scholarly journals Network Analysis Provides Insight into Tomato Lipid Metabolism

Metabolites ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 152 ◽  
Author(s):  
Anastasiya Kuhalskaya ◽  
Micha Wijesingha Ahchige ◽  
Leonardo Perez de Souza ◽  
José Vallarino ◽  
Yariv Brotman ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Network Analysis ◽  
Volatile Compounds ◽  
Tomato Fruit ◽  
Major Influence ◽  
Phenotypic Traits ◽  
Solanum Pennellii ◽  
Metabolic Network Analysis ◽  
Wide Range ◽  
Insight Into

Metabolic correlation networks have been used in several instances to obtain a deeper insight into the complexity of plant metabolism as a whole. In tomato (Solanum lycopersicum), metabolites have a major influence on taste and overall fruit quality traits. Previously a broad spectrum of metabolic and phenotypic traits has been described using a Solanum pennellii introgression-lines (ILs) population. To obtain insights into tomato fruit metabolism, we performed metabolic network analysis from existing data, covering a wide range of metabolic traits, including lipophilic and volatile compounds, for the first time. We provide a comprehensive fruit correlation network and show how primary, secondary, lipophilic, and volatile compounds connect to each other and how the individual metabolic classes are linked to yield-related phenotypic traits. Results revealed a high connectivity within and between different classes of lipophilic compounds, as well as between lipophilic and secondary metabolites. We focused on lipid metabolism and generated a gene-expression network with lipophilic metabolites to identify new putative lipid-related genes. Metabolite–transcript correlation analysis revealed key putative genes involved in lipid biosynthesis pathways. The overall results will help to deepen our understanding of tomato metabolism and provide candidate genes for transgenic approaches toward improving nutritional qualities in tomato.

scholarly journals Two-component signaling systems regulate diverse virulence-associated traits in Pseudomonas aeruginosa

2021 ◽  
Author(s):  
Benjamin X. Wang ◽  
Kyle C. Cady ◽  
Gerardo C. Oyarce ◽  
Katharina Ribbeck ◽  
Michael T. Laub
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Sensory Systems ◽  
Phenotypic Traits ◽  
Signaling Proteins ◽  
Histidine Kinases ◽  
Signaling Systems ◽  
Wide Range ◽  
Two Component ◽  
Sense And Respond ◽  
Insight Into

Pseudomonas aeruginosa is an opportunistic pathogen that can cause problematic infections at different sites throughout the human body. P. aeruginosa encodes a large suite of over 60 two-component signaling systems that enable cells to rapidly sense and respond to external signals. Previous work has shown that some of these sensory systems contribute to P. aeruginosa pathogenesis, but the virulence-associated processes and phenotypic traits that each of these systems controls is still largely unclear. To aid investigations of these sensory systems, we have generated deletion strains for each of 64 genes encoding histidine kinases and one histidine phosphotransferase in P. aeruginosa PA14. We provide initial phenotypic characterizations of this collection by assaying these mutants for over a dozen virulence-associated traits, and find that each of these phenotypes is regulated by multiple sensory systems. Our work highlights the usefulness of this collection for further studies of P. aeruginosa two-component signaling systems and provides insight into how these systems may contribute to P. aeruginosa infection. Importance Pseudomonas aeruginosa can grow and survive in a wide range of conditions, including as a human pathogen. As such, P. aeruginosa must be able to sense and respond to diverse signals and cues in its environment. This sensory capability is endowed in part by the hundreds of two-component signaling proteins encoded in the P. aeruginosa genome, but the precise roles of each remain poorly defined. To facilitate systematic study of the signaling repertoire of P. aeruginosa PA14, we generated a library of deletion strains, each lacking one of the 65 histidine kinases. By subjecting these strains to a battery of phenotypic assays, we confirm the functions of many and unveil roles for dozens of previously uncharacterized histidine kinases in controlling various traits, many of which are associated with P. aeruginosa virulence. Thus, this work provides new insight into the functions of two-component signaling proteins and provides a resource for future investigations.

scholarly journals Skill networks and measures of complex human capital

2017 ◽  
Vol 114 (48) ◽  
pp. 12720-12724 ◽  
Author(s):  
Katharine A. Anderson
Keyword(s):  
Human Capital ◽  
Labor Market ◽  
Network Analysis ◽  
Additional Insight ◽  
Wide Range ◽  
Different Types ◽  
Using Data ◽  
Insight Into

We propose a network-based method for measuring worker skills. We illustrate the method using data from an online freelance website. Using the tools of network analysis, we divide skills into endogenous categories based on their relationship with other skills in the market. Workers who specialize in these different areas earn dramatically different wages. We then show that, in this market, network-based measures of human capital provide additional insight into wages beyond traditional measures. In particular, we show that workers with diverse skills earn higher wages than those with more specialized skills. Moreover, we can distinguish between two different types of workers benefiting from skill diversity: jacks-of-all-trades, whose skills can be applied independently on a wide range of jobs, and synergistic workers, whose skills are useful in combination and fill a hole in the labor market. On average, workers whose skills are synergistic earn more than jacks-of-all-trades.

Sentence-Based Experience Logging in New Hearing Aid Users

2020 ◽  
Vol 29 (3S) ◽  
pp. 631-637
Author(s):  
Katja Lund ◽  
Rodrigo Ordoñez ◽  
Jens Bo Nielsen ◽  
Dorte Hammershøi
Keyword(s):  
Hearing Aid ◽  
Patient Experiences ◽  
Online Tool ◽  
Rehabilitation Process ◽  
Hearing Rehabilitation ◽  
Clinical Observations ◽  
Hearing Aid Use ◽  
Wide Range ◽  
Insight Into ◽  
Shed Light

Purpose The aim of this study was to develop a tool to gain insight into the daily experiences of new hearing aid users and to shed light on aspects of aided performance that may not be unveiled through standard questionnaires. Method The tool is developed based on clinical observations, patient experiences, expert involvement, and existing validated hearing rehabilitation questionnaires. Results An online tool for collecting data related to hearing aid use was developed. The tool is based on 453 prefabricated sentences representing experiences within 13 categories related to hearing aid use. Conclusions The tool has the potential to reflect a wide range of individual experiences with hearing aid use, including auditory and nonauditory aspects. These experiences may hold important knowledge for both the patient and the professional in the hearing rehabilitation process.

Aromatic Volatile Composition of Celery and Celeriac Cultivars

HortScience ◽  
1990 ◽  
Vol 25 (5) ◽  
pp. 556-559 ◽  
Author(s):  
Fredy Van Wassenhove ◽  
Patrick Dirinck ◽  
Georges Vulsteke ◽  
Niceas Schamp
Keyword(s):  
Volatile Compounds ◽  
Chromatographic Method ◽  
Apium Graveolens ◽  
Volatile Components ◽  
Two Dimensional ◽  
Qualitative Composition ◽  
Volatile Composition ◽  
Wide Range ◽  
Gas Chromatographic Method ◽  
Identification And Quantification

A two-dimensional capillary gas chromatographic method was developed to separate and quantify aromatic volatiles of celery in one analysis. The isolation, identification, and quantification of the volatile compounds of four cultivars of blanching celery (Apium graveolens L. var. dulce) and six cultivars of celeriac (Apium graveolens L. var. rapaceum) are described. The qualitative composition of Likens-Nickerson extracts of both cultivars is similar. The concentration of terpenes and phthalides, the key volatile components, found in various cultivars of both celery and celeriac varied over a wide range.

scholarly journals Engineering the Interface between Inorganic Nanoparticles and Biological Systems through Ligand Design

Nanomaterials ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 1001
Author(s):  
Rui Huang ◽  
David C. Luther ◽  
Xianzhi Zhang ◽  
Aarohi Gupta ◽  
Samantha A. Tufts ◽  
...  
Keyword(s):  
Organic Synthesis ◽  
Molecular Design ◽  
Biological Systems ◽  
Ligand Design ◽  
Inorganic Nanoparticles ◽  
Organic Ligands ◽  
Biological Applications ◽  
Wide Range ◽  
Insight Into

Nanoparticles (NPs) provide multipurpose platforms for a wide range of biological applications. These applications are enabled through molecular design of surface coverages, modulating NP interactions with biosystems. In this review, we highlight approaches to functionalize nanoparticles with ”small” organic ligands (Mw < 1000), providing insight into how organic synthesis can be used to engineer NPs for nanobiology and nanomedicine.

scholarly journals Gas Damping in Capacitive MEMS Transducers in the Free Molecular Flow Regime

Sensors ◽  
2021 ◽  
Vol 21 (7) ◽  
pp. 2566
Author(s):  
Boris A. Boom ◽  
Alessandro Bertolini ◽  
Eric Hennes ◽  
Johannes F. J. van den Brand
Keyword(s):  
Flow Regime ◽  
Gas Diffusion ◽  
Diffusion Time ◽  
Molecular Flow ◽  
Free Molecular Flow ◽  
Simple Analytical Model ◽  
Gas Damping ◽  
Wide Range ◽  
Capacitive Mems ◽  
Insight Into

We present a novel analysis of gas damping in capacitive MEMS transducers that is based on a simple analytical model, assisted by Monte-Carlo simulations performed in Molflow+ to obtain an estimate for the geometry dependent gas diffusion time. This combination provides results with minimal computational expense and through freely available software, as well as insight into how the gas damping depends on the transducer geometry in the molecular flow regime. The results can be used to predict damping for arbitrary gas mixtures. The analysis was verified by experimental results for both air and helium atmospheres and matches these data to within 15% over a wide range of pressures.

scholarly journals Prediction of Dead Oil Viscosity: Machine Learning vs. Classical Correlations

Energies ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 930
Author(s):  
Fahimeh Hadavimoghaddam ◽  
Mehdi Ostadhassan ◽  
Ehsan Heidaryan ◽  
Mohammad Ali Sadri ◽  
Inna Chapanova ◽  
...  
Keyword(s):  
Machine Learning ◽  
Viscosity Data ◽  
Oil Viscosity ◽  
Pvt Data ◽  
Proposed Model ◽  
Wide Range ◽  
Engineering Problems ◽  
Functional Forms ◽  
Insight Into

Dead oil viscosity is a critical parameter to solve numerous reservoir engineering problems and one of the most unreliable properties to predict with classical black oil correlations. Determination of dead oil viscosity by experiments is expensive and time-consuming, which means developing an accurate and quick prediction model is required. This paper implements six machine learning models: random forest (RF), lightgbm, XGBoost, multilayer perceptron (MLP) neural network, stochastic real-valued (SRV) and SuperLearner to predict dead oil viscosity. More than 2000 pressure–volume–temperature (PVT) data were used for developing and testing these models. A huge range of viscosity data were used, from light intermediate to heavy oil. In this study, we give insight into the performance of different functional forms that have been used in the literature to formulate dead oil viscosity. The results show that the functional form f(γAPI,T), has the best performance, and additional correlating parameters might be unnecessary. Furthermore, SuperLearner outperformed other machine learning (ML) algorithms as well as common correlations that are based on the metric analysis. The SuperLearner model can potentially replace the empirical models for viscosity predictions on a wide range of viscosities (any oil type). Ultimately, the proposed model is capable of simulating the true physical trend of the dead oil viscosity with variations of oil API gravity, temperature and shear rate.

A new species of Sclerocephalus with a fully ossified endocranium gives insight into braincase evolution in temnospondyls

2021 ◽  
pp. 1-13
Author(s):  
Rainer R. Schoch ◽  
Gabriela Sobral
Keyword(s):  
New Species ◽  
Character Evolution ◽  
Late Paleozoic ◽  
New Taxon ◽  
Early Permian ◽  
Top Predator ◽  
Central European ◽  
Wide Range ◽  
A New Species ◽  
Insight Into

Abstract The late Paleozoic temnospondyl Sclerocephalus formed an aquatic top predator in various central European lakes of the late Carboniferous and early Permian. Despite hundreds of specimens spanning a wide range of sizes, knowledge of the endocranium (braincase and palatoquadrate) remained very insufficient in Sclerocephalus and other stereospondylomorphs because even large skulls had unossified endocrania. A new specimen from a stratigraphically ancient deposit at St. Wendel in southwestern Germany is recognized as representing a new taxon, S. concordiae new species, and reveals a completely ossified endocranium. The sphenethmoid was completely ossified from the basisphenoid to the anterior ethmoid region, co-ossified with the parasphenoid, and the basipterygoid joint was fully established. The pterygoid bears a slender, S-shaped epipterygoid, which formed a robust pillar lateral to the braincase. The massive stapes was firmly sutured to the parasphenoid. In the temnospondyl endocranium, character evolution involved various changes in the epipterygoid region, which evolved distinct morphologies in each of the major clades. UUID: http://zoobank.org/5e6d2078-eacf-4467-84cf-a12efcae7c0b

scholarly journals Visualising Ostia’s Processional Landscape Through a Multi-Layered Computational Approach: Case Study of the Cult of the Magna Mater

2019 ◽  
Vol 5 (1) ◽  
pp. 444-467
Author(s):  
Katherine A. Crawford
Keyword(s):  
Network Analysis ◽  
Computational Approach ◽  
Urban Network ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Existing Problems ◽  
Layered Approach ◽  
Religious Landscape ◽  
Insight Into

AbstractOstia, the ancient port of Rome, had a rich religious landscape. How processional rituals further contributed to this landscape, however, has seen little consideration. This is largely due to a lack of evidence that attests to the routes taken by processional rituals. The present study aims to address existing problems in studying processions by questioning what factors motivated processional movement routes. A novel computational approach that integrates GIS, urban network analysis, and agent-based modelling is introduced. This multi-layered approach is used to question how spectators served as attractors in the creation of a processional landscape using Ostia’s Campo della Magna Mater as a case study. The analysis of these results is subsequently used to gain new insight into how a greater processional landscape was created surrounding the sanctuary of the Magna Mater.

scholarly journals Transcriptomic and Metabolic Network Analysis of Metabolic Reprogramming and IGF-1 Modulation in SCA3 Transgenic Mice

2021 ◽  
Vol 22 (15) ◽  
pp. 7974
Author(s):  
Yu-Te Lin ◽  
Yong-Shiou Lin ◽  
Wen-Ling Cheng ◽  
Jui-Chih Chang ◽  
Yi-Chun Chao ◽  
...  
Keyword(s):  
Network Analysis ◽  
Transgenic Mice ◽  
Signaling Pathways ◽  
Metabolic Network ◽  
Metabolic Reprogramming ◽  
Spinocerebellar Ataxia Type ◽  
Positive Effects ◽  
Metabolic Network Analysis ◽  
Potential Biomarker ◽  
Metabolic Remodeling

Spinocerebellar ataxia type 3 (SCA3) is a genetic neurodegenerative disease for which a cure is still needed. Growth hormone (GH) therapy has shown positive effects on the exercise behavior of mice with cerebellar atrophy, retains more Purkinje cells, and exhibits less DNA damage after GH intervention. Insulin-like growth factor 1 (IGF-1) is the downstream mediator of GH that participates in signaling and metabolic regulation for cell growth and modulation pathways, including SCA3-affected pathways. However, the underlying therapeutic mechanisms of GH or IGF-1 in SCA3 are not fully understood. In the present study, tissue-specific genome-scale metabolic network models for SCA3 transgenic mice were proposed based on RNA-seq. An integrative transcriptomic and metabolic network analysis of a SCA3 transgenic mouse model revealed that metabolic signaling pathways were activated to compensate for the metabolic remodeling caused by SCA3 genetic modifications. The effect of IGF-1 intervention on the pathology and balance of SCA3 disease was also explored. IGF-1 has been shown to invoke signaling pathways and improve mitochondrial function and glycolysis pathways to restore cellular functions. As one of the downregulated factors in SCA3 transgenic mice, IGF-1 could be a potential biomarker and therapeutic target.

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