tbuckley/cabot-search huggingface dataset:
Representing cancer clinical trial criteria and attributes using ontologies: An NLP-assisted approach.
Authors: Kyeryoung Lee, Zhongzhi Liu, Meng Ma, Chris Gilman, Yun Mai, Xiang Zhou, Krish Ghosh, Rong Chen, Eric Schadt, Xiaoyan Wang
Journal: Journal of Clinical Oncology (2020)

e14079 Background: Low patient recruitment is one of the main reasons clinical trials fail. Identifying eligible patients for clinical trials using electric health records (EHRs) can help reach accrual targets. Ontology reasoning implemented in Trial2Patient, a scalable system we developed for matching patient to clinical trials, forms the basis for generating patient cohorts in our system. For efficient cohort definition, an attribute ontology for eligibility criteria and entity categorization is a necessary first step. To meet this requirement, we constructed an ontology platform for lung cancer trials. Methods: We classified 128 non-small cell lung cancer and 38 small cell lung cancer trials into different therapy groups. Among the 166 trials we examined, 110 were immuno-oncology therapy-based, 48 were targeted therapy-based, and 8 were chemotherapy or device trials. We analyzed the eligibility criteria for each trial manually to identify entities from all trials as well as indication specific and further therapy group specific entities. To incorporate a semi-automated, natural language process (NLP)-assisted named entity recognition (NER) into the future cohort definition process, we trained NLP and deep learning models for NER and ontology encoding. Attributes generated from 50 processed NSCLC trials were evaluated with our manually curated attributes. The ontology generated from lung cancer was tested in 74 prostate cancer trials for generalizability. Results: The ontology for lung cancer trials, which is generalizable to prostate cancer and other cancer clinical trials, were constructed. Total 507 attributes were extracted and entities were categorized into 8 groups. Evaluation of attributes generated by NLP and deep learning models compared with manually extracted attributes showed high consistency and accuracy. The average precision, recall and F1 values of 15 most commonly appearing entities (disease, histology, targeted therapy, immunotherapy, radiotherapy, neoadjuvant therapy, age, gender, test, vitals, value, drug, gene, mutation, problem) are 0.873, 0.769, and 0.805, respectively. Conclusions: We contribute to a clinical trial ontology platform for lung cancer and prostate cancer trial recruitment. This ontology platform can be expanded to other solid tumors or hematologic malignancies for clinical trial analysis, and can also be applied to generate synthetic control arm cohorts. We believe NLP-assisted NER can be successfully incorporated for the future work of large scale of clinical trial cohort definition.
Clinical characteristics and treatment of severe hyperlipidemic pancreatitis
Authors: Jian-guo Jia, Jia-bang Sun, Da-chuan Liu, Fei Li
Journal: BMJ (2008)

Objective To summarize clinical characteristics and experiences in treatment of severe hyperlipidemic pancreatitis (SHLP). Methods A retrospective analysis for 22 cases of SHLP and 91 cases of severe acute biliary pancreatitis (SABP) hospitalized during January 1, 2000 to December 31, 2006 was carried out to compare their clinical characteristics and treatment outcomes. Results Activities of serum and urine amylase in SHLP patients at admission were (715 ± 99) and (382 ± 56) U/L, respectively, significantly lower than those in SABP patients (1551 ± 107) and (773 ± 66) U/L, respectively (P < 0.01). About 55% (12/22) of SHLP patients had pulmonary infection, 36% (8/22) with circulatory failure, 41% (9/22) with respiratory failure and 23 % (5/22) with renal failure, all significantly higher than those in SABP patients SABP [32% (29/91), 14% (13/91), 7% (6/91) and 5% (5/91), respectively, P < 0.01]. Two died of SHLP and 11 of SABP, respectively. Conclusions In diagnosis of SHLP, it should be noticed that no remarkable elevation of activities in serum and urine amylase usually, so during the course of treatment for SHLP, it is important to prevent and treat multi-organ failure, respiratory failure and renal failure in an active way.

Key words: 
Pancreatitis;  Hypertriglyceridemia;  Disease attributes;  Treatment outcome
经纤维支气管镜救治幼儿气道异物误诊重症肺炎一例
Authors: 王文建
Journal: BMJ (2008)

患儿女,26个月.因发热咳嗽3 d伴气急于2006年8月23日21:00急诊收入儿童监护病房,否认有进食呛咳史,既往无类似病史.入院查体:体温40%,心率200次/min,呼吸26次/min,神志清,烦躁不安,呼吸促,口唇无紫绀,未见吸气三凹征,咽红,心音有力,未闻杂音,左肺未及呼吸音,右肺呼吸音粗,无干湿啰音,腹平软,肝脾肋下未及,四肢末梢无青紫及畸形.血白细胞16.1×109/L,分类中性粒细胞0.77,血红蛋白119 g/L,C反应蛋白19 mg/L。
Outcomes and toxicities in patients (pts) non-randomly assigned to immunotherapy Children’s Oncology Group (COG) ANBL0032.
Authors: Ami Vijay Desai, Andrew Gilman, Mehmet Fevzi Ozkaynak, Arlene Naranjo, Wendy B London, Sheena Cretella Tenney, Malcolm Smith, Nita Seibel, Hiroyuki Shimada, Katherine K. Matthay, Susan Lerner Cohn, John M. Maris, Rochelle Bagatell, Paul M. Sondel, Julie R. Park, Alice L. Yu
Journal: Journal of Clinical Oncology (2020)

10523 Background: Immunotherapy with the anti-GD2 antibody dinutuximab plus sargramostim (GM-CSF), aldesleukin (IL-2) and isotretinoin following consolidation therapy improved outcome for high-risk neuroblastoma (HRNBL) pts enrolled on COG ANBL0032. Randomization was halted in 2009; subsequent pts were non-randomly assigned to immunotherapy. Toxicities and survival were evaluated. Methods: HRNBL pts &lt; 31 years old with a pre-autologous stem cell transplant (ASCT) response of ≥ partial response (PR) were eligible. Demographics, INSS stage, tumor biology, 1993 INRC pre-ASCT response and toxicities were summarized using descriptive statistics. Five-year (yr) EFS and OS from time of study enrollment were estimated. Results: From 2009-2015, 1,183 pts were non-randomly assigned to immunotherapy. 96.7% (n = 1,144) were ≥18 months old and 83.1% (n = 765/921) had stage 4 disease. 45.1% (n = 363/805) of tumors with known biology were MYCN amplified, 94.5% (n = 749/793) had unfavorable histology, and 54.9% (n = 397/723) were diploid. Pre-ASCT, 352 (29.8%) pts had complete response (CR), 418 (35.3%) had very good partial response (VGPR), and 413 (34.9%) had PR. 1,042 (88.1%) pts underwent a single and 141 (11.9%) underwent tandem ASCT. For the entire cohort, 5-yr EFS was 61.1±1.9% and 5-yr OS was 71.9±1.7%. 5-yr EFS and OS for pts ≥18 months of age with stage 4 disease (n = 746) were 58.4±2.3% and 71.0±2.1%. 5-yr EFS and OS were 82.3±4.8% and 86.7±4.2% among pts with stage 3 disease (n = 110). EFS but not OS was superior for those with a CR/VGPR pre-ASCT vs. PR (5-yr EFS: 64.2±2.2% vs. 55.4±3.2%, p = 0.0133; OS: 72.7±2.1% vs. 70.5±2.9%, p = 0.3811). There was a trend toward improved OS for those treated with tandem vs. single transplant (5-yr EFS: 65.9±4.3% vs. 60.4±2.1%, p = 0.1282; OS: 76.5±3.8% vs. 71.2±1.9%, p = 0.0704). Grade ≥3 toxicities ( &gt; 10% of pts) during GM-CSF and IL-2-containing cycles, respectively, included pain (15.6/11.4%), fever (15.1/32.7%), anemia (18.9/21.7%), thrombocytopenia (13.9/17.4%), lymphopenia (12.3/16.0%), and hypokalemia (13.3/25.2%). Additional Grade ≥3 toxicities ( &gt; 10% of pts) included hypoxia (10.1%) during GM-CSF-containing cycles, and anaphylaxis (12.0%), neutropenia (16.1%), hyponatremia (16.5%), and hypotension (13.8%) during IL-2-containing cycles. Conclusions: In this large cohort of HRNBL pts treated with immunotherapy, 5-yr EFS was 61.1%. Superior EFS was observed for pts with stage 3 disease and for those with CR/VGPR pre-ASCT. IL-2-containing cycles were associated with increased toxicity. Clinical trial information: NCT00026312.
Developing South Asia’s first structured head and neck surgery multicenter fellowship initiative.
Authors: Shamit Chopra, Dushyant Mandlik, Deepak Balasubramanian, Vikram Kekatpure, Subramania Iyer, Jyoti Dabholkar, Kaustubh Patel
Journal: Journal of Clinical Oncology (2020)

11037 Background: Despite high head neck cancer incidence in South Asia, there exist few fellowship programs, which are limited by lack of structure, review processes and standard curricula. Our aim was a regionwide multicenter head and neck fellowship initiative to address the above limitations. Methods: A 10-member task force was constituted in January 2018 under the aegis of the Foundation for Head and Neck Oncology. First phase: Initial curriculum drafted by incorporating region-specific perspectives, aided by multiple source documents. Candidate eligibility criteria outlined, accommodating multiple pertinent disciplines and an international applicant base. Format for a structured entrance examination, and a mandatory/desirable rotation schedule were developed. Second Subcommittee(SC) phase: Creation of a web portal ( www.fhnofellowship.org ) by Outreach SC, approval of applicant centers by Accreditation SC, layout of exam structure by the Examination SC, and defining a rank order list-driven match process by the Match SC. Third phase: Development of standard documentation including suggested bibliography, log book format, recommended grand rounds topics, common minimum criteria for fellowship graduation. A common entrance exam was conducted in Feb 2019, which incorporated written screening, center-candidate interactions, objective interview, and the merit-based institution-fellow match. Results: Total number of applicants: 92, the majority Oral Maxillofacial Surgeons(83.7%). Seventeen fellows matched in the first cycle, the initial and 6-month program compliance 94.1% and 88.2% respectively. More eligible institutions accredited(36.8% increase) prior to the second cycle in Nov 2019, during which 19 fellows(11.8% increase) were matched. An interim review was done in Oct 2019, and periodic reviewing set at 6-month intervals. Planned fourth phase: Objective center/candidate feedback, surgical video repository, online training schedule, develop the fellowship exit examination, and expand outreach to other countries. Conclusions: Owing to high head neck cancer incidence in the subcontinent, anatomic complexity, need to balance outcomes/toxicities and requirement of expert multidisciplinary care; structured head neck fellowship training is imperative. Despite inherent challenges of concept and implementation in a diverse multicultural resource-limited setting, we foresee the application of region-relevant perspectives helping us achieve the objective of furthering subspecialty head neck training in South Asia.
Neutrophil to lymphocyte ratio and monocyte to lymphocyte ratio in early pregnant women with hypertensive disorders
Authors: Jie Gao, Mei Luo, Wei Ma
Journal: BMJ (2019)

Objective
To investigate the correlation of systemic inflammation parameters including neutrophil to lymphocyte ratio (NLR) and monocyte-lymphocyte ratio (MLR) with the pregnancy outcome of hypertension disorders of pregnancy.


Methods
Two hundred and twelve pregnant women in first-trimester with hypertensive disorders and 212 matched healthy subjects (control group) were enrolled in the study. The differences in white blood cell count (WBC), neutrophil (N), lymphocyte (L), monocyte (M), NLR and MLR were compared between groups.


Results
The WBC, N, M, NLR and MLR values were significantly higher in pregnant women with hypertensive disorders than those in healthy controls (9.1×109/L vs.8.5×109/L,Z=4.89, P 0.05). Multivariate logistic regression analysis showed that NLR was a predictive factor of hypertensive disorders of pregnancy (OR=1.68, 95%CI: 1.07-2.62, P<0.05).


Conclusions
NLR might be a useful systemic inflammation marker for the prediction of hypertensive disorders in women with early pregnancy.


Key words: 
Hypertension, pregnancy-induced; Neutrophil to lymphocyte ratio; Monocyte to lymphocyte ratio
Patient journey and quality of life (QOL) among diffuse-type TGCT in the U.S.
Authors: Nicholas M. Bernthal, Geert Spierenburg, Michiel van de Sande, John H. Healey, Silvia Stacchiotti, Sebastian Bauer, Hans Gelderblom, Eric Staals, Julio López Bastida, Eva-Maria Fronk, Xin Ye, Petra Laeis, Emanuela Palmerini
Journal: Journal of Clinical Oncology (2020)

e23565 Background: Diffuse Tenosynovial Giant Cell Tumor (d-TGCT) is a rare, locally aggressive neoplasm of joint and tendon sheath synovia, which may severely affect patients (pts) QOL due to pain, limited joint function and destruction of bone and local tissues. This study analyzes real-world data to describe d-TGCT pt journey and QOL in the US. Methods: The TGCT Observational Platform Project (TOPP), the first non-interventional prospective disease registry, enrolled d-TGCT pts at 10 Western European (EU) and 2 US sarcoma centers from Nov 2016 to Mar 2019, with prospective follow-up of 24 mo. Pts demographics, disease history and ongoing medical treatment and pt-reported outcomes (PROs) (pain, stiffness, PROMIS Physical Function [PF] and EQ-5D) were collected at baseline and every 6 mo during follow-up periods. Descriptive analyses from baseline compared US pts with Western EU pts (Table). Results: Of 166 d-TGCT pts, 30 were enrolled in the US. Mean age was 40.6 ± 12.82 y, with 63.3% female and 66.7% with tumor in knee. Median time from first symptom to diagnosis was 12 mo (range; 0–153). 28 pts (93.3%) had surgery, 4 pts (13.3%) had tyrosine kinase inhibitors (TKI), no pts had radiotherapy. 18 pts (60%) experienced &gt;1 locoregional recurrence. Median Pain Severity Score (PSS) and Pain Interference Score (PIS) were 2.8 and 3.0, respectively. Median PROMIS PF Score was 39.8. Mean EQ-5D index score and visual analogue scale (VAS) were 0.73 ±0.229 and 75.5 ±13.31, respectively. Compared with Western EU pts, US pts reported similar PROs and QOL, were younger, had shorter delay in diagnosis, and lower use of systemic therapy or radiotherapy (Table). Conclusions: d-TGCT affects a relatively young population in the US, similar to Western EU, resulting in serious impairment in daily activities and QOL. Shorter diagnostic delay and less frequent use of non–surgical approach was observed in the US. [Table: see text]
Characterization of MET exon 14 skipping in Chinese non-small cell lung cancer (NSCLC) patients.
Authors: Baihua Zhang, Yu Xia, Jiujin Zhang, Jin Yu, Min Chen, Wei Yao, Juan Zhao, Jiqiang He, Tony S. K. Mok, Kai Wang
Journal: Journal of Clinical Oncology (2020)

e21525 Background: MET exon 14 skipping ( METex14) has been identified as a precise biomarker for MET-targeted therapy. Most METex14 alterations occur in patients (pts) with non-small cell lung cancer (NSCLC). Here, we present the clinical, pathological, and genomic characteristics of Chinese NSCLC pts harboring METex14. Methods: Formalin-fixed, paraffin-embedded (FFPE) tumor and matched blood samples from 3433 pts were collected from December 2017 to January 2019 for a 450 cancer gene targeted next-generation sequencing (NGS) panel. Genomic alterations (GAs) including single nucleotide variations, short and long insertions/deletions (Indels), copy number variations, and gene rearrangements were assessed. The testing was carried out by a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory. Results: A total of 35 (1.0%) pts harbored the GAs predicted to cause METex14, which was lower than that of the Western population (3%), and comparable to data in previously reported Chinese NSCLC pts. METex14 mutation rates were 10.5% in sarcomatoid carcinoma, 1.5% in adenosquamous carcinoma and 1.0% in adenocarcinoma. The median age of pts with METex14 was 65 years (range 46-85) and 46% were female. Compared with wild-type (WT) pts, those harboring METex14 were significantly associated with older age (median age: 65 vs. 60 years, respectively, p = 0.005) and earlier stage (stage I &amp; II ratio: 67.7% vs 42.0%, respectively, p &lt; 0.0001). METex14 alterations included 17 samples (48.6%) that were base substitutions located on the non-coding adjacent splice acceptor (1), donors (7), and other splice acceptors (9), and 18 (48.6%) Indels located on the non-coding adjacent splice acceptors (8), donor (1), other splice acceptor (1), and exon/intron junctions (7). MDM2, FRS2, and CDK4 amplification was observed in 22.9%, 20.0%, and 17.1%, respectively, of pts with METex14, which was significantly higher than in WT pts (P &lt; 0.001). Concurrent EGFR mutations were rarely observed with METex14 compared with WT pts (8.6% vs. 51.7%, respectively, p &lt; 0.0001). Concurrent MET amplification was identified in 3 samples with METex14, and no other driver genes were found. Conclusions: METex14 occurred in 1.0% of Chinese NSCLC pts and showed a significantly higher prevalence in sarcomatoid carcinoma. METex14 observed in pts with NSCLC were associated with increased concurrent MDM2, FRS2, and CDK4 amplification and decreased EGFR mutation, suggesting that METex14 acts as a driving oncogenic factor in NSCLC.
Evaluation of prescribing practices of denosumab and zoledronic acid in breast and prostate cancer patients at University of Chicago Medicine.
Authors: Heng Yang, Randall W Knoebel, Sandeep Parsad, Emma Carroll, Walter Michael Stadler
Journal: Journal of Clinical Oncology (2020)

e24144 Background: Zoledronic acid (ZA) and denosumab are both bone-modifying agents (BMAs) approved for use in patients with bone metastases with breast or prostate cancer as well as patients who are receiving aromatase inhibitors (breast cancer) or androgen deprivation therapy (prostate cancer). There are various frequencies of administration, doses, and duration of these agents depending on indication and extent of disease. Currently there is data to show that ZA can be given every 3 months in patients with metastatic breast and prostate cancer, however, there is no data that clearly indicates that denosumab every 3 months is non-inferior to every 28 days. This study aimed to analyze current prescribing patterns of ZA and denosumab in metastatic breast cancer and metastatic castration resistant prostate cancer patients at The University of Chicago Medicine (UCM). Methods: This was a retrospective study of 80 patients who received at least one dose of ZA or denosumab between July 1 st 2018 to June 30 th 2019 from UCM outpatient oncology clinic for the purpose of treating metastatic breast cancer or metastatic castration resistant prostate cancer in conjunction with standard antineoplastic therapy. All included patients must have bone metastases. Patients were divided into four groups by disease state (breast or prostate cancer) and BMA agent (ZA or denosumab). The primary outcome was BMA therapy adherence rate, which was defined by those who received greater than or equal to 80% of appropriately scheduled doses. Descriptive statistics were used for skeletal-related events (SREs) and BMA associated adverse effects. Results: Patients who received ZA achieved higher adherence rates (100% breast, 86% prostate) compared to patients that received denosumab (63% breast, 23% prostate). The most common reason for the lower adherence rate in denosumab groups was scheduling convenience. During the study period, there were 3, 0, 2 and 5 patients had SREs in the above four groups respectively. The predominant adverse event across all groups was hypocalcemia and two patients with prostate cancer on denosumab developed osteonecrosis of the jaw. The cost analysis showed using ZA as primary BMA agent might save up to 2.5 million dollars per year at UCM. Conclusions: The use ofZA was associated with higher adherence rates compared to denosumab. Implementing a pharmacy driven protocol for ZA use for patients with metastatic breast and prostate cancer may improve BMA regimen adherence rates and significantly reduce costs.
Hepatitis B, preventive, treatable, but challengeable
Authors: 王永怡, 张玲霞
Journal: BMJ (2010)

1992年至1995年病毒性肝炎流行病学调查显示,我国原有慢性乙型肝炎病毒(HBV)感染者约1.2亿,约占全球3.5亿感染者的1/3.随着20世纪90年代乙型肝炎(乙肝)基因重组疫苗接种计划的实施,绝大多数新生儿在出生24 h内获得首针接种,2006年抽样调查公布,我国慢性HBV感染者已降到9300万人[1]。
异物致胃肠穿孔三例临床分析
Authors: 何玉成, 王皓晨, 肖兰华, 周海军, 黄忠雄
Journal: BMJ (2012)

回顾分析2008年8月至2011年4月我院收治的3例异物致胃肠穿孔病例,总结其临床及影像表现.3例中男性2例、女性1例,全部经手术证实,均以不明原因腹痛入院,术前CT可见穿透胃肠壁的高密度异物影。
A urine exosomal circRNA classifier for detection of high-grade prostate cancer at initial biopsy: A multicenter, retrospective study.
Authors: Liaoyuan Li, Wen Tao, Yadi He, Tao He, Qing Li, Zhenquan Wu, Weiming Deng, Lingxiao Zhang
Journal: Journal of Clinical Oncology (2020)

5522 Background: The low specificity of prostate-specific antigen (PSA) has resulted in the overdiagnosis and overtreatment of clinically indolent prostate cancer (PCa). We aimed to identify a urine exosomal circular RNA (circRNA) classifier that could detect high-grade (Gleason score [GS]7 or greater) PCa. Methods: We did a three-stage study that enrolled eligible participants, including PCa-free men, 45 years or older, scheduled for an initial prostate biopsy due to suspicious digital rectal examination findings and/or PSA levels (limit range, 2.0-20.0 ng/mL), from four hospitals in China. We used RNA sequencing and digital droplet polymerase chain reaction to identify 18 candidate urine exosomal circRNAs that were increased in 11 patients with high-grade PCa compared with 11 case-matched patients with benign prostatic hyperplasia. Using a training cohort of eligible participants, we built a urine exosomal circRNA classifier (Ccirc) to detect high-grade PCa. We then evaluated the classifier in discrimination of GS7 or greater from GS6 and benign disease on initial biopsy in two independent cohorts. We used the sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) to evaluate diagnostic performance, and compared Ccirc with standard of care (SOC) (ie, PSA level, age, race, and family history). Results: Between June 1, 2016, and July 31, 2019, we recruited 356 participants to the training cohort, and 442 and 325 participants to the two independent validation cohorts. We identified a Ccirc containing five differentially expressed circRNAs (circ_0049335, circ_0056536, circ_0004028, circ_0008475, and circ_0126027) that could detect high-grade PCa. Ccirc showed higher accuracy than SOC to distinguish individuals with high-grade PCa from controls in both the training cohort and the validation cohorts. (AUC 0.831 [95% CI 0.765-0.883] vs 0.724 [0.705-0.852], P = 0.032 in the training cohort; 0.823 [0.762-0.871] vs 0.706 [0.649-0.762], P = 0.007 in validation cohort 1; and 0.878 [0.802-0.943] vs 0.785 [0.701-0.890], P = 0.021 for validation cohort 2). In all three cohorts, Ccirc had higher sensitivity (range 71.6-87.2%) and specificity (82.3-90.7%) than did SOC (sensitivity, 42.3-68.2%; specificity, 40.1-62.3%) to detect high-grade PCa. Using a predefined cut point, 202 of 767 (26.3%) biopsies would have been avoided, missing only 6% of patients with dominant pattern 4 high-risk GS 7 disease. Conclusions: Ccirc is a potential biomarker for high-grade PCa among suspicious men.
甲状腺峡部癌19例诊治分析
Authors: 童彦初, 杨辉
Journal: BMJ (2011)

甲状腺峡部占位病变较为常见.我院自2003年6月至2010年7月共收治120例,其中甲状腺峡部癌19例,约占15.8％,现对其临床资料做同顾性分析,报告如下.一、临床资料1.一般情况:19例中,男3例,女16例,年龄20～ 65岁,平均37岁.因发现颈前无痛性包块就诊,无怕热、多汗、心慌,无畏冷、乏力,其中1例男性患者并左侧颈部淋巴结明显肿大,1例女性患者并右侧颈部淋巴结明显肿大,1例女性患者颈部呈环形增粗质硬包块,呈冰冻状,有声嘶、吞咽和呼吸困难,瞳孔缩小、眼裂变窄、一侧面部无汗等Honer综合征的临床表现. 关键词：甲状腺肿瘤