Mapping Interactomes with High Coverage and Efficiency Using the Shifted Transversal Design

2011 ◽  
pp. 147-159
Author(s):  
Xiaofeng Xin ◽  
Charles Boone ◽  
Nicolas Thierry-Mieg
Keyword(s):  
Transversal Design ◽  
High Coverage

scholarly journals Shifted Transversal Design smart-pooling for high coverage interactome mapping

2009 ◽  
Vol 19 (7) ◽  
pp. 1262-1269 ◽  
Author(s):  
X. Xin ◽  
J.-F. Rual ◽  
T. Hirozane-Kishikawa ◽  
D. E. Hill ◽  
M. Vidal ◽  
...  
Keyword(s):  
Transversal Design ◽  
High Coverage ◽  
Interactome Mapping

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

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 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.

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

2020 ◽  
Author(s):  
Tianyang Yan ◽  
Heta Desai ◽  
Lisa Boatner ◽  
Stephanie Yen ◽  
Jian Cao ◽  
...  
Keyword(s):  
High Throughput ◽  
High Coverage ◽  
Method Integration ◽  
Coverage Analysis

<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>

Self-Assembled Fluid Phase Floating Membranes with Tuneable Water Interlayers

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

<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>

scholarly journals Clique Size in Sensor Networks with Key Pre-Distribution Based on Transversal Design

2005 ◽  
Vol 1 (3-4) ◽  
pp. 345-354 ◽  
Author(s):  
Dibyendu Chakrabarti ◽  
Subhamoy Maitra ◽  
Bimal Roy
Keyword(s):  
Sensor Networks ◽  
Distributed Computing ◽  
Secure Communication ◽  
Sensor Nodes ◽  
Transversal Design ◽  
Secret Key ◽  
Distributed Sensor Networks ◽  
Distributed Sensor

Key pre-distribution is an important area of research in Distributed Sensor Networks (DSN). Two sensor nodes are considered connected for secure communication if they share one or more common secret key(s). It is important to analyse the largest subset of nodes in a DSN where each node is connected to every other node in that subset (i.e., the largest clique). This parameter (largest clique size) is important in terms of resiliency and capability towards efficient distributed computing in a DSN. In this paper, we concentrate on the schemes where the key pre-distribution strategies are based on transversal design and study the largest clique sizes. We show that merging of blocks to construct a node provides larger clique sizes than considering a block itself as a node in a transversal design.

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

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

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

Animals ◽  
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.

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

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.

scholarly journals Childhood vaccination coverage in Australia: an equity perspective

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.

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

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.

Sign in / Sign up

Export Citation Format

Share Document