tbuckley/cabot-search huggingface dataset:
Characteristics and Prognosis of Acquired Resistance to Immune Checkpoint Inhibitors in Gastrointestinal Cancer
Authors: Na Zhuo, Chang Liu, Qi Zhang, Jian Li, Xiaotian Zhang, Jifang Gong, Ming Lu, Zhi Peng, Jun Zhou, Xicheng Wang, Xi Jiao, Yujiao Wang, Yanni Wang, Mengting Gao, Lin Shen, Zhihao Lu
Journal: JAMA Network Open (2022)

With the expanding use of immune checkpoint inhibitors (ICIs) in gastrointestinal (GI) cancer, the occurrence of acquired resistance (AR) has gradually emerged. However, the progression patterns and survival of patients with AR to ICIs are still unknown.To explore the characteristics and prognosis of AR after ICI therapy in patients with advanced GI cancer.This cohort study screened patients with advanced GI cancer treated with ICIs between January 14, 2016, and December 31, 2020, at Peking University Cancer Hospital. Initial response was defined as complete response, partial response, or stable disease longer than 6 months as assessed by Response Evaluation Criteria in Solid Tumors version 1.1. Progression was also based on Response Evaluation Criteria in Solid Tumors version 1.1. Progression or death after the initial response was defined as AR. Oligoprogression of AR was defined as 2 or more disease sites progression. The current status of AR in GI cancer and the patterns of AR and its prognosis were evaluated. The site of AR and subsequent management were also assessed. Data were analyzed from June to August 2021.Patients in the cohort were treated with mono-ICI or combination therapy.Kaplan-Meier analyses and log-rank tests were conducted for overall survival analyses. Univariate and multivariate Cox analyses were conducted to determine the prognostic implications of each variable.Of the 1124 patients who received ICIs, 373 (33.2%) patients (282 men [75.6%]; median [IQR] age, 62 [54-68] years) achieved an initial response, and 173 (46.4%) patients (137 men [79.2%]; median [IQR] age, 61 [54-67] years) developed AR. Almost all patients (167 patients [96.5%]) developed AR within 24.0 months. Progression patterns of AR were most commonly oligoprogression (122 patients [70.5%]) rather than polymetastatic progression (38 patients [22.0%]) and were associated with a good prognosis (38.5 vs 14.0 months; hazard ratio, 0.37; 95% CI, 0.18-0.74; P < .001). Lymph nodes (101 patients [58.4%]) appeared to be the most common site of AR. Management after AR was mainly systemic therapy (96 patients [55.5%]).Oligoprogression was the most common pattern of AR progression, and lymph nodes were the most susceptible site for AR. Further study will be needed to determine the most favorable management for AR.
Nationwide study on SARS-CoV-2 transmission within households from lockdown to reopening, Denmark, 27 February 2020 to 1 August 2020
Authors: Frederik Plesner Lyngse, Carsten Kirkeby, Tariq Halasa, Viggo Andreasen, Robert Leo Skov, Frederik Trier Møller, Tyra Grove Krause, Kåre Mølbak
Journal: Eurosurveillance (2022)

Background The COVID-19 pandemic is one of the most serious global public health threats of recent times. Understanding SARS-CoV-2 transmission is key for outbreak response and to take action against the spread of disease. Transmission within the household is a concern, especially because infection control is difficult to apply within this setting. Aim The objective of this observational study was to investigate SARS-CoV-2 transmission in Danish households during the early stages of the COVID-19 pandemic. Methods We used comprehensive administrative register data from Denmark, comprising the full population and all COVID-19 tests from 27 February 2020 to 1 August 2020, to estimate household transmission risk and attack rate. Results We found that the day after receiving a positive test result within the household, 35% (788/2,226) of potential secondary cases were tested and 13% (98/779) of these were positive. In 6,782 households, we found that 82% (1,827/2,226) of potential secondary cases were tested within 14 days and 17% (371/2,226) tested positive as secondary cases, implying an attack rate of 17%. We found an approximate linear increasing relationship between age and attack rate. We investigated the transmission risk from primary cases by age, and found an increasing risk with age of primary cases for adults (aged ≥ 15 years), while the risk seems to decrease with age for children (aged &lt; 15 years). Conclusions Although there is an increasing attack rate and transmission risk of SARS-CoV-2 with age, children are also able to transmit SARS-CoV-2 within the household.
LIPID-LOWERING THERAPY INTENSIFICATION AMONG UNITED STATES VETERANS FOLLOWING MYOCARDIAL INFARCTION OR CORONARY REVASCULARIZATION BETWEEN 2015 AND 2019
Authors: Alexander R. Zheutlin, Catherine G. Derington, Jennifer S. Herrick, James Cook, Robert S. Rosenson, Bharat Poudel, Monika M. Safford, Todd M. Brown, Elizabeth A. Jackson, Mark Woodward, Stephanie Reading, Jason Exter, Kate Orroth, Salim S. Virani, Paul Muntner, Adam Phillip Bress
Journal: Journal of the American College of Cardiology (2022)
Ending the covid-19 pandemic means helping countries to catch-up with vaccination, not giving up
Authors: Seth Berkley
Journal: BMJ (2022)

The comparative analysis of National Tuberculosis Control Programmes (NTPs) in industrialised, low-tuberculosis-incidence countries is limited. Analysis of applied methods, function and accumulated experience contributes to improving global tuberculosis control. A questionnaire addressing NTP surveillance infrastructure and characteristics was completed in 19 industrialised countries, with populations of &gt;3 million and annual notified tuberculosis incidence rates of &lt;16 cases per 100,000 population (2003 data). All European countries surveyed adopted World Health Organization Collaborating Centre for the Surveillance of Tuberculosis in Europe (EuroTB) definitions. Surveillance information, which usually includes names, was transferred electronically to the national level in 17 out of the 19 countries. Surveillance systems capture process and social determinants. Case notification to the central level occurred within a median period of 7 days, independent of mandatory notification requirements. The mean completeness of tuberculosis case-reporting was estimated to be 93.5% (range 65–100%). Integration between HIV and tuberculosis registries was performed in two countries, and, in seven others, both databases were cross-matched periodically. National Tuberculosis Control Programme function in industrialised low-incidence countries utilises well-established infrastructure and relies upon centralised operations. Approaches are consistent with current World Health Organization surveillance recommendations. The present study lays collaborative groundwork for additional multinational analyses for the enhancement of global tuberculosis surveillance, which may assist policy-makers in countries moving from medium to low rates of incidence.
Executable network of SARS-CoV-2-host interaction predicts drug combination treatments
Authors: Rowan Howell, Matthew A. Clarke, Ann-Kathrin Reuschl, Tianyi Chen, Sean Abbott-Imboden, Mervyn Singer, David M. Lowe, Clare L. Bennett, Benjamin Chain, Clare Jolly, Jasmin Fisher
Journal: npj Digital Medicine (2022)

The COVID-19 pandemic has pushed healthcare systems globally to a breaking point. The urgent need for effective and affordable COVID-19 treatments calls for repurposing combinations of approved drugs. The challenge is to identify which combinations are likely to be most effective and at what stages of the disease. Here, we present the first disease-stage executable signalling network model of SARS-CoV-2-host interactions used to predict effective repurposed drug combinations for treating early- and late stage severe disease. Using our executable model, we performed in silico screening of 9870 pairs of 140 potential targets and have identified nine new drug combinations. Camostat and Apilimod were predicted to be the most promising combination in effectively supressing viral replication in the early stages of severe disease and were validated experimentally in human Caco-2 cells. Our study further demonstrates the power of executable mechanistic modelling to enable rapid pre-clinical evaluation of combination therapies tailored to disease progression. It also presents a novel resource and expandable model system that can respond to further needs in the pandemic.
Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma
Authors: Samuel S. Freeman, Moshe Sade-Feldman, Jaegil Kim, Chip Stewart, Anna L.K. Gonye, Arvind Ravi, Monica B. Arniella, Irena Gushterova, Thomas J. LaSalle, Emily M. Blaum, Keren Yizhak, Dennie T. Frederick, Tatyana Sharova, Ignaty Leshchiner, Liudmila Elagina, Oliver G. Spiro, Dimitri Livitz, Daniel Rosebrock, François Aguet, Jian Carrot-Zhang, Gavin Ha, Ziao Lin, Jonathan H. Chen, Michal Barzily-Rokni, Marc R. Hammond, Hans C. Vitzthum von Eckstaedt, Shauna M. Blackmon, Yunxin J. Jiao, Stacey Gabriel, Donald P. Lawrence, Lyn M. Duncan, Anat O. Stemmer-Rachamimov, Jennifer A. Wargo, Keith T. Flaherty, Ryan J. Sullivan, Genevieve M. Boland, Matthew Meyerson, Gad Getz, Nir Hacohen
Journal: Cell Reports Medicine (2022)

Immune checkpoint blockade (CPB) improves melanoma outcomes, but many patients still do not respond. Tumor mutational burden (TMB) and tumor-infiltrating T cells are associated with response, and integrative models improve survival prediction. However, integrating immune/tumor-intrinsic features using data from a single assay (DNA/RNA) remains underexplored. Here, we analyze whole-exome and bulk RNA sequencing of tumors from new and published cohorts of 189 and 178 patients with melanoma receiving CPB, respectively. Using DNA, we calculate T cell and B cell burdens (TCB/BCB) from rearranged TCR/Ig sequences and find that patients with TMBhigh and TCBhigh or BCBhigh have improved outcomes compared to other patients. By combining pairs of immune- and tumor-expressed genes, we identify three gene pairs associated with response and survival, which validate in independent cohorts. The top model includes lymphocyte-expressed MAP4K1 and tumor-expressed TBX3. Overall, RNA or DNA-based models combining immune and tumor measures improve predictions of melanoma CPB outcomes.
THE LONG-TERM EFFICACY AND SAFETY OF EVINACUMAB IN PATIENTS WITH REFRACTORY HYPERCHOLESTEROLEMIA
Authors: Robert S. Rosenson, Lesley J. Burgess, Christoph F. Ebenbichler, Seth J. Baum, Erik S.G. Stroes, Shazia Ali, Nagwa Khilla, Robert Pordy, Divya Singh, Daniel Gaudet
Journal: Journal of the American College of Cardiology (2022)
FULLY AUTOMATED ANALYSIS OF CARDIAC POINT OF CARE ULTRASOUND: FEASIBILITY AND CLINICAL RELEVANCE IN COVID-19 PATIENTS.
Authors: Will Hawkes, Martin G. Keane, Benjamin Khazan, SALIMA QAMRUDDIN, Austen Tutor, Ritu Thamman, Tasneem Z. Naqvi, Deepa Mandale, Jordan B. Strom, Gabriel Pajares Hurtado, Eric Peterson, Fahad I. Gul, Shivani Watson, Katherine Tilkes, Halley Davidson, Christopher Scott, Hania Piotrowska, William H. Hansen, Gary Woodward, Patricia A. Pellikka
Journal: Journal of the American College of Cardiology (2022)
Long-Term Efficacy of Colchicine in Patients With Chronic Coronary Disease: Insights From LoDoCo2
Authors: Tjerk S.J. Opstal, Amber van Broekhoven, Aernoud T.L. Fiolet, Arend Mosterd, John W. Eikelboom, Stefan M. Nidorf, Peter L. Thompson, Charley A. Budgeon, Louis Bartels, Ron de Nooijer, Willem A. Bax, Jan G.P. Tijssen, Saloua El Messaoudi, Jan H. Cornel
Journal: Circulation (2022)
Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients
Authors: Maria Paz Ventero, Oscar Moreno-Perez, Carmen Molina-Pardines, Andreu Paytuví-Gallart, Vicente Boix, Isabel Escribano, Irene Galan, Pilar González-delaAleja, Mario López-Pérez, Rosario Sánchez-Martínez, Esperanza Merino, Juan Carlos Rodríguez
Journal: Journal of Infection (2021)
SEX DIFFERENCES IN EFFECTIVENESS AND SAFETY OF ASPIRIN IN SECONDARY PREVENTION OF CARDIOVASCULAR OUTCOMES IN PATIENTS: A SUBGROUP ANALYSIS FROM THE ADAPTABLE STUDY
Authors: Catherine P. Benziger, Amanda Stebbins, Wruck Lisa, Guillaume Marquis-Gravel, Faraz S. Ahmad, Peter M. Farrehi, Saket Girotra, Kamal Gupta, Sunil Kripalani, Harsh Mehta, Daniel Munoz, Tamar Polonsky, Amber Sharlow, Jeffrey Whittle, Adrian F. Hernandez, W. Schuyler Jones
Journal: Journal of the American College of Cardiology (2022)
Colchicine prophylaxis is associated with fewer gout flares after COVID-19 vaccination
Authors: Jie Lu, Yuwei He, Robert Terkeltaub, Mingshu Sun, Zijing Ran, Xinmiao Xu, Can Wang, Xinde Li, Shuhui Hu, Xiaomei Xue, Fei Yan, Hui Zhang, Huiyong Yin, Yongyong Shi, Nicola Dalbeth, Changgui Li
Journal: Annals of the Rheumatic Diseases (2022)

COVID-19 vaccination often triggers a constellation of transitory inflammatory symptoms. Gout is associated with several comorbidities linked to poor outcomes in COVID-19, and gout flares can be triggered by some vaccinations. We analysed the risk of gout flares in the first 3 months after COVID-19 vaccination with inactivated virus, and whether colchicine can prevent gout flares following post-COVID-19 vaccination.A clinical delivery population-based cross-sectional study was conducted in the Gout Clinic at the Affiliated Hospital of Qingdao University between February and October 2021. Study participants were selected using a systematic random sampling technique among follow-up patients with gout. We collected data, including vaccinations and potential risk factors, using a combination of interviews, health QR codes and medical records. Logistic regression was used to adjust for covariates.We enrolled 549 gout participants (median age 39 years, 84.2% vaccinated). For the 462 patients who received COVID-19 vaccine, 203 (43.9%) developed at least one gout flare in the 3 months after vaccination. Most of these flares were experienced within 1 month after the first (99/119 (83.2%)) or second (70/115 (60.9%)) dose of vaccine. Compared with unvaccinated participants, COVID-19 vaccination was associated with higher odds of gout flare within 3 months (adjusted OR 6.02; 95% CI 3.00 to 12.08). Colchicine use was associated with 47% less likelihood of postvaccine gout flare.COVID-19 vaccination was associated with increased odds of gout flare, which developed mainly in month 1 after each vaccine dose, and was negatively associated with colchicine prophylaxis.
CONQUERING THE SUMMIT WITH BIPOLAR ABLATION: BIPOLAR ABLATION FROM THE ANTERIOR INTERVENTRICULAR BRANCH TO THE LEFT VENTRICLE
Authors: James Mann, Shu Chang, Syed Rafay Ali Sabzwari, Christopher Barrett, Lukasz Patrick Cerbin, Lohit Garg, Alexis Z. Tumolo, Amneet Sandhu, Jason J. West, Michael Rosenberg, Matthew Michael Zipse, Paul D. Varosy, Wendy S. Tzou, Ryan G. Aleong
Journal: Journal of the American College of Cardiology (2022)
Uterine HOXA11 antisense long non-coding RNA prevents decidualization: A new pathway-regulating pregnancy
Authors: Hugh S. Taylor
Journal: Molecular Therapy (2022)

To achieve a successful pregnancy, coordinated development of the embryo and uterine endometrium are normally archived by coupling ovulation to progesterone production. A surge of pituitary luteinizing hormone triggers the release of oocytes and simultaneously initiates the conversion of the ovarian follicle to the corpus luteum, which produces large quantities of progesterone. Progesterone, in turn, drives endometrial differentiation, also known as decidualization. The decidualized endometrium is briefly receptive to the developing embryo, allowing the embryo to attach and implant in the uterine endometrium, thus establishing the early pregnancy.
A real-world, single-center experience and the immediate impact of granulocyte and monocyte adsorption apheresis on generalized pustular psoriasis
Authors: Hideaki Uchida, Masahiro Kamata, Shota Egawa, Mayumi Nagata, Saki Fukaya, Kotaro Hayashi, Atsuko Fukuyasu, Takamitsu Tanaka, Takeko Ishikawa, Takamitsu Ohnishi, Kazumitsu Sugiura, Yayoi Tada
Journal: Journal of the American Academy of Dermatology (2022)
TRENDS IN FOOD INSECURITY AMONG THOSE WITH CARDIOVASCULAR DISEASE AND CARDIOMETABOLIC RISK FACTORS ACROSS RACE AND ETHNICITY FROM 1999-2018
Authors: Eric J. Brandt, John Z. Ayanian, Tammy Chang, Cindy Leung, Brahmajee K. Nallamothu
Journal: Journal of the American College of Cardiology (2022)
NCCN Guidelines® Insights: Head and Neck Cancers, Version 1.2022
Authors: Jimmy J. Caudell, Maura L. Gillison, Ellie Maghami, Sharon Spencer, David G. Pfister, Douglas Adkins, Andrew C. Birkeland, David M. Brizel, Paul M. Busse, Anthony J. Cmelak, A. Dimitrios Colevas, David W. Eisele, Thomas Galloway, Jessica L. Geiger, Robert I. Haddad, Wesley L. Hicks, Ying J. Hitchcock, Antonio Jimeno, Debra Leizman, Loren K. Mell, Bharat B. Mittal, Harlan A. Pinto, James W. Rocco, Cristina P. Rodriguez, Panayiotis S. Savvides, David Schwartz, Jatin P. Shah, David Sher, Maie St. John, Randal S. Weber, Gregory Weinstein, Frank Worden, Justine Yang Bruce, Sue S. Yom, Weining Zhen, Jennifer L. Burns, Susan D. Darlow
Journal: Journal of the National Comprehensive Cancer Network (2022)

The NCCN Guidelines for Head and Neck Cancers address tumors arising in the oral cavity (including mucosal lip), pharynx, larynx, and paranasal sinuses. Occult primary cancer, salivary gland cancer, and mucosal melanoma (MM) are also addressed. The specific site of disease, stage, and pathologic findings guide treatment (eg, the appropriate surgical procedure, radiation targets, dose and fractionation of radiation, indications for systemic therapy). The NCCN Head and Neck Cancers Panel meets at least annually to review comments from reviewers within their institutions, examine relevant new data from publications and abstracts, and reevaluate and update their recommendations. These NCCN Guidelines Insights summarize the panel's most recent recommendations regarding management of HPV-positive oropharynx cancer and ongoing research in this area.
MORTALITY AMONGST PATIENTS WITH ATRIAL FIBRILLATION AND VALVULAR HEART DISEASE (VHD) FOLLOWING DOAC VS VKA- AMETA-ANALYSIS
Authors: Beshoy Iskander, Ghanshyam Patel, Vandit Vandit Vyas, Siddhant Jain, Tanvi Singla, Nikhila Chelikam Chelikam, Lavanya Dondapati, Ali Bombaywala, Daniel Zarrate, Nitesh Jain, Urvish Patel, Appala Peela, Amit Sharma
Journal: Journal of the American College of Cardiology (2022)
DIAGNOSTIC PERFORMANCE OF CORONARY ANGIOGRAPHY-BASED INDEX OF MICROCIRCULATORY RESISTANCE ASSESSMENT: A SYSTEMIC REVIEW AND META ANALYSIS
Authors: Weijia Li, Tatsunori Takahashi, Saul Rios, Azeem Latib, Joo Myung Lee, William Fuller Fearon, Yuhei Kobayashi
Journal: Journal of the American College of Cardiology (2022)
LONG-TERM OUTCOMES FOLLOWING TRANSCATHETER AORTIC VALVE REPLACEMENT IN PATIENTS WITH HISTORY OF RADIATION THERAPY
Authors: Kris Kumar, Ashraf Samhan, Craig C. Morris, Trisha Chau, Tessa Herman, Gurion Lantz, Scott M. Chadderdon, Howard K. Song, Firas E. Zahr, Harsh Golwala
Journal: Journal of the American College of Cardiology (2022)
INTER-PACEMAKER CROSSTALK - A CAUSE FOR CRT FAILURE
Authors: Nikky Bardia, Usman Sarwar, Maulikkumar Patel, Nupur Shah, Siva Chiranjeevi, Nilarun Chowdhuri, Christopher Michael Malozzi, Farnoosh Rahimi, Ghulam Mustafa Awan, Amod Amritphale, Bassam A. Omar
Journal: Journal of the American College of Cardiology (2022)
PREDICTORS OF ACUTE GOUT IN ACUTE DECOMPENSATED SYSTOLIC HEART FAILURE-ANALYSIS FROM NATIONAL INPATIENT SAMPLE
Authors: Shakeel Jamal, Ehizogie Edigin, Asim Kichloo, Preeti Kansal, Augustine Manadan, Anwar Zaitun, Timir K. Paul
Journal: Journal of the American College of Cardiology (2022)
Abstract P3-19-05: Genomic machine learning model predicts radiation therapy benefit in early-stage breast cancer patients with high accuracy
Authors: Kimberly Badal, Jerome Foster, Rajini Haraksingh, Melford John
Journal: Cancer Research (2022)

Abstract Background: Radiation therapy (RT) is frequently recommended for post-surgery treatment of early-stage breast cancer (BC) patients, though not all benefit. Clinical factors currently guide RT treatment decisions. This work presents a high-accuracy genomic machine learning (ML) model to predict RT-benefit in early-stage BC patients and a novel method for selecting genomic features for ML algorithms. Methods: Gene expression data from 477 early-stage BC patients treated with surgery and RT from the METABRIC cohort were obtained. Wilcoxon Rank Sum (Wilcox RS) test and Cox Proportional Hazards (Cox PH) were used to reduce the number of genes used to train 8 ML algorithms. Each ML algorithm was trained on a random subset of 80% of the data using 10-fold cross-validation and tested on the remaining 20% to assess its performance in predicting relapse status within 30 years. Results: The genomic data were reduced using Wilcox RS and Cox PH to a 1,596 gene set and a 977 gene set. These gene sets when used to train the 8 ML algorithms resulted in models that ranged in performance accuracies from 54.01% to 95.6%. The highest accuracies were obtained using Support Vector Machine (SVM977 - 93.41%, SVM1596 - 95.6%) and Neural Networks (NN977 - 92.31%, NN1596 - 93.41%). The accuracy of all models when tested on RT-untreated patients was 30-40% lower compared to RT-treated patients. SVM977 had the highest sensitivity of 91.09%. Members of the 977 gene set were enriched with genes involved in the cell cycle and differentiation as well as radiogenes. Conclusion: We developed an SVM model that used 977 differentially expressed genes as features that predicted RT-benefit in early-stage BC patients with 93.41% accuracy and 91.09% sensitivity. We also developed a novel genomic feature selection approach that used Wilcoxon RS followed by Cox PH that resulted in expression values of only 4% of all genes being used as features in the models. Citation Format: Kimberly Badal, Jerome Foster, Rajini Haraksingh, Melford John. Genomic machine learning model predicts radiation therapy benefit in early-stage breast cancer patients with high accuracy [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-19-05.