tbuckley/cabot-search huggingface dataset:
COVID-19 mRNA vaccines drive differential antibody Fc-functional profiles in pregnant, lactating, and nonpregnant women
Authors: Caroline Atyeo, Elizabeth A. DeRiso, Christine Davis, Evan A. Bordt, Rose M. De Guzman, Lydia L. Shook, Lael M. Yonker, Alessio Fasano, Babatunde Akinwunmi, Douglas A. Lauffenburger, Michal A. Elovitz, Kathryn J. Gray, Andrea G. Edlow, Galit Alter
Journal: Science Translational Medicine (2021)

Substantial immunological changes occur throughout pregnancy to render the mother immunologically tolerant to the fetus and allow fetal growth. However, additional local and systemic immunological adaptations also occur, allowing the maternal immune system to continue to protect the dyad against pathogens both during pregnancy and after birth through lactation. This fine balance of tolerance and immunity, along with physiological and hormonal changes, contributes to increased susceptibility to particular infections in pregnancy, including more severe coronavirus disease 2019 (COVID-19). Whether these changes also make pregnant women less responsive to vaccination or induce altered immune responses to vaccination remains incompletely understood. To define potential changes in vaccine response during pregnancy and lactation, we undertook deep sequencing of the humoral vaccine response in a group of pregnant and lactating women and nonpregnant age-matched controls. Vaccine-specific titers were comparable between pregnant women, lactating women, and nonpregnant controls. However, Fc receptor (FcR) binding and antibody effector functions were induced with delayed kinetics in both pregnant and lactating women compared with nonpregnant women after the first vaccine dose, which normalized after the second dose. Vaccine boosting resulted in high FcR-binding titers in breastmilk. These data suggest that pregnancy promotes resistance to generating proinflammatory antibodies and indicates that there is a critical need to follow prime-boost timelines in this vulnerable population to ensure full immunity is attained.
OA15.04 Telisotuzumab Vedotin (teliso-v) Monotherapy in Patients With Previously Treated c-Met+ Advanced Non-Small Cell Lung Cancer
Authors: D.R. Camidge, F. Moiseenko, I. Cicin, H. Horinouchi, E. Filippova, J. Bar, S. Lu, P. Tomasini, C. Ocampo, D. Sullivan, D. Maag, J. Goldman
Journal: Journal of Thoracic Oncology (2021)
OA06.04 Constructing a Global Molecular Database for Thoracic Malignancies: The IASLC Molecular Subcommittee Lung Cancer Dataset
Authors: R. Osarogiagbon, K. Nishimura, R. Rami Porta, L. Montuenga, D. Giroux, K. Suda, L. Araujo, F. Detterbeck, O. Gautschi, K. Kerr, P. Kneuertz, P. Mack, J. Matilla, A. Nicholson, H. Pass, C. Presley, R. Terra, I. Wistuba, D. Yang, Y. Yatabe, W. Travis, M. Tsao, H. Asamura, V. Rusch, F. Hirsch, D. Carbone
Journal: Journal of Thoracic Oncology (2021)
P62.03 Survival After Distant Recurrent Versus De Novo Stage IV Metastatic Lung Cancer Under Low-Dose Computed Tomography Screening
Authors: C. Su, E. Choi, J. Wu, J. Neal, A. Kurian, L. Backhus, A. Leung, H. Wakelee, S. Han
Journal: Journal of Thoracic Oncology (2021)
Gut microbiome features associated with liver fibrosis in Hispanics, a population at high risk for fatty liver disease
Authors: Suet‐Ying Kwan, Jingjing Jiao, Aron Joon, Peng Wei, Lauren E. Petty, Jennifer E. Below, Carrie R. Daniel, Xiaogang Wu, Jianhua Zhang, Robert R. Jenq, P. Andrew Futreal, Ernest T. Hawk, Joseph B. McCormick, Susan P. Fisher‐Hoch, Laura Beretta
Journal: Hepatology (2021)

Hispanics are disproportionately affected by NAFLD, liver fibrosis, cirrhosis, and HCC. Preventive strategies and noninvasive means to identify those in this population at high risk for liver fibrosis, are urgently needed. We aimed to characterize the gut microbiome signatures and related biological functions associated with liver fibrosis in Hispanics and identify environmental and genetic factors affecting them.
P40.19 Efficacy and Toxicity of Third-Line Chemotherapy in Advanced Non-Small Cell Lung Cancer
Authors: T. Beninato, S. Manglaviti, E. Zattarin, G. Apollonio, E. Galli, M. Bini, C. Sposetti, G. Massa, A. Bottiglieri, M. Ganzinelli, C. Proto, R. Ferrara, A. Prelaj, G. Galli, A. De Toma, M. Brambilla, M. Occhipinti, F.G.M. De Braud, M.C. Garassino, G. Lo Russo
Journal: Journal of Thoracic Oncology (2021)
MA01.02 Surgical Complexity of Pulmonary Resections Performed for Oligometastatic Non-Small Cell Lung Cancer
Authors: M. Antonoff, H. Feldman, K. Mitchell, A. Farooqi, E. Ludmir, W. Hofstetter, R. Mehran, R. Rajaram, D. Rice, B. Sepesi, S. Swisher, A. Vaporciyan, G. Walsh, S. Gandhi, D. Gomez
Journal: Journal of Thoracic Oncology (2021)
Trying to Block SARS-CoV-2 Transmission With Intranasal Vaccines
Authors: Rita Rubin
Journal: JAMA (2021)

urrently available COVID-19 vaccines are highly effective at reducing symptom severity, but they don't appear to prevent SARS-CoV-2 from gaining a toehold in the nose.Ensconced there, the virus can stealthily replicate and then, expelled by coughing or sneezing, go on to infect others.The vaccines, all administered as intramuscular injections, induce circulating antibodies in the blood but not mucosal antibodies in the lining of the nose."It's actually very hard to protect the upper respiratory tract with these [injected] systemic vaccines," Vincent Munster, PhD, chief of the Virus Ecology Section of the National Institute of Allergy and Infectious Diseases (NIAID) Rocky Mountain Laboratories, said in an interview.But what if a COVID-19 vaccine could be sprayed or squirted into the nose?Could such a vaccine induce an immune response in the nasal mucosa, thus stopping SARS-CoV-2 from hitching a ride and spreading?That's the goal of Munster and other scientists in a handful of countries who've been investigating intranasal COVID-19 vaccine candidates.Tests in animal models have looked promising, and phase 1 clinical trials in healthy, COVID-19 vaccine-naive individuals are underway."We think intranasal vaccines are important because they have the potential to block transmission," unlike the available injected vaccines, said Martin Moore, PhD, the CEO and cofounder of Meissa Vaccines in Redwood City, California, which has launched a phase 1 trial of its intranasal vaccine.Studies suggest that individuals who receive injected COVID-19 vaccines may be protected against serious illness from SARS-CoV-2 but can still become infected and spread the virus.For example, research by Munster and coauthors found that the intramuscular Oxford/AstraZeneca vaccine, which isn't authorized in the US, protected rhesus monkeys exposed to SARS-CoV-2 against pneumonia but didn't reduce viral shedding from their upper respiratory tract.And in the 469 cases identified in this past July's COVID-19 outbreak in Provincetown,
Clinical Features at Presentation for Glioblastoma Patients Impact Survival Predictions in a Machine Learning Model
Authors: Alistair Lawrence, Rohit Sinha, Stefan Mitrasinovic, Stephen Price
Journal: Neuro-Oncology (2021)

Abstract Aims To generate an accurate prediction model for greater than median survival using Random Forest machine learning analysis and to compare the model to a traditional logistic regression analysis model on the same Glioblastoma Dataset. Method In this single centre retrospective cohort study, all patients with histologically diagnosed primary GB from October 2014 to April 2019 were included (n=466). Machine learning algorithms encompassing multiple logistic regression and a Random Forest, Gini index-based decision tree model with 100,000 trees were used. 17 clinical, molecular and treatment specific binarily categorised variables were used. The dataset was split 70:30 into training and validating sets. Results The dataset contained 466 patients. 326 patients made up the training set and 140 the validation set. The Random Forest model’s accuracy for predicting 18-month survival was 86.4% compared to the Logistic Regression model’s accuracy of 85.7%. The top 5 factors that the Random Forest model used to predict survival over 18 months were; mean MGMT status &amp;gt;10%, if the patient underwent gross total resection, whether the patient had adjuvant temozolomide, whether the patient had a neurological deficit on presentation, and the sex of the patient. Conclusion Machine learning can be applied in the context of GB prognostic modelling. The models show that as well as the known factors that affect GB survival, the presenting symptom may also have an impact on prognostication.
Evaluation of the Cost-effectiveness of Drug Treatment for Alzheimer Disease in a Simulation Model That Includes Caregiver and Societal Factors
Authors: Kouta Ito, Rick Chapman, Steven D. Pearson, Ali Tafazzoli, Kristine Yaffe, Jerry H. Gurwitz
Journal: JAMA Network Open (2021)

The possibility of widespread use of a novel effective therapy for Alzheimer disease (AD) will present important clinical, policy, and financial challenges.
Endoscopic Treatment of Large Bile Duct Stones: A Systematic Review and Network Meta-Analysis
Authors: Antonio Facciorusso, Paraskevas Gkolfakis, Daryl Ramai, Georgios Tziatzios, Janice Lester, Stefano Francesco Crinò, Leonardo Frazzoni, Ioannis S. Papanikolaou, Marianna Arvanitakis, Daniel Blero, Arnaud Lemmers, Pierre Eisendrath, Lorenzo Fuccio, Konstantinos Triantafyllou, Armando Gabbrielli, Jacques Devière
Journal: Clinical Gastroenterology and Hepatology (2021)
Two subclasses of advanced serous ovarian adenocarcinoma with different gene expression profilings by hierarchical clustering and non-negative matrix factorization
Authors: Kosuke Yoshihara, Masayuki Sekine, Atsushi Tajima, Ituro Inoue, Kenichi Tanaka
Journal: Cancer Research (2007)

2976  Ovarian cancer is the most lethal malignancy in gynecological field. The current classification method applied for epithelial ovarian cancer mainly based on pathological examination is far from sufficient to predict clinical outcome. To ensure a clinically useful classification by gene expression signature, we used Agilent Human 1A(v2) Oligo microarrays to profile gene expression of 18716 genes in a series of seventeen advanced serous ovarian adenocarcinoma samples and six normal peritoneum samples as control.  1209 genes were differentially expressed between serous adenocarcinomas and peritoneums; 457 genes were up-regulated and 734 genes were down-regulated in serous adenocarcinomas. Hierarchical clustering (HC) with the 1209 genes classified serous adenocarcinomas into two subgroups. To confirm the classification provided by HC, we applied a non-negative matrix factorization (NMF) analysis that is an unsupervised classification method. NMF analysis also provided two subgroups, comprising the same adenocarcinomas samples as indicated with the HC dendrogram. To further characterize the two subgroups from the clinical aspect, we first compared these groups according to overall survival, however, there was no difference (p=0.963; logrank test). We noticed an enrichment of lymph node metastasis in one subgroup (six out of fourteen patients) whereas no metastasis patient in the other group (zero out of six patients). Reflecting the metastasis condition there appears to be a slight difference between the two subgroups in disease-free survival (p=0.097; logrank test). Subsequent statistical analysis showed that 29 genes were differentially expressed between the two subgroups, assuming that the gene expression pattern may predict the prognosis of serous adenocarcinoma. This work represents the first step to the identification of useful classification for serous ovarian adenocarcinoma.
P57.16 Inflammatory Markers as Predictors of Treatment Response and Survival in Patients With Non-Small Cell Lung Cancer Treated with PD-1 Inhibitors
Authors: I. Tourkantonis, I. Gkiozos, D. Grapsa, A. Charpidou, H. Gogas, D. Psyrri, K. Syrigos
Journal: Journal of Thoracic Oncology (2021)
P60.12 Prevalence of c-Met overexpression (c-Met+) and Impact of Prior Lines of Treatment on c-Met Protein Expression in NSCLC
Authors: M. Motwani, S. Panchabhai, J. Bar, N. Girard, P. Bradbury, S. Lu, J. Jin, A. Hotson, D. Maag, D. Planchard, D.R. Camidge
Journal: Journal of Thoracic Oncology (2021)
Abstract 15109: Atrial Fibrillation Treatment and Outcomes in Pregnancy
Authors: Fahd N Yunus, Mariam Askari, Jun Fan, Alexander C Perino, Mintu P Turakhia
Journal: Circulation (2018)

Background: Atrial fibrillation (AF) is the most common arrhythmia during pregnancy, yet there is limited data on management and outcomes. We attempted to describe the burden of AF during pregnancy...
Phase II study of crizotinib in east Asian patients (pts) with ROS1-positive advanced non-small cell lung cancer (NSCLC).
Authors: Koichi Goto, James Chih-Hsin Yang, Dong-Wan Kim, Shun Lu, Takashi Seto, Jin-Ji Yang, Noboru Yamamoto, Myung-Ju Ahn, Toshiaki Takahashi, Takeharu Yamanaka, Allison Margaret Kemner, Debasish Roychowdhury, Jolanda Paolini, Keith D. Wilner, Yi-Long Wu
Journal: Journal of Clinical Oncology (2016)

9022 Background: Approximately 1–2% of NSCLCs harbor a rearrangement of the ROS1 gene, an oncogene for which screening is difficult due to its low incidence. Crizotinib, an inhibitor of anaplastic lymphoma kinase (ALK), ROS1, and MET, showed marked antitumor activity in ROS1-positive advanced NSCLC (Shaw, N Engl J Med 2014). In the present study, we assessed the antitumor activity and safety of crizotinib in East Asian pts with ROS1-positive advanced NSCLC. Methods: In this ongoing open-label, single-arm phase II study (NCT01945021), pts with ROS1-positive, ALK-negative advanced NSCLC who had received ≤ 3 lines of prior systemic therapy were administered crizotinib at a starting dose of 250 mg BID. Treatment was continued until RECIST-defined progression (determined by independent radiology review [IRR]), unacceptable toxicity, or withdrawal of consent, or at the investigator's discretion for ongoing clinical benefit. The primary endpoint was ORR by IRR. Results: Between September 2013 and January 2015, 129 pts were enrolled at 37 sites in China, Japan, Korea, and Taiwan, making this the largest study of ROS1-positive NSCLC to date. Crizotinib was administered to 127 pts (all were included in the antitumor and safety analyses), and 63% were ongoing at data cutoff (6 months after the last pt enrolled). ORR by IRR was 69% (95% CI: 61–77) and was similar (63−80%) irrespective of the number of prior lines of therapy. For most pts, responses were observed within the first 2 months. Disease control rates were 84% at week 8 and 76% at week 16. At data cutoff, responses were durable (median duration of response: not reached [NR]; 95% CI: 8.5 months – NR). The median duration of crizotinib treatment was 7.8 months. The most frequently reported all-causality AEs (any grade) were elevated transaminases (58%), vision disorder (47%), diarrhea (46%), and nausea (44%). Of 18 deaths on study (15 due to PD, 2 to pneumonia, and 1 to respiratory failure), none were attributed to crizotinib. Conclusions: This study supports the clinical benefit of crizotinib in East Asian pts with ROS1-positive advanced NSCLC. Crizotinib was generally well tolerated, with a safety profile consistent with that previously reported. Clinical trial information: NCT01945021.
Shining light on chiral inorganic nanomaterials for biological issues
Authors: Yining Shao, Guilin Yang, Jiaying Lin, Xiaofeng Fan, Yue Guo, Wentao Zhu, Ying Cai, Huiyu Huang, Die Hu, Wei Pang, Yanjun Liu, Yiwen Li, Jiaji Cheng, Xiaoqian Xu
Journal: Theranostics (2021)

The rapid development of chiral inorganic nanostructures has greatly expanded from intrinsically chiral nanoparticles to more sophisticated assemblies made by organics, metals, semiconductors, and their hybrids. Among them, lots of studies concerning on hybrid complex of chiral molecules with achiral nanoparticles (NPs) and superstructures with chiral configurations were accordingly conducted due to the great advances such as highly enhanced biocompatibility with low cytotoxicity and enhanced penetration and retention capability, programmable surface functionality with engineerable building blocks, and more importantly tunable chirality in a controlled manner, leading to revolutionary designs of new biomaterials for synergistic cancer therapy, control of enantiomeric enzymatic reactions, integration of metabolism and pathology
P04.01 Presence of Ground Glass Opacity Component is True Determinant of Prognosis in Clinical Stage I Non-Small Cell Lung Cancer
Authors: A. Hamada, K. Suda, S. Ohara, M. Chiba, M. Shimoji, M. Endo, T. Takemoto, J. Soh, S. Shiono, T. Mitsudomi
Journal: Journal of Thoracic Oncology (2021)
Chemogenetic sensory fMRI reveals behaviorally relevant bidirectional changes in primate somatosensory network
Authors: Toshiyuki Hirabayashi, Yuji Nagai, Yukiko Hori, Ken-ichi Inoue, Ichio Aoki, Masahiko Takada, Tetsuya Suhara, Makoto Higuchi, Takafumi Minamimoto
Journal: Neuron (2021)
HHV-6 Prophylaxis with Foscanet Improves Hematopoietic Engraftment after Umbilical Cord Blood Transplantation
Authors: Nelli Bejanyan, John Rogosheske, Todd E. DeFor, Jaime Green, Troy C Lund, Daniel J. Weisdorf, John E. Wagner, Claudio G Brunstein
Journal: Blood (2017)
P62.02 A Predictive Model to Guide Brain MRI Surveillance in Patients With Metastatic Lung Cancer: Impact on Real World Outcomes
Authors: J. Wu, V. Ding, S. Luo, E. Choi, J. Hellyer, N. Myall, S. Henry, D. Wood, H. Stehr, H. Ji, S. Nagpal, M. Hayden Gephart, H. Wakelee, J. Neal, S. Han
Journal: Journal of Thoracic Oncology (2021)
P48.11 ctDNA Dynamic Detection Reveals the Advantages of EGFR Tyrosine Kinase Inhibitors Combined With Chemotherapy in NSCLC Patients
Authors: W. Feng, W. Gu, H. Zhang, Y. Lu, W. Gu, M. Li, S. Yang, Z. Ye, J. Liu, Q. Lin, Y. Liang, J. Zhang, H. Chen, X. Shi, F. Wang, D. You
Journal: Journal of Thoracic Oncology (2021)
Peripheral blood RNA biomarkers for cardiovascular disease from bench to bedside: a position paper from the EU-CardioRNA COST action CA17129
Authors: Maarten Vanhaverbeke, Ritienne Attard, Monika Bartekova, Soumaya Ben-Aicha, Timo Brandenburger, David de Gonzalo-Calvo, Costanza Emanueli, Rosienne Farrugia, Johannes Grillari, Matthias Hackl, Barbora Kalocayova, Fabio Martelli, Markus Scholz, Stephanie Bezzina Wettinger, Yvan Devaux
Journal: Cardiovascular Research (2021)

Abstract Despite significant advances in the diagnosis and treatment of cardiovascular diseases, recent calls have emphasized the unmet need to improve precision-based approaches in cardiovascular disease. Although some studies provide preliminary evidence of the diagnostic and prognostic potential of circulating coding and non-coding RNAs, the complex RNA biology and lack of standardization have hampered the translation of these markers into clinical practice. In this position paper of the CardioRNA COST action CA17129, we provide recommendations to standardize the RNA development process in order to catalyse efforts to investigate novel RNAs for clinical use. We list the unmet clinical needs in cardiovascular disease, such as the identification of high-risk patients with ischaemic heart disease or heart failure who require more intensive therapies. The advantages and pitfalls of the different sample types, including RNAs from plasma, extracellular vesicles, and whole blood, are discussed in the sample matrix, together with their respective analytical methods. The effect of patient demographics and highly prevalent comorbidities, such as metabolic disorders, on the expression of the candidate RNA is presented and should be reported in biomarker studies. We discuss the statistical and regulatory aspects to translate a candidate RNA from a research use only assay to an in-vitro diagnostic test for clinical use. Optimal planning of this development track is required, with input from the researcher, statistician, industry, and regulatory partners.
Overlap and cumulative effects of pancreatic duct obstruction, abnormal pain processing and psychological distress on patient-reported outcomes in chronic pancreatitis
Authors: Søren S Olesen, Anna E Phillips, Mahya Faghih, Louise Kuhlmann, Emily Steinkohl, Jens B Frøkjær, Benjamin L Bick, Mitchell L Ramsey, Phil A Hart, Pramod K Garg, Vikesh K Singh, Dhiraj Yadav, Asbjørn M Drewes
Journal: Gut (2021)

Objective Several factors have been suggested to mediate pain in patients with chronic pancreatitis. However, it is unknown whether these factors are overlapping and if they have cumulative effects on patient-reported outcomes (PROs). Design We performed a multicentre cross-sectional study of 201 prospectively enrolled subjects with definitive chronic pancreatitis. All subjects underwent evaluation for pancreatic duct obstruction, abnormalities in pain processing using quantitative sensory testing, and screening for psychological distress (anxiety, depression and pain catastrophising) based on validated questionnaires. Abnormality was defined by normal reference values. PROs included pain symptom severity (Brief Pain Inventory short form) and quality of life (EORTC-QLQ-C30 questionnaire). Associations between pain-related factors and PROs were investigated by linear trend analyses, multiple regression models and mediation analyses. Results Clinical evaluation suggestive of pancreatic duct obstruction was observed in 29%, abnormal pain processing in 23%, anxiety in 47%, depression in 39% and pain catastrophising in 28%; each of these factors was associated with severity of at least one PRO. Two or more factors were present in 51% of subjects. With an increasing number of factors, there was an increase in pain severity scores (p&lt;0.001) and pain interference scores (p&lt;0.001), and a reduction in quality of life (p&lt;0.001). All factors had independent and direct effects on PROs, with the strongest effect size observed for psychological distress. Conclusion Pain-related factors in chronic pancreatitis are often present in an overlapping manner and have a cumulative detrimental effect on PROs. These findings support a multidisciplinary strategy for pain management. Trial registration number The study was registered with ClinicalTrials.gov ( NCT03434392 ).
MA03.01 EPICAL Trial. A Phase Ib StudyCombining Anti-Epidermal Growth Factor (EGF) Vaccination With Afatinib in EGFR-Mutant Non-Small Cell Lung Cancer
Authors: D. Rodriguez Abreu, M. Cobo, S. Viteri, A. Aguilar-Hernández, N. Reguart, M. Gonzalez-Cao, C. Cabrera-Gálvez, I. Moya, S. Garcia-Roman, J. Codony-Servat, B. García Peláez, N. Jordana Ariza, M.A. Molina-Vila, E. D'Hondt, R. Rosell
Journal: Journal of Thoracic Oncology (2021)