased biosynthesis of seed storage globulins, specifically vicilin-like globulins. Overall, this study has provided insights into protein compositional changes after malting in celiac-friendly barley varieties

Proteome changes resulting from malting in hordein-reduced barley lines

Hordeum vulgare L., commonly known as barley, is primarily used for animal feed and malting. The major storage proteins in barley are hordeins, known triggers of celiac disease (CD). Here, sequential window acquisition of all theoretical mass spectra (SWATH)-MS proteomics was employed to investigate the proteome profile of grain and malt samples from the malting barley cultivar Sloop and single-, double-, and triple hordein-reduced lines bred in a Sloop background. Using a discovery proteomics approach, 2688 and 3034 proteins were detected from the grain and malt samples, respectively. By utilizing label-free relative quantitation through SWATH-MS, a total of 2654 proteins have been quantified from grain and malt. The comparative analyses between the barley grain and malt samples revealed that the C-hordein-reduced lines have a more significant impact on proteome level changes due to malting than B- and D-hordein-reduced lines. Upregulated proteins in C-hordein-reduced lines were primarily involved in the tricarboxylic acid cycle and fatty acid peroxidation processes to provide more energy for seed germination during malting. By applying proteomics approaches after malting in hordein-reduced barley lines, we uncovered additional changes in the proteome driven by the genetic background that were not apparent in the sound grain. Our findings offer valuable insights for barley breeders and maltsters seeking to understand and optimize the performance of gluten-free grains in malt products

Application of mass spectrometry-based proteomics to barley research

Barley (Hordeum vulgare) is the fourth most cultivated crop in the world in terms of production volume, and it is also the most important raw material of the malting and brewing industries. Barley belongs to the grass (Poaceae) family and plays an important role in food security and food safety for both humans and livestock. With the global population set to reach 9.7 billion by 2050, but with less available and/or suitable land for agriculture, the use of biotechnology tools in breeding programs are of considerable importance in the quest to meet the growing food gap. Proteomics as a member of the “omics” technologies has become popular for the investigation of proteins in cereal crops and particularly barley and its related products such as malt and beer. This technology has been applied to study how proteins in barley respond to adverse environmental conditions including abiotic and/or biotic stresses, how they are impacted during food processing including malting and brewing, and the presence of proteins implicated in celiac disease. Moreover, proteomics can be used in the future to inform breeding programs that aim to enhance the nutritional value and broaden the application of this crop in new food and beverage products. Mass spectrometry analysis is a valuable tool that, along with genomics and transcriptomics, can inform plant breeding strategies that aim to produce superior barley varieties. In this review, recent studies employing both qualitative and quantitative mass spectrometry approaches are explored with a focus on their application in cultivation, manufacturing, processing, quality, and the safety of barley and its related products

Three-dimensional micromechanical assessment of bio-inspired composites with non-uniformly dispersed inclusions

The final publication is available at Elsevier via https://doi.org/10.1016/j.compstruct.2019.01.056 © 2019. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Bio-inspired composites with hexagonal platelet and cylindrical inclusions were studied. A novel algorithm termed staggered hardcore algorithm (SHCA) was used to rapidly generate 3D periodic representative volume elements (RVE) for bio-inspired composites with staggered non-uniformly dispersed inclusions. The spatial dispersions of inclusions in these generated RVEs were assessed using autocorrelation analysis, demonstrating the effectiveness of the SHCA algorithm. Orthotropic elastic properties of two different bio-inspired composites were computed and compared with analytical models, namely modified shear-lag, Mori-Tanaka and Halpin-Tsai, as well as available experimental data from the literature. For lower inclusion volume fractions, the computed results correlated well with experimental data and the analytical results. However, for higher inclusion volume fractions and aspect ratios the analytical results diverged, particularly Mori-Tanaka and modified shear-lag models which was similarly reported in previous studies. The capabilities of the computational model were further demonstrated through a comparative study of orthotropic elastic constants for the cylindrical and hexagonal inclusion composites. The study revealed the necessity to use 3D micromechanical models with realistic inclusion dispersions for accurately assessing the response of high inclusion volume fraction bio-inspired composites.Natural Sciences and Engineering Research Council of CanadaChina Scholarship Counci

Proteome and nutritional shifts observed in hordein double-mutant barley lines

Lysine is the most limiting essential amino acid in cereals, and efforts have been made over the decades to improve the nutritional quality of these grains by limiting storage protein accumulation and increasing lysine content, while maintaining desired agronomic traits. The single lys3 mutation in barley has been shown to significantly increase lysine content but also reduces grain size. Herein, the regulatory effect of the lys3 mutation that controls storage protein accumulation as well as a plethora of critically important processes in cereal seeds was investigated in double mutant barley lines. This was enabled through the generation of three hordein double-mutants by inter-crossing three single hordein mutants, that had all been backcrossed three times to the malting barley cultivar Sloop. Proteome abundance measurements were integrated with their phenotype measurements; proteins were mapped to chromosomal locations and to their corresponding functional classes. These models enabled the prediction of previously unknown points of crosstalk that connect the impact of lys3 mutations to other signalling pathways. In combination, these results provide an improved understanding of how the mutation at the lys3 locus remodels cellular functions and impact phenotype that can be used in selective breeding to generate favourable agronomic traits

Extrudable hydroxyapatite/plant oil-based biopolymer nanocomposites for biomedical applications: Mechanical testing and modeling

Towards developing bone-inspired, high performance composite biomaterials, two nanocomposite inks, consisting of a plant oil-based biopolymer resin (soybean oil epoxidized acrylate (SOEA)) and silanized nano-hydroxyapatite (Si-nHA) particles with and without diluent hydroxyethyl acrylate (HEA), were extruded using direct ink writing to fabricate filaments of differing volume fractions. HEA was hypothesized to lower ink viscosity, improve Si-nHA dispersion and extrudability, and therefore result in better relative improvements in mechanical properties over those of the base resin. Thermogravimetric analysis, scanning electron microscopy and uniaxial tensile tests were conducted. Strength, toughness, and stiffness of both resins were improved by the addition of Si-nHA. The HEA improved dispersion and extrudability. This resulted in better particle alignment and relatively greater augmentation of mechanical properties. The experimental data for both biopolymer resins were used to calibrate 3D representative volume element (RVE) finite element micromechanical models, while the experimental data for the nanocomposite filaments were employed to validate these models. The Young's moduli from the computational models were also compared with experimental data and with analytical predictions calculated using the Mori-Tanaka method. The predictions of 3D RVE models correlated well with the experimental data while, for higher volume fractions, the Mori-Tanaka results diverged, similar to previous reports.The authors thank the University of Waterloo and the Natural Sciences and Engineering Research Council of Canada (NSERC) for funding awarded to TLW and JM in support of this research

The stability of money demand in the long-run: Italy 1861–2011

Money demand stability is a crucial issue for monetary policy efficacy, and it is particularly endangered when substantial changes occur in the monetary system. By implementing the ARDL technique, this study intends to estimate the impact of money demand determinants in Italy over a long period (1861–2011) and to investigate the stability of the estimated relations. We show that instability cannot be excluded when a standard money demand function is estimated, irrespectively of the use of M1 or M2. Then, we argue that the reason for possible instability resides in the omission of relevant variables, as we show that a fully stable demand for narrow money (M1) can be obtained from an augmented money demand function involving real exchange rate and its volatility as additional explanatory variables. These results also allow us to argue that narrower monetary aggregates should be employed in order to obtain a stable estimated relation