The editors regret there was an error in“Shotgun metagenome library construction and sequencing”section.“The raw sequences can be found in BGID(CRA000815)”should be corrected to“The raw metagenome sequencing data...
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The editors regret there was an error in“Shotgun metagenome library construction and sequencing”section.“The raw sequences can be found in BGID(CRA000815)”should be corrected to“The raw metagenome sequencing data have been deposited in the Genome Sequence Archive at Beijing Institute of Genomics,Chinese Academy of sciences(GSA:CRA000815),and are publicly accessible at https://***/gsa/”.The correct section is shown *** editors would like to apologize for any inconvenience caused.
Background: Physicians invest hours creating patient notes, which are rich in information but difficult for computers to analyze due to their unstructured format. GPT-4 reshaped our ability to process text, yet it is ...
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Background: Physicians invest hours creating patient notes, which are rich in information but difficult for computers to analyze due to their unstructured format. GPT-4 reshaped our ability to process text, yet it is unknown how well this model can handle medical notes. This project aims to compare GPT-4’s ability to annotate medical notes against experienced physicians across three different languages at multiple institutions and countries. Methods: This study included eight sites from four countries - the united States, Colombia, Singapore, and Italy. Each site contributed seven de-identified notes (admission, progress, or consult) from hospitalized patients. GPT-4 assessed each note by answering 14 questions, including demographic information, clinical judgments, data quality, and patients’ eligibility for a hypothetical study enrollment. For validation, two physicians from each site independently evaluated GPT-4's responses. Findings: Overall, 56 medical notes, written in English, Italian, and Spanish, were analyzed. A total of 784 responses from GPT-4 were generated. Both physicians agreed with GPT-4’s response 79% of the time (622/784, 95%CI 76-82%). Only one of the two physicians agreed with GPT-4’s response 10% of the time (82/784, 95%CI 8-13%). Neither physician agreed with GPT-4’s response 10% of the time (80/784, 95%CI 8-13%). Both physicians agreed with GPT-4 more often in notes written in Spanish and Italian than in English, with agreement rates of 88% (86/98, 95%CI 79-93%), 84% (82/98, 95%CI 75-90%), and 77% (454/588, 95%CI 74-80%), respectively. Hallucinations were rare (10/784, 95%CI 0-2%). GPT-4 correctly selected patients for a hypothetical study enrollment based on three criteria 90% of the time (95%CI 81-98%). Interpretation: The findings indicate that GPT-4 annotations demonstrated a high agreement rate with physicians across all languages. We also demonstrate GPT-4's potential to assist in patient selection for studies. Funding: None. Declarati
The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Rec...
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Morphological mapping is a fundamental step in studying the processes that shaped an asteroid surface. Yet, it is challenging and often requires multiple independent assessments by trained experts. Here, we present fa...
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In this report, we summarize the first NTIRE challenge on light field (LF) image super-resolution (SR), which aims at super-resolving LF images under the standard bicubic degradation with a magnification factor of 4. ...
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BACKGROUND:Extracting clinical entities from unstructured medical documents is critical for improving clinical decision support and documentation workflows. This study examines the performance of various encoder and d...
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BACKGROUND:Extracting clinical entities from unstructured medical documents is critical for improving clinical decision support and documentation workflows. This study examines the performance of various encoder and decoder models trained for Named Entity Recognition (NER) of clinical parameters in pathology and radiology reports, highlighting the applicability of Large Language Models (LLMs) for this task.
METHODS:Three NER methods were evaluated: (1) flat NER using transformer-based models, (2) nested NER with a multi-task learning setup, and (3) instruction-based NER utilizing LLMs. A dataset of 2013 pathology reports and 413 radiology reports, annotated by medical students, was used for training and testing.
RESULTS:The performance of encoder-based NER models (flat and nested) was superior to that of LLM-based approaches. The best-performing flat NER models achieved F1-scores of 0.87-0.88 on pathology reports and up to 0.78 on radiology reports, while nested NER models performed slightly lower. In contrast, multiple LLMs, despite achieving high precision, yielded significantly lower F1-scores (ranging from 0.18 to 0.30) due to poor recall. A contributing factor appears to be that these LLMs produce fewer but more accurate entities, suggesting they become overly conservative when generating outputs.
CONCLUSION:LLMs in their current form are unsuitable for comprehensive entity extraction tasks in clinical domains, particularly when faced with a high number of entity types per document, though instructing them to return more entities in subsequent refinements may improve recall. Additionally, their computational overhead does not provide proportional performance gains. Encoder-based NER models, particularly those pre-trained on biomedical data, remain the preferred choice for extracting information from unstructured medical documents.
Anthropogenic emissions of black carbon (BC) aerosols are generally thought to warm the climate. However, the magnitude of this warming remains highly uncertain due to limited knowledge of BC sources; optical properti...
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Anthropogenic emissions of black carbon (BC) aerosols are generally thought to warm the climate. However, the magnitude of this warming remains highly uncertain due to limited knowledge of BC sources; optical properties; and atmospheric processes such as transport, removal, and cloud interactions. Here, we assess and constrain estimates of the historical warming influence of BC using recent observations and emission inventories. Based on simulations from four climate models, we show that the current global mean surface temperature change from anthropogenic BC due to aerosol-radiation interaction spans a factor of three—from +0.02 ± 0.02 K to +0.06 ± 0.05 K. Rapid atmospheric adjustments reduce the instantaneous radiative forcing by nearly 50% (multi-model mean), substantially lowering the net warming. Yet, recent satellite constraints suggest a stronger effect, highlighting the need for a more comprehensive reassessment of BC’s climate influence.
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