Removing 65 Years of Approximation in Rotating Ring Disk Electrode Theory with Physics-Informed Neural Networks

The rotating Ring Disk Electrode (RRDE), since its introduction in 1959 by Frumkin and Nekrasov, has become indispensable with diverse applications in electrochemistry, catalysis, and material science. The collection efficiency ( N ) is an important parameter extracted from the ring and disk currents of the RRDE, providing valuable information about reaction mechanism, kinetics, and pathways. The theoretical prediction of N is a challenging task: requiring solution of the complete convective diffusion mass transport equation with complex velocity profiles. Previous efforts, including by Albery and Bruckenstein who developed the most widely used analytical equations, heavily relied on approximations by removing radial diffusion and using approximate velocity profiles. 65 years after the introduction of RRDE, we employ a physics-informed neural network to solve the complete convective diffusion mass transport equation, to reveal the formerly neglected edge effects and velocity corrections on N , and to provide a guideline where conventional approximation is applicable

Divide and Conquer: Chromosomal Approach to Cope with the Wheat Genome

Póster presentado en el Olomouc Biotech. Plant Biotechnology: green for good, celebrado en Olomouc (República Checa) del 19 al 21 de junio de 2011.Peer Reviewe

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules

Sequencing of 15 622 Gene-bearing BACs Clarifies the Gene-dense Regions of the Barley Genome

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley–Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST: Barley provides facile access to BAC sequences and their annotations, along with the barley– Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.Keywords: Aegilops tauschii, Barley, centromere BACs, HarvEST:Barley, gene distribution, synteny, recombination frequency, Hordeum vulgare L., BAC sequencingThis is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by John Wiley & Sons Ltd. on behalf of the Society for Experimental Biology. The published article can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-313X. Supporting information is available online at: http://onlinelibrary.wiley.com/doi/10.1111/tpj.12959/abstrac

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Fault-Tolerant Fuzzy Control for Semi-Markov Jump Nonlinear Systems Subject to Incomplete SMK and Actuator Failures

International audienceThis article focuses on the problem of fuzzy-model-based fault-tolerant control for nonlinear semi-Markov jump systems in the discrete-time context. The discrete-time semi-Markov process is employed to describe the mode jumping among several subsystems in the investigated systems. Moreover, the nonlinear characteristics are effectively tackled through utilizing the Takagi–Sugeno fuzzy model. Unlike some previous results, the information of the semi-Markov kernel (SMK) in this article is assumed to be partially available, which conforms better with the practical scenarios. Besides, considering the case that actuators may encounter some unexpected failures during system operation, the fault-tolerant mechanism is introduced in the process of controller design to enhance the fault tolerance of the studied systems. By means of SMK approach and Lyapunov stability theory, some elapsed-time-dependent criteria for guaranteeing the mean-square stability of the closed-loop system are established. According to these criteria, the design methodology of the reliable fuzzy state feedback controller is developed. Eventually, in order to verify the practicability and rationality of the developed control scheme, a single-link robot arm model is presented

Robust Nonlinear Predictive Current Control Techniques for PMSM

This paper proposes a robust nonlinear predictive current control (RNPCC) method for permanent magnet synchronous motor (PMSM) drives, which can optimize the current control loop performance of the PMSM system with model parameter perturbation. First, the disturbance caused by parameter perturbation was considered in the modeling of PMSM. Based on this model, the influence of parameter perturbation on the conventional predictive current control (PCC) was analyzed. The composite integral terminal sliding mode observer (SMO) was then designed to estimate the disturbance caused by the parameter perturbation in real time. Finally, a RNPCC method is developed without relying on the mathematical model of PMSM, which can effectively eliminate the influence of parameter perturbation by injecting the estimated disturbance value. Simulations and experiments verified that the proposed RNPCC method was able to remove the current error caused by the parameter perturbation during steady state operation

Common-Mode Reduction SVPWM for Three-Phase Motor Fed by Two-Level Voltage Source Inverter

Aiming at the problem of large magnitude and high frequency of common-mode voltage (CMV) when space vector pulse width modulation (SVPWM) is used in a three-phase motor fed by a two-level voltage source inverter, a common-mode reduction SVPWM (CMRSVPWM) is studied. In this method, six new sectors are obtained by rotating six sectors of conventional SVPWM by 30°. In odd-numbered sectors, only three non-zero vectors with odd subscripts are used for synthesis, while in even-numbered sectors, only three non-zero vectors with even subscripts are used for synthesis. The actuation durations of three non-zero vectors in each switching period in each sector are given. Simulation and experimental results show that, compared with the conventional SVPWM, the CMV magnitude of CMRSVPWM is reduced by 66.67% and the CMV frequency of CMRSVPWM is reduced from the original switching frequency to the triple fundamental frequency. At the same time, the current, torque and speed of the motor are still good

Feasibility and safety of Stanford A aortic dissection complete endovascular repair system in a porcine model

Abstract Background Acute type A aortic dissection (ATAAD) is a catastrophic disease with high morbidity and mortality. Although open surgery is still the gold standard for the treatment of ATAAD, some patients, with advanced age and multiple comorbidities, can only receive medical management alone. Nowadays, thoracic aortic endovascular repair (TEVAR) provides a potential treatment option for the patient with ATAAD, but traditional stent grafts (SGs), which are not designed for the ATAAD, are inapplicable to the unique anatomy of the aortic arch. Therefore, we innovatively created the BRIDGE system (Chuangxin Medical, Shenzhen, China), a complete endovascular reconstruction system designed to treat ATAAD. This study aimed to evaluate the feasibility and safety of the novel Stanford A aortic dissection complete endovascular reconstruction system in a porcine model. Method The BRIDGE system consists of the type A stent system and the type C stent system. Between November 2020 and March 2021, three white swine were utilized in the study. The BRIDGE system was deployed via the transcatheter approach under angiographic guidance. The swine(n = 3) treated with our system were evaluated using angiography before sacrifice 1-month after implantation, which was followed by gross specimen evaluation and histological examination of harvested tissues. Result The acute procedure success rate was 100% (3/3). The immediate post-procedural angiography showed that both type A SGs and type C SGs were deployed in satisfactory locations, with patency of the supra-aortic trunk and no endoleak. The cumulative mortality of 30-day was 0% without any adverse events. No device migration or leakage was observed angiographically, before sacrifice. The gross observation confirmed a type A SG covered part of the entry of anonyma. Favorable endothelialization, no thrombogenesis, and slight inflammatory infiltration of the tissues around the device were confirmed by microscopic examinations in all pigs. Conclusion It was feasible and secure to use Stanford A aortic dissection complete endovascular reconstruction system to implement a transcatheter endovascular repair in a porcine model. With this novel system, treating acute type A aortic dissection may be more efficient and secure in human