128 research outputs found
BI-RADS BERT & Using Section Segmentation to Understand Radiology Reports
Radiology reports are one of the main forms of communication between
radiologists and other clinicians and contain important information for patient
care. In order to use this information for research and automated patient care
programs, it is necessary to convert the raw text into structured data suitable
for analysis. State-of-the-art natural language processing (NLP)
domain-specific contextual word embeddings have been shown to achieve
impressive accuracy for these tasks in medicine, but have yet to be utilized
for section structure segmentation. In this work, we pre-trained a contextual
embedding BERT model using breast radiology reports and developed a classifier
that incorporated the embedding with auxiliary global textual features in order
to perform section segmentation. This model achieved a 98% accuracy at
segregating free text reports sentence by sentence into sections of information
outlined in the Breast Imaging Reporting and Data System (BI-RADS) lexicon, a
significant improvement over the Classic BERT model without auxiliary
information. We then evaluated whether using section segmentation improved the
downstream extraction of clinically relevant information such as
modality/procedure, previous cancer, menopausal status, the purpose of the
exam, breast density, and breast MRI background parenchymal enhancement. Using
the BERT model pre-trained on breast radiology reports combined with section
segmentation resulted in an overall accuracy of 95.9% in the field extraction
tasks. This is a 17% improvement compared to an overall accuracy of 78.9% for
field extraction with models using Classic BERT embeddings and not using
section segmentation. Our work shows the strength of using BERT in radiology
report analysis and the advantages of section segmentation in identifying key
features of patient factors recorded in breast radiology reports
Solution structure of the cytochrome P450 reductase–cytochrome c complex determined by neutron scattering
Electron transfer in all living organisms critically relies on formation of complexes between the proteins involved. The function of these complexes requires specificity of the interaction to allow for selective electron transfer but also a fast turnover of the complex, and they are therefore often transient in nature, making them challenging to study. Here, using small-angle neutron scattering with contrast matching with deuterated protein, we report the solution structure of the electron transfer complex between cytochrome P450 reductase (CPR) and its electron transfer partner cytochrome c This is the first reported solution structure of a complex between CPR and an electron transfer partner. The structure shows that the interprotein interface includes residues from both the FMN- and FAD-binding domains of CPR. In addition, the FMN is close to the heme of cytochrome c but distant from the FAD, indicating that domain movement is required between the electron transfer steps in the catalytic cycle of CPR. In summary, our results reveal key details of the CPR catalytic mechanism, including interactions of two domains of the reductase with cytochrome c and motions of these domains relative to one another. These findings shed light on interprotein electron transfer in this system and illustrate a powerful approach for studying solution structures of protein-protein complexes
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