Advanced Quantum Poisson Solver in the NISQ era

The Poisson equation has many applications across the broad areas of science and engineering. Most quantum algorithms for the Poisson solver presented so far, either suffer from lack of accuracy and/or are limited to very small sizes of the problem, and thus have no practical usage. Here we present an advanced quantum algorithm for solving the Poisson equation with high accuracy and dynamically tunable problem size. After converting the Poisson equation to the linear systems through the finite difference method, we adopt the Harrow-Hassidim-Lloyd (HHL) algorithm as the basic framework. Particularly, in this work we present an advanced circuit that ensures the accuracy of the solution by implementing non-truncated eigenvalues through eigenvalue amplification as well as by increasing the accuracy of the controlled rotation angular coefficients, which are the critical factors in the HHL algorithm. We show that our algorithm not only increases the accuracy of the solutions, but also composes more practical and scalable circuits by dynamically controlling problem size in the NISQ devices. We present both simulated and experimental solutions, and conclude that overall results on the quantum hardware are dominated by the error in the CNOT gates.Comment: Quantum Week QCE 2022, poster pape

Advancing Algorithm to Scale and Accurately Solve Quantum Poisson Equation on Near-term Quantum Hardware

The Poisson equation has many applications across the broad areas of science and engineering. Most quantum algorithms for the Poisson solver presented so far either suffer from lack of accuracy and/or are limited to very small sizes of the problem, and thus have no practical usage. Here we present an advanced quantum algorithm for solving the Poisson equation with high accuracy and dynamically tunable problem size. After converting the Poisson equation to a linear system through the finite difference method, we adopt the HHL algorithm as the basic framework. Particularly, in this work we present an advanced circuit that ensures the accuracy of the solution by implementing non-truncated eigenvalues through eigenvalue amplification, as well as by increasing the accuracy of the controlled rotation angular coefficients, which are the critical factors in the HHL algorithm. Consequently, we are able to drastically reduce the relative error in the solution while achieving higher success probability as the amplification level is increased. We show that our algorithm not only increases the accuracy of the solutions but also composes more practical and scalable circuits by dynamically controlling problem size in NISQ devices. We present both simulated and experimental results and discuss the sources of errors. Finally, we conclude that though overall results on the existing NISQ hardware are dominated by the error in the CNOT gates, this work opens a path to realizing a multidimensional Poisson solver on near-term quantum hardware.Comment: 13 pages, 11 figures, 1 tabl

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023.

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with >3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC

Inhaled Tranexamic Acid for Massive Hemoptysis in the Setting of Oral Anticoagulation: A Case Report

Introduction: We discuss a case of massive hemoptysis in the setting of a direct-acting oral anticoagulant (DOAC) successfully managed with nebulized tranexamic acid (TXA).Case Report: Per the American College of Cardiology and the American Society of Hematology, it is recommended that significant bleeding associated with a DOAC be treated with either 4-factor prothrombin complex concentrate or andexanet alfa. However, our patient was at high risk for thrombotic complications given a recent pulmonary embolism.Conclusion: We demonstrate that it is reasonable to trial nebulized TXA given its low cost, ease of administration, and safety profile. Additionally, this report discusses a unique dosing strategy and a previously unreported complication associated with nebulization of undiluted TXA

VEuPathDB/web-monorepo: v1.0.86

<h2>What's Changed</h2> <ul> <li>Genomics: Finalize menu code for maps by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/477</li> <li>Interim non-handling of date variables for bubble markers (but allows EdaDataService#309 to be merged) by @bobular in https://github.com/VEuPathDB/web-monorepo/pull/453</li> <li>Add new analysis button to all analyses component in map by @chowington in https://github.com/VEuPathDB/web-monorepo/pull/459</li> <li>Genes phyletic tree search box by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/561</li> <li>Collection map type by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/399</li> <li>Incorporate p value floor from backend by @asizemore in https://github.com/VEuPathDB/web-monorepo/pull/565</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/VEuPathDB/web-monorepo/compare/v1.0.85...v1.0.86</p&gt

VEuPathDB/web-monorepo: v1.0.93

<h2>What's Changed</h2> <ul> <li>Display useful message to user when analysis fails to load by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/645</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/VEuPathDB/web-monorepo/compare/v1.0.92...v1.0.93</p&gt

VEuPathDB/web-monorepo: v1.0.88

<h2>What's Changed</h2> <ul> <li>Add more reference org filters by @jernestmyers in https://github.com/VEuPathDB/web-monorepo/pull/577</li> <li>Eda study type error by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/590</li> <li>Eda categorical collection type by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/592</li> <li>Increase row count font size in beta Downloads table by @jernestmyers in https://github.com/VEuPathDB/web-monorepo/pull/593</li> <li>Reposition reference filter by @jernestmyers in https://github.com/VEuPathDB/web-monorepo/pull/591</li> <li>Add min-width to prevent confusing overflow UX by @jernestmyers in https://github.com/VEuPathDB/web-monorepo/pull/599</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/VEuPathDB/web-monorepo/compare/v1.0.87...v1.0.88</p&gt

VEuPathDB/web-monorepo: v1.0.90

A monorepo that contains all frontend code for VEuPathDB website

VEuPathDB/web-monorepo: v1.0.95

<h2>What's Changed</h2> <ul> <li>Feature 556 connect correlation backend by @asizemore in https://github.com/VEuPathDB/web-monorepo/pull/560</li> <li>Fix breakage from variableId -> collectionId changes by @jernestmyers in https://github.com/VEuPathDB/web-monorepo/pull/655</li> <li>Studies menu filter bug by @jernestmyers in https://github.com/VEuPathDB/web-monorepo/pull/656</li> <li>update default effect size and var names by @asizemore in https://github.com/VEuPathDB/web-monorepo/pull/664</li> <li>add maaslin citation and link by @asizemore in https://github.com/VEuPathDB/web-monorepo/pull/653</li> <li>Allow for displayOrder values < 1 by @dmfalke in https://github.com/VEuPathDB/web-monorepo/pull/660</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/VEuPathDB/web-monorepo/compare/v1.0.94...v1.0.95</p&gt