HPC-driven computational reproducibility

Reproducibility of results is a cornerstone of the scientific method. Scientific computing encounters two challenges when aiming for this goal. Firstly, reproducibility should not depend on details of the runtime environment, such as the compiler version or computing environment, so results are verifiable by third-parties. Secondly, different versions of software code executed in the same runtime environment should produce consistent numerical results for physical quantities. In this manuscript, we test the feasibility of reproducing scientific results obtained using the IllinoisGRMHD code that is part of an open-source community software for simulation in relativistic astrophysics, the Einstein Toolkit. We verify that numerical results of simulating a single isolated neutron star with IllinoisGRMHD can be reproduced, and compare them to results reported by the code authors in 2015. We use two different supercomputers: Expanse at SDSC, and Stampede2 at TACC. By compiling the source code archived along with the paper on both Expanse and Stampede2, we find that IllinoisGRMHD reproduces results published in its announcement paper up to errors comparable to round-off level changes in initial data parameters. We also verify that a current version of IlliinoisGRMHD reproduces these results once we account for bug fixes which has occurred since the original publicationComment: 22 pages, 6 figures, submitted to Classical and Quantum Gravit

The C-terminal α–α superhelix of Pat is required for mRNA decapping in metazoa

Pat proteins regulate the transition of mRNAs from a state that is translationally active to one that is repressed, committing targeted mRNAs to degradation. Pat proteins contain a conserved N-terminal sequence, a proline-rich region, a Mid domain and a C-terminal domain (Pat-C). We show that Pat-C is essential for the interaction with mRNA decapping factors (i.e. DCP2, EDC4 and LSm1–7), whereas the P-rich region and Mid domain have distinct functions in modulating these interactions. DCP2 and EDC4 binding is enhanced by the P-rich region and does not require LSm1–7. LSm1–7 binding is assisted by the Mid domain and is reduced by the P-rich region. Structural analysis revealed that Pat-C folds into an α–α superhelix, exposing conserved and basic residues on one side of the domain. This conserved and basic surface is required for RNA, DCP2, EDC4 and LSm1–7 binding. The multiplicity of interactions mediated by Pat-C suggests that certain of these interactions are mutually exclusive and, therefore, that Pat proteins switch decapping partners allowing transitions between sequential steps in the mRNA decapping pathway

A ruptured ectopic pregnancy in a patient with an intrauterine device: A case report.

Intrauterine devices (IUDs) are used worldwide. The 2 types that are used are the levonorgestrel IUD and a copper containing IUD. This is a case study of a 30-year-old female with a levonorgestrel IUD who was diagnosed with a ruptured ectopic pregnancy in the emergency department (ED). Point-of-care urine pregnancy test and point-of-care ultrasound (POCUS) were vital in making this diagnosis and should be utilized in patients assigned female at birth who present with abdominal pain

Formation of large viroplasms and virulence of Cauliflower mosaic virus in turnip plants depend on the N-terminal EKI sequence of viral protein TAV

International audienc