tbuckley/cabot-search huggingface dataset:
Abstract P4-09-14: Evaluation of the relationship between antioxidant gene polymorphisms and breast cancer
Authors: Turkan Ozturk Topcu, Nilgun ısıksacan, Zisan Asal Kilic, Sacide Pehlivan, Meral Gunaldi
Journal: Cancer Research (2020)

Abstract Background: Myeloperoxidase (MPO) is a lysosomal enzyme found in monocytes, macrophages and primary granules of neutrophils. MPO participates in the biotransformation reaction of specific carcinogens by catalyzing the formation of hypochloric acid. The destruction of malignant and non-malignant cells is achieved via MPO enzyme. An important mechanism in oxidative stress regulation is the function of uncoupling proteins (UCP), which are among the mitochondrial membrane proteins. They control free radical formation. Theaim of thisstudywastodeterminetherelationshipbetweenpolymorphisms of myeloperoxidase (MPO), uncoupling protein 2 (UCP-2)genesanddevelopment of breastcancer. Methods: Thedistributions of genotypeandallelefrequencywascomparedamongthe groups.Thirty-seven caseswithbreastcancerandseventyhealthycontrolswereenrolled in thepresentstudy. Thestudyfocused on threefunctionalvariants; a variant in a variable number of 27 bp tandem repeatsin a variant in thepromoter region (G463A) of MPO gene and a variant in thepromoterregion(-866G/A) of UCP-2 gene. Wegenotypedthesevariantsusingthepolymerasechainreaction (PCR) and/or PCR- restrictionfragmentlengthpolymorphism (RFLP) method. Thedistribution of alleleand genotype in MPO and UCP-2 geneswerecomparedbetweencaseswithbreastcancer andhealthycontrolsusingchi-square test. Results: Significantlydecreasedbreastcancerriskswerefoundfor UCP-2 AA, and AG polymorphisms(For UCP-2 AA polymorphism OR=8.167; 95%CI:2.785-23.951; p=0.001, for UCP2 AG polymorphism OR=4.341; 95%CI:1.679-11.222; p=0.002).Significantly increasedbreastcancer risk wasfoundfor UCP-2 GG polymorphism (OR:5.0; 95%CI:2.207-11.327; p=0.001).Therewerenostatisticallysignificantdifference in any genotype of MPO whencaseswithbreastcancerandhealthycontrolswerecompared. Conclusion: In the current study, UCP-2 AA, AG and GG genotypes were found to be associated with breast cancer. In contrast, MPO GG, GA genotypes were not associated with breast cancer. Further studies are needed to determine whether these gene polymorphisms have a place in diagnosis or determining the risk of disease. Citation Format: Turkan Ozturk Topcu, Nilgun ısıksacan, Zisan Asal Kilic, Sacide Pehlivan, Meral Gunaldi. Evaluation of the relationship between antioxidant gene polymorphisms and breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-09-14.
An intestinal organoid–based platform that recreates susceptibility to T-cell–mediated tissue injury
Authors: Yu Matsuzawa-Ishimoto, Ashley Hine, Yusuke Shono, Eugene Rudensky, Amina Lazrak, Frank Yeung, Jessica A. Neil, Xiaomin Yao, Ying-Han Chen, Thomas Heaney, Samantha L. Schuster, Erin E. Zwack, Jordan E. Axelrad, David Hudesman, Jennifer J. Tsai, Katherine Nichols, M. Zahidunnabi Dewan, Michael Cammer, Allison Beal, Sandra Hoffman, Brad Geddes, John Bertin, Chen Liu, Victor J. Torres, P’ng Loke, Marcel R. M. van den Brink, Ken Cadwell
Journal: Blood (2020)
Abstract 17238: Delayed Left Atrial Decompression is Associated With Prolonged Duration of Veno-arterial Extracorporeal Membrane Oxygenation Support: Results of a Multicenter Pediatric Interventional Cardiology Early Career Society (PICES) Study
Authors: Jeffrey D Zampi, Fares Alghanem, Sunkyung Yu, Ryan Callahan, Christopher L Curzon, Jeffrey W Delaney, Robert G Gray, Carrie E Herbert, Ryan A Leahy, Ray Lowery, Sara K Pasquali, Priti M Patel, Diego Porras, Shabana Shahanavaz, Ravi R Thiagarajan, Sara M Trucco, Mariel E Turner, Surendranath R Veeran Reddy, Shawn C West, Wendy Whiteside, Bryan H Goldstein
Journal: Circulation (2017)

Introduction: Patients with severe left ventricular dysfunction requiring veno-arterial extracorporeal membrane oxygenation (VA ECMO) support may develop left ventricular distension and left atrial...
Abstract P4-09-13: Spectrum analysis of the inherited mutations of BRCA1/-2 genes that associated with high risk breast cancer in Saudi population
Authors: Yousef MohammedRabaa Hawsawi, Abdelrazak Meliti, Edward Cupler, Turki Sobahy, Samar Zailaie, Mohammed Baghdadi, Hosam Alardati
Journal: Cancer Research (2020)

Abstract Background: Breast cancer (BC) is the most common prevalent cancer among female worldwide, despite the advances in molecular biology. In Saudi Arabia, the disease represents 19.9% of the total cancer-related deaths in women. Inherited mutations of BRCA1/-2 are well documented to be associated with higher risk of breast cancer. Aim: To investigate the role of inherited mutation in BRCA1/-2 genes that associated with breast cancer in Saudi population. Methodology: A total of 41 FFPE samples were collected from BC patients admitted to KFSHRC-Jeddah from 2013 to 2018. Genomic DNA was extracted using the Qiagen FFPE kit. A100ng of each DNA samples were used for library preparation using Ion AmpliSeq™ Library Kit Plus with Saudi Inherited Cancer Panel. Ion Torrent Proton platforms were used for DNA sequencing on Ion Torrent PGM using Ion PI™ Hi-Q™ Sequencing 200 Kit. Results: A total of 26 distinct heterozygous BRCA1/-2 variants were identified in Saudi population, 15 variants in BRCA1 gene and 11 in BRCA2 gene. In BRCA1, one variant was nonframeshift deletion and 11 were missense, 3 variants likely benign, while in BRCA 2, one was stopgain and 6 were missense and 4 variants likely benign. Conclusion: Screening of BRCA1/-2 genes mutations helps in understanding the risk associated with mutations of other forms of cancer in Saudi population. The preliminary data is used as an establishing of a high-throughput NGS molecular profiling for Saudi breast cancer patients Citation Format: Yousef MohammedRabaa Hawsawi, Abdelrazak Meliti, Edward Cupler, Turki Sobahy, Samar Zailaie, Mohammed Baghdadi, Hosam Alardati. Spectrum analysis of the inherited mutations of BRCA1/-2 genes that associated with high risk breast cancer in Saudi population [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-09-13.
Health-Status Outcomes with Invasive or Conservative Care in Coronary Disease
Authors: John A. Spertus, Philip G. Jones, David J. Maron, Sean M. O’Brien, Harmony R. Reynolds, Yves Rosenberg, Gregg W. Stone, Frank E. Harrell, William E. Boden, William S. Weintraub, Khaula Baloch, Kreton Mavromatis, Ariel Diaz, Gilbert Gosselin, Jonathan D. Newman, Stavroula Mavromichalis, Karen P. Alexander, David J. Cohen, Sripal Bangalore, Judith S. Hochman, Daniel B. Mark
Journal: New England Journal of Medicine (2020)

In the ISCHEMIA trial, an invasive strategy with angiographic assessment and revascularization did not reduce clinical events among patients with stable ischemic heart disease and moderate or severe ischemia. A secondary objective of the trial was to assess angina-related health status among these patients.
Status Update on Data Required to Build a Learning Health System
Authors: Monica M. Bertagnolli, Brian Anderson, Kelly Norsworthy, Steven Piantadosi, Andre Quina, Richard L. Schilsky, Robert S. Miller, Sean Khozin
Journal: Journal of Clinical Oncology (2020)

Wide adoption of electronic health records (EHRs) has raised the expectation that data obtained during routine clinical care, termed “real-world” data, will be accumulated across health care systems and analyzed on a large scale to produce improvements in patient outcomes and the use of health care resources. To facilitate a learning health system, EHRs must contain clinically meaningful structured data elements that can be readily exchanged, and the data must be of adequate quality to draw valid inferences. At the present time, the majority of EHR content is unstructured and locked into proprietary systems that pose significant challenges to conducting accurate analyses of many clinical outcomes. This article details the current state of data obtained at the point of care and describes the changes necessary to use the EHR to build a learning health system.
Long-term efficacy and safety of secukinumab in patients with psoriatic arthritis: 5-year (end-of-study) results from the phase 3 FUTURE 2 study
Authors: Iain B McInnes, Philip J Mease, Alan J Kivitz, Peter Nash, Proton Rahman, Jürgen Rech, Philip G Conaghan, Bruce Kirkham, Sandra Navarra, Ashwini D Belsare, Eumoprhia M Delicha, Luminita Pricop
Journal: The Lancet Rheumatology (2020)
Abstract 108: Optimal In-Hospital Defibrillator Placement
Authors: Kwan Hon Benjamin Leung, Matthew Yang, Christopher Sun, Katherine S Allan, Natalie Wong, Timothy Chan
Journal: Circulation (2019)

Introduction: Delays in defibrillation of in-hospital cardiac arrests (IHCAs) can reduce the likelihood of survival. Mathematical optimization has been shown to improve public location defibrillator placement but has not been applied to in-hospital defibrillator placement. Objective: To determine if mathematical optimization of in-hospital defibrillator placements can reduce distances to IHCAs compared to current placements in a large academic teaching hospital. Methods: We identified all treated IHCAs and defibrillator placements in St. Michael’s Hospital in Toronto, Canada from Jan. 2007 to Jun. 2017 and mapped them to a 3-D representation of the hospital that we developed from blueprints. An equal number of optimal defibrillator locations was identified using a mathematical optimization model that minimizes the average distance between IHCAs and the closest defibrillator in a 10-fold cross-validation approach. The optimized and current defibrillator locations were compared in terms of average distance to the out-of-sample IHCAs in each fold. We repeated the analysis excluding IHCAs and defibrillators in intensive care units (ICUs), operating theaters (OTs), and the emergency department (ED). Significance in the difference of average distance was determined using a Wilcoxon signed-rank test. Results: We identified 537 treated IHCAs and 53 defibrillators within the hospital during the study period. Of these, 236 IHCAs and 38 defibrillators were outside of ICUs, OTs, and the ED. Optimal defibrillator placements reduced the average defibrillator-to-IHCA distance from 17.1 m to 3.8 m, a relative decrease of 77.8% (P&lt;0.01) on all IHCAs compared to current defibrillator placements. For non-ICU/OT/ED IHCAs, the average distance was reduced from 18.3 m to 9.8 m, a relative decrease of 46.4% (P&lt;0.01). Conclusion: Optimization-guided placement of in-hospital defibrillators can significantly reduce the distance from an IHCA to the closest defibrillator.
When do athletes benefit from cardiac genetic testing?
Authors: Christopher Semsarian, Jessica Orchard, Belinda Gray, John Orchard
Journal: British Journal of Sports Medicine (2020)

Genetic testing has had a major impact in many areas of medicine, including sports cardiology. Here we discuss cardiac genetic testing not as a screening tool but rather as an evidence-based follow-up test in an athlete with an abnormal ECG or medical history to identify those athletes who have a potentially life-threatening cardiac genetic disorder.

Cardiac genetic testing is a valuable investigation for the diagnosis of over 40 cardiovascular diseases including the inherited cardiomyopathies and primary arrhythmogenic disorders. A positive genetic diagnosis can impact on the individual in terms of diagnosis, guiding treatment options and prognosis, as well as in screening family members. Advances in next generation sequencing technologies has resulted in the ability to test for panels of genes, quickly and at relatively low cost, making cardiac genetic testing more commonplace in clinical practice. Perhaps the greatest challenge is not the actual sequencing of cardiac genes but the detailed and comprehensive analysis and interpretation of the genetic data to determine the pathogenicity of the DNA variants identified and which of the findings are clinically relevant to the individual’s phenotype.1 As a result, cardiac genetic testing is best undertaken in a specialised multidisciplinary clinic setting where specific clinical and genetic expertise is available.2 3 In Australia and the UK, a referral to a specified cardiogenetics programme typically comes from a general cardiologist. These clinics are found in a number of …
Choriocapillaris Compression Correlates with Choroidal Nevus–Associated Subretinal Fluid: OCT Analysis of 3431 Cases
Authors: Michael D. Yu, Lauren A. Dalvin, David Ancona-Lezama, Antonio Yaghy, Sandor R. Ferenczy, Tatyana Milman, Ralph C. Eagle, Carol L. Shields
Journal: Ophthalmology (2020)
Abstract ES1-2: Detecting and Managing Immunotherapy-related Toxicities Wisely
Authors: P Schmid
Journal: Cancer Research (2020)

Abstract With the increasing use of immunotherapy, multidisciplinary breast cancer teams have to get used to recognising and managing immune-related side effects. Although immune checkpoint inhibitors are generally well tolerated, they can cause a wide range of side effects which often differ from those commonly seen with other types of cancer treatment. These immune-mediated side effects include inflammatory or autoimmune reactions which can resemble autoimmune diseases. Side effect patterns can be highly variable in terms of timing, severity and organ manifestation. They appear at any time, sometimes even months after the last treatment, and can affect any part of the body. The risk of developing immune-related side effects generally increases with longer treatment-duration. Most commonly affected body systems are skin, endocrine organs, the gastrointestinal tract, liver and lungs, but even very rare manifestations such as neurological disorders or myocarditis need to be considered as they can be serious. Before considering patients for immunotherapy, they should be carefully assessed with regards the risk of developing immune-related side effects. Patients with a history of autoimmune disorders are generally at risk of worsening of their autoimmune disease with immunotherapy. Early recognition and intervention are critical for the effective management which often includes the use of corticosteroids and occasionally additional immunosuppressive agents. Interdisciplinary working within oncology groups as well as with associated specialties is critical for optimal patients management. With effective management most immune-related side effects resolve and patients can continue their treatment. Citation Format: P Schmid. Detecting and Managing Immunotherapy-related Toxicities Wisely [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr ES1-2.
Abstract 13012: Apolipoprotein L1 Risk Alleles Are Associated With Risk of Plaque Rupture in Coronary Artery Disease
Authors: Liang Guo, Marco Delsante, Anne Cornelissen, Xiaoqing Zhao, Robert Kutys, Raquel Fernandez, Ka Hyun Paek, Atsushi Sakamoto, Hiroyuki Jinnouchi, Dipti Surve, Maria E Romero, Frank D Kolodgie, Myung K Shin, Maarten Hoek, Jeffrey B Kopp, Avi Z Rosenberg, Harry R Davis, Renu Virmani, Aloke V Finn
Journal: Circulation (2019)

Introduction: Two genetic risk variants in Apolipoprotein L1 gene have been associated with high rate of kidney disease in African Americans, but it is still controversial whether these variants ar...
Mega‐trials in heart failure: effects of dilution in examination of new therapies
Authors: Beth A. Davison, Koji Takagi, Stefanie Senger, Gary Koch, Marco Metra, Antoine Kimmoun, Alexandre Mebazaa, Adriaan A. Voors, Olav W. Nielsen, Ovidiu Chioncel, Peter S. Pang, Barry H. Greenberg, Aldo P. Maggioni, Alain Cohen‐Solal, Georg Ertl, Naoki Sato, John R. Teerlink, Gerasimos Filippatos, Piotr Ponikowski, Etienne Gayat, Christopher Edwards, Gad Cotter
Journal: European Journal of Heart Failure (2020)
Organ donation: educating the public about the “opt-out” system is crucial
Authors: Matthew H V Byrne, James Ashcroft
Journal: BMJ (2020)

The switch to an “opt-out” system for organ donation is eagerly anticipated and represents a positive change.1 But it will not solve the organ donor deficit on its own. The policy change has been effective in Wales, but a systematic review of 35 countries found that the effectiveness of an opt-out system at improving donation …
Abstract P2-16-07: Randomized controlled trial of neoadjuvant eribulin mesylate versus paclitaxel in women with operable breast cancer (JONIE-3 study)
Authors: Takahiko Kawate, Takashi Ishikawa, Daishu Miura, Yoshie Hasegawa, Akihiko Tachibana, Jun Horiguchi, Mitsuhiro Hayashi, Masaru Miyashita, Tomoyuki Kubota, Kazutaka Narui, Masato Suzuki, Kouhei Akazawa, Norio Kohno
Journal: Cancer Research (2020)

Abstract Background: Eribulin mesylate (ERI) improved the overall survival in metastatic breast cancer (BC) patients. However, the efficacy has not been reported in early breast cancer. We performed the neoadjuvant chemotherapy (NAC) study based on hypothesis that ERI is less toxic, particularly in peripheral neuropathy, and has similar efficacy to paclitaxel (PTX) in patients with operable BC. Methods: This is a multicenter open label randomized phase 2 study (UMIN000012817). Patients were randomly assigned to either ERI (1.4mg/m2, d1 and d8, q21 days, 4 cycles) followed by FEC (fluorouracil 500 mg/m2, epirubicin 100 mg/m2, and cyclophosphamide 500 mg/m2) (ERI-FEC) or PTX (80mg/m2, weekly, 12 cycles) followed by FEC (PTX-FEC) with stratified by ER, HER2, and menopausal status. Trastuzumab was added in patients with HER2 positive disease. Primary endpoint was the incidence of peripheral sensory and motor neuropathy (PSN and PMN) with Grade 1 or higher according to CTCAE ver.4.0. Secondary endpoints were pathological complete response (pCR) rates (ypT0/is/ypN0), clinical response rates (CR+PR), adverse events, disease-free survival (DFS) and patient neurotoxicity questionnaire (PNQ) analysis. Here, we report 3 year’s DFS and PNQ analysis in this study Results: Between December 2013 to March 2016, 121 cases were enrolled and 5 cases were excluded from the primary assessment. One hundred sixteen cases were finally randomized and treated by ERI-FEC in 58 cases and PTX-FEC in 57 cases. A median follow-up time of ERI-FEC and PTX-FEC was 54.2 and 51.4 months, respectively. Three year-DFS rate were 89.7% in the ERI-FEC group (95% CI 51.1 - 57.3) and 86.0% in the PTX-FEC group. (p=0.561). The incidences of PSN and PMN were significantly lower in the ERI-FEC group than the PAX-FEC group at the end of treatments (previously reported). PNQ analysis after treatments is now undergone. Conclusion: DFS was not different between them. Although the pCR rate was lower in ERI-FEC than PAC-FEC as reported at the previous meeting. ERI was more favorable on adverse events than PTX during NAC treatments. Long-term results on neurotoxicity of these two drugs will be presented at the meeting. Citation Format: Takahiko Kawate, Takashi Ishikawa, Daishu Miura, Yoshie Hasegawa, Akihiko Tachibana, Jun Horiguchi, Mitsuhiro Hayashi, Masaru Miyashita, Tomoyuki Kubota, Kazutaka Narui, Masato Suzuki, Kouhei Akazawa, Norio Kohno. Randomized controlled trial of neoadjuvant eribulin mesylate versus paclitaxel in women with operable breast cancer (JONIE-3 study) [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-16-07.
Ultrasound Doppler and tenosynovial fluid analysis in tenosynovitis
Authors: Fawad Aslam, Bryant R England, Amy Cannella, Veronika Sharp, Lily Kao, Jon Arnason, Jemima Albayda, Catherine Bakewell, Shruti Sanghvi, Robert Fairchild, Karina D Torralba, Amy Evangelisto, Paul J DeMarco, Narandra Bethina, Eugene Y Kissin
Journal: Annals of the Rheumatic Diseases (2020)

To assess Doppler ultrasound (US) and tenosynovial fluid (TSF) characteristics in tenosynovitis within common rheumatic conditions, as well as their diagnostic utility.Subjects with tenosynovitis underwent Doppler US and US-guided TSF aspiration for white cell count (WCC) and crystal analysis. Tenosynovial Doppler scores (DS) were semiquantitatively graded. TSF WCC and DS were compared using Kruskal-Wallis tests and logistic regression between non-inflammatory conditions (NIC), inflammatory conditions (IC) and crystal-related conditions (CRC). Receiver operating curves, sensitivity and specificity assessed the ability of WCC and DS to discriminate IC from NIC.We analysed 100 subjects from 14 sites. The mean age was 62 years, 65% were female, and the mean TSF volume was 1.2 mL. Doppler signal was present in 93.7% of the IC group and was more frequent in IC than in NIC group (OR 6.82, 95% CI 1.41 to 32.97). The TSF median WCC per 109/L was significantly higher in the IC (2.58, p<0.001) and CRC (1.07, p<0.01) groups versus the NIC group (0.38). A TSF cut-off of ≥0.67 WCC per 109/L optimally discriminated IC versus NIC with a sensitivity and specificity each of 81.3%. In the IC group, 20 of 48 (41.7%) subjects had a TSF WCC <2.00 per 109/L.A negative DS helps rule out IC in tenosynovitis, but a positive DS is non-specific and merits TSF testing. Unlike synovial fluid, a lower TSF WCC better discriminates IC from NIC. US guidance facilitates aspiration of minute TSF volume, which is critical for diagnosing tenosynovial CRC.
Machine learning for microbial identification and antimicrobial susceptibility testing on MALDI-TOF mass spectra: a systematic review
Authors: C.V. Weis, C.R. Jutzeler, K. Borgwardt
Journal: Clinical Microbiology and Infection (2020)

The matrix assisted laser desorption/ionization and time-of-flight mass spectrometry (MALDI-TOF MS) technology has revolutionized the field of microbiology by facilitating precise and rapid species identification. Recently, machine learning techniques have been leveraged to maximally exploit the information contained in MALDI-TOF MS, with the ultimate goal to refine species identification and streamline antimicrobial resistance determination.The aim was to systematically review and evaluate studies employing machine learning for the analysis of MALDI-TOF mass spectra.Using PubMed/Medline, Scopus and Web of Science, we searched the existing literature for machine learning-supported applications of MALDI-TOF mass spectra for microbial species and antimicrobial susceptibility identification.Original research studies using machine learning to exploit MALDI-TOF mass spectra for microbial specie and antimicrobial susceptibility identification were included. Studies focusing on single proteins and peptides, case studies and review articles were excluded.A systematic review according to the PRISMA guidelines was performed and a quality assessment of the machine learning models conducted.From the 36 studies that met our inclusion criteria, 27 employed machine learning for species identification and nine for antimicrobial susceptibility testing. Support Vector Machines, Genetic Algorithms, Artificial Neural Networks and Quick Classifiers were the most frequently used machine learning algorithms. The quality of the studies ranged between poor and very good. The majority of the studies reported how to interpret the predictors (88.89%) and suggested possible clinical applications of the developed algorithm (100%), but only four studies (11.11%) validated machine learning algorithms on external datasets.A growing number of studies utilize machine learning to optimize the analysis of MALDI-TOF mass spectra. This review, however, demonstrates that there are certain shortcomings of current machine learning-supported approaches that have to be addressed to make them widely available and incorporated them in the clinical routine.