tbuckley/cabot-search huggingface dataset:
Abstract PO-01: Transcriptional dimensions provide a framework for describing tumor heterogeneity in CLL
Authors: Julie E. Feusier, Rosalie G. Waller, Michael J. Madsen, Brian Avery, Nicola J. Camp
Journal: Blood Cancer Discovery (2020)

Abstract Our goal is to define multiple informative transcriptome variables that capture sources of heterogeneity in chronic lymphocytic leukemia (CLL) cells, for flexible modeling in epidemiology and clinical studies. CD19+/CD5+ B-cells were sorted from whole blood of 227 CLL patients and RNA was sequenced on the HiSeq4000 or NovaSeq platforms as part of the ORIEN Avatar Initiative. Transcript-based read counts were generated from FASTQ files using Salmon. High-quality genes were selected and read counts internally normalized and corrected for batch effects using ComBat. Preprocessing resulted in a final set of 8,716 quality-controlled, autosomal, protein-coding genes. PCA was performed and, using a scree test, we selected 14 dimensions that represented 55.9% of the total variance across the CLL patients' transcriptomes. Fourteen quantitative, orthogonal CLL dimension variables were calculated for all 227 patients. By design, these CLL dimensions capture transcriptome variance and provide novel multi-gene expression biomarkers. We assessed whether these CLL transcriptome dimensions captured known clinically relevant molecular differences. First, we investigated associations with IGVH mutational status (determined using MiXCR). CLL dimension variables 1, 5, 6, and 8 predicted IGHV mutational status (p=4.6x10-16). Next, we investigated associations with ZAP70 and CD38 biomarkers, calculated by their expression in the RNA sequencing data using a separate pipeline and correcting for batch effects by ComBat (neither gene was in the 8,716 genes retained for PCA). CLL dimension variables 3, 5, 6, 7, and 8 significantly predicted Zap70 expression (p=1.6x10-38). CLL dimension variables 2, 3, 5, and 6 significantly predicted CD38 expression (p=3.1x10-31). Transcriptome dimension variables provide a flexible intrinsic framework to describe heterogeneity across CLL patients. We have shown that our transcriptome dimensions capture IGHV mutational status and ZAP70 and CD38 expression, all biomarkers for prognosis. Future work will include exploring the ability of the 14 dimensions to capture other known important molecular markers for CLL, including somatic deletion of 17p deletion, somatic mutational patterns, microsatellite instability, and previously described expression-based subgroups. Transcriptome dimensions are designed for utility as predictor variables, alongside other covariates, in parametric modeling, and have the potential to improve both epidemiology and clinical studies. Citation Format: Julie E. Feusier, Rosalie G. Waller, Michael J. Madsen, Brian Avery, Nicola J. Camp. Transcriptional dimensions provide a framework for describing tumor heterogeneity in CLL [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-01.
A “dual-guide” bioinspired drug delivery strategy of a macrophage-based carrier against postoperative triple-negative breast cancer recurrence
Authors: Yue Qiu, Kebai Ren, Wei Zhao, Qianwen Yu, Rong Guo, Jiao He, Ling Mei, Yayuan Liu, Jiajing Tang, Shanshan Xu, Jianping Li, Jiaojie Wei, Man Li, Zhirong Zhang, Qin He
Journal: Journal of Controlled Release (2020)
Abstract 14903: Evaluation of the Effectiveness of Warfarin Anticoagulation in Welsh Patients With Non-Valvular Atrial Fibrillation: The Sail Warfarin Out of Range Descriptors Study (SWORDS)
Authors: Daniel Harris, Daniel Thayer, Caroline Brooks, Gravenor Michael, Nathan Hill, Geoff Murley, Francisca Vargas-Lopes, Ting Wang, Steven Lister, Julian Halcox
Journal: Circulation (2018)

Introduction: The target International Normalised Range (INR) for patients with non-valvular atrial fibrillation (NVAF) prescribed vitamin K antagonist (VKA) therapy is 2-3. The net clinical benefi...
The impact of primary care supported shielding on the risk of mortality in people vulnerable to COVID-19: English sentinel network matched cohort study
Authors: Azmaeen Zarif, Mark Joy, Julian Sherlock, James P Sheppard, Rachel Byford, Oluwafunmi Akinyemi, Clare R Bankhead, Alexandra Deeks, Filipa Ferreira, Nicholas Jones, Harshana Liyanage, Dylan McGagh, Brian Nicholson, Jason Oke, Cecilia Okusi, Manasa Tripathy, John Williams, Richard Hobbs, Simon de Lusignan
Journal: Journal of Infection (2021)

To mitigate risk of mortality from coronavirus 2019 infection (COVID-19), the UK government recommended 'shielding' of vulnerable people through self-isolation for 12 weeks.A retrospective cohort study using a nationally representative English primary care database comparing people aged >= 40 years who were recorded as being advised to shield using a fixed ratio of 1:1, matching to people with the same diagnoses not advised to shield (n = 77,360 per group). Time-to-death was compared using Cox regression, reporting the hazard ratio (HR) of mortality between groups. A sensitivity analysis compared exact matched cohorts (n = 24,752 shielded, n = 61,566 exact matches).We found a time-varying HR of mortality between groups. In the first 21 days, the mortality risk in people shielding was half those not (HR = 0.50, 95%CI:0.41-0.59. p < 0.0001). Over the remaining nine weeks, mortality risk was 54% higher in the shielded group (HR=1.54, 95%CI:1.41-1.70, p < 0.0001). Beyond the shielding period, mortality risk was over two-and-a-half times higher in the shielded group (HR=2.61, 95%CI:2.38-2.87, p < 0.0001).Shielding halved the risk of mortality for 21 days. Mortality risk became higher across the remainder of the shielding period, rising to two-and-a-half times greater post-shielding. Shielding may be beneficial in the next wave of COVID-19.
Thermo‐Triggered In Situ Chitosan‐Based Gelation System for Repeated and Enhanced Sonodynamic Therapy Post a Single Injection
Authors: Jialin She, Xuanfang Zhou, Yaojia Zhang, Rui Zhang, Quguang Li, Wenju Zhu, Zhouqi Meng, Zhuang Liu
Journal: Advanced Healthcare Materials (2020)

Sonodynamic therapy (SDT) by utilizing ultrasonic waves triggers the generation of reactive oxygen species (ROS) with the help of sonosensitizers to destruct deep-seated tumors has attracted great attention. However, the efficacy of SDT may not be robust enough due to the insufficient oxygen supply within solid tumors. Additionally, repeated injections and treatments, which are often required to achieve the optimal therapeutic responses, may cause additional side effects and patient incompliance. Herein, a thermo-triggered in situ hydrogel system is developed in which catalase (CAT) conjugated with sonosensitizer meso-tetra (4-carboxyphenyl) porphine (TCPP) is mixed into chitosan (CS) and beta-glycerol phosphate disodium (GP) to form the precursor solution. After injection of the precursor solution into tumors, the in situ sol-gel transformation will occur as triggered by the body temperature, resulting in the localized tumor retention of TCPP-CAT. The locally restrained TCPP-CAT not only produces ROS under ultrasonic treatment, but also sustainably reverses the oxygen-deficient status in solid tumors by triggering the O2 generation from the decomposition of endogenous H2 O2 , further promoting the efficacy of SDT. As a result, the repeated SDT after a single dose injection of such a hydrogel can offer robust treatment effects to effectively eradicate tumors.
Caring for colleagues during the pandemic: Deepa Janga
Authors: Marika Davies
Journal: BMJ (2020)

When Deepa Janga moved to the UK in 2005, she planned to complete her membership examinations and then return to India.But she fell in love with the NHS and found she couldn't leave."Where I come from, you can't imagine that everything, like cancer treatment, is the same for everyone," she says."The concept that you can have anything and everything free for everyone is unique, very few countries in the world have something like this.
Epicutaneous immunotherapy for treatment of peanut allergy: Follow-up from the Consortium for Food Allergy Research
Authors: Amy M. Scurlock, A. Wesley Burks, Scott H. Sicherer, Donald Y.M. Leung, Edwin H. Kim, Alice K. Henning, Peter Dawson, Robert W. Lindblad, M. Cecilia Berin, Christine B. Cho, Wendy F. Davidson, Marshall Plaut, Hugh A. Sampson, Robert A. Wood, Stacie M. Jones
Journal: Journal of Allergy and Clinical Immunology (2020)
16644 Utilizing Fibrosis-4 Score to assess risk for hepatic fibrosis in patients with psoriasis on methotrexate
Authors: Alana Deutsch, Roya Nazarian, Elizabeth Yim, Beth N. McLellan, Danielle A. Espinoza, Allan W. Wolkoff, Steven R. Cohen
Journal: Journal of the American Academy of Dermatology (2020)
Abstract 18212: Von Willebrand Factor-ADAMTS13 System and Clinical Outcome in Patients With Non-valvular Atrial Fibrillation
Authors: Waldemar E Wysokinski, Rayya Saadiq, Robert McBane, Rowlens Melduni, Ewa Konik, Kevin Cohoon, Naser Ammash, Samuel Asirvatham, Joshua Slusser, Diane Grill
Journal: Circulation (2017)

Introduction: We previously documented a direct relationship between Von Willebrand factor (VWF) concentration/activity regulated by cleaving protease - ADAMTS13 and echocardiographic measures of l...
Abstract 14553: A Deep Learning Based Model for Predicting Heart Failure in Hypertrophic Cardiomyopathy Patients With Left Ventricular Outflow Tract Obstruction
Authors: Ahmed S Fahmy
Journal: Circulation (2019)

Introduction: Heart Failure (HF) is highly amenable to effective treatment in hypertrophic cardiomyopathy (HCM) patients. However, there is no reliable model for predicting progressive HF. We sough...
18277 Development of a patient decision aid for hidradenitis suppurativa: Facilitating informed shared decision making
Authors: Jerry Tan, Olivia McBride, Donna McLean, Tanja Samardzic, Christine A. Yannuzzi, Robert P. Dellavalle, Christopher Sayed, Barry Resnik, Sandra Guilbault
Journal: Journal of the American Academy of Dermatology (2020)
Abstract 15644: Proinflammatory Diet Independently Predicts Shorter Event-free Survival in Patients With Heart Failure
Authors: Junghee Kang, Debra K Moser, Martha J Biddle, Terry A Lennie
Journal: Circulation (2020)

Introduction: Inflammation is a common biological process accompanying chronic conditions, such as heart failure (HF) that can be moderated by diet. The association between foods thought to promote inflammation and event-free survival in patients with HF has not been investigated. Hypothesis: The inflammatory potential of individuals’ diets, measured using the dietary inflammatory index (DII), will be associated with event-free survival in patients with HF. Methods: The DII scores were calculated from 4-day food diaries recorded at baseline by 213 patients with HF (age 61±12years, 35% female, 43% NYHA III/IV). Patients were followed for a median of 365 days by monthly phone calls, medical record review, and death records to determine time to all cause-hospitalization or death. The DII scores were dichotomized using median value for the Cox regression model. Hierarchical multivariate Cox proportional hazards model was used to determine whether DII scores predicted event-free survival after controlling for age, gender, body mass index, prescribed angiotensin-converting-enzyme inhibitor, beta-blocker, cholesterol lowering agent, antiinflammatory agent, N-terminal pro B-type natriuretic peptide, comorbidity, depressive symptoms, and the New York Heart Association functional classification. Results: The DII scores independently predicted event-free survival in the model constant ( p = 0.012). Higher DII scores were associated with more than double the risk of an event compared to lower DII scores (HR: 2.28, 95% Confidence Interval =1.21-4.36). Conclusions: Greater intake of foods considered to promote inflammation was associated with shorter event-free survival in patients with HF. These results provide further evidence of the importance of diet to HF outcomes.
183P Textbook outcome as a measure of surgical quality assessment and prognosis in gastric neuroendocrine carcinoma: A large multicenter sample analysis
Authors: Y-X. Gao, H-G. Wang, D. Wu, C-H. Zheng, P. Li, J-W. Xie, J-B. Wang, J-X. Lin, J. Lu, Q-Y. Chen, L-L. Cao, M. Lin, R-H. Tu, Z-N. Huang, J-L. Lin, H-L. Zheng, C. Huang
Journal: Annals of Oncology (2020)
Corrections to Assessment of Variation in State Regulation of Generic Drug and Interchangeable Biologic Substitutions
Authors: Ameet Sarpatwari
Journal: JAMA Internal Medicine (2020)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Internal Medicine HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Internal Medicine journal
Abstract 16811: Discharge Initiation of Digoxin is Associated With Lower 30-Day All-Cause Readmission in Hospitalized Older Patients With Heart Failure and Reduced Ejection Fraction Receiving Beta-Blockers
Authors: Taimoor Hashim, Sridivya Parvataneni, Gregg C Fonarow, Robert C Bourge, Sumanth D Prabhu, Javed Butler, Kanan Patel, Charity J Morgan, Prakash Deedwania, Gerasimos Filippatos, Wilbert S Aronow, Stefan D Anker, Richard M Allman, Clyde W Yancy, Ali Ahmed
Journal: Circulation (2013)

Background: Digoxin reduces 30-day all-cause hospital admission in older patients with heart failure and reduced ejection fraction (HFrEF) (PMID: 23490060). We examined if digoxin use is associated...
Retraction in the era of COVID-19 and its influence on evidence-based medicine: is science in jeopardy?
Authors: Matheus Negri Boschiero, Tatiana Aline Carvalho, Fernando Augusto de Lima Marson
Journal: Pulmonology (2020)

Studies related to the coronavirus disease 2019 (COVID-19) were frequently published as pre-prints prior to undergoing peer-review. However, several publications were later retracted due to ethical concerns or study misconduct. Although these studies have been retracted, the availability of their corresponding pre-prints has never been formally investigated, and may result in the spread of misinformation if they are being used to inform decision-making.Our objective was to conduct a systematic survey of retracted COVID-19 publications listed on the Retraction Watch database as of August 15th, 2021. We assessed the availability of corresponding pre-prints for retracted publications, and documented the number of citations and online views.Our study included 140 retracted COVID-19 publications, and we could not retrieve corresponding pre-prints for 132 retracted publications in our study (94%). Although we were unable to find the majority of pre-prints, they had already been disseminated, with a maximal citation count of 593 and Altmetric score of 558,928.While it is reassuring that most corresponding pre-prints could not be retrieved, our study highlights the need for online platforms and journals to employ quality assurance methods to prevent the spread of misinformation through citation of retracted papers.
14188 Wearable UV/HEV light sensor and smartphone application for personal monitoring and personalized recommendations
Authors: Rafal Pielak, Pinghung Wei, Haruna Peyret, Guive Balooch, Dominique Moyal, Daphine Clemente, Janet Wangeri-Talbot, Jyotsna Paturi, Anthony Banks, John Rogers
Journal: Journal of the American Academy of Dermatology (2020)
13677 Time to relapse in patients with moderate to severe psoriasis who were tildrakizumab responders at week 28: Post hoc analysis through 64 weeks from the reSURFACE 1 trial
Authors: Kristian Reich, José-Manuel Carrascosa, Emilio Fumero, Andreu Schoenenberger López, Mark Lebwohl
Journal: Journal of the American Academy of Dermatology (2020)
16349 Rates of herpes zoster, hepatitis C, and tuberculosis among patients with psoriasis treated with apremilast, biologics, disease-modifying antirheumatic drugs, and corticosteroids: A cohort study in the US MarketScan database
Authors: Susan Jick, Katrina Wilcox Hagberg, Rebecca Persson, Catherine Vasilakis-Scaramozza, Steve J. Niemcryk, Michael Peng, Maria Paris, Anders Lindholm
Journal: Journal of the American Academy of Dermatology (2020)
Tissue is the issue?
Authors: Anthony Yuen Bun Teoh
Journal: Endoscopy (2020)

In the randomized crossover study by Seicean et al., the authors compared endoscopic ultrasound (EUS)-guided fine-needle aspiration (FNA) with or without contrast-enhanced harmonic imaging (CE-EUS) [1]. With the use of CE-EUS, the authors postulated that any necrotic area could be visualized and avoided during FNA, resulting in improved diagnostic accuracy. However, after completion of the study, the authors noted that the diagnostic accuracies were similar between the two groups and the combined diagnostic rate after two passes was 93.8 %. The results remained similar after subgroup analysis on mass location, presence of necrosis, portal hypertension, biliary stenting, and diagnosis.
Radiofrequency vapor ablation for Barrett’s esophagus: feasibility, safety and proof of concept in a stepwise study with in vitro, animal, and the first in-human application
Authors: Sanne N. van Munster, Roos E. Pouw, Virender K. Sharma, Sybren L. Meijer, Bas L. A. M. Weusten, Jacques J. G. H. M. Bergman
Journal: Endoscopy (2020)

Abstract Introduction The Radiofrequency Vapor Ablation (RFVA) System (AquaMedical, Inc., Santa Ana, CA) is a novel ablation system for eradication of Barrett’s esophagus, that generates vapor at 100 °C using an RF electrode located in the catheter tip. We performed in-vitro dosimetry studies and the first in-human feasibility study. Methods The system includes an RFVA generator with syringe pump and a through-the-scope-catheter. The RFVA system was tested in-vitro (lean-beef and porcine study) and ablation depth was compared to focal RFA. Two doses were selected for further in-vivo testing in dysplatic BE patients. Repeat endoscopy with histology was performed after 8 weeks to assess squamous conversion. Results In porcine, RFVA 3-seconds was comparable to RFA, whereas RFVA 5-seconds produced slightly deeper ablation. We selected a conservative 1-second and 3-seconds for human study. Fifty-three ablations were successfully applied in 15 patients with no adverse events. Follow-up endoscopy showed a median squamous conversion of 55 % (IQR 33 – 74) and 98 % (56 – 99) for 1 and 3-seconds, respectively. Conclusions In this 3-phase study with lean-beef, porcine and the first in-human application, the RFVA system was feasible for esophageal ablation and successfully and safely converted targeted BE areas into squamous epithelium.
Slowing late infantile Batten disease by direct brain parenchymal administration of a rh.10 adeno-associated virus expressing <i>CLN2</i>
Authors: Dolan Sondhi, Stephen M. Kaminsky, Neil R. Hackett, Odelya E. Pagovich, Jonathan B. Rosenberg, Bishnu P. De, Alvin Chen, Benjamin Van de Graaf, Jason G. Mezey, Grace W. Mammen, Denesy Mancenido, Fang Xu, Barry Kosofsky, Kaleb Yohay, Stefan Worgall, Robert J. Kaner, Mark Souwedaine, Bruce M. Greenwald, Michael Kaplitt, Jonathan P. Dyke, Douglas J. Ballon, Linda A. Heier, Szilard Kiss, Ronald G. Crystal
Journal: Science Translational Medicine (2020)

Administration of an adeno-associated virus coding for the CLN2 gene into the brain parenchyma slows the progression of CLN2 disease in children.
PET-CT Does Not Impact on the Outcome of the Patients Affected By Multiple Myeloma after Autologous Transplantation: A Real Life Experience
Authors: Walter Bertolami, Paola Anna Erba, Francesco Caracciolo, Edoardo Benedetti, Enrico Orciuolo, Gabriele Buda, Riccardo Morganti, Sara Galimberti, Mario Petrini
Journal: Blood (2017)
Association between neuraxial anaesthesia or general anaesthesia for lower limb revascularisation surgery in adults and clinical outcomes: population based comparative effectiveness study
Authors: Derek J Roberts, Sudhir K Nagpal, Dalibor Kubelik, Timothy Brandys, Henry T Stelfox, Manoj M Lalu, Alan J Forster, Colin JL McCartney, Daniel I McIsaac
Journal: BMJ (2020)

Abstract Objective To examine the associations between neuraxial anaesthesia or general anaesthesia and clinical outcomes, length of hospital stay, and readmission in adults undergoing lower limb revascularisation surgery. Design Comparative effectiveness study using linked, validated, population based databases. Setting Ontario, Canada, 1 April 2002 to 31 March 2015. Participants 20 988 patients Ontario residents aged 18 years or older who underwent their first lower limb revascularisation surgery in hospitals performing 50 or more of these surgeries annually. Main outcome measures Primary outcome was 30 day all cause mortality. Secondary outcomes were in-hospital cardiopulmonary and renal complications, length of hospital stay, and 30 day readmissions. Multivariable, mixed effects regression models, adjusting for patient, procedural, and hospital characteristics, were used to estimate associations between anaesthetic technique and outcomes. Robustness of analyses were evaluated by conducting instrumental variable, propensity score matched, and survival sensitivity analyses. Results Of 20 988 patients who underwent lower limb revascularisation surgery, 6453 (30.7%) received neuraxial anaesthesia and 14 535 (69.3%) received general anaesthesia. The percentage of neuraxial anaesthesia use ranged from 0.6% to 90.6% across included hospitals. Furthermore, use of neuraxial anaesthesia declined by 17% over the study period. Death within 30 days occurred in 204 (3.2%) patients who received neuraxial anaesthesia and 646 (4.4%) patients who received general anaesthesia. After multivariable, multilevel adjustment, use of neuraxial anaesthesia compared with use of general anaesthesia was associated with decreased 30 day mortality (absolute risk reduction 0.72%, 95% confidence interval 0.65% to 0.79%; odds ratio 0.68, 95% confidence interval 0.57 to 0.83; number needed to treat to prevent one death=139). A similar direction and magnitude of association was found in instrumental variable, propensity score matched, and survival analyses. Use of neuraxial anaesthesia compared with use of general anaesthesia was also associated with decreased in-hospital cardiopulmonary and renal complications (odds ratio 0.73, 0.63 to 0.85) and a reduced length of hospital stay (−0.5 days, −0.3 to−0.6 days). Conclusions Use of neuraxial anaesthesia compared with general anaesthesia for lower limb revascularisation surgery was associated with decreased 30 day mortality and hospital length of stay. These findings might have been related to reduced cardiopulmonary and renal complications after neuraxial anaesthesia and support the increased use of neuraxial anaesthesia in patients undergoing these surgeries until the results of a large, confirmatory randomised trial become available.
Mohs micrographic surgery for male genital tumors: Local recurrence rates and patient-reported outcomes
Authors: Tess M. Lukowiak, Allison M. Perz, Leora Aizman, Robert Caleb Kovell, Stephen Kovach, John P. Fischer, Aimee Krausz, Cerrene Giordano, H. William Higgins, Thuzar M. Shin, Joseph F. Sobanko, Jeremy R. Etzkorn, Stacy McMurray, Raju Chelluri, Thomas Guzzo, Christopher J. Miller
Journal: Journal of the American Academy of Dermatology (2020)