tbuckley/cabot-search huggingface dataset:
Automated Radiology Report Generation: A Review of Recent Advances
Authors: Phillip Sloan, Philip Clatworthy, Edwin Simpson, Majid Mirmehdi
Journal: IEEE Reviews in Biomedical Engineering (2024)

Increasing demands on medical imaging departments are taking a toll on the radiologist's ability to deliver timely and accurate reports. Recent technological advances in artificial intelligence have demonstrated great potential for automatic radiology report generation (ARRG), sparking an explosion of research. This survey paper conducts a methodological review of contemporary ARRG approaches by way of (i) assessing datasets based on characteristics, such as availability, size, and adoption rate, (ii) examining deep learning training methods, such as contrastive learning and reinforcement learning, (iii) exploring state-of-the-art model architectures, including variations of CNN and transformer models, (iv) outlining techniques integrating clinical knowledge through multimodal inputs and knowledge graphs, and (v) scrutinising current model evaluation techniques, including commonly applied NLP metrics and qualitative clinical reviews. Furthermore, the quantitative results of the reviewed models are analysed, where the top performing models are examined to seek further insights. Finally, potential new directions are highlighted, with the adoption of additional datasets from other radiological modalities and improved evaluation methods predicted as important areas of future development.
Smart responsive staple for dynamic promotion of anastomotic stoma healing
Authors: Qi Sun, Zifeng Yang, Ruijun Xu, Renjie Li, Yang Li, Feng Wang, Yong Li
Journal: Bioactive Materials (2024)

The precise combination of conflicting biological properties through sophisticated structural and functional design to meet all the requirements of anastomotic healing is of great demand but remains challenging. Here, we develop a smart responsive anastomotic staple (Ti-OH-MC) by integrating porous titanium anastomotic staple with multifunctional polytannic acid/tannic acid coating. This design achieves dynamic sequential regulation of antibacterial, anti-inflammatory, and cell proliferation properties. During the inflammatory phase of the anastomotic stoma, our Ti-OH-MC can release tannic acid to provide antibacterial and anti-inflammatory properties, together with immune microenvironment regulation function. At the same time, as the healing progresses, the multifunctional coating gradually falls off to expose the porous structure of the titanium anastomotic staple, which promotes cell adhesion and proliferation during the later proliferative and remodeling phases. As a result, our Ti-OH-MC exceeds the properties of clinically used titanium anastomotic staple, and can effectively promote the healing. The staple's preparation strategy is simple and biocompatible, promising for industrialisation and clinical application. This work provides an effective anastomotic staple for anastomotic stoma healing and serve as a reference for the functional design and preparation of other types of titanium-based tissue repair materials.
Phase II Efficacy and Safety of 80 mg Osimertinib in Patients With Leptomeningeal Metastases Associated With Epidermal Growth Factor Receptor Mutation–Positive Non–Small Cell Lung Cancer (BLOSSOM)
Authors: Sehhoon Park, Richard Baldry, Hyun Ae Jung, Jong-Mu Sun, Se-Hoon Lee, Jin Seok Ahn, Yu Jung Kim, Youngjoo Lee, Dong-Wan Kim, Sang-We Kim, Ki Hyeong Lee, Won Jae Lee, Jung Won Choi, Kyuha Chong, Jung-Il Lee, So-Hyeon Gwon, Nak-Hoon Son, Myung-Ju Ahn
Journal: Journal of Clinical Oncology (2024)

Leptomeningeal metastases (LMs) exhibit a high incidence in patients with epidermal growth factor receptor (EGFR)-mutated non-small cell lung cancer (NSCLC) post-treatment with first- or second-generation EGFR tyrosine kinase inhibitors (TKIs). This investigation evaluates the efficacy, safety, and pharmacokinetics of 80 mg once daily osimertinib in patients with LMs resistant to prior first- or second-generation EGFR TKIs.
Psychological adjustment and perception of patients’ relatives and healthcare providers regarding continuous deep sedation until death: A mixed-methods study.
Authors: Leonor Fasse, Marie Locatelli, Ines Maria Vaz Duarte Luis, Jean Bernard Le-Provost, Florian Scotte, Ingrid Joffin, Adrien Evin, Cécile Flahault
Journal: Journal of Clinical Oncology (2024)

12098 Background: France is currently in the midst of societal discussions concerning new legislation on active assistance in dying. Continuous Deep Sedation Until Death (CDSUD) is considered by some a “French exception” since 2016, but 8 years later, findings suggest that this procedure is not really clear to all, including patients, their relatives and their healthcare providers (HCP). The primary objective of this original research is to document the psychological adjustment of patients’ relatives and HCPs in the cancer context. Methods: APSY-SED (ID-RCB 2021-A03042-39) is a multicentric prospective, longitudinal and observational study, using a mixed-methods design. A lexicometric analysis of the semi-structured interviews was performed using Iramuteq software. A questionnaire survey was conducted, encompassing for relatives: anxiety and depressive symptoms (STAI-S, BDI-II); for HCPs: Professional Stress and Professional experience (Karasek questionnaire). We present here the main results at T1 (when CDSUD is implemented). Results: Main quantitative results are presented in Table I. Regarding qualitative findings, fifteen research interviews with relatives and 15 interviews with HCP were analyzed. Most frequent words associated with CDSUD were its “objectives”, its specific “temporality”, the mention of “euthanasia”, and “saying goodbye”. Confusion between CDSUD and euthanasia persists in relatives and HCPs. Conclusions: On average, relatives reported severe anxiety in the context of CDSUD. The qualitative findings regarding the main concerns shared by the relatives concerning the CDSUD temporality perceived as brutal, shed light on this anxiety. The second assessment time of this study, 6 months after death, including measures of depression, anxiety, intensity of grief reactions, will allow to specify the adjustement at mid-term. This is the first empirical study carried out in France on the adjustment of relatives and HCPs caring for patients with cancer for whom CDSUD is discussed. [Table: see text]
Shaping the future of molecular neurosurgery: towards epigenetic precision in surgical neuro-oncology?
Authors: Philipp Karschnia, Joerg-Christian Tonn
Journal: Neuro-Oncology (2024)

Journal Article Accepted manuscript Shaping the future of molecular neurosurgery: towards epigenetic precision in surgical neuro-oncology? Get access Philipp Karschnia, Philipp Karschnia Department of Neurosurgery, LMU University Hospital of the Ludwig-Maximilians-University Munich, Munich, GermanyGerman Cancer Consortium (DKTK), Partner Site Munich, Germany https://orcid.org/0000-0002-1254-5310 Search for other works by this author on: Oxford Academic PubMed Google Scholar Joerg-Christian Tonn Joerg-Christian Tonn Department of Neurosurgery, LMU University Hospital of the Ludwig-Maximilians-University Munich, Munich, GermanyGerman Cancer Consortium (DKTK), Partner Site Munich, Germany Corresponding Author: Prof. Joerg-Christian Tonn, MD, Department of Neurosurgery, Ludwig-Maximilians-University Munich, Marchioninistrasse 15 / 81377 Munich, Germany, phone: +49-(0)89-4400-72591, fax: +49-(0)89-4400-72592, e-mail: Joerg.Christian.Tonn@med.uni-muenchen.de https://orcid.org/0009-0004-1756-423X Search for other works by this author on: Oxford Academic PubMed Google Scholar Neuro-Oncology, noae100, https://doi.org/10.1093/neuonc/noae100 Published: 04 June 2024 Article history Received: 25 May 2024 Published: 04 June 2024
NTRK positivity and conversion to appropriate personalized treatment.
Authors: Bethany Michelle Slifko, Howard L. McLeod, Wendy Moore, Inês Abrunhosa Amaral, Susanne Munksted
Journal: Journal of Clinical Oncology (2024)

e15163 Background: The field of precision medicine continues to grow in size and complexity. In oncology alone, the FDA has approved companion diagnostics for 53 unique biomarkers across 28 different indications linking to 59 separate drugs to treat cancer patients beyond traditional options (FDA 21 December 2023). Two of these drugs, entrectinib and larotrectinib, are approved across all tumor types for NTRK fusions, which while rare in common cancer indications are more common in understudied, rare cancers (Cocco et al Nature 2018). These treatment options have significant outcomes for patients, however, there is still a large barrier for patients to access the right treatment (Sadik et al JCO 2022). We hypothesized not all patients with identified NTRK alterations are being prescribed these treatments and assessed this in real-world data for US oncology patients. Methods: Diaceutics proprietary DXRX database contains real-world claims, specialty pharmacy and laboratory data that enables the identification of patients positive for biomarker alterations and resultant treatment pathways in the US. The result-level laboratory data was filtered to solid tumor patients who were positive for NTRK alterations in the 2-year window between 2022 and 2023. The identified NTRK positive patients were then tokenized and joined to our medical claims and pharmacy data to assess which treatment combinations these patients received. Results: A total of 4,251 cancer patients were identified as having tumors with NTRK alterations. Of the patients that could be linked to treatment (800 patients), 1.5% (n = 12) patients went on to receive a targeted treatment for their NTRK alteration, either entrectinib (n = 8), larotrectinib (n = 3), or both entrectinib and larotrectinib (n = 1). When not prescribed either of these, 43.25% (n = 346) patients received different targeted treatment, possibly because of other alterations identified. There were still 55.25% (n = 442) receiving no targeted treatment, either being prescribed chemotherapy (chemo) alone (28.25%, n = 226), immunotherapy (IO) alone (21.1%, n = 169), or an IO/chemo combination (5.9%, n = 47). Conclusions: Despite the established significant disease control from targeted NTRK treatments, most patients with these alterationsdo not have an opportunity to benefit from the most effective personalized treatment for their cancer. These findings may suggest that targeted therapy for rarer and/or tissue agnostic alterations may get deprioritized or overlooked. Therefore, we advocate that a new, different approach for bringing targeted treatments for rare biomarkers to patients is still needed. Different economic models and an optimized approach to engage and inform key stakeholders including oncologists of the presence and benefit of targeted treatments is critical and needs further investigation.
An economic analysis of low-energy contact x-ray brachytherapy for treatment of rectal cancer.
Authors: Arthur Sun Myint, Hayley Bennett, Christopher Rao, Leona Batten, Elise Hasler, David Jarrom, Matthew Prettyjohns, Craig Barrington
Journal: Journal of Clinical Oncology (2024)

e15622 Background: Health Technology Wales sought to evaluate the clinical and cost-effectiveness of contact x-ray brachytherapy (CXB) in conjunction with external-beam radiotherapy (EBRT), compared to EBRT alone for early-stage (T2–3b, N0–1, M0) rectal cancer in a surgically fit population. Methods: An economic analysis was performed using a decision analytical, state transition model. Analysis was performed from a third-party payer perspective over a life-time horizon. The model was populated using data from the Organ Preservation in Early Rectal Adenocarcinoma (OPERA) trial. Results: . CXB was estimated to provide 0.2 quality-adjusted life years (QALYs) per patient at an additional cost of $1118 per person. CXB was cost-effective compared with external beam boost at a cost of $5623 per QALY gained. These findings did not change in deterministic sensitivity analysis and CXB was cost-effective in over 90% of probabilistic sensitivity analyses. Conclusions: CXB is likely to be cost-effective with a high degree of certainty in this patient population.
Digital droplet PCR-based detection of KRAS, NRAS, and BRAF mutation in plasma samples from patients with colorectal cancer.
Authors: Jin-Soo Kim, Mi Young Kim, Donghwa Lee, Rumi Shin, Jin Hyun Park, Jun Ho Ko, In Sil Choi, Seung Chul Heo, Mi Ran Kang
Journal: Journal of Clinical Oncology (2024)

e15626 Background: Digital droplet PCR (ddPCR) is known for high sensitivity to detect mutated DNA in plasma. The aim of this study was to investigate the concordance of KRAS, NRAS and BRAF mutation detection in patients with colorectal cancers (CRCs) between plasma samples (PSs) and tissue samples (TSs) in pair. Methods: We prospectively collected paired PS and TS from patients with CRC (N = 200) who underwent surgery or biopsy for metastasis at Seoul National University Boramae Medical Center from Mar 2017 to January 2020. The ddPCR was performed using QX200™ Droplet Digital PCR System (Bio-Rad, USA) according to the manufacturer's recommended protocol with PCR kits developed for each gene (Gencurix, South Korea). Results: A total of 187 TSs and PSs were valid for ddPCR. Among these, 111 had results for KRAS, 51 had results for NRAS and 21 had results for BRAF, which were tested through routine clinical practice (RCP) using the pyrosequencing or Sanger sequencing method. The experiment's outcomes were analyzed for KRAS, NRAS, and BRAF, respectively. The analysis initially compared the results of RCP TS and ddPCR TS, and subsequently, intended to compare the mutation detection rates between TS and PS by comparing the results of ddPCR TS and ddPCR PS for FFPE/PS paired specimens. For KRAS, compared to RCP TS, the sensitivity of ddPCR TS was 100%, specificity was 66.7%, and the overall concordance rate was 79.3%. In TS/PS paired specimens, the sensitivity of ddPCR PS for ddPCR TS results was 38.5%, specificity was 97.6%, and the overall concordance rate was 64.7%. For NRAS, compared to RCP TS, the sensitivity of ddPCR TS was 100%, specificity was 98.0%, and the overall concordance rate was 98.0%. In TS/PS paired specimens, the sensitivity of ddPCR PS for ddPCR TS results was 33.3%, specificity was 100%, and the overall concordance rate was 97.4%. For BRAF, sensitivity of ddPCR TS was not available (no RCP positive sample), specificity was 85.7% compared to RCP, corresponded to a concordance rate of 97.0%. The sensitivity of ddPCR PS for ddPCR TS results was 71.4%, specificity was 100%, and the overall concordance rate was 97.4%. The sensitivity of ddPCR PS for ddPCR TS results was 71.4%, specificity was 100%, and the overall concordance rate was 97.4%. Conclusions: The present study showed that ddPCR has high accuracy in detecting KRAS, NRAS and BRAF mutation in plasma samples from patients with CRC. Analysis of PS could be useful in early response assessment and longitudinal disease monitoring for patient with metastatic CRC with specific mutation.
Gene fusions: A retrospective analysis of therapies and treatments of MTB patients over 7 years.
Authors: Jamie Randall, Whitney Rose Swain, Safae Chouraichi, Hongkun Wang, Arthur Winer, Jasmine Huynh, Raymond Couric Wadlow, Timothy Lewis Cannon
Journal: Journal of Clinical Oncology (2024)

e15183 Background: Gene fusions (GF) are less common than single nucleotide variants, amplifications, and deletions, but have been suggested to be more predictive of responses to specific molecularly targeted therapies than other types of molecular alterations. We reviewed our institutional trends for overall survival in our molecular tumor board database based on the receipt of molecularly targeted therapy. Methods: We identified patients with non-hematologic malignancies and gene fusions (GF) identified by DNA based next generation sequencing (NGS) and reviewed by the Inova Schar Cancer Institute Molecular Tumor Board (ISCI MTB) between March 1, 2016 and March 1, 2023. GFs were confirmed by re-evaluation of next generation sequencing, and we determined the number of patients who received molecularly targeted therapy (RTT) specific for the GF. We evaluated overall survival (OS) in the RTT cohort and in the cohort that did not receive targeted therapy (NTT). TMPRSS fusions in prostate cancer were excluded from this analysis. Results: There were 93 patients with gene fusions in advanced staged cancers that met study criteria. Twenty-three were lost to follow up, transferred care outside ISCI, or enrolled in hospice. Of 70 stage IV patients reviewed, thirty-seven were found to have received GF targeted therapy. OS for all patients was 28.5 months. Patients in the RTT cohort had a median OS of 45 months and patients in the NTT cohort had an OS of 26.8 months (p-value = 0.16, Log-rank test). Conclusions: Targeted therapy in solid tumors with gene fusions is associated with prolonged overall survival. It is critical for MTBs to use NGS platforms that identify GF. Further studies examining OS and GF are warranted. [Table: see text]
A phase Ib study of JMT103, a receptor activator of NF-kB ligand (RANKL) antibody, in patients (pts) with bone metastases from solid tumors.
Authors: Ran Ran, Hongtao Li, Huan Zhou, Tao Sun, Ai-min Zang, Guo Hongqian, Hua Xie, Shikai Wu, Yong Yan, Xing Yin, Hailin Xiong, Hong Li, Jing Yuan, Huiping Li, Jin Li
Journal: Journal of Clinical Oncology (2024)

e15190 Background: JMT103 is a human IgG4 monoclonal antibody against RANKL and blocks the RANK signaling in osteoclasts, thus suppressing bone resorption. This phase Ib study aims to demonstrate the activity of JMT103 in bone metastases patients with solid tumors. Methods: In this randomized, multi-center, open-label, phase Ib study, adult pts with bone metastases from solid tumors were enrolled and randomized at a 1:1:1 ratio to receive JMT103 subcutaneously at 120mg every 4 weeks (Q4W, Cohort 1), 120mg every 8 weeks (Q8W, Cohort 2) and 180mg Q8W (Cohort 3) up to 49 weeks. The primary endpoint was the percent change from baseline to week 13 in creatinine-adjusted urinary N-telopeptide (uNTx/Cr). Secondary endpoints included safety, anti-drug antibodies (ADA) positivity, the percentage of patients who experienced on-study skeletal-related events (SREs), and ≥ 2-point decreases in pain with Brief Pain Inventory – Short Form. Results: At database lock (Mar. 31, 2023), 295 pts were enrolled; 293 were treated with JMT103 and eligible for efficacy and safety evaluation (96 pts in Cohort 1, 97 pts in Cohort 2, and 100 pts in Cohort 3). The median age was 58 years (Interquartile range [IQR] 51, 66), and the primary tumor types were mainly breast (145, 50%) and prostate cancer (44, 15%). At week 13, the median (IQR) percent change in uNTx/Cr was - 80% (- 93%, - 50%) in Cohort 1, - 73% (- 94%, - 34%) in Cohort 2, and - 76% (- 92%, - 40%) in Cohort 3, respectively. The incidence of SREs in the three cohorts was 3%, 6%, and 7%, respectively. Among the 33 pts in Cohort 1, 35 pts in Cohort 2, and 37 pts in Cohort 3 with baseline pain scores ≥ 2, 61% in Cohort 1, 46% in Cohort 2, and 54% in Cohort 3 experienced ≥ 2-point decreases in pain at the first post-treatment visit (Day 15). For ADA analysis, only 1 (1%) pt in Cohort 2 with a negative result at baseline tested positive after treatment. The table shows the overall summary of the safety profile. Most of TRAEs were low in grade and resolved quickly. The most common TRAEs (any grade) were hypocalcemia (68, 23%), hypophosphatemia (67, 23%), and increased aspartate transaminase (35, 12%). Among the 40 cases of grade-5 TEAE, only 1 was reported as a TRAE (pneumonia); the rest were unrelated to JMT103. Conclusions: Our study demonstrated a promising efficacy of JMT103 in reducing bone metabolism biomarker and a good safety profile with low immunogenicity. Clinical trial information: NCT04630522 . [Table: see text]
Real-world use of a CSF circulating tumor cell assay in the diagnosis and management of leptomeningeal metastasis.
Authors: Nicholas Alfred Blondin, Nicholas Haberli
Journal: Journal of Clinical Oncology (2024)

2029 Background: The diagnosis of leptomeningeal metastasis (LM) can be challenging due to variability in clinical symptoms, radiographic, and cerebrospinal fluid (CSF) findings. The National Comprehensive Cancer Network (NCCN) guidelines recommend assessment of circulating tumor DNA (ctDNA) to increase sensitivity of tumor cell detection and assess the response to treatment. We hypothesize that the real-world use of an assay for the direct detection and enumeration of circulating tumor cells (CTCs) in the CSF is clinically useful for accurate diagnosis of LM, particularly in an early stage of disease. Methods: We report a series of 55 patients treated at our institution with a cancer diagnosis and either neurological symptoms or radiographic findings that suggested LM. All patients underwent a lumbar puncture, assessment for CSF CTCs, and conventional hospital-based cytology testing between 6/1/2020 and 8/1/2023. Survival data cutoff was 12/31/2023. Patient outcomes are reported. Results: 55 patients were tested, and 30 patients were found to be positive for CTCs and diagnosed with LM. Only 10 patients were concurrently positive for CTCs and cytology at our institution, whereas 20 patients with positive CTCs had a negative or ambiguous cytology. No patients with a negative CTC result (25 patients) were subsequently diagnosed with LM, whereas 4 patients with a positive CTC result remained without progressive neurological symptoms. 5 patients diagnosed with LM were alive at the time of data cutoff. The histologic breakdown for LM was: breast (11), non-small cell lung cancer (NSCLC) (16), gastrointestinal (GI) (3). Median overall survival (OS) was longer in patients with a positive CTC and negative cytology result compared to patients with concurrent positive CTC and cytology (172 vs. 63 days, p = 0.06). Median OS was also longer in breast cancer LM compared to NSCLC LM (235 vs. 63 days, p = 0.008). Most patients diagnosed with LM received therapies including Ommaya reservoir placement, intrathecal chemotherapy, and/or radiation. Conclusions: The use of a CSF circulating tumor cell assay aided the diagnosis of LM and led to timely initiation of treatment. A negative result of the CTC assay was associated with ruling out LM. Diagnosis of LM with the CTC assay and negative cytology was associated with longer survival, possibly due to earlier treatment initiation, and not solely a lead time bias. Breast cancer LM patients had improved survival compared to NSCLC and GI cancer patients, possibly due to more effective treatment options.