tbuckley/cabot-search huggingface dataset:
Systematic analysis of extracting data on advance directives from patient electronic health records in terminal oncology patients.
Authors: William Paul Skelton, Jason Scott Starr, Kiarash Rahmanian, Robert Guenther, William L. Allen, Thomas J. George, Ray E. Moseley
Journal: Journal of Clinical Oncology (2020)

e24011 Background: Advanced care planning and living wills are critical components of caring for patients at the end of their lives. Advance directives are designed to be implemented when a patient meets the legal definition of terminal and is deemed incapacitated. By reviewing the electronic health record (EHR) in patients with terminal cancer, we sought to evaluate whether advance directives were appropriately implemented. Methods: A retrospective analysis of the EHR of 500 cancer patients from 1/1/2013 to 12/31/2016 was performed. Data points were manually collected and entered in a central database, and data analysis was completed using SAS. Results: Of the 500 patients, 160 (32%) had an advance directive (AD). The most common clinical terminology used by physicians indicating a terminal diagnosis was “progressive” (36.6%) and “palliative” (31%). The most common clinical terminology indicating incapacity was “altered mental status” (25.6%), and “not oriented” (14%). 34 patients (6.8%) met all criteria of having a terminal diagnosis, a documented AD, and deemed incapacitated. Of these patients who met all of these data points, their ADs were implemented on average 1.7 days (SD: 4.4 days) after which they should have been. This resulted in a total of 58 days of additional care provided to these patients. Conclusions: End-of-life care is a challenging albeit vital part of the practice of medicine. This study provided insight on to how ADs are managed in day to day practice in a hospital. From our analysis, it is clear that physicians are able to identify when a patient is terminal; however, it is typically later than it should have been recognized (and thereby, leading to delays in the implementation of the patient’s AD). Further studies should be performed focusing on harnessing the power of the EHR and providing physicians formative and evaluative feedback of practice patterns to ensure that ADs are honored when appropriate.
Impact of travel distance on timeliness of adjuvant chemotherapy in veterans with colorectal cancer.
Authors: Richard Lewis Martin, Gretchen C. Edwards, Lauren R. Samuels, Cathy Eng, Christianne L. Roumie
Journal: Journal of Clinical Oncology (2020)

e19159 Background: Rural patients have well described disparities in quality cancer care. The VA Budget and Choice Improvement Act (2015) and VA Mission Act (2018) were passed to increase timely access to cancer care for veterans living at greater distances from VA facilities by paying for community oncology care. We sought to evaluate the baseline timeliness of adjuvant colorectal cancer (CRC) chemotherapy among patients living at increased distances from the Veterans Health Administration Tennessee Valley Healthcare System (VHA-TVHS) to determine local metrics for quality improvement initiatives. Methods: We reviewed 1,107 electronic medical records of patients with colorectal surgeries from January 1, 2000 to December 31, 2015 at the VHA-TVHS. We included patients with NCCN eligible pathologic high-risk stage II (T4/perf, R1, &lt; 12LN, LVI) or stage III CRC and excluded those age ≥80, age ≥75 hospitalized in the prior year with a major co-morbidity, and death or hospice within 30 days of surgery. Primary exposure was travel distance from central zip code of patient residence to VHA-TVHS, categorized &lt; 50 miles (N = 64), 55-99 miles (N = 60), and ≥ 100 miles (N = 56) to account for changes in referral patterns. Outcomes were days from surgery to first chemotherapy treatment and achieving a VHA timeliness standard of 56 days. Eligible patients not receiving chemotherapy were capped at 120 days per Commission on Cancer standard. Results: Of 1,107 colorectal resections, we excluded 623 for non-cancer, 212 for stage I or low risk stage II, 47 for metastases, and 45 for age, co-morbidity, death, and hospice, yielding a final cohort of 121 colon and 59 rectal cancer patients. Patients were predominantly male (96%), white (79%), and median age 64 years [Interquartile Range 60, 70]. Median days to chemotherapy were 62.5 days [48.5, 120] for those who lived &lt; 50 miles, 58.5 days[46.5, 120] for distance 50-99 miles, and 84 days [50.5, 120]) for distance ≥ 100 miles. There were only 41%, 48%, and 32% in each distance group meeting the 56-day standard, respectively. Adjusting for known correlates, time to chemotherapy was 10.6 days longer for patients living ≥ 100 miles compared to &lt; 50 miles (p = 0.08). Conclusions: Distance to care may influence timeliness of chemotherapy among southeast regional veterans. Given the observed overall low rate of timely chemotherapy, understanding modifiable health system factors associated with omissions and delays, as well as the impact of recent VA legislation merits further exploration.
Long-term proteasome inhibition in US community multiple myeloma (MM) patients (pts) following in-class transition (iCT) from parenteral bortezomib (V) to oral ixazomib (I): Updated real-world (RW) data from US MM-6.
Authors: Saulius Kazmiems Girnius, Habte Aragaw Yimer, Sudhir Manda, Christopher A. Yasenchak, Veena Charu, Roger M. Lyons, Suman Kambhampati, Reumu E. Birhiray, Haresh S. Jhangiani, Ralph V. Boccia, Presley Whidden, Kim Bogard, Dasha Cherepanov, Stephen Joseph Noga, Robert M. Rifkin
Journal: Journal of Clinical Oncology (2020)

e19332 Background: US MM-6 is investigating iCT from parenteral V-based induction to all-oral I-lenalidomide-dexamethasone (IRd) with the aim of increasing proteasome inhibitor (PI)-based treatment adherence/duration while maintaining quality of life (QoL) &amp; further improving outcomes in the diverse US community population. Methods: 21 US community sites, including VA hospitals, are enrolling non-transplant-eligible newly diagnosed MM pts with ≥stable disease after 3 cycles of V-based therapy to receive IRd. Pts use mobile &amp; digital devices to collect actigraphy (activity/sleep) data, complete QoL &amp; treatment satisfaction questionnaires, &amp; self-report medication adherence. Primary endpoint: progression-free survival (PFS); key secondary endpoints include: response rates &amp; duration of therapy. Results: As of Nov 18, 2019, 84 pts had been treated (median age 73 [range 49–90] yrs; 44% ≥75 yrs; 49% male; 15% black/African American; 10% Hispanic/Latino; 35% International Staging System stage III disease; 42% lytic bone disease). Comorbidities included hypertension (57%), anemia (44%), fatigue (43%), &amp; peripheral neuropathy (13%). 85% of pts were receiving VRd at the time of iCT. 62% of pts are still on therapy &amp; enrollment is ongoing. After initiating iCT, ≥complete response (CR) rate increased from 4% to 26% (Table). At 8 mos median follow-up, 6 pts had progressed &amp; there were 2 on-study deaths. The 12-mo PFS rate was 86% (95% CI, 73–93) from the start of V-based regimen &amp; from the start of IRd. During IRd treatment, 92% of pts had treatment-emergent adverse events (TEAEs) (48% grade [G] ≥3). G3 TEAEs (≥5% of pts) were diarrhea (7%), pneumonia (6%), syncope (6%), &amp; anemia (5%). TEAEs led to study drug discontinuation in 7% of pts; 36% had serious TEAEs. I/R/d dose was adjusted due to AEs in 39%/39%/29% of pts. Medication adherence (cycles 1–5) was ‘excellent’/‘very good’ in ≥78% of pts reporting adherence. QoL/treatment satisfaction were maintained in pts completing questionnaires. Actigraphy data showed normal activity levels &amp; sleep durations. Conclusions: US MM-6 pts are representative of the RW US MM population &amp; results show that iCT to an oral PI may permit prolonged PI-based therapy with promising efficacy &amp; without impacting pts’ QoL or treatment satisfaction. Clinical trial information: NCT03173092 . [Table: see text]
Case series of acute arthritis during COVID-19 admission
Authors: María-del-Carmen López-González, Maria Luisa Peral-Garrido, Irene Calabuig, Ernesto Tovar-Sugrañes, Vega Jovani, Pilar Bernabeu, Raquel García-Sevila, Jose-Manuel León-Ramírez, Oscar Moreno-Perez, Vicente Boix, Joan Gil, Esperanza Merino, Paloma Vela, Mariano Andrés
Journal: Annals of the Rheumatic Diseases (2020)

The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has changed life significantly worldwide. Rheumatologists also had to get used to the new context, prioritising remote over in-person consultations or solving doubts and giving advice to our immunocompromised patients. Besides, international collaborations have provided opinions concerning decisions that may affect people with rheumatic diseases; for instance, a major provision and use of hydroxychloroquine for COVID-19 might lead to a shortage for patients with lupus or rheumatoid arthritis, as Graef and colleagues point out in their recent viewpoint.1 

In areas of higher impact of the outbreak, as occurred in Spain, some of us have collaborated with colleagues from respiratory medicine and infectious diseases within multidisciplinary teams to face COVID-19. A collateral advantage has been the …
Tumor sequencing aids to identify individuals with hereditary cancer.
Authors: Teresa Imizcoz-Fabra, Eva Cañada-Higueras, Nerea García de Vicuña-Bilbao, Beatriz Ramírez-Horcada, Arancha Bielsa-Colás, Maria Isabel Mora, Javier Ursúa-Noain, Olga Prat-Barásoain, Marta Abengozar, Gorka Alkorta-Aranburu, Maite Herraiz
Journal: Journal of Clinical Oncology (2020)

e13678 Background: Early identification of individuals with hereditary cancer significantly improves survival in patients and relatives. New genomic tools can identify germline pathogenic variants via tumor-only genomic sequencing in addition to treatment guiding biomarkers. Methods: Our tumor sequencing protocol in medical practice since 2018 via Oncomine Comprehensive Assay (OCA) interrogates several hereditary cancer associated genes; therefore, we aimed to evaluate OCA’s capacity to point out individuals’ with hereditary cancer. But first, OCA’s technical validity was evaluated by testing up to 20 year old FFPE block isolated tumor genomes of individuals known to carry 19 pathogenic variants. Results: All variants were present in the OCA raw dataset but 26% were not called by the commercial software due to specificity of the variant calling algorithm and bias caused by amplicon-based enrichment and limited coverage. Even with this limitation, OCA’s clinical utility was evaluated next. A pathogenic variant candidate to be germline was identified in 5% (26/510) of tumor genomes routinely tested looking for treatment guiding biomarkers, but up to 8% (26/317) when excluding lung cancer patients. Importantly, 73% (14/19) of the ones that were followed-up by peripheral blood testing were confirmed to be germline, so inherited nature of the cancer was confirmed in 9% of ovarian, 8% of endometrium, 5% of biliary tract, 4% of breast, 1% of colorectal and 1% of lung cancer patients whose tumor genome was tested for routine treatment guiding biomarker identification. Conclusions: OCA is a useful genomic tool for identifying individuals with hereditary cancer that opens a new era in clinical practice in oncology. An increased awareness among physicians about this new genomic tool includes understanding the importance of peripheral blood confirmation to define the germline nature of the OCA-identified candidate variant; and proper genetic counseling and germline testing when OCA does not find a candidate variant in a patient with strong family history due to the lack of comprehensive identification of every type of pathogenic variants in all known genes associated with inherited cancer via tumor sequencing tools like OCA.
Phenotyping clinical trial treatment regimens in cancer: An integrative ontology, artificial intelligence and knowledge engineering approach.
Authors: Yun Mai, Kyeryoung Lee, Zongzhi Liu, Zhiqiang Li, Scott Jones, Meng Ma, Marc Fink, Krish Ghosh, Rong Chen, Eric Schadt, Xiaoyan Wang
Journal: Journal of Clinical Oncology (2020)

e14054 Background: Matching clinical attributes (i.e. indications, lab tests, treatment regimens) of clinical trial eligibility criteria with real world patient data is extremely challenging. Attribute phenotyping is one of the key components of Trial2Patient, a customized system developed by Sema4 to find patients for clinical trials. Transforming treatment regimens to a standard ontology and encoding drugs with standard nomenclatures will facilitate the semantic retrieval of treatments mentioned in clinical trial criteria. This will also enable the interoperation between different data sources that is often required for fast-learning and scalable healthcare information system. Methods: Free text containing treatment regimen/medication terms were extracted and preprocessed from three sources: 1) clinical trials listed in a commercial database citeline.com, 2) clinical trials listed in clinicaltrials.gov, and 3) National Comprehensive Cancer Network (NCCN) Guidelines. The regimen terms such as neoadjuvant therapy for non-small cell lung cancer, checkpoint inhibitor, EGFR inhibitor, androgen deprivation therapy (ADT), among many others, were profiled by AI methods (i.e. pattern reorganization and rule-based) and knowledge engineering via Sema4’s in-house knowledge base (CAV), Pharmaprojects in citline.com and NCCN Guidelines. The drugs related to each regimen were identified and mapped to RxCUI via RxNorm ontology. Results: We identified 76 regimen terms for non-small cell lung cancer (NSCLC), small cell lung cancer (SCLC) and prostate cancer (e.g. PD-L1 ≥1% nonsquamous NSCLC, bone antiresorptive therapy for M1 castration resistant prostate cancer), and 14,476 drug-category pair (e.g. pembrolizumab is a PD-1 inhibitor, pembrolizumab is used as the third line and beyond systemic therapy for M1 CRPC). All drugs identified were mapped to RxCUI for real world patient matching. Conclusions: This approach systematically extracted and normalized regimens and medications mentioned in clinical trials in NSCLC, SCLC and prostate cancer to standard codes. These standardized data can be used in mapping treatment histories of a patient to the eligibility criteria for clinical studies or for identifying studies relevant to a patient. The outcome of profiling cancer treatment regimens through standard ontology RxNorm may be particularly valuable in cancer studies based on real-world evidence.
Use of iodixanol incoronary intervention for patients with diabetic renal insufficiency
Authors: 柳弘, 吕树铮, 陈韵岱, 吴小凡, 周渊, 葛长江
Journal: BMJ (2007)

目的 评价应用碘克沙醇对糖尿病伴肾功能异常患者进行冠状动脉(冠脉)介入治疗的安全性.方法分析2004年6月至2006年6月进行冠脉介入治疗的糖尿病伴肾功能异常患者97例的临床资料,其中50例应用等渗造影剂碘克沙醇(碘克沙醇组),47例应用低渗造影剂碘普罗胺(碘普罗胺组).通过冠脉造影发现病变血管167支,其中前降支65支,回旋支44支,右冠脉58支.全部病例于术前、手术当天及术后第3、7天测定血清肌酐、尿素氮水平,并观察造影剂1肾病的发生情况.结果167支病变血管植入192个支架,成功率100%.无急性、亚急性血栓形成及主要心脏不良事件发生.术后全部患者心绞痛症状消失.碘克沙醇组有2例发生造影剂肾病(4%),碘普罗胺组有10例(21%),两组差异有统计学意义(P＜0.01).经血液透析治疗,连续临床随访3个月,全部病例存活,无肾功能恶化及心绞痛症状发生.结论选择等渗造影剂碘克沙醇对糖尿病伴肾功能异常患者进行冠脉介入治疗安全,可减少造影剂肾病的发生。
遗传性出血性毛细血管扩张症致黑便一例
Authors: 王慧, 崔维刚, 付金栋, 刘金贤, 王玲, 刘京营
Journal: BMJ (2011)

患者男,44岁,因“间断黑便5年,加重伴头晕20余天”入院.患者5年前无明显诱因出现黑便,为黑色成形软便,呈间断性,无腹痛,无呕血,近5年未觉明显不适,未就诊.入院前20余天患者黑便加重,每日排黑便1～2次,量不定,稀软不成形,自觉头晕,乏力加重,无鼻衄及齿龈出血,无皮肤出血,遂来我院就诊.既往有长期牙龈出血史,无鼻衄史.个人吸烟10余年,10支/d;偶有饮酒.家族无鼻衄史、无消化道出血史,经严格调查无遗传性出血性毛细血管扩张症家族史. 关键词：毛细血管扩张;遗传性出血性
Knockdown of KREMEN2 inhibits tumor proliferation and metastasis in gastric cancer.
Authors: Beibei Chen, Saiqi Wang, Jinxi Huang, Jitian Li, Jianying Zhang, Weifeng Xu, Huifang Lv, Caiyun Nie, Jianzheng Wang, Yingjun Liu, Xiaobing Chen
Journal: Journal of Clinical Oncology (2020)

e16555 Background: KREMEN2 is an important regulator of classical Wnt/β-catenin signaling pathway. However, the relationship between KREMEN2 and gastric cancer is not clear. The aim of this study was to explore the regulatory role of KREMEN2 in the tumorigenesis and metastasis of gastric cancer. Methods: We measured the protein level of KREMEN2 in 156 gastric adenocarcinoma, 40 metastatic gastric adenocarcinoma, 8 marginal and 4 normal tissues using tissue microarray. The differences in KREMEN2 expression were tested with Mann-Whitney U test. The relationship between KREMEN2 expression and pathologic data was determined with Pearson’s correlation analysis. The mRNA and protein level in cultured cell lines were detected by qRT-PCR and western blotting, respectively. Lentivirus was transfected by repressing KREMEN2. Cell viability was determined by the MTT assay. Apoptosis and cell cycle distribution were detected using flow cytometry. The cell migration was investigated by wound healing and transwell assay. Antibody array was performed to explore the underlying molecule mechanism. In vivo, Xenograft assay was established using nude mice to explore the role of KREMEN2 in gastric cancer cell and bioluminescence was observed via an in vivo imaging system. Results: It was demonstrated that, compared to para-cancerous tissues, KREMEN2 was significantly up-regulated in gastric cancer tissues, and was positively correlated with the pathological grade of gastric cancer patients. Given that KREMEN2 is abundantly expressed in most tested gastric cancer cell lines, KREMEN2 knockdown cell models were established and further used to construct mice xenograft model. After knocking down KREMEN2, the proliferation of gastric cancer cells was inhibited both in vivo and in vitro. At the same time, knockdown of KREMEN2 induced apoptosis, cell cycle arrest at G2/M phase and inhibition of migration in gastric cancer cells in vitro. Mechanistically, we found that knockdown of KREMEN2 suppressed PI3K/Akt pathway. Conclusions: Therefore, we revealed that the overexpression of KREMEN2 in gastric cancer may promote the carcinogenesis and metastasis of gastric cancer by activating the PI3K/Akt pathway.
Unplanned hospital admissions are a marker of decreased overall survival in patients with solid tumor malignancies.
Authors: Zachary L. Quinn, Maria Vershvovsky, Alexander Xu, Allison M. Zibelli
Journal: Journal of Clinical Oncology (2020)

e19118 Background: For patients being treated for solid tumor malignancies, an unplanned hospitalization is a significant event that may help predict outcomes. Prior studies have demonstrated a 1 year mortality rate as high as 73% for oncology patients following an unplanned admission. As our therapies continue to improve, better understanding of the significance of acute hospitalizations is needed to help influence management decisions for oncology providers. Methods: We conducted a retrospective review of all patients admitted to a solid oncology inpatient service at Thomas Jefferson University Hospital (TJUH) who were discharged between January 1 st and March 31 st 2019. We excluded all patients who had not established care with a provider at TJUH prior to the index admission. We collected data on age, sex, length of stay (LOS), diagnosis, treatment activity, ECOG performance status (PS), 30 day and total re-admissions, survival and whether hospice was discussed during index admission. We censored data at 180 days after date of index discharge. We evaluated overall survival (OS) using the Kaplan-Meier method and compared survival to 30-day readmission and ECOG status using a log-rank test. Results: During our investigational time period there were 263 discharges, which yielded a study population of 182 patients. Median LOS was 5 days and 55% of patients were female. Gastrointestinal and genitourinary cancers were the most prevalent, observed in 32% and 28% of patients respectively. 75% of patients were on active treatment at time of admission. Survival data was available in 174 patients and at 6 months, OS was found to be 47%. 35% of patients were readmitted within 30 days of their index discharge. Patients readmitted within 30 days had a significantly lower OS than patients without a readmission (31% vs. 56%, P = 0.002). 70% of patients had a PS of 0 or 1 prior to index admission and OS in this group was significantly better in comparison to patients with a higher ECOG score (57% vs. 33%, P = 0.001). Hospice was discussed with 31% patients during index admission. Conclusions: We observed a 6 month overall survival of 47% following an unplanned admission and this was lower for patients that were re-admitted within 30 days. Higher PS scores predicted worse outcomes; however, the majority of patients had a favorable PS prior to index admission. This study suggests that following an unplanned admission, oncology patients are at elevated risk for poor outcomes and that providers should reassess goals of care at follow up clinic visits.
Minimally invasive Nuss procedure for pectus excavatum repair in 7 patients
Authors: Hong-can Shi, Chao Sun, Yu-sheng Shu, Wei-ping Shi
Journal: BMJ (2008)

This study retrospectively analyzed 7 patients with severe pectus excavatum who underwent thoracoscope-assistant Nuss procedure from July 2006 to June 2008.All the participants were followed up for 1 to 24 months(mean,15.7 months).No intraoperative or postoperative complications were found in any of the patients.The operating time was 40 to 55 minutes.Mean hospital stay was 5 days (range,4 to 7days).Our experience with the minimally invasive repair of pectus excavatum might be encouraging.thoracoscope-assistant Nuss could effectively treat pectus excavatum in children,associated with minimal invasion,lower morbidity,less hospital stay,and considerable improvement in physiologic and psychological function.

Key words: 
Funnel chest; Thoracic surgery,video-assisted
Monitoring early clearance of circulating tumor DNA as an effective tool to predict clinical benefits of immune checkpoint inhibitors in lung cancer patients: The preliminary results from clinical trial NCT04203095.
Authors: Di Zheng, Jian Ni, Yi Zhong, Qian Ziliang, Baiyun Wang
Journal: Journal of Clinical Oncology (2020)

e15056 Background: Immuno-checkpoint inhibitors (ICI)is the stand-of-care of lung cancer treatment nowadays. But it’s still challenging to find an effective biomarker to predict clinical benefits from ICIs. Early data suggested that monitoring early clearance of circulating tumor DNA (ctDNA) as a tool to predict clinical benefits. Here we started a clinical trial (NCT04203095) to further validate it. Methods: 19 advanced non-small cell lung cancer patients who were planned to be treated with ICIs with or without chemotherapy were recruited consecutively since April 2019 ( NCT04203095 ). Clinical response was evaluated by RECIST 1.1 assessments at 12 weeks of treatments and afterward during 3-month interval visiting in the first year. Fresh plasma samples were collected -1 (before),+3 weeks and +12 weeks after the first dose. Plasma cell-free DNA(cfDNA) was send to low-coverage whole genome sequencing, followed by chromosomal instability (CIN) analyses by a customized workflow (UCAD). CIN scores were calculated by summarizing the copy number variations genome wide. Results: Early clearance of ctDNA was defined as Pearson correlations co-efficiency of copy number variations of cf DNA was below 0.65 between the baseline and 3 weeks after ICIs were administered. These 19 patients included 11 squamous cell carcinoma (SCC) and 8 adenocarcinomas. 8 of 11 respoonding patients showed early clearance of ctDNA, and 7 of 8 patients with SD or PD didn’t obtain early clearance of ctDNA. Meanwhile, clinical stage, histology, treatments (PD1 single or PD1+chemo combinations), sequence of treatment (first line, second line or multiple lines) did not predict clinical response, and baseline CIN score was not significantly correlated with clinical responses. In summary, only ctDNA early clearance was statistically significantly associated with clinical response (P = 0.020). Conclusions: Early clearance of plasma circulating tumor DNA at 3 weeks after treatments might be used a predictive biomarker of immune-checkpoint inhibition response. Clinical trial information: NCT04203095 .