Benjamin F. Mann
YOU?
Author Swipe
View article: $k\ell$-refinement: An adaptive mesh refinement scheme for hiearchical hybrid grids
$k\ell$-refinement: An adaptive mesh refinement scheme for hiearchical hybrid grids Open
This work introduces an adaptive mesh refinement technique for hierarchical hybrid grids with the goal to reach scalability and maintain excellent performance on massively parallel computer systems. On the block structured hierarchical hyb…
View article: Resistance to antibacterial antifolates in multidrug-resistant <i>Staphylococcus aureus</i>: prevalence estimates and genetic basis
Resistance to antibacterial antifolates in multidrug-resistant <i>Staphylococcus aureus</i>: prevalence estimates and genetic basis Open
Objectives Antibacterial antifolate drugs might have a wider role in the management of staphylococcal infection. One factor that could potentially limit their use in this context is pre-existing resistance. Here we explored the prevalence …
View article: Evaluating the Effectiveness of Large Language Models in Representing Textual Descriptions of Geometry and Spatial Relations (Short Paper)
Evaluating the Effectiveness of Large Language Models in Representing Textual Descriptions of Geometry and Spatial Relations (Short Paper) Open
This research focuses on assessing the ability of large language models (LLMs) in representing geometries and their spatial relations. We utilize LLMs including GPT-2 and BERT to encode the well-known text (WKT) format of geometries and th…
View article: Discovering Language Model Behaviors with Model-Written Evaluations
Discovering Language Model Behaviors with Model-Written Evaluations Open
Ethan Perez, Sam Ringer, Kamile Lukosiute, Karina Nguyen, Edwin Chen, Scott Heiner, Craig Pettit, Catherine Olsson, Sandipan Kundu, Saurav Kadavath, Andy Jones, Anna Chen, Benjamin Mann, Brian Israel, Bryan Seethor, Cameron McKinnon, Chris…
View article: Multi-material design optimization of optical properties of particulate products by discrete dipole approximation and sequential global programming
Multi-material design optimization of optical properties of particulate products by discrete dipole approximation and sequential global programming Open
The optimal design of nanoparticles with respect to their optical properties is one of the main foci within nanoparticle technology. In this contribution, we suggest a new design optimization method in the framework of which the discrete d…
View article: Structural remodeling of SARS-CoV-2 spike protein glycans reveals the regulatory roles in receptor-binding affinity
Structural remodeling of SARS-CoV-2 spike protein glycans reveals the regulatory roles in receptor-binding affinity Open
Glycans of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein are speculated to play functional roles in the infection processes as they extensively cover the protein surface and are highly conserved across the …
View article: Ninth Workshop on Speech and Language Processing for Assistive Technologies (SLPAT-2022)
Ninth Workshop on Speech and Language Processing for Assistive Technologies (SLPAT-2022) Open
We present MozoLM, an open-source language model microservice package intended for use in AAC text-entry applications, with a particular focus on the design principles of the library.The intent of the library is to allow the ensembling of …
View article: Successive remodeling of IgG glycans using a solid-phase enzymatic platform
Successive remodeling of IgG glycans using a solid-phase enzymatic platform Open
The success of glycoprotein-based drugs in various disease treatments has become widespread. Frequently, therapeutic glycoproteins exhibit a heterogeneous array of glycans that are intended to mimic human glycopatterns. While immunogenic r…
View article: Structural remodeling of SARS-CoV-2 spike protein glycans reveals the regulatory roles in receptor binding affinity
Structural remodeling of SARS-CoV-2 spike protein glycans reveals the regulatory roles in receptor binding affinity Open
Glycans of the SARS-CoV-2 spike protein are speculated to play functional roles in the infection processes as they extensively cover the protein surface and are highly conserved across the variants. To date, the spike protein has become th…
View article: Design and Study of PEG Linkers That Enable Robust Characterization of PEGylated Proteins
Design and Study of PEG Linkers That Enable Robust Characterization of PEGylated Proteins Open
Several PEGylated therapeutic proteins are approved drugs, and more are under development. However, the synthesis and characterization of these bioconjugates, especially heterogeneous mixtures of PEGylated proteins, are challenging. The pr…
View article: Drug Metabolism in Drug Discovery and Preclinical Development
Drug Metabolism in Drug Discovery and Preclinical Development Open
Drug metabolism or more generally, xenobiotic metabolism, is the biotransformation of exogenous compounds by living organisms, usually through specialized enzymatic systems. The metabolism of experimental therapeutics is an important aspec…
View article: Proceedings of the Fourth Workshop on NLP for Internet Freedom: Censorship, Disinformation, and Propaganda
Proceedings of the Fourth Workshop on NLP for Internet Freedom: Censorship, Disinformation, and Propaganda Open
Welcome to the fourth edition of the Workshop on NLP for Internet Freedom: Censorship, Disinformation, and Propaganda.This is the second time we are running the workshop virtually, due to the COVID-19 pandemic.The pandemic has had a profou…
View article: Mass Activated Droplet Sorting (MADS) Enables High‐Throughput Screening of Enzymatic Reactions at Nanoliter Scale
Mass Activated Droplet Sorting (MADS) Enables High‐Throughput Screening of Enzymatic Reactions at Nanoliter Scale Open
Microfluidic droplet sorting enables the high‐throughput screening and selection of water‐in‐oil microreactors at speeds and volumes unparalleled by traditional well‐plate approaches. Most such systems sort using fluorescent reporters on m…
View article: Mass Activated Droplet Sorting (MADS) Enables High‐Throughput Screening of Enzymatic Reactions at Nanoliter Scale
Mass Activated Droplet Sorting (MADS) Enables High‐Throughput Screening of Enzymatic Reactions at Nanoliter Scale Open
Microfluidic droplet sorting enables the high‐throughput screening and selection of water‐in‐oil microreactors at speeds and volumes unparalleled by traditional well‐plate approaches. Most such systems sort using fluorescent reporters on m…
View article: What is the evidence for the use of parenteral nutrition (PN) in critically ill surgical patients: a systematic review and meta-analysis
What is the evidence for the use of parenteral nutrition (PN) in critically ill surgical patients: a systematic review and meta-analysis Open
PN may offer benefit in critically ill surgical patients. The size and quality of studies lead to uncertainty around the estimates of clinical effect, meaning a robust trial is required.
View article: Determination of Pharmacokinetic Parameters of Subcutaneous Zyklophin by Quantitative Determination of Zyklophin in Mouse Plasma by LCMS/MS Analysis For Assessment As A Potential Therapeutic Agent In The Treatment of Cocaine Addiction
Determination of Pharmacokinetic Parameters of Subcutaneous Zyklophin by Quantitative Determination of Zyklophin in Mouse Plasma by LCMS/MS Analysis For Assessment As A Potential Therapeutic Agent In The Treatment of Cocaine Addiction Open
Pharmaceutical agents targeting the μ opioid receptors (MOR) have been widely used in the treatment and management of pain. However, serious side effects and the prevalence of abuse have complicated their administration. This has increased…
View article: Identification of Mercury and Dissolved Organic Matter Complexes Using Ultrahigh Resolution Mass Spectrometry
Identification of Mercury and Dissolved Organic Matter Complexes Using Ultrahigh Resolution Mass Spectrometry Open
The chemical speciation and bioavailability of mercury (Hg) is markedly influenced by its complexation with naturally dissolved organic matter (DOM) in aquatic environments. To date, however, analytical methodologies capable of identifying…
View article: Evaluating Mobile Survey Tools (MSTs) for Field-Level Monitoring and Data Collection: Development of a Novel Evaluation Framework, and Application to MSTs for Rural Water and Sanitation Monitoring
Evaluating Mobile Survey Tools (MSTs) for Field-Level Monitoring and Data Collection: Development of a Novel Evaluation Framework, and Application to MSTs for Rural Water and Sanitation Monitoring Open
Information and communications technologies (ICTs) such as mobile survey tools (MSTs) can facilitate field-level data collection to drive improvements in national and international development programs. MSTs allow users to gather and trans…
View article: Global Proteome Response to Deletion of Genes Related to Mercury Methylation and Dissimilatory Metal Reduction Reveals Changes in Respiratory Metabolism in <i>Geobacter sulfurreducens</i> PCA
Global Proteome Response to Deletion of Genes Related to Mercury Methylation and Dissimilatory Metal Reduction Reveals Changes in Respiratory Metabolism in <i>Geobacter sulfurreducens</i> PCA Open
Geobacter sulfurreducens PCA can reduce, sorb, and methylate mercury (Hg); however, the underlying biochemical mechanisms of these processes and interdependent metabolic pathways remain unknown. In this study, shotgun proteomics was used t…
View article: Pathways of anaerobic organic matter decomposition in tundra soils from Barrow, Alaska
Pathways of anaerobic organic matter decomposition in tundra soils from Barrow, Alaska Open
Arctic tundra soils store a large quantity of organic carbon that is susceptible to decomposition and release to the atmosphere as methane (CH 4 ) and carbon dioxide (CO 2 ) under a warming climate. Anaerobic processes that generate CH 4 a…
View article: Indexing Permafrost Soil Organic Matter Degradation Using High-Resolution Mass Spectrometry
Indexing Permafrost Soil Organic Matter Degradation Using High-Resolution Mass Spectrometry Open
Microbial degradation of soil organic matter (SOM) is a key process for terrestrial carbon cycling, although the molecular details of these transformations remain unclear. This study reports the application of ultrahigh resolution mass spe…