SP3‐FAIMS Chemoproteomics for High‐Coverage Profiling of the Human Cysteinome**

Scalable Approach to High Coverages on Oxides via Iterative Training of a Machine-Learning Algorithm

10.26434/chemrxiv.10288514.v1 ◽

2019 ◽

Author(s):

Andrew Medford ◽

Shengchun Yang ◽

Fuzhu Liu

Keyword(s):

Machine Learning ◽

Chemical Potential ◽

Learning Algorithm ◽

Absolute Error ◽

Low Energy ◽

Training Data ◽

High Coverage ◽

Metal Compounds ◽

Adsorption Energies ◽

The Stability

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 CHx, NHx and OHx species on the oxygen vacancy and pristine rutile TiO2(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 (N1.12) 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.

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SP3-FAIMS Chemoproteomics for High Coverage Profiling of the Human Cysteinome

10.26434/chemrxiv.13487364.v1 ◽

2020 ◽

Author(s):

Tianyang Yan ◽

Heta Desai ◽

Lisa Boatner ◽

Stephanie Yen ◽

Jian Cao ◽

...

Keyword(s):

High Throughput ◽

High Coverage ◽

Method Integration ◽

Coverage Analysis

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.

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Self-Assembled Fluid Phase Floating Membranes with Tuneable Water Interlayers

10.26434/chemrxiv.8307419 ◽

2019 ◽

Author(s):

Luke Clifton ◽

Nicoló Paracini ◽

Arwel V. Hughes ◽

Jeremy H. Lakey ◽

Nina-Juliane Seinke ◽

...

Keyword(s):

Fluid Phase ◽

Interlayer Thickness ◽

Supported Bilayers ◽

Self Assembled Monolayer ◽

High Coverage ◽

Nano Technology ◽

Surface Distance ◽

Potential Applications ◽

Self Assembled ◽

Coated Surfaces

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.

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Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Animals ◽

10.3390/ani11030899 ◽

2021 ◽

Vol 11 (3) ◽

pp. 899

Author(s):

Fotis Pappas ◽

Christos Palaiokostas

Keyword(s):

Genetic Diversity ◽

Salvelinus Alpinus ◽

Arctic Charr ◽

Cost Effective ◽

Limiting Factors ◽

Phenotypic Traits ◽

Production Volume ◽

High Coverage ◽

Genomic Relationships ◽

Low Coverage

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.

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A deep database of medical abbreviations and acronyms for natural language processing

Scientific Data ◽

10.1038/s41597-021-00929-4 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Lisa Grossman Liu ◽

Raymond H. Grossman ◽

Elliot G. Mitchell ◽

Chunhua Weng ◽

Karthik Natarajan ◽

...

Keyword(s):

Natural Language Processing ◽

Natural Language ◽

Language Processing ◽

American English ◽

Substantial Improvement ◽

Future Application ◽

Multiple Sources ◽

High Coverage ◽

Clinical Text ◽

Automated Quality Control

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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Childhood vaccination coverage in Australia: an equity perspective

BMC Public Health ◽

10.1186/s12889-021-11345-z ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Arzu Arat ◽

Hannah C. Moore ◽

Sharon Goldfeld ◽

Viveca Östberg ◽

Vicky Sheppeard ◽

...

Keyword(s):

Vaccination Coverage ◽

Economic Status ◽

Childhood Vaccination ◽

High Coverage ◽

Socio Economic Status ◽

Policy Interventions ◽

South Wales ◽

Social Inequities ◽

Future Policy ◽

Aboriginal Children

Abstract Background This study describes trends in social inequities in first dose measles-mumps-rubella (MMR1) vaccination coverage in Western Australia (WA) and New South Wales (NSW). Using probabilistically-linked administrative data for 1.2 million children born between 2002 and 2011, we compared levels and trends in MMR1 vaccination coverage measured at age 24 months by maternal country of birth, Aboriginal status, maternal age at delivery, socio-economic status, and remoteness in two states. Results Vaccination coverage was 3–4% points lower among children of mothers who gave birth before the age of 20 years, mothers born overseas, mothers with an Aboriginal background, and parents with a low socio-economic status compared to children that did not belong to these social groups. In both states, between 2007 and 2011 there was a decline of 2.1% points in MMR1 vaccination coverage for children whose mothers were born overseas. In 2011, WA had lower coverage among the Aboriginal population (89.5%) and children of young mothers (89.3%) compared to NSW (92.2 and 92.1% respectively). Conclusion Despite overall high coverage of MMR1 vaccination, coverage inequalities increased especially for children of mothers born overseas. Strategic immunisation plans and policy interventions are important for equitable vaccination levels. Future policy should target children of mothers born overseas and Aboriginal children.

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Is an integrated model of school eye health delivery more cost-effective than a vertical model? An implementation research in Zanzibar

BMJ Open Ophthalmology ◽

10.1136/bmjophth-2020-000561 ◽

2021 ◽

Vol 6 (1) ◽

pp. e000561

Author(s):

Ving Fai Chan ◽

Fatma Omar ◽

Elodie Yard ◽

Eden Mashayo ◽

Damaris Mulewa ◽

...

Keyword(s):

Implementation Research ◽

Cost Savings ◽

Cost Effective ◽

Integrated Model ◽

Health Screening ◽

High Coverage ◽

Health Delivery ◽

Screening Cost ◽

Eye Health ◽

The Cost

ObjectiveTo review and compare the cost-effectiveness of the integrated model (IM) and vertical model (VM) of school eye health programme in Zanzibar.Methods and analysisThis 6-month implementation research was conducted in four districts in Zanzibar. Nine and ten schools were recruited into the IM and VM, respectively. In the VM, teachers conducted eye health screening and education only while these eye health components were added to the existing school feeding programme (IM). The number of children aged 6–13 years old screened and identified was collected monthly. A review of project account records was conducted with 19 key informants. The actual costs were calculated for each cost categories, and costs per child screened and cost per child identified were compared between the two models.ResultsScreening coverage was 96% and 90% in the IM and VM with 297 children (69.5%) from the IM and 130 children (30.5%) from VM failed eye health screening. The 6-month eye health screening cost for VM and IM was US$6 728 and US$7 355. The cost per child screened for IM and VM was US$1.23 and US$1.31, and the cost per child identified was US$24.76 and US$51.75, respectively.ConclusionBoth models achieved high coverage of eye health screening with the IM being a more cost-effective school eye health delivery screening compared with VM with great opportunities for cost savings.

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High-coverage, unbounded sound predictive race detection

ACM SIGPLAN Notices ◽

10.1145/3296979.3192385 ◽

2018 ◽

Vol 53 (4) ◽

pp. 374-389 ◽

Cited By ~ 2

Author(s):

Jake Roemer ◽

Kaan Genç ◽

Michael D. Bond

Keyword(s):

High Coverage ◽

Race Detection

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Genome diversity in Ukraine

GigaScience ◽

10.1093/gigascience/giaa159 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Taras K Oleksyk ◽

Walter W Wolfsberger ◽

Alexandra M Weber ◽

Khrystyna Shchubelka ◽

Olga T Oleksyk ◽

...

Keyword(s):

Sequence Data ◽

Copy Number Variations ◽

Genomic Variation ◽

High Coverage ◽

Genome Data ◽

New Information ◽

Genome Wide ◽

Public Data ◽

Genome Wide Data ◽

Multiple Samples

Abstract Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.

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