LLM-AIx: An open source pipeline for Information Extraction from unstructured medical text based on privacy preserving Large Language Models.

In clinical science and practice, text data, such as clinical letters or procedure reports, is stored in an unstructured way. This type of data is not a quantifiable resource for any kind of quantitative investigations and any manual review or structured information retrieval is time-consuming and costly. The capabilities of Large Language Models (LLMs) mark a paradigm shift in natural language processing and offer new possibilities for structured Information Extraction (IE) from medical free text. This protocol describes a workflow for LLM based information extraction (LLM-AIx), enabling extraction of predefined entities from unstructured text using privacy preserving LLMs. By converting unstructured clinical text into structured data, LLM-AIx addresses a critical barrier in clinical research and practice, where the efficient extraction of information is essential for improving clinical decision-making, enhancing patient outcomes, and facilitating large-scale data analysis. The protocol consists of four main processing steps: 1) Problem definition and data preparation, 2) data preprocessing, 3) LLM-based IE and 4) output evaluation. LLM-AIx allows integration on local hospital hardware without the need of transferring any patient data to external servers. As example tasks, we applied LLM-AIx for the anonymization of fictitious clinical letters from patients with pulmonary embolism. Additionally, we extracted symptoms and laterality of the pulmonary embolism of these fictitious letters. We demonstrate troubleshooting for potential problems within the pipeline with an IE on a real-world dataset, 100 pathology reports from the Cancer Genome Atlas Program (TCGA), for TNM stage extraction. LLM-AIx can be executed without any programming knowledge via an easy-to-use interface and in no more than a few minutes or hours, depending on the LLM model selected.

Scheme for Quantum-Logic Based Transfer of Accuracy in Polarizability Measurement for Trapped Ions Using a Moving Optical Lattice.

Optical atomic clocks based on trapped ions suffer from systematic frequency shifts of the clock transition due to interaction with blackbody radiation from the environment. These shifts can be compensated if the blackbody radiation spectrum and the differential dynamic polarizability is known to a sufficient precision. Here, we present a new measurement scheme, based on quantum logic that allows a direct transfer of precision for polarizability measurements from one species to the other. This measurement circumvents the necessity of calibrating laser power below the percent level, which is the limitation for state-of-the-art polarizability measurements in trapped ions. Furthermore, the presented technique allows one to reference the polarizability transfer to hydrogenlike ions for which the polarizability can be calculated with high precision.

Marine heatwaves and upwelling shape stress responses in a keystone predator.

Climate change increases the frequency and intensifies the magnitude and duration of extreme events in the sea, particularly so in coastal habitats. However, the interplay of multiple extremes and the consequences for species and ecosystems remain unknown. We experimentally tested the impacts of summer heatwaves of differing intensities and durations, and a subsequent upwelling event on a temperate keystone predator, the starfish Asterias rubens. We recorded mussel consumption throughout the experiment and assessed activity and growth at strategically chosen time points. The upwelling event overall impaired starfish feeding and activity, likely driven by the acidification and low oxygen concentrations in the upwelled seawater. Prior exposure to a present-day heatwave (+5°C above climatology) alleviated upwelling-induced stress, indicating cross-stress tolerance. Heatwaves of present-day intensity decreased starfish feeding and growth. While the imposed heatwaves of limited duration (9 days) caused slight impacts but allowed for recovery, the prolonged (13 days) heatwave impaired overall growth. Projected future heatwaves (+8°C above climatology) caused 100% mortality of starfish. Our findings indicate a positive ecological memory imposed by successive stress events. Yet, starfish populations may still suffer extensive mortality during intensified end-of-century heatwave conditions.

Ocean winter warming induced starvation of predator and prey.

Ocean warming impacts the fitness of marine ectothermic species, leading to poleward range shifts, re-shuffling of communities, and changes in ecosystem services. While the detrimental effects of summer heat waves have been widely studied, little is known about the impacts of winter warming on marine species in temperate regions. Many species benefit from low winter temperature-induced reductions in metabolism, as these permit conservation of energy reserves that are needed to support reproduction in spring. Here, we used a unique outdoor mesocosm system to expose a coastal predator-prey system, the sea star Asterias and the blue mussel Mytilus, to different winter warming scenarios under near-natural conditions. We found that the body condition of mussels decreased in a linear fashion with increasing temperature. Sea star growth also decreased with increasing temperature, which was a function of unaltered predation rates and decreased mussel body condition. Asterias relative digestive gland mass strongly declined over the studied temperature interval (ca twofold). This could have severe implications for reproductive capacity in the following spring, as digestive glands provide reserve compounds to maturing gonads. Thus, both predator and prey suffered from a mismatch of energy acquisition versus consumption in warmer winter scenarios, with pronounced consequences for food web energy transfer in future oceans.

Warming and temperature variability determine the performance of two invertebrate predators.

In a warming ocean, temperature variability imposes intensified peak stress, but offers periods of stress release. While field observations on organismic responses to heatwaves are emerging, experimental evidence is rare and almost lacking for shorter-scale environmental variability. For two major invertebrate predators, we simulated sinusoidal temperature variability (±3 °C) around todays' warm summer temperatures and around a future warming scenario (+4 °C) over two months, based on high-resolution 15-year temperature data that allowed implementation of realistic seasonal temperature shifts peaking midpoint. Warming decreased sea stars' (Asterias rubens) energy uptake (Mytilus edulis consumption) and overall growth. Variability around the warming scenario imposed additional stress onto Asterias leading to an earlier collapse in feeding under sinusoidal fluctuations. High-peak temperatures prevented feeding, which was not compensated during phases of stress release (low-temperature peaks). In contrast, increased temperatures increased feeding on Mytilus but not growth rates of the recent invader Hemigrapsus takanoi, irrespective of the scale at which temperature variability was imposed. This study highlights species-specific impacts of warming and identifies temperature variability at the scale of days to weeks/months as important driver of thermal responses. When species' thermal limits are exceeded, temperature variability represents an additional source of stress as seen from future warming scenarios.

Initialization of quantum simulators by sympathetic cooling.

Simulating computationally intractable many-body problems on a quantum simulator holds great potential to deliver insights into physical, chemical, and biological systems. While the implementation of Hamiltonian dynamics within a quantum simulator has already been demonstrated in many experiments, the problem of initialization of quantum simulators to a suitable quantum state has hitherto remained mostly unsolved. Here, we show that already a single dissipatively driven auxiliary particle can efficiently prepare the quantum simulator in a low-energy state of largely arbitrary Hamiltonians. We demonstrate the scalability of our approach and show that it is robust against unwanted sources of decoherence. While our initialization protocol is largely independent of the physical realization of the simulation device, we provide an implementation example for a trapped ion quantum simulator.

Motional Fock states for quantum-enhanced amplitude and phase measurements with trapped ions.

The quantum noise of the vacuum limits the achievable sensitivity of quantum sensors. In non-classical measurement schemes the noise can be reduced to overcome this limitation. However, schemes based on squeezed or Schrödinger cat states require alignment of the relative phase between the measured interaction and the non-classical quantum state. Here we present two measurement schemes on a trapped ion prepared in a motional Fock state for displacement and frequency metrology that are insensitive to this phase. The achieved statistical uncertainty is below the standard quantum limit set by quantum vacuum fluctuations, enabling applications in spectroscopy and mass measurements.

Non-destructive state detection for quantum logic spectroscopy of molecular ions.

Precision laser spectroscopy of cold and trapped molecular ions is a powerful tool in fundamental physics--used, for example, in determining fundamental constants, testing for their possible variation in the laboratory, and searching for a possible electric dipole moment of the electron. However, the absence of cycling transitions in molecules poses a challenge for direct laser cooling of the ions, and for controlling and detecting their quantum states. Previously used state-detection techniques based on photodissociation or chemical reactions are destructive and therefore inefficient, restricting the achievable resolution in laser spectroscopy. Here, we experimentally demonstrate non-destructive detection of the quantum state of a single trapped molecular ion through its strong Coulomb coupling to a well controlled, co-trapped atomic ion. An algorithm based on a state-dependent optical dipole force changes the internal state of the atom according to the internal state of the molecule. We show that individual quantum states in the molecular ion can be distinguished by the strength of their coupling to the optical dipole force. We also observe quantum jumps (induced by black-body radiation) between rotational states of a single molecular ion. Using the detuning dependence of the state-detection signal, we implement a variant of quantum logic spectroscopy of a molecular resonance. Our state-detection technique is relevant to a wide range of molecular ions, and could be applied to state-controlled quantum chemistry and to spectroscopic investigations of molecules that serve as probes for interstellar clouds.

Precision Isotope Shift Measurements in Calcium Ions Using Quantum Logic Detection Schemes.

We demonstrate an efficient high-precision optical spectroscopy technique for single trapped ions with nonclosed transitions. In a double-shelving technique, the absorption of a single photon is first amplified to several phonons of a normal motional mode shared with a cotrapped cooling ion of a different species, before being further amplified to thousands of fluorescence photons emitted by the cooling ion using the standard electron shelving technique. We employ this extension of the photon recoil spectroscopy technique to perform the first high precision absolute frequency measurement of the 2D(3/2)→2P(1/2) transition in calcium, resulting in a transition frequency of f=346 000 234 867(96) kHz. Furthermore, we determine the isotope shift of this transition and the 2S(1/2)→2P(1/2) transition for 42Ca+, 44Ca+, and 48Ca+ ions relative to 40Ca+ with an accuracy below 100 kHz. Improved field and mass shift constants of these transitions as well as changes in mean square nuclear charge radii are extracted from this high resolution data.