Ariel - Volume 3 Number 8

Editors Richard J. Bonanno Robin A. Edwards Associate Editors Steven Ager Tom Williams Lay-out Editor Eugenia Miller Contributing Editors Paul Bialas Robert Breckenridge David Jacoby Mike LeWitt Terry Burt Michael Leo Editors Emeritus Delvyn C. Case, Jr. Paul M. Fernhof

Autoregressive fragment-based diffusion for pocket-aware ligand design

In this work, we introduce AutoFragDiff, a fragment-based autoregressive diffusion model for generating 3D molecular structures conditioned on target protein structures. We employ geometric vector perceptrons to predict atom types and spatial coordinates of new molecular fragments conditioned on molecular scaffolds and protein pockets. Our approach improves the local geometry of the resulting 3D molecules while maintaining high predicted binding affinity to protein targets. The model can also perform scaffold extension from user-provided starting molecular scaffold.Comment: Accepted, NeurIPS 2023 Generative AI and Biology Workshop. OpenReview: https://openreview.net/forum?id=E3HN48zja

The first assessment of Batrachochytrium dendrobatidis in amphibian populations in the Kanuku Mountains Protected Area of Guyana

- Batrachochytrium dendrobatidis (Bd) is a fungal pathogen threatening hundreds of amphibian species with extinction across the globe, especially in Latin America. Extensive investigations have revealed the presence of Bd in many South American countries, but there has been a lack of such research conducted in Guyana. We assessed the presence of Bd in the amphibian populations of the Kanuku Mountains Protected Area, in the south-west of the country. We swabbed two hundred and fifty anurans and processed the samples using standard Polymerase Chain Reaction analysis to identify cutaneous presence of Bd, making this the most comprehensive investigation into the existence of Bd in Guyana. All samples were negative for the presence of Bd DNA. Given the presence of Bd in countries neighbouring Guyana, and the severe declines it has caused in amphibian populations, we consider Guyana to be under severe threat. We advocate further surveillance in Guyana to fully determine the presence or absence of Bd, and we emphasise the importance of biosecurity and monitoring in mitigating a potential outbreak of this fungal pathogen

Polarization mode dispersion compensator field trial and field fiber characterization

Two high-PMD long distance routes were characterized and used to test an optical polarization mode dispersion compensator (PMDC) under field conditions. For this trial, 110 km routes with mean PMD values of 25 and 26.5 ps were provisioned with commercial WDM transport equipment and tested for several weeks. The route was comprised of three spans of characterized fiber that followed railroad tracks. We show the temporal variation of the output polarization state and the evolution of first- and second-order PMD spectra over 7 days. The deployment of a variable-length PMDC on these links allowed error-free transmission of an OC-192 signal. Splitting the output to receivers with and without PMDC demonstrated specific PMD events that caused errors in the absence of a PMDC. (C) 2002 Optical Society of America

On Petition for a Writ of Certiorari to The United States Court of Appeals for The Eighth Circuit, Brief of Law Professors Paul F. Rothstein, et. al., Office of the President v. Office of Independent Counsel

This Court should grant review not only because this is a case of national importance and prominence, but also because the decision below is a conspicuous departure from settled principles of evidence law. The panel majority concluded that communications between government lawyers and government officials are not protected by the attorney-client privilege, at least when those communications are sought by a federal grand jury. That conclusion conflicts with the predominant common-law understanding that the attorney-client privilege applies to government entities and that where the privilege applies, it is absolute (i.e., it protects against disclosure in all types of legal and investigative proceedings). In particular, the Court of Appeals\u27 decision rests on a fundamental misunderstanding of this Court\u27s decisions in Upjohn Co. v. United States, 449 U.S. 383 (1981), and United States v. Nixon, 418 U.s. 683 (1974). Moreover, this case warrants further review because the decision below has profound implications beyond the parties to this dispute. The Court of Appeals\u27 ruling, if allowed to stand, will create widespread uncertainty among federal, state, and local officials concerning the extent to which their communications with their agency lawyers, for the purpose of seeking legal advice in the conduct of governmental affairs, are protected by the attorney-client privilege. Unless this Court grants review and resolves this uncertainty, the decision below will likely have an adverse effect on the current and future operation of not only the Office of the President of the United States, but also government at all levels. At the very least, a decision of such vast implications (as in the present case) should be made by the highest court in the land. We accordingly urge the Court to grant the petition for review

Staying true with the help of others: doxastic self-control through interpersonal commitment

I explore the possibility and rationality of interpersonal mechanisms of doxastic self-control, that is, ways in which individuals can make use of other people in order to get themselves to stick to their beliefs. I look, in particular, at two ways in which people can make interpersonal epistemic commitments, and thereby willingly undertake accountability to others, in order to get themselves to maintain their beliefs in the face of anticipated “epistemic temptations”. The first way is through the avowal of belief, and the second is through the establishment of collective belief. I argue that both of these forms of interpersonal epistemic commitment can function as effective tools for doxastic self-control, and, moreover, that the control they facilitate should not be dismissed as irrational from an epistemic perspective