High-coverage, unbounded sound predictive race detection

2018 ◽  
Vol 53 (4) ◽  
pp. 374-389 ◽  
Author(s):  
Jake Roemer ◽  
Kaan Genç ◽  
Michael D. Bond
Keyword(s):  
2019 ◽  
Author(s):  
Andrew Medford ◽  
Shengchun Yang ◽  
Fuzhu Liu

Understanding the interaction of multiple types of adsorbate molecules on solid surfaces is crucial to establishing the stability of catalysts under various chemical environments. Computational studies on the high coverage and mixed coverages of reaction intermediates are still challenging, especially for transition-metal compounds. In this work, we present a framework to predict differential adsorption energies and identify low-energy structures under high- and mixed-adsorbate coverages on oxide materials. The approach uses Gaussian process machine-learning models with quantified uncertainty in conjunction with an iterative training algorithm to actively identify the training set. The framework is demonstrated for the mixed adsorption of CH<sub>x</sub>, NH<sub>x</sub> and OH<sub>x</sub> species on the oxygen vacancy and pristine rutile TiO<sub>2</sub>(110) surface sites. The results indicate that the proposed algorithm is highly efficient at identifying the most valuable training data, and is able to predict differential adsorption energies with a mean absolute error of ~0.3 eV based on <25% of the total DFT data. The algorithm is also used to identify 76% of the low-energy structures based on <30% of the total DFT data, enabling construction of surface phase diagrams that account for high and mixed coverage as a function of the chemical potential of C, H, O, and N. Furthermore, the computational scaling indicates the algorithm scales nearly linearly (N<sup>1.12</sup>) as the number of adsorbates increases. This framework can be directly extended to metals, metal oxides, and other materials, providing a practical route toward the investigation of the behavior of catalysts under high-coverage conditions.


2020 ◽  
Author(s):  
Tianyang Yan ◽  
Heta Desai ◽  
Lisa Boatner ◽  
Stephanie Yen ◽  
Jian Cao ◽  
...  

<p>We report a new cysteine chemoproteomic method, termed SP3-FAIMS chemoproteomics, which enables rapid and high coverage analysis of the human cysteinome. By combining enhanced cysteine biotinylation with SP3 sample decontamination and FAIMS online fraction, we identified in aggregate 34,225 unique cysteines found on 7,243 proteins. Showcasing the versatility of our method, integration with the isoTOP-ABPP workflow enabled the high throughput discovery of cysteines labelled by electrophilic compounds. </p>


2019 ◽  
Author(s):  
Luke Clifton ◽  
Nicoló Paracini ◽  
Arwel V. Hughes ◽  
Jeremy H. Lakey ◽  
Nina-Juliane Seinke ◽  
...  

<p>We present a reliable method for the fabrication of fluid phase unsaturated bilayers which are readily self-assembled on charged self-assembled monolayer (SAM) surfaces producing high coverage floating supported bilayers where the membrane to surface distance could be controlled with nanometer precision. Vesicle fusion was used to deposit the bilayers onto anionic SAM coated surfaces. Upon assembly the bilayer to SAM solution interlayer thickness was 7-10 Å with evidence suggesting that this layer was present due to SAM hydration repulsion of the bilayer from the surface. This distance could be increased using low concentrations of salts which caused the interlayer thickness to enlarge to ~33 Å. Reducing the salt concentration resulted in a return to a shorter bilayer to surface distance. These accessible and controllable membrane models are well suited to a range of potential applications in biophysical studies, bio-sensors and Nano-technology.</p><br>


2019 ◽  
Vol 44 (4) ◽  
pp. 18-18 ◽  
Author(s):  
Egor Namakonov ◽  
Eric Mercer ◽  
Pavel Parizek ◽  
Kyle Storey

ChemBioChem ◽  
2021 ◽  
Author(s):  
Tianyang Yan ◽  
Heta S. Desai ◽  
Lisa M. Boatner ◽  
Stephanie L. Yen ◽  
Jian Cao ◽  
...  
Keyword(s):  

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 899
Author(s):  
Fotis Pappas ◽  
Christos Palaiokostas

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.


2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Lisa Grossman Liu ◽  
Raymond H. Grossman ◽  
Elliot G. Mitchell ◽  
Chunhua Weng ◽  
Karthik Natarajan ◽  
...  

AbstractThe recognition, disambiguation, and expansion of medical abbreviations and acronyms is of upmost importance to prevent medically-dangerous misinterpretation in natural language processing. To support recognition, disambiguation, and expansion, we present the Medical Abbreviation and Acronym Meta-Inventory, a deep database of medical abbreviations. A systematic harmonization of eight source inventories across multiple healthcare specialties and settings identified 104,057 abbreviations with 170,426 corresponding senses. Automated cross-mapping of synonymous records using state-of-the-art machine learning reduced redundancy, which simplifies future application. Additional features include semi-automated quality control to remove errors. The Meta-Inventory demonstrated high completeness or coverage of abbreviations and senses in new clinical text, a substantial improvement over the next largest repository (6–14% increase in abbreviation coverage; 28–52% increase in sense coverage). To our knowledge, the Meta-Inventory is the most complete compilation of medical abbreviations and acronyms in American English to-date. The multiple sources and high coverage support application in varied specialties and settings. This allows for cross-institutional natural language processing, which previous inventories did not support. The Meta-Inventory is available at https://bit.ly/github-clinical-abbreviations.


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