Tootfinder

Methylation Operation Wizard (MeOW): Identification of differentially methylated regions in long-read sequencing data
Miranda PG Zalusky, Danny E Miller
https://arxiv.org/abs/2402.17182

Methylation Operation Wizard (MeOW): Identification of differentially methylated regions in long-read sequencing data
Long-read sequencing (LRS) is able to simultaneously capture information about both DNA sequence and modifications, such as CpG methylation in a single sequencing experiment. Here we present Methylation Operation Wizard (MeOW), a program to identify and prioritize differentially methylated regions (DMRs) genome-wide using LRS data. MeOW can be run using either a file containing counts of per-nucleotide methylated CpG sites or with a bam file containing modified base tags.

Real Acoustic Fields: An Audio-Visual Room Acoustics Dataset and Benchmark
Ziyang Chen, Israel D. Gebru, Christian Richardt, Anurag Kumar, William Laney, Andrew Owens, Alexander Richard
https://arxiv.org/abs/2403.18821

Real Acoustic Fields: An Audio-Visual Room Acoustics Dataset and Benchmark
We present a new dataset called Real Acoustic Fields (RAF) that captures real acoustic room data from multiple modalities. The dataset includes high-quality and densely captured room impulse response data paired with multi-view images, and precise 6DoF pose tracking data for sound emitters and listeners in the rooms. We used this dataset to evaluate existing methods for novel-view acoustic synthesis and impulse response generation which previously relied on synthetic data. In our evaluation, we…

AI auditing: The Broken Bus on the Road to AI Accountability
Abeba Birhane, Ryan Steed, Victor Ojewale, Briana Vecchione, Inioluwa Deborah Raji
https://arXiv.org/abs/2401.14462

AI auditing: The Broken Bus on the Road to AI Accountability
One of the most concrete measures to take towards meaningful AI accountability is to consequentially assess and report the systems' performance and impact. However, the practical nature of the "AI audit" ecosystem is muddled and imprecise, making it difficult to work through various concepts and map out the stakeholders involved in the practice. First, we taxonomize current AI audit practices as completed by regulators, law firms, civil society, journalism, academia, consulting agencies. Next, …

Real Acoustic Fields: An Audio-Visual Room Acoustics Dataset and Benchmark
Ziyang Chen, Israel D. Gebru, Christian Richardt, Anurag Kumar, William Laney, Andrew Owens, Alexander Richard
https://arxiv.org/abs/2403.18821

Real Acoustic Fields: An Audio-Visual Room Acoustics Dataset and Benchmark
We present a new dataset called Real Acoustic Fields (RAF) that captures real acoustic room data from multiple modalities. The dataset includes high-quality and densely captured room impulse response data paired with multi-view images, and precise 6DoF pose tracking data for sound emitters and listeners in the rooms. We used this dataset to evaluate existing methods for novel-view acoustic synthesis and impulse response generation which previously relied on synthetic data. In our evaluation, we…

Transmission IR Microscopy for the Quantitation of Biomolecular Mass In Live Cells
Yow-Ren Chang, Seong-Min Kim, Young Jong Lee
https://arxiv.org/abs/2403.18881

Transmission IR Microscopy for the Quantitation of Biomolecular Mass In Live Cells
Absolute quantity imaging of biomolecules on a single cell level is critical for measurement assurance in biosciences and bioindustries. While infrared (IR) transmission microscopy is a powerful label-free imaging modality capable of chemical quantification, its applicability to hydrated biological samples remains challenging due to the strong water absorption. We overcome this challenge by applying a solvent absorption compensation (SAC) technique to a home-built quantum cascade laser IR micro…

Metronom rechnet mit Zug-Ausfällen zwischen Bremen und Hamburg
Wie das Unternehmen mitteilt, müssen wegen Bauarbeiten im Großraum Hamburg zusätzliche Schichten gefahren werden. Das lasse die dünne Personaldecke aber nicht zu.
https://www.butenunbinnen.de/nachrichten/m<…

Metronom rechnet mit Zug-Ausfällen zwischen Bremen und Hamburg
Wie das Unternehmen mitteilt, müssen wegen Bauarbeiten im Großraum Hamburg zusätzliche Schichten gefahren werden. Das lasse die dünne Personaldecke aber nicht zu.

Segment anything model for head and neck tumor segmentation with CT, PET and MRI multi-modality images
Jintao Ren, Mathis Rasmussen, Jasper Nijkamp, Jesper Grau Eriksen, Stine Korreman
https://arxiv.org/abs/2402.17454

Segment anything model for head and neck tumor segmentation with CT, PET and MRI multi-modality images
Deep learning presents novel opportunities for the auto-segmentation of gross tumor volume (GTV) in head and neck cancer (HNC), yet fully automatic methods usually necessitate significant manual refinement. This study investigates the Segment Anything Model (SAM), recognized for requiring minimal human prompting and its zero-shot generalization ability across natural images. We specifically examine MedSAM, a version of SAM fine-tuned with large-scale public medical images. Despite its progress,…

Galaxies with grains: unraveling dust evolution and extinction curves with hydrodynamical simulations
Yohan Dubois, Francisco Rodr\'iguez Montero, Corentin Guerra, Maxime Trebitsch, San Han, Ricarda Beckmann, Sukyoung K. Yi, Joseph Lewis, J. K. Jang
https://arxiv.org/abs/2402.18515 <…

Galaxies with grains: unraveling dust evolution and extinction curves with hydrodynamical simulations
We introduce a model for dust evolution in the {\sc ramses} code for simulations of galaxies with a resolved multiphase interstellar medium. Dust is modelled as a fluid transported with the gas component, and is decomposed into two sizes, 5 nm and $0.1 \, μ\rm m$, and two chemical compositions for carbonaceous and silicate grains. Using a suite of isolated disc simulations with different masses and metallicities, the simulations can explore the role of these processes in shaping the key proper…

Giant Strain Response of Charge Modulation and Singularity in a Kagome Superconductor
Chun Lin, Armando Consiglio, Ola Kenji Forslund, Julia Kuspert, M. Michael Denner, Hechang Lei, Alex Louat, Matthew D. Watson, Timur K. Kim, Cephise Cacho, Dina Carbone, Mats Leandersson, Craig Polley, Thiagarajan Balasubramanian, Domenico Di Sante, Ronny Thomale, Zurab Guguchia, Giorgio Sangiovanni, Titus Neupert, Johan Chang

Giant Strain Response of Charge Modulation and Singularity in a Kagome Superconductor
Tunable quantum materials hold great potential for applications. Of special interest are materials in which small lattice strain induces giant electronic responses. The kagome compounds AV3Sb5 (A = K, Rb, Cs) provide a testbed for such singular electronic states. In this study, through angle-resolved photoemission spectroscopy, we provide comprehensive spectroscopic measurements of the giant responses induced by compressive and tensile strains on the charge-density-wave (CDW) order parameter an…

Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
Valerio Piomponi, Miroslav Krepl, Jiri Sponer, Giovanni Bussi
https://arxiv.org/abs/2404.14821

Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
N6-methyladenosine (m6A) is a prevalent RNA post-transcriptional modification that plays crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT521-B (YTH) family of proteins, which are notable m6A readers, function through their highly conserved YTH domain. Recent structural investigations and molecular dynamics (MD) simulations have shed light on the recognition mechanism of m6A by the YTHDC1 protein. Despite advancements, using MD to predict the stabilizat…