tbuckley/cabot-search huggingface dataset:
Who gets a referral to oncologists and subsequent treatments for stages III and IV non-small cell lung cancer (NSCLC)?
Authors: Bernardo Haddock Lobo Goulart, Catherine R. Fedorenko, David G Mummy, David K Blough, Lisel Koepl, Sacha Satram-Hoang, Carolina M. Reyes, Scott David Ramsey
Journal: Journal of Clinical Oncology (2012)

6007 Background: We identified the physicians initially involved in the management of stages III and IV NSCLC, and explored associations of patient and their initial physician factors with referrals to oncologists and subsequent receipt of guideline-based therapies (GBTs) endorsed by the National Comprehensive Cancer Network. Methods: Using a retrospective cohort design, we identified patients with a new diagnosis of stages III and IV NSCLC from 01/01/2000 to 12/31/2005 included in the Surveillance, Epidemiology, and End Results-Medicare database. After collecting patient sociodemographic, tumor, and treatment data, we linked Unique Physician Identifier Numbers (UPINs) from Medicare claims to the American Medical Association Masterfile database to identify the initial physicians and subsequent referrals to cancer specialists, defined as surgeons, radiation oncologists and oncologists. We used logistic regression to explore associations between: 1) patient and initial physician independent variables with referrals to oncologists; 2) referrals to different combinations of cancer specialists with receipt of stage-specific GBTs, adjusted for confounders. The follow-up period was 12 months or up to 12/31/2006. Results: For 28,977 patients, mean age was 75 years, 53% were male, 83% were white, 51% had stage IV, 37% initially saw an internal medicine doctor, 84% saw at least an oncologist, 31% saw all 3 types of cancer specialists, and 44% received GBTs. Younger age, white race, stage IV, higher income, lower co-morbidity index, initial physicians other than family practice doctors, and referral to pulmonologists were associated with higher likelihood of referral to oncologists (P&lt;0.01 for all factors). Compared to those who saw only an oncologist, those who saw only a surgeon and/or a radiation specialist were less likely to receive GBTs (OR=0.3; 95%CI=0.3-0.4). Among patients who had no referrals or who saw specialties other than oncology, 14% received GBTs. Conclusions: Seeing an oncologist is a critical step in the standard treatment of advanced NSCLC. Yet, race, income, and the type of initial physician may constitute barriers of access to oncologists, which can result in substandard care.
THE PREVALENCE OF SUBCLINICAL LEFT VENTRICULAR SYSTOLIC DYSFUNCTION BY 3D-GLOBAL LONGITUDINAL STRAIN IN SOUTH ASIANS COMPARED TO WHITES EUROPEANS AND THE ROLE OF CENTRAL OBESITY: THE SOUTHALL AND BRENT REVISITED (SABRE) STUDY
Authors: Lamia Al Saikhan, Chloe Park, Therese Tillin, Jamil Mayet, Nish Chaturvedi, Alun Hughes
Journal: Journal of the American College of Cardiology (2020)
SEX-BASED DIFFERENCES IN RATES OF DEVICE REMOVAL FOLLOWING CARDIAC IMPLANTABLE ELECTRONIC DEVICE INFECTIONS: DATA FROM THE NATIONWIDE READMISSIONS DATABASE 2010 - 2014
Authors: Edward Cheng, George Thomas, James Edmund Ip, Christopher F. Liu, Steven Markowitz, Ilhwan Yeo, Luke Kim, Bruce Lerman, Jim Cheung
Journal: Journal of the American College of Cardiology (2020)
ARM EXERCISE ELECTROCARDIOGRAPHIC STRESS TESTING VERSUS REGADENASON MYOCARDIAL PERFUSION IMAGING AND EXERCISE TREADMILL TESTING FOR CLINICAL OUTCOME PREDICTION
Authors: Douglas Kyrouac, Anandita Kulkarni, Divya Kapoor, Jiafu Ou, C. William Balke, Hong Xian, Medhat Osman, Wade Martin
Journal: Journal of the American College of Cardiology (2020)
Integrating Mouse and Human Genetic Data to Move beyond GWAS and Identify Causal Genes in Cholesterol Metabolism
Authors: Zhonggang Li, James A. Votava, Gregory J.M. Zajac, Jenny N. Nguyen, Fernanda B. Leyva Jaimes, Sophia M. Ly, Jacqueline A. Brinkman, Marco De Giorgi, Sushma Kaul, Cara L. Green, Samantha L. St. Clair, Sabrina L. Belisle, Julia M. Rios, David W. Nelson, Mary G. Sorci-Thomas, William R. Lagor, Dudley W. Lamming, Chi-Liang Eric Yen, Brian W. Parks
Journal: Cell Metabolism (2020)
Impact of survival on health care charges during melanoma treatment.
Authors: Diana I. Brixner, Brandon Kyle Bellows, Arati Dahal, David D. Stenehjem
Journal: Journal of Clinical Oncology (2013)

e20043 Background: Treatment charges increase during the last year of life in patients with melanoma, but it remains unknown if charges differ between patients who die during treatment and survivors. The objective of this study was to examine annualized mean charges by melanoma survival status. Methods: The University of Utah Enterprise Data Warehouse was used to analyze patients ≥18 years with a diagnosis of melanoma identified by ICD-9 code (first diagnosis defined as index date) treated at the Huntsman Cancer institute (HCI) from 2002-2010. The HCI tumor registry was used to determine stage at diagnosis and other cancer diagnoses. Cause and date of death was captured from the Utah Population Database. Cancer-related (CR) and non-CR charges were assessed by ICD-9 codes from index date until death or end of the follow-up period, were weighted by the inverse probability of survival, and annualized. Generalized linear models (GLM) with gamma distribution and log link function were used to examine charges by survival status, adjusting for baseline characteristics including demographics, disease stage, and comorbidities. Results: A total of 1205 patients were included, of which 218 (18%) died. Compared to alive patients, deceased patients were older (60 vs. 56), more female (40% vs. 28%), more were diagnosed with stage IV disease (19% vs. 3%), and less with stage I disease (26% vs. 66%) (all p≤0.001). Mean unadjusted annualized charges were not significantly different between the two groups for CR charges (deceased $15,109 vs. alive $14,519; p=0.89), but non-CR charges were higher for deceased patients ($77,390 vs. $18,719; p&lt;0.001). GLM results indicated deceased patients, relative to survivors, had 59% higher annualized CR charges (p&lt;0.001) overall, with higher CR charges at stages I and II (86% and 76%, respectively; both p&lt;0.001), and lower CR charges at stage IV (-127%; p&lt;0.001). Death was associated with 154% higher annualized non-CR charges (p&lt;0.001) at stages I, II, III, and IV (210%, 167%, 119%, and 73%, respectively; all p&lt;0.05). Conclusions: When adjusting for confounders, deceased melanoma patients had higher charges overall compared to melanoma survivors. The exception was for decreased CR charges in stage IV, most likely related to earlier death.
ADDITIONAL PROGNOSTIC ROLE OF STRAIN WITH STRESS CARDIAC MAGNETIC RESONANCE
Authors: Marco Guglielmo, Laura Fusini, Giuseppe Muscogiuri, Andrea Baggiano, Francesca Baessato, Antonella Loffreno, Ludovica Danza, Elisabetta Tonet, Mauro Pepi, Gianluca Pontone
Journal: Journal of the American College of Cardiology (2020)
CHARACTERIZING AND QUANTIFYING MITRAL ANNULAR CALCIFICATION FOR PATIENT-PREDICTIVE MODELING IN THE ERA OF TMVR
Authors: Sophia Alexis, Talal Alzahrani, Omar K. Khalique, Annapoorna Subhash Kini, Samin K. Sharma, George D. Dangas, Rebecca T. Hahn, Susheel K. Kodali, Martin Leon, David Adams, Isaac George, Gilbert Tang
Journal: Journal of the American College of Cardiology (2020)
LONG-TERM EFFECTS OF ASPIRIN ON CARDIAC ALLOGRAFT VASCULOPATHY PROGRESSION AND ADVERSE OUTCOMES AFTER HEART TRANSPLANTATION
Authors: Rabea Asleh, Alexandros Briasoulis, Amir Lerman, Byron Smith, Camden Lopez, Naveen Pereira, Brooks Edwards, John Stulak, Walter Kremers, Alfredo Clavell, Richard Daly, Sudhir Kushwaha
Journal: Journal of the American College of Cardiology (2020)
Elective Termination of Pregnancy in Autoimmune Rheumatic Diseases: Experience From Two Databases
Authors: Michael D. Lockshin, Marta Guerra, Jane E. Salmon
Journal: Arthritis & Rheumatology (2020)

Objective To provide reference data regarding the frequency and safety of elective termination of pregnancy in women with autoimmune rheumatic diseases followed up in 2 referral databases. Methods Two large databases, one from an autoimmune rheumatic disease referral clinical practice with a known interest in pregnancy (the Barbara Volcker Center for Women and Rheumatic Disease [ BVC ]), and one from an observational study of systemic lupus erythematosus– and antiphospholipid antibody–associated pregnancies (Predictors of Pregnancy Outcome: Biomarkers in Antiphospholipid Antibody Syndrome and Systemic Lupus Erythematosus [ PROMISSE ]), were interrogated for histories of prior elective termination of pregnancy and complications related to incident pregnancy termination. Results Of women who had had prior pregnancies, 21.7% of 1,307 in the BVC database and 25.3% of 297 in the PROMISSE database gave histories of 1–5 prior elective terminations of pregnancy; BVC patients reported no flares or hospitalizable complications due to pregnancy termination. Of 674 incident pregnancies, termination for fetal or maternal reasons was recommended for 15 (2%); of these, 2 fetuses died before the procedure was carried out and 1 woman declined termination and, though gravely ill, successfully delivered. She died of cardiomyopathy 3 years later. Conclusion Many patients with autoimmune rheumatic disease undergo elective termination of pregnancy; few report complications. In medically indicated termination of pregnancy, there are no adverse signals of unusual complications or disease flare.
<i>Paulinia CUPANA</i> (PC) (GUARANÁ) dry extract for breast cancer (BC) women with HOT flashes (HFS): Results of a PILOT study.
Authors: Auro Del Giglio, Adriana Braz del Giglio, Saulo silva Oliveira, Rebecca Melo Zanellato, Livia tiemi Cavicchioli, Lucas Reifur, Tatiana Goberstein Lerner
Journal: Journal of Clinical Oncology (2013)

e20631 Background: HFs are very disturbing for BC patients, affecting about two thirds of them. PC is an amazonic plant that was shown to have anti-fatigue activity for BC women undergoing chemotherapy. Methods: we included BC women at least 3 months after finishing their treatment with at least 14 HFs per week. Patients received 50 mg PO of PC dry extract twice daily for 6 weeks. We assessed both HF frequency and its severity and patients graded their own toxicities weekly. We employed a phase II Simon design in which 9 out of 15 patients would be required to have at least a 50% decrease in their HF severity score. Results: We included 24 women with a median age of 50.2(36-65). Only 18 started PC and 15 completed the 6 weeks of the study. Three patients declined participation right after starting PC for difficulty in participation and for noncompliance. Ten out of 15 patients had a more than 50% decrease in their HF severity score. Throughout the 6 weeks of treatment we observed statistically significant decreases in HFs number (p =0.0331) and Severity Scores (p=0,0039). As compared to week 0, patients reported worsening of anorexia (1), insomnia (1), nausea (1), fatigue (1), sweating (1), constipation (1), anxiety (1), humor change (1) and headache (1). None of these toxicities warranted discontinuation of the study. Conclusions: We conclude that PC was effective for HF control achieving the pre-specified threshold with acceptable toxicity and warrants further confirmatory studies.
IMPROVING CARDIAC REHABILITATION REFERRAL AND PARTICIPATION RATES AMONG INDIVIDUALS WITH ACUTE CORONARY SYNDROME WITH THE IMPLEMENTATION OF ELECTRONIC ORDER SETS
Authors: Alex Maloof, Santiago R. Nuño, Armando Gallegos, Nainjot Bains, Hyeri You, Wesley K. Thompson, Ignacio A. Zepeda, Jia Shen, Robert El-Kareh, Luis R. Castellanos
Journal: Journal of the American College of Cardiology (2020)
Impact of dendritic cells combining with cytokine-induced killer cells synergized chemotherapy in patients of advanced non-small cell lung cancer.
Authors: Runbo Zhong, Hua Zhong, Baohui Han
Journal: Journal of Clinical Oncology (2013)

e19018 Background: Advanced non-small cell lung cancer (NSCLC) remains an incurable disease by following conventional chemotherapy and is the major cause of cancer–related mortality worldwide. Dendritic cells (DC) play a central role in the induction of an effective antitumor immune response. Cytokine-induced killer (CIK) cells, the subset of T lymphocytes, have a profound capacity to cytolytically eliminate cancer cells. This study was designed to evaluate how the times of receiving DC/CIKs vaccination following regular chemotherapy impact the overall survival time in patients of advanced lung cancer. Methods: 43 patients suffering from III B -IV NSCLC were enrolled in the study between August 2004 and December 2008, and all received four courses of vinolbine-platinum (NP) chemotherapy followed by vaccinated with carcinoembryonic antigen (CEA) peptide-pulsed autologus dendritic cells and CIK cells. Vaccination was repeated at 30-day intervals until the patient refused to accept. The adverse effect and overall survival (OS) were evaluated. Results: Median survival time (MST) of all patients was 19.50 months. The 1-, 2- and 3-year overall survival rate was 66.50%, 41.04%, 28.14% respectively. The 1-, 2- and 3-year overall survival rate of patients who received no less than two times of vaccination therapy was 83.92%, 74.59%, 49.73% and who received only one time was 59.44%, 23.71%, 17.78% respectively. A statistically significant difference between the two groups was identified (p=0.0052). The adverse effect as a result of chemoimmunotherapy was tolerable. Conclusions: Advanced NSCLC patients can benefit from the combination of DC-CIK vaccination followed conventional chemotherapy,and the more vaccination therapy received the longer overall survival time observed.
Interleukin-33 Induces the Enzyme Tryptophan Hydroxylase 1 to Promote Inflammatory Group 2 Innate Lymphoid Cell-Mediated Immunity
Authors: Anne-Laure Flamar, Christoph S.N. Klose, Jesper B. Moeller, Tanel Mahlakõiv, Nicholas J. Bessman, Wen Zhang, Saya Moriyama, Vladislava Stokic-Trtica, Lucille C. Rankin, Gregory Garbès Putzel, Hans-Reimer Rodewald, Zhengxiang He, Lili Chen, Sergio A. Lira, Gerard Karsenty, David Artis
Journal: Immunity (2020)
Discovering new targeted therapies for BRAF mutant-like colorectal cancers.
Authors: F. Anthony San Lucas, Scott Kopetz, Paul A. Scheet, Eduardo Vilar Sanchez
Journal: Journal of Clinical Oncology (2013)

3623 Background: Approximately 10% of colorectal cancers (CRCs) harbor a BRAF mutation (BRAFm). Patients with BRAFm tumors have poor prognosis and are a therapeutic challenge. A BRAFm gene expression signature has been communicated (Popovici et al, JCO 2012), which can identify BRAFm tumors as well as BRAF wild-type tumors that display a similar expression pattern. Collectively, these tumors are termed BRAFm-like. Our goal was to validate this signature using next-generation sequencing and to discover novel therapies for BRAFm-like CRCs using a systems biology approach. Methods: We developed a semi-automated workflow that integrates publicly available tools named the Cancer In-silico Drug Discovery (CIDD). To validate the BRAFm-like signature, we used CIDD to analyze the CRC dataset from the The Cancer Genome Atlas Network (TCGA). Samples were stratified on BRAFm status using exome-sequencing, and expression profiles were inferred from RNA-sequencing. We matched expression profiles with drug-induced signatures inferred from the Connectivity Map (CMap) – a systems biology tool that contains expression data of cell lines treated with 1,500 compounds. CIDD statistically ranks candidate compounds and annotates them to pathways using public databases. Results: When applied to TCGA RNA-sequencing data, a classifier based on the BRAFm-like signature resulted in 93.3% sensitivity and 83.5% specificity for detecting BRAFm samples. When applied to Agilent gene expression data, this resulted in 80% sensitivity and 91.1% specificity. 41% of KRAS-mutated samples and 14% of double wild-type samples were predicted to be BRAFm-like. 100% of MSI-high and 18% of MSS samples were predicted to be BRAFm-like. Compounds near the top of our drug rankings include Gefitinib and MG-262 a proteasome inhibitor. Conclusions: We have validated the BRAFm-like signature using RNA-sequencing and Agilent expression data from the TCGA, and showed a high degree of robustness across technologies. We have identified EGFR and proteasome inhibitors as potential compounds to target BRAFm-like CRCs.
Abstract 9988: Sudden Cardiac Death Due to Valvular Heart Disease
Authors: Lauri Holmstroem, Jarkko Piuhola, Juha Vähätalo, Anette Haukilahti, Tuomas Kentta, Lasse Pakanen, Juha Perkiomaki, Matti Niemela, Kari Kervinen, Heikki Huikuri, Juhani Junttila
Journal: Circulation (2019)

Background: In approximately half of sudden cardiac death (SCD) victims cardiac disease has not been diagnosed during lifetime. Coronary artery disease and nonischemic cardiomyopathies are the most...
Optimisation of EGFR TKI efficiency in the therapeutic scheme of EGFR wild-type lung cancer.
Authors: Mathilde Cabart, Judith Raimbourg, Lisenn Lalier, Jaafar Bennouna, Francois Vallette
Journal: Journal of Clinical Oncology (2013)

e18532 Background: EGFR tyrosine kinase inhibitors (EGFR TKI) have improved the therapeutic care of lung cancer patients but only a small sub-population of patients, namely those harboring EGFR-mutated tumors, benefit from this therapy. The observation that EGFR TKI enhance prognosis and quality of life in all patients when used as second line or maintenance treatment impelled us into the search of potential markers of the optimal introduction kinetics of EGFR TKI in the therapeutic scheme. Methods: We used lung cancer cell lines harboring either wild-type or mutated EGFR (NCI-H1650, NCI-H1975) to study the consequences of cisplatin treatment in vitro on the consecutive sensitivity to erlotinib. Results: Sub-lethal cisplatin pretreatment (3µM) enhances erlotinib toxicity in EGFR wild-type, but not EGFR mutated cells (A549 IC50 drops from 28 to 15µM for short-term or 12µM for long-term exposure). This correlates with EGFR activation following short-term or prolonged cisplatin treatment through the secretion of EGFR ligands. This activation of EGFR is concomitant to the decrease in other receptor tyrosine kinases phosphorylation including Met. Conclusions: The sensitivity of EGFR wild-type lung cancer cells to erlotinib in vitro is enhanced by cisplatin pretreatment. We identified potential markers of this sensitization, namely EGFR ligands, which serum level might be predicitive of the optimal efficiency of EGFR TKI. In vivo validation of these markers is under investigation. The concomitant decrease in other receptor tyrosine kinases phosphorylation suggests that the targeting of other receptor tyrosine kinases might potentiate EGFR TKI efficiency.
NORDSTAR: paving the way for a new era in asthma research
Authors: Kirk Geale, Hatef Darabi, Maria Lindh, Hanna Fues Wahl, Oskar Ström, Hui Cao, Luisa Alvares, Rikke Dodge, Emil Loefroth, Alan Altraja, Vibeke Backer, Helena Backman, Leif Bjermer, Apostolos Bossios, Bernt Bøgvald Aarli, Barbro Dahlén, Ole Hilberg, Christer Janson, Hannu Kankaanranta, Jussi Karjalainen, Paula Kauppi, Maritta Kilpeläinen, Sverre Lehmann, Lauri Lehtimäki, Bo Lundbäck, Thomas Sandström, Charlotte Suppli Ulrik, Asger Sverrild, Arja Viinanen, Anna von Bülow, Valentyna Yasinska, Celeste Porsbjerg
Journal: European Respiratory Journal (2020)

<b>NORDSTAR is a longitudinal dataset for the study of asthma comprising 3.3 million individuals and over 50 million person-years in 4 Nordic countries. The data include diagnoses, medication dispensing, use of resources and costs, socio-demographics, and mortality.</b>http://bit.ly/2HueyEt
COMPARISON OF TRANSRADIAL VERSUS TRANSFEMORAL ACCESS FOR PERCUTANEOUS CORONARY INTERVENTION IN STEMI PATIENTS: A META-ANALYSIS OF RANDOMIZED TRIALS
Authors: Aravdeep Jhand, Varunsiri Atti, Rahul Dhawan, Mohit Turagam, Mamas A. Mamas, Emmanouil Brilakis, Arnav Kumar, Natraj Katta, Yiannis S. Chatzizisis, J. Abbott, Ajay Kirtane, Deepak Bhatt, Poonam Velagapudi
Journal: Journal of the American College of Cardiology (2020)
Aortic Pulse Wave Velocity Predicts All-Cause Mortality in Chronic Obstructive Pulmonary Disease
Authors: Marie Fisk, Ian Wilkinson
Journal: American Journal of Respiratory and Critical Care Medicine (2020)

We really want to thank Suri and colleagues for their interest in our study (1) and for indicating that similar observations were made by other studies (2).However, as pointed out by them regarding erroneously citing the paper in which transmission occurred after symptom resolution, we want to clarify.In the cited study, the authors indicated that the transmission between index patients and other patients happened before symptom onset and not after the resolution of the symptoms, which is indeed correct (3).However, in the same study, the transmission was also reported between patient 1 and other patients (3, 4) who had no contact with the index patient.Patient 1 returned to work after the resolution of symptoms but was unaware of his infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).After confirmation of infection in the index patient upon return to China, patient 1 presented to the Division of Infectious Diseases and Tropical Medicine in Munich for further assessment.Patient 1 was found to be well with no signs of fever but had a very elevated viral load (.10 8 copies).Our citation referred to the transmission from patient 1 to patients 3 and 4 rather than from the index patient as was suggested by authors.Another major point raised by the authors is the comparison between coronavirus and influenza infections.In the ferret model, the infective viral shedding time is limited to 5 days, whereas quantitative PCR (qPCR) positivity remains until Days 11-13.However, there are stark differences between influenza infection and coronavirus disease .Patients succumbing to COVID-19 remain positive for the virus until their death, even if it occurs 30-40 days after symptom onset, suggesting the ability of SARS-CoV-2 to persist in the body for prolonged times (4).However, we agree with the need to find a better way to ascertain the shedding time in infected patients, as resources have been scarce to test all patients, especially multiple times, before being discharged from hospitals.In these conditions, patients are suggested to remain in isolation to avoid any spread of infection.However, we agree with the authors that it is possible that many of these patients do not shed the active virus despite being positive on qPCR.These findings need to be confirmed by large-scale studies in which throat swabs are indeed tested in a sufficient number of patients to determine if viral positivity on qPCR represents infective virus or just viral remnants that are unable to transmit along with the time kinetics.
An invited commentary on “Ekser B, Contreras AG, Andraus W, Taner T. Current status of combined liver-kidney transplantation. Int J Surg. 2020 Feb 19. pii: S1743-9191(20)30171–0. doi: 10.1016/j.ijsu.2020.02.008.”
Authors: Aaron Shanker, Mohammad Bashashati
Journal: International Journal of Surgery (2020)
One-two punch injury to tolerance mechanisms in graft-versus-host disease
Authors: Léolène J Carrington, Ivan Maillard
Journal: Journal of Clinical Investigation (2020)

Chronic graft-versus-host disease (GVHD) is a major complication of allogeneic hematopoietic cell transplantation that resembles autoimmunity, with unclear pathogenesis and few effective therapeutic options. In this issue of the JCI, Dertschnig et al. used mouse models to investigate the basis of T cell autoreactivity following GVHD. Notably, GVHD caused irreversible damage to a population of tolerogenic stromal cells that display peripheral tissue-restricted antigens in lymph nodes, which impaired their capacity to purge and suppress autoreactive T cells. Together with damage to central tolerance mechanisms in the thymus, these findings outline a critical one-two punch injury that profoundly disrupts immune tolerance in this devastating disease.