Medical Information Extraction with Large Language Models

The increase in clinical text data following the adoption of electronic health records offers benefits for medical practice and introduces challenges in automatic data extraction. Since manual extraction is often inefficient and error-prone, with this work, we explore the use of open, small-scale, Large Language Models (LLMs) to automate and improve the extraction of medication and timeline data. With our experiments, we aim to assess the effectiveness of different prompting strategies –zero-shot, few-shots, and sequential prompting– on LLMs to generate a mixture of structured and unstructured information starting from a reference document. The results show that even a zero-shot learning approach can be sufficient to extract medication information with high precision. The main issues in generating the required information seem to be completeness and redundancy. However, prompt tuning alone seems to be sufficient to achieve good results using these LLMs, even in specific domains like the medical one. Besides medical information extraction, in this work, we address the problem of explainability, introducing a line-number referencing method to enhance transparency and trust in the generated results. Finally, to underscore the viability of applying these LLM-based solutions to medical information extraction, we deployed the developed pipelines within a demo application

Response of a benthic food web to hydrocarbon contamination

Direct and indirect effects of diesel-contaminated sediment on microalgae, meiofauna, and meiofauna-microalgae trophic interactions were examined in a microcosm study of the sediment community from a Spartina alterniflora salt marsh. Microcosms of natural sediment were given small dally doses of contaminated sediment over a 28-d period, creating low-, medium-, and high-diesel treatment concentrations of ~ 0.5, 5.5, and 55 ppm PAH, respectively. Diesel caused initial (within 7 h) reductions in microalgal grazing by meiobenthic harpacticoid copepods. Over longer periods of exposure (7-28 d), grazing on microalgae by copepods as a group was reduced in high-diesel treatments, primarily because of high copepod mortality. In contrast, grazing by and abundance of Cletocamptus deitersi (a copepod) was significantly enhanced in high-diesel treatments. Concurrent with reduced grazing by copepods, nematode grazing rates increased significantly in high-diesel treatments, indicating possible competition for microalgae between copepods and nematodes. In spite of transiently enhanced grazing by nematodes and C. deitersi, total meiofaunal grazing on microalgae was reduced in high-diesel treatments. Increased Chl a : pheopigment ratios in contaminated sediments were also indicative of reduced grazing pressure. A large (10x) increase in microalgal biomass was observed in high-diesel treatments and was likely a consequence of reduced meiofaunal grazing. The general responses observed in microcosms were also observed in a field study of polycyclic aromatic hydrocarbon contamination. Collectively, our data indicate that benthic microalgal biomass is controlled by meiofaunal grazing and that meiofauna may compete for limited algal resources. Furthermore, consideration of multiple trophic levels and their interactions allows a more complete and ecologically meaningful understanding of the mechanisms by which contaminants induce changes in natural communities

Generation of ultra-short light pulses by a rapidly ionizing thin foil

A thin and dense plasma layer is created when a sufficiently strong laser pulse impinges on a solid target. The nonlinearity introduced by the time-dependent electron density leads to the generation of harmonics. The pulse duration of the harmonic radiation is related to the risetime of the electron density and thus can be affected by the shape of the incident pulse and its peak field strength. Results are presented from numerical particle-in-cell-simulations of an intense laser pulse interacting with a thin foil target. An analytical model which shows how the harmonics are created is introduced. The proposed scheme might be a promising way towards the generation of attosecond pulses. PACS number(s): 52.40.Nk, 52.50.Jm, 52.65.RrComment: Second Revised Version, 13 pages (REVTeX), 3 figures in ps-format, submitted for publication to Physical Review E, WWW: http://www.physik.tu-darmstadt.de/tqe

The wall shear rate distribution for flow in random sphere packings

The wall shear rate distribution P(gamma) is investigated for pressure-driven Stokes flow through random arrangements of spheres at packing fractions 0.1 <= phi <= 0.64. For dense packings, P(gamma) is monotonic and approximately exponential. As phi --> 0.1, P(gamma) picks up additional structure which corresponds to the flow around isolated spheres, for which an exact result can be obtained. A simple expression for the mean wall shear rate is presented, based on a force-balance argument.Comment: 4 pages, 3 figures, 1 table, RevTeX 4; significantly revised with significantly extended scop

Exclusive electromagnetic production of strangeness on the nucleon : review of recent data in a Regge approach

In view of the numerous experimental results recently released, we provide in this letter an update on the performance of our simple Regge model for strangeness electroproduction on the nucleon. Without refitting any parameters, a decent description of all measured observables and channels is achieved. We also give predictions for spin transfer observables, recently measured at Jefferson Lab which have high sensitivity to discriminate between different theoretical approaches.Comment: 5 pages, 5 figure

Ascidians at the Pacific and Atlantic entrances to the Panama Canal

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aquatic Invasions 6 (2011): 371-380, doi:10.3391/ai.2011.6.4.02.The Panama Canal region is susceptible to non-native species introductions due to the heavy international shipping traffic through the area. Ascidian introductions are occurring worldwide but little is known about introductions at the Panama Canal. Surveys were conducted in 2002, 2008, and 2009 within the Pacific and Atlantic entrances to the canal. We found a high diversity of ascidians on both sides of the canal, dominated by non-native species; six species occurred at both Pacific and Atlantic Panama sites. This is the first report of Polyandrocarpa anguinea and P. sagamiensis in Atlantic Panama waters and Ascidia incrassata, Ascidia sydneiensis, Botrylloides nigrum, Botryllus planus, Didemnum perlucidum, Diplosoma listerianum, Microcosmus exasperatus, Polyandrocarpa zorritensis, Polyclinum constellatum, Symplegma brakenhielmi, Symplegma rubra, and Trididemnum orbiculatum in Pacific Panama waters. The canal may serve as a major invasion corridor for ascidians and should be monitored over time.Funding for this project came from WHOI Ocean Life Institute-Tropical Research Initiative to Carman and CNPq to Rocha

The Effect of Air on Granular Size Separation in a Vibrated Granular Bed

Using high-speed video and magnetic resonance imaging (MRI) we study the motion of a large sphere in a vertically vibrated bed of smaller grains. As previously reported we find a non-monotonic density dependence of the rise and sink time of the large sphere. We find that this density dependence is solely due to air drag. We investigate in detail how the motion of the intruder sphere is influenced by size of the background particles, initial vertical position in the bed, ambient pressure and convection. We explain our results in the framework of a simple model and find quantitative agreement in key aspects with numerical simulations to the model equations.Comment: 14 pages, 16 figures, submitted to PRE, corrected typos, slight change

A NOVEL APPROACH TO IMPROVING THE AVAILABLE POWER OUTPUT OF PIEZOELECTRIC ULTRASONIC MOTORS

ABSTRACT Piezoelectric actuators have attractive operating properties because they do not generate electromagnetic fields and are not affected by them, and their power output characteristics scale linearly with decreasing size. These actuators have not see

Abundance and diversity of ascidians in the southern Gulf of Chiriquí, Pacific Panama

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aquatic Invasions 6 (2011): 381-390, doi:10.3391/ai.2011.6.4.03.Little is known about the ascidian fauna of Pacific Panama. Ascidian surveys were conducted in the southern Gulf of Chiriquí on the Pacific coast of Panama in January 2008 and 2009. Surveys along linear transects at 2-3 m depth (snorkel, 2008) and 5 and 12 m depth (SCUBA, 2009) were conducted at multiple sites within a chain of islands extending out from the mainland. Twelve different ascidian taxa were observed with mean densities of up to ~17 ascidians m-2. The most abundant species was Rhopalaea birkelandi. Two of the most abundant taxa (Ascidia sp., Pyura sp.) appear to represent previously undescribed species. Several species of didemnids were also abundant. Ascidians were most abundant near the coast of the mainland and were less abundant near the islands farthest offshore. These data on Panamanian ascidian communities provide a baseline of local biodiversity against which it will be possible to determine whether the communities change over time, if additional species become introduced to the region, or if native Panamanian species become invasive in other parts of the world.This research was supported by Ocean Life Institute Exploratory Grant (250513.38) to Carman and Sievert, Tropical Research Initiative Grant (253750.09) to Carman, Molyneaux and Sievert, a University of Hartford International Center Faculty Grant to Bullard, and CNPq senior postdoctoral grant to Rocha (200914/2008-1)