tbuckley/cabot-search huggingface dataset:
Reveal, Don’t Conceal
Authors: Tracey L. Weissgerber, Stacey J. Winham, Ethan P. Heinzen, Jelena S. Milin-Lazovic, Oscar Garcia-Valencia, Zoran Bukumiric, Marko D. Savic, Vesna D. Garovic, Natasa M. Milic
Journal: Circulation (2019)

Reports highlighting the problems with the standard practice of using bar graphs to show continuous data have prompted many journals to adopt new visualization policies. These policies encourage authors to avoid bar graphs and use graphics that show the data distribution; however, they provide little guidance on how to effectively display data. We conducted a systematic review of studies published in top peripheral vascular disease journals to determine what types of figures are used, and to assess the prevalence of suboptimal data visualization practices. Among papers with data figures, 47.7% of papers used bar graphs to present continuous data. This primer provides a detailed overview of strategies for addressing this issue by (1) outlining strategies for selecting the correct type of figure depending on the study design, sample size, and the type of variable; (2) examining techniques for making effective dot plots, box plots, and violin plots; and (3) illustrating how to avoid sending mixed messages by aligning the figure structure with the study design and statistical analysis. We also present solutions to other common problems identified in the systematic review. Resources include a list of free tools and templates that authors can use to create more informative figures and an online simulator that illustrates why summary statistics are meaningful only when there are enough data to summarize. Last, we consider steps that investigators can take to improve figures in the scientific literature.
P2.01-14 Phase 3 Trial of Sitravatinib Plus Nivolumab vs Docetaxel for Treatment of NSCLC After Platinum-Based Chemoimmunotherapy
Authors: E. Nidhiry, T. Mekhail, E. Thara, M. Nagasaka, C. Chen, B.G. Gopurala, N. Campbell, K. Eaton, Y. Homsi, R. Yanagihara, R. Vaddepally, X. Yan, V. Tassell, S. Neuteboom, R. Chao, R. Keresztes
Journal: Journal of Thoracic Oncology (2019)
Relatively Low Sensitivity of CD109(-) Hematopoietic Stem/Progenitor Cells (HSPCs) to TGF-β: A Possible Mechanism Responsible for the Preferential Commitment of Piga Mutant HSPCs in Immune-Mediated Bone Marrow Failure
Authors: Noriharu Nakagawa, Kohei Hosokawa, Luis Espinoza, Kana Maruyama, Takamasa Katagiri, Hirohito Yamazaki, Shinji Nakao
Journal: Blood (2016)
P1.01-99 EGFR-Wild Type Patients Responding to TKI: Revisiting Pathology with Newer Technology
Authors: A. Papadakis, G. Kasymjanova, D. Small, C. Pepe, L. Sakr, G. Chong, H. Wang, A. Spatz, J. Agulnik, V. Cohen
Journal: Journal of Thoracic Oncology (2019)
Clonal hematopoiesis in elderly twins: concordance, discordance, and mortality
Authors: Jakob Werner Hansen, Dorthe Almind Pedersen, Lisbeth Aagaard Larsen, Simon Husby, Signe Bedsted Clemmensen, Jacob Hjelmborg, Francesco Favero, Joachim Weischenfeldt, Kaare Christensen, Kirsten Grønbæk
Journal: Blood (2019)
Global Routine Vaccination Coverage, 2018
Authors: Megan Peck, Marta Gacic-Dobo, Mamadou S. Diallo, Yoann Nedelec, Samir S. Sodha, Aaron S. Wallace
Journal: MMWR Morbidity and Mortality Weekly Report (2019)

Endorsed by the World Health Assembly in 2012, the Global Vaccine Action Plan 2011-2020 (GVAP) (1) calls on all countries to reach ≥90% national coverage with all vaccines in the country's national immunization schedule by 2020. Building on previous analyses (2) and using the World Health Organization (WHO) and United Nations Children's Fund (UNICEF) global vaccination coverage estimates as of 2018, this report presents global, regional, and national vaccination coverage estimates and trends, including vaccination dropout rates. According to these estimates, global coverage with the first dose of diphtheria and tetanus toxoids and pertussis-containing vaccine (DTP1) remained relatively unchanged from 2010 (89%) to 2018 (90%). Global coverage with the third DTP dose (DTP3) followed a similar global trend to that of DTP1, remaining relatively consistent from 2010 (84%) to 2018 (86%) (3). Globally, 19.4 million children (14%) were not fully vaccinated in 2018, and among them, 13.5 million (70%) did not receive any DTP doses. Overall, dropout rates from DTP1 to DTP3 decreased globally from 6% in 2010 to 4% in 2018. Global coverage with the first dose of measles-containing vaccine (MCV1) remained between 84% and 86% during 2010-2018. Among countries that offer a second MCV dose (MCV2) during the second year of life, coverage increased from 19% in 2007 to 54% in 2018; among countries offering MCV2 to older age groups (children aged 3-14 years), coverage also increased, from 36% in 2007 to 69% in 2018 (3). Globally, the estimated difference in coverage with MCV1 and MCV2 in 2018 was 17%. However, among new and underused vaccines, global coverage increased from 2007 to 2018 for completed series of rotavirus vaccine, pneumococcal conjugate vaccine (PCV), rubella vaccine, Haemophilus influenzae type b vaccine (Hib), and hepatitis B vaccine (HepB). To reach global vaccination coverage goals for vaccines recommended during childhood, adolescence, and adulthood, tailored strategies that address local determinants for incomplete vaccination are needed, including targeting hard-to-reach and hard-to-vaccinate populations.
P1.11-38 Frequency and Prognostic Impact of Concomitant Mutations in KRAS and TP53 or STK11 in Brazilian Lung Adenocarcinoma Patients
Authors: V. De Sa, J. Chinoca, M. Spina Donadio, V. De Lima, G. Torrezan, D. Carraro, H. Freitas
Journal: Journal of Thoracic Oncology (2019)
P1.04-17 Phase I/II Study of Nivolumab and Vorolanib in Patients with Refractory Thoracic Tumors
Authors: J. Whisenant, K. Beckermann, H. Borghaei, T. Owonikoko, J. Patel, L. Berry, Y. Shyr, K. Harrow, C. Liang, A. Holzhausen, G. Selvaggi, H. Wakelee, L. Horn
Journal: Journal of Thoracic Oncology (2019)
EP1.01-28 Real World Use of Afatinib in NSCLC EGFRm+ Patients Outside Clinical Trials: A FAETT Experience
Authors: I. Ramos García, A. Sánchez, A.L. Ortega, J. Pradera, M. Cobo, M.Á. Moreno, I. Barneto, S. Ruiz, I. Fernández, T. García, F. Toscano, J.M. Trigo Perez
Journal: Journal of Thoracic Oncology (2019)
Cys34 Adductomics Links Colorectal Cancer with the Gut Microbiota and Redox Biology
Authors: Hasmik Grigoryan, Courtney Schiffman, Marc J. Gunter, Alessio Naccarati, Silvia Polidoro, Sonia Dagnino, Sandrine Dudoit, Paolo Vineis, Stephen M. Rappaport
Journal: Cancer Research (2019)

Abstract Chronic inflammation is an established risk factor for colorectal cancer. To study reactive products of gut inflammation and redox signaling on colorectal cancer development, we used untargeted adductomics to detect adduct features in prediagnostic serum from the EPIC Italy cohort. We focused on modifications to Cys34 in human serum albumin, which is responsible for scavenging small reactive electrophiles that might initiate cancers. Employing a combination of statistical methods, we selected seven Cys34 adducts associated with colorectal cancer, as well as body mass index (BMI; a well-known risk factor). Five adducts were more abundant in colorectal cancer cases than controls and clustered with each other, suggesting a common pathway. Because two of these adducts were Cys34 modifications by methanethiol, a microbial–human cometabolite, and crotonaldehyde, a product of lipid peroxidation, these findings further implicate infiltration of gut microbes into the intestinal mucosa and the corresponding inflammatory response as causes of colorectal cancer. The other two associated adducts were Cys34 disulfides of homocysteine that were less abundant in colorectal cancer cases than controls and may implicate homocysteine metabolism as another causal pathway. The selected adducts and BMI ranked higher as potentially causal factors than variables previously associated with colorectal cancer (smoking, alcohol consumption, physical activity, and total meat consumption). Regressions of case–control differences in adduct levels on days to diagnosis showed no statistical evidence that disease progression, rather than causal factors at recruitment, contributed to the observed differences. These findings support the hypothesis that infiltration of gut microbes into the intestinal mucosa and the resulting inflammation are causal factors for colorectal cancer. Significance: Infiltration of gut microbes into the intestinal mucosa and the resulting inflammation are causal factors for colorectal cancer.
New frontiers in proton therapy: applications in cancers
Authors: Tai‐Ze Yuan, Ze‐Jiang Zhan, Chao‐Nan Qian
Journal: Cancer Communications (2019)

Proton therapy offers dominant advantages over photon therapy due to the unique depth-dose characteristics of proton, which can cause a dramatic reduction in normal tissue doses both distal and proximal to the tumor target volume. In turn, this feature may allow dose escalation to the tumor target volume while sparing the tumor-neighboring susceptible organs at risk, which has the potential to reduce treatment toxicity and improve local control rate, quality of life and survival. Some dosimetric studies in various cancers have demonstrated the advantages over photon therapy in dose distributions. Further, it has been observed that proton therapy confers to substantial clinical advantage over photon therapy in head and neck, breast, hepatocellular, and non-small cell lung cancers. As such, proton therapy is regarded as the standard modality of radiotherapy in many pediatric cancers from the technical point of view. However, due to the limited clinical evidence, there have been concerns about the high cost of proton therapy from an economic point of view. Considering the treatment expenses for late radiation-induced toxicities, cost-effective analysis in many studies have shown that proton therapy is the most cost-effective option for brain, head and neck and selected breast cancers. Additional studies are warranted to better unveil the cost-effective values of proton therapy and to develop newer ways for better protection of normal tissues. This review aims at reviewing the recent studies on proton therapy to explore its benefits and cost-effectiveness in cancers. We strongly believe that proton therapy will be a common radiotherapy modality for most types of solid cancers in the future.
OA12.06 A Prospective Randomized Phase Ⅲ Study of Precise PORT for Patients with pⅢA-N2 NSCLC After Complete Resection and Adjuvant Chemotherapy
Authors: Z. Hui, Y. Men, C. Hu, Z. Zhou, J. Liang, Q. Feng, B. Nan, X. Wang, D. Chen, Z. Xiao, J. Lv, L. Deng, T. Zhang, W. Wang, S. Gao, J. He, L. Wang
Journal: Journal of Thoracic Oncology (2019)
MA23.11 Analysis of Immune Phenotype Composition in Malignant Pleural Mesothelioma (MPM) Using Bulk RNA Sequencing
Authors: A. Mandal, A. Nastase, S.K. Lu, S. Gennatas, H. Anbunathan, M. Edwards, D. Morris-Rosendahl, A. Newman Taylor, R.C. Rintoul, E. Lim, S. Popat, A. Nicholson, A. Bowcock, M. Lathrop, M. Moffatt, W. Cookson
Journal: Journal of Thoracic Oncology (2019)
Primary squamous cell carcinoma of the oral cavity at presentation in Pakistan
Authors: A. Jamshed, R. Hussain, K. Rehman, H. Iqbal, S. Hameed, U. Majeed, M. A. Shah, R. Azhar, Q. Ahmed, Z. Faruqui
Journal: Journal of Clinical Oncology (2009)

e17002 Background: Squamous cell carcinoma of oral cavity (SCCOC) is characterized by marked geographical differences in frequency and site distribution. Pakistan is situated within the high risk zone on the global oral cancer map. However, no reliable data exists on oral cancer in this area. Our aim was to determine clinicopathological features and patterns at presentation of primary SCCOC in a comprehensive cancer centre in Pakistan. Methods: Demographic, risk factors, pathological and AJCC staging data for SCCOC treated at Shaukat Khanum Memorial Hospital for the period November 2003-October 2008 were obtained from the head and neck unit database. Results: The database identified 666 patients with biopsy proven primary SCCOC. Mean age was 53 years (range 12 - 90 years). Male (428): Female (238) ratio was M64%:F36%. The occurrence of major risk factors for oral cancer specifically smoking, betel quid chewing, naswar (smokeless tobacco) and alcohol use in males (428) was 45% (193), 28% (118), 29% (126), 3% (13), and in females (238) was 8% (20), 29% (68), 13% (30), 0% (0), respectively. Thirty-eight percent (411/666) had no association with tobacco, betel quid or alcohol use. Subsite within oral cavity; anterior tongue 41.1% (274), buccal mucosa 26.6% (177), lower gingival and alveolus 19.5% (130), upper gingival and alveolus 4.1% (27), lips 3.6% (24), retromolar trigone 2.9% (19), hard palate 1.7% (11), and floor mouth 0.6 (4). Broder's/World Health Organization histological grade; grade I 52% (334), grade II 34% (226), grade III 7% (49), and unknown 5% (36). According to AJCC 2002 system 0.2% (1), 10.8% (72), 12.2% (81), 13.2% (88), and 63.7% (420) had stage 0, I, II, III, and IV, respectively. Conclusions: Approximately 80% of patients with primary SCCOC present with stage III or IV disease with anterior tongue as the most common subsite in our hospital. While tobacco and betel quid chewing can be attributed to development of SCCOC in a significant proportion of patients, nearly 38% are unlinked to typical risks factors suggesting other environmental and genetic agents as etiological factors in this region. No significant financial relationships to disclose.
EP1.12-18 NET-001: A Phase II Study of ABI-009 in Metastatic Neuroendocrine Tumors of the Lung or Gastroenteropancreatic System
Authors: R. Ramirez, M. Matrana, S. Satti, R. Griffin, B. Voros, A. Mohammed, R. Thiagarajan, J.P. Boudreaux, E. Woltering
Journal: Journal of Thoracic Oncology (2019)
PARAGON-HF — Why We Do Randomized, Controlled Clinical Trials
Authors: Christopher M. O’Connor, Christopher deFilippi
Journal: New England Journal of Medicine (2019)

Patients with heart failure and preserved ejection fraction have high morbidity and mortality, as well as reduced quality of life, and there are no approved therapies. The complex pathophysiological mechanisms contributing to this condition have made therapeutic development difficult. The PARAMOUNT (Prospective Comparison of ARNI [angiotensin receptor–neprilysin inhibitor] with ARB [angiotensin-receptor blocker] on Management of Heart Failure with Preserved Ejection Fraction) trial,1 a phase 2 trial of sacubitril–valsartan (a combination angiotensin receptor–neprilysin inhibitor) as compared with valsartan alone in patients with heart failure with preserved ejection fraction, showed a significant reduction in natriuretic peptide levels at 12 weeks. PARADIGM-HF (Prospective . . .
Physical activity: government must tackle “stark inequalities,” says BMA
Authors: Elisabeth Mahase
Journal: BMJ (2019)

The UK government must take urgent action to improve low levels of physical activity around the country, with particular focus on deprived areas, the BMA has said.1

The BMA warned of “stark inequalities” in exercise between people living in deprived areas and the rest of the country, in its report on increasing physical activity in the UK. It said that 34% of adults in the most deprived areas of England were classified as inactive, compared with the national average of 23%.

The report also highlighted that Asian (31%), black (29%), and other …
Neuronal network activity controls microglial process surveillance in awake mice via norepinephrine signaling
Authors: Yong U. Liu, Yanlu Ying, Yujiao Li, Ukpong B. Eyo, Tingjun Chen, Jiaying Zheng, Anthony D. Umpierre, Jia Zhu, Dale B. Bosco, Hailong Dong, Long-Jun Wu
Journal: Nature Neuroscience (2019)
P1.04-76 Predictive Factors of Early Therapeutic Failure to Immunotherapy in Patients with Metastatic NSCLC
Authors: V.A. Ramos Sousa, V. Fonseca De Jesus, T. Pimentel Muniz, M. Da Rosa Barbosa, H. Freitas, V. De Lima
Journal: Journal of Thoracic Oncology (2019)
Increased T Cell Plasticity With Dysregulation of Follicular Helper T, Peripheral Helper T, and Treg Cell Responses in Children With Juvenile Idiopathic Arthritis and Down Syndrome–Associated Arthritis
Authors: C. Foley, A. Floudas, M. Canavan, M. Biniecka, E. J. MacDermott, D. J. Veale, R. H. Mullan, O. G. Killeen, U. Fearon
Journal: Arthritis & Rheumatology (2019)

Objective Juvenile idiopathic arthritis ( JIA ) is the most common inflammatory arthritis in children; however, an aggressive, erosive arthritis of little‐known immunologic mechanism occurs 20 times more frequently in children with Down syndrome. This study was undertaken to characterize T cell and B cell polyreactivity, follicular helper T (Tfh) cell, peripheral helper T (Tph) cell, and Treg cell responses, and synovial inflammation in Down syndrome–associated arthritis ( DA ). Methods Multiparametric flow cytometric analysis and Simplified Presentation of Incredibly Complex Evaluations ( SPICE ) software were used to examine peripheral blood B cell populations and T cell cytokine responses in patients with DA , JIA , Down syndrome (trisomy 21 [T21]), and in healthy controls. Tfh and Tph cell frequency and origin, in addition to Treg cell frequency, were also evaluated. Synovial inflammation was assessed by immunohistology. Results Expansion of IgM‐only memory B cells was demonstrated in DA compared to JIA (mean ± SEM 22.48 ± 3.278 versus 9.011 ± 1.317; P = 0.005), paralleled by decreased frequency of transitional B cells. T cell responses in DA were characterized by marked functional plasticity, as was evident from the increased frequency of polyfunctional CD 8+ Th cells ( P &lt; 0.05), CD 161+ Th cells ( P &lt; 0.05), and CD 8− Th cells ( P &lt; 0.001), and positivity for tumor necrosis factor, interferon‐γ, interleukin‐17A, or granulocyte–macrophage colony‐stimulating factor, compared to all other groups. Significant expansion of CXCR 3+ CCR 6+ (Th1/Th17) Tfh cells ( P = 0.003) and CXCR 3+ CCR 6+ Tph cells ( P = 0.01), paralleled by a decrease in CXCR 3− CCR 6− (Th2) Tfh cells was observed in DA compared to T21. Treg cells were significantly reduced in DA compared to T21 (mean ± SEM 7.111 ± 0.9518 versus 11.96 ± 1.055 versus; P = 0.0028), with a specific reduction in the naive:memory Treg cell ratio. Marked synovial tissue inflammation and increased T cell and B cell infiltrations were demonstrated in DA compared to JIA . Conclusion DA is more common and more aggressive than JIA . It is characterized by increased polyreactive Th, Tfh, and Tph cell responses, reduced Treg cell frequency, and evidence of increased synovial inflammation, all of which are potentially distinct from JIA and T21.
New Insights into Malaria Pathogenesis
Authors: Christopher A. Moxon, Matthew P. Gibbins, Dagmara McGuinness, Danny A. Milner, Matthias Marti
Journal: Annual Review of Pathology Mechanisms of Disease (2019)

Malaria remains a major public health threat in tropical and subtropical regions across the world. Even though less than 1% of malaria infections are fatal, this leads to about 430,000 deaths per year, predominantly in young children in sub-Saharan Africa. Therefore, it is imperative to understand why a subset of infected individuals develop severe syndromes and some of them die and what differentiates these cases from the majority that recovers. Here, we discuss progress made during the past decade in our understanding of malaria pathogenesis, focusing on the major human parasite Plasmodium falciparum.
P2.05-05 Availability of Four Dimensional Computed Tomography (4DCT) for Lung Cancer
Authors: H. Arai, M. Tajiri, Y. Mishina, S. Nakamura, H. Masuda, K. Shiino, K. Okudela, T. Iwasawa, M. Masuda
Journal: Journal of Thoracic Oncology (2019)
Glucuronidation of tamoxifen and 4-hydroxytamoxifen by human UGT1A4 variants
Authors: Dongxiao Sun, Kimberly Duncan, Gang Chen, Ryan Dellinger, L. Michael Carastro, Philip Lazarus
Journal: Cancer Research (2005)

4915  Tamoxifen (TAM) is an antiestrogen that has been widely used for chemotherapy and chemoprevention of breast cancer in women. One of the major mechanisms of metabolism of TAM and its active metabolite, trans-4-hydroxytamoxifen (4-HO-TAM), is via glucuronidation. In this study, the glucuronidating activities of three common variants of the human UDP-glucuronosyltransferase (UGT) 1A4 gene were compared using TAM and 4-OH-TAM. Using high performance liquid chromatography (HPLC), microsomes from wild-type UGT1A4 (UGT1A4*1)-over-expressing HK293 cells exhibited significant activity against TAM and 4-OH-TAM, forming exclusively the TAM-N+- and 4-OH-TAM-N+-glucuronides, respectively, as determined by treatment with 1N NaOH, with apparent Km’s of 86 and 115 μM, respectively. After normalizing for differences in UGT1A4 expression between cell lines, the rate of TAM-N+-glucuronide and 4-OH-TAM-N+-glucuronide formation was significantly (p
Clinical Utility and Implications of Asparaginase Antibodies in Acute Lymphoblastic Leukemia
Authors: Chengcheng Liu, Jitesh D. Kawedia, Cheng Cheng, Deqing Pei, Christian A Fernandez, Xiangjun Cai, Kristine Crews, Sue Kaste, John C Panetta, W. Paul Bowman, Sima Jeha, John Sandlund, William E. Evans, Ching-Hon Pui, Mary V. Relling
Journal: Blood (2011)
P2.04-88 Surgical Outcomes of a Multicenter Phase II Trial of Neoadjuvant Atezolizumab in Resectable Stages IB-IIIB NSCLC: Update on LCMC3 Clinical Trial
Authors: J. Lee, J. Chaft, A. Nicholas, G. Patterson, S. Waqar, E. Toloza, E. Haura, D. Raz, K. Reckamp, R. Merritt, D. Owen, D. Finley, C. Mcnamee, J. Blasberg, E. Garon, J. Mitchell, R. Doebele, F. Baciewicz, M. Nagasaka, H. Pass, A. Johnson, S. Phan, K. Schulze, P. Bunn, B. Johnson, M. Kris, D. Kwiatkowski, I. Wistuba, D. Carbone, V. Rusch
Journal: Journal of Thoracic Oncology (2019)
P2.03-56 Polymorphism ICAM-1 and Beta-3 Integrin Are Associated with the Development of Non-Small Cell Lung Cancer and the Prognostic Role of ICAM-1
Authors: H. Fındık Kıyan, İ. Yaylım, S. Demirkol, M. Hakan, O. Küçükhüseyin, I. Sarbay, A. Turna
Journal: Journal of Thoracic Oncology (2019)
EP1.18-23 Is Salvage Lung Resection Necessary After Definitive Chemoradiation Therapy for Stage IIIA(N2) Non-Small Cell Lung Cancer?
Authors: A. Turna, H. Melek, M. Agkoç, C. Gebitekin, H. Turna, F. Dinçbaş, S. Erturan, G. Aydın, K. Kaynak
Journal: Journal of Thoracic Oncology (2019)
P2.17-28 Examination of the Indication and Validity of Segmental Resection as Intentional and Palliative Limited Resection for Lung Cancer
Authors: K. Kojima, Y. Morifuji, H. Inoue, H. Umeguchi, M. Kato, C. Takasaki, M. Yano, K. Okubo
Journal: Journal of Thoracic Oncology (2019)
Abstract 16089: Pulmonary Hypertension-Induced Right Ventricular Pressure Overload Stimulates Cardiac Fibroblast Periostin Expression and Dedifferentiation of Adult Cardiac Myocytes
Authors: Danielle R Bruns, Philip D Tatman, Roshni S Kalkur, R D Brown, Kurt R Stenmark, Peter M Buttrick, Lori A Walker
Journal: Circulation (2018)

Our group has previously reported that conditioned media derived from cardiac fibroblasts (Cfib) from the pulmonary hypertensive (PH)-right ventricle (RV) causes rapid and marked dedifferentiation ...