DNA-Mediated Electron Transfer in Naphthalene-Modified Oligonucleotides

Naphthalene-modified oligonucleotides have been synthesized and characterized with respect to electron transfer chemistry. Using the Sonogashira coupling reaction, naphthalene can be covalently anchored onto a modified uridine through an ethynyl linkage. This tethering allows for effective electronic coupling with the DNA bases, resulting in a significant red shift of the absorption bands of the naphthalenic chromophore. Modification with this chromophore does not appear to affect the overall stability and structure of the DNA. Upon selective irradiation of the naphthalene moiety at 340 nm, photoreduction of a distal electron trap, 5-bromouridine, embedded in the DNA base stack occurs. This DNA-mediated reduction from a distance was found to be significantly more efficient with substitution of 5-bromouridine toward the 5′-end than toward the 3′-end. These results support a general preference for electron transfer through DNA toward the 5′-end, irrespective of the donor. In addition, differences in efficiency of photoreduction through intrastrand and interstrand pathways are observed. For DNA-mediated reduction, as with DNA-mediated oxidation, significant differences in the charge transfer reaction are apparent that depend upon subtle differences in coupling into the DNA base stack

Two-dimensional flows of foam: drag exerted on circular obstacles and dissipation

A Stokes experiment for foams is proposed. It consists in a two-dimensional flow of a foam, confined between a water subphase and a top plate, around a fixed circular obstacle. We present systematic measurements of the drag exerted by the flowing foam on the obstacle, \emph{versus} various separately controlled parameters: flow rate, bubble volume, solution viscosity, obstacle size and boundary conditions. We separate the drag into two contributions, an elastic one (yield drag) at vanishing flow rate, and a fluid one (viscous coefficient) increasing with flow rate. We quantify the influence of each control parameter on the drag. The results exhibit in particular a power-law dependence of the drag as a function of the solution viscosity and the flow rate with two different exponents. Moreover, we show that the drag decreases with bubble size, increases with obstacle size, and that the effect of boundary conditions is small. Measurements of the streamwise pressure gradient, associated to the dissipation along the flow of foam, are also presented: they show no dependence on the presence of an obstacle, and pressure gradient depends on flow rate, bubble volume and solution viscosity with three independent power laws.Comment: 23 pages, 13 figures, proceeding of Eufoam 2004 conferenc

Did You Mean...? Confidence-based Trade-offs in Semantic Parsing

We illustrate how a calibrated model can help balance common trade-offs in task-oriented parsing. In a simulated annotator-in-the-loop experiment, we show that well-calibrated confidence scores allow us to balance cost with annotator load, improving accuracy with a small number of interactions. We then examine how confidence scores can help optimize the trade-off between usability and safety. We show that confidence-based thresholding can substantially reduce the number of incorrect low-confidence programs executed; however, this comes at a cost to usability. We propose the DidYouMean system which better balances usability and safety.Comment: 9 pages. arXiv admin note: substantial text overlap with arXiv:2211.0744

Calibrated Interpretation: Confidence Estimation in Semantic Parsing

Sequence generation models are increasingly being used to translate natural language into programs, i.e. to perform executable semantic parsing. The fact that semantic parsing aims to predict programs that can lead to executed actions in the real world motivates developing safe systems. This in turn makes measuring calibration -- a central component to safety -- particularly important. We investigate the calibration of popular generation models across four popular semantic parsing datasets, finding that it varies across models and datasets. We then analyze factors associated with calibration error and release new confidence-based challenge splits of two parsing datasets. To facilitate the inclusion of calibration in semantic parsing evaluations, we release a library for computing calibration metrics.Comment: TACL Camera-read

The eruptive history and magmatic evolution of Aluto volcano: new insights into silicic peralkaline volcanism in the Ethiopian rift

The silicic peralkaline volcanoes of the East African Rift are some of the least studied volcanoes on Earth. Here we bring together new constraints from fieldwork, remote sensing, geochronology and geochemistry to present the first detailed account of the eruptive history of Aluto, a restless silicic volcano located in a densely populated section of the Main Ethiopian Rift. Prior to the growth of the Aluto volcanic complex (before 500 ka) the region was characterized by a significant period of fault development and mafic fissure eruptions. The earliest volcanism at Aluto built up a trachytic complex over 8 km in diameter. Aluto then underwent large-volume ignimbrite eruptions at 316 ± 19 ka and 306 ± 12 ka developing a ~ 42 km2 collapse structure. After a hiatus of ~ 250 ka, a phase of post-caldera volcanism initiated at 55 ± 19 ka and the most recent eruption of Aluto has a radiocarbon age of 0.40 ± 0.05 cal. ka BP. During this post-caldera phase highly-evolved peralkaline rhyolite lavas, ignimbrites and pumice fall deposits have erupted from vents across the complex. Geochemical modelling is consistent with rhyolite genesis from protracted fractionation (> 80%) of basalt that is compositionally similar to rift-related basalts found east of the complex. Based on the style and volume of recent eruptions we suggest that silicic eruptions occur at an average rate of 1 per 1000 years, and that future eruptions of Aluto will involve explosive emplacement of localised pumice cones and effusive obsidian coulees of volumes in the range 1–100 × 106 m3

The impact of the COVID-19 pandemic on cancer care.

The COVID-19 pandemic has disrupted the spectrum of cancer care, including delaying diagnoses and treatment and halting clinical trials. In response, healthcare systems are rapidly reorganizing cancer services to ensure that patients continue to receive essential care while minimizing exposure to SARS-CoV-2 infection

Why Did the Chicken Cross the Road? Rephrasing and Analyzing Ambiguous Questions in VQA

Natural language is ambiguous. Resolving ambiguous questions is key to successfully answering them. Focusing on questions about images, we create a dataset of ambiguous examples. We annotate these, grouping answers by the underlying question they address and rephrasing the question for each group to reduce ambiguity. Our analysis reveals a linguistically-aligned ontology of reasons for ambiguity in visual questions. We then develop an English question-generation model which we demonstrate via automatic and human evaluation produces less ambiguous questions. We further show that the question generation objective we use allows the model to integrate answer group information without any direct supervision.Comment: ACL 2023. Code and data: https://github.com/esteng/ambiguous_vq