tbuckley/cabot-search huggingface dataset:
P235 Epigenetic landscape of the asthmatic airways
Authors: P McErlean, A Kelly, J Dhariwal, J Watson, N Jurdzinski, J Smith, R Solari, MR Edwards, A Van Oosterhout, SL Johnston, P Lavender
Journal: Thorax (2016)

The airway epithelium of asthmatics exhibits distinct genomic and phenotypic characteristics. However the mechanisms underlying the establishment and chronicity of these characteristics remains unknown. We investigated if epigenetic changes underpin the genomic characteristics of the asthmatic airways by determining the chromatin landscape of bronchial epithelial cells (BECs) in healthy and asthmatic adults. We employed ChIP-seq of histone H3 acetylation (H3K27ac) to determine the chromatin landscape in e<i>x vivo</i> cultured BECs from healthy and allergic-atopic asthmatics (n = 3 donors each). Regions of differential enrichment were identified (MEDIPS) and associated genes and pathways determined (GREAT). Gene expression profiles were investigated by microarray (Illumina) and differential analysis conducted (Partek Genome Suite). Super enhancers (SEs) were identified (ROSE) and enrichment of transcription factor motifs (MEME) and their tissue distribution (protienatlas.org) determined. We identified 33,744 differentially enriched regions (DERs) of H3K27ac between asthma and healthy BECs. DERs were associated with genes (e.g. SERPINB2, TSLP) and pathways (e.g. leukotriene synthesis, antiviral response) previously implicated in asthma and had little overlap with known glucocorticoid receptor binding sites (1.7% of total). DERs occurred up to 100kb from gene promoters and gain or loss of H3K27ac was associated with increased and decreased gene expression in asthmatics respectively. Using a comparative approach, we identified SEs that were common (i.e., present across all donors) and distinct to health and asthma. In addition to established asthma genes (e.g. CLCA1) and transcription factors (e.g. TP63), asthma-SEs encompassed non-coding RNAs (up to 32% of genes) and epithelial-specific transcription factors (e.g. GCM2) previously unreported in asthma. Our data indicates that asthma influences the chromatin landscape of BECs and suggests the genomic differences observed in the asthmatic airway epithelium are underpinned by established epigenetic mechanisms.
P3.02b-014 Monitoring of T790M Mutation in Serum for Prediction of Response to Third Generation Inhibitors
Authors: Teresa Morán, Enric Carcereny, Joaquim Bosch-Barrera, Carles Mesia, Remedios Blanco, Yolanda Garcia, Diana Roa, Elia Sais, Eudald Felip, Cristina Queralt, Itziar De Aguirre, Jose Luis Ramirez, Olga Fernandez, Rafael Rosell
Journal: Journal of Thoracic Oncology (2017)
P3.01-064 The Overexpression and Cleavage of SASH1 by Caspase-3 Stimulates Cell Death in Lung Cancer Cells
Authors: Joshua Burgess, Emma Bolderson, Steven Gray, Martin Barr, Kathy Gately, Shu-Dong Zhang, Anne-Marie Baird, Derek Richard, Kenneth O’Byrne
Journal: Journal of Thoracic Oncology (2017)
P2.01-008 SiRe Next Generation Sequencing Panel: Effective Diagnostic Tool for Circulating Free DNA Analysis
Authors: Umberto Malapelle, Clara Mayo, Danilo Rocco, Monica Garzon, Pasquale Pisapia, Nuria Jordana Ariza, Riccardo Smeraglio, Roberta Sgariglia, Caterina De Luca, Francesco Pepe, Alejandro Martinez-Bueno, Daniela Morales-Espinosa, María González-Cao, Niki Karachaliou, Santiago Viteri, Claudio Bellevicine, Christian Rolfo, Miguel Angel Molina Vila, Rafael Rosell, Giancarlo Troncone
Journal: Journal of Thoracic Oncology (2017)
P3.02b-020 Gender and Ethnicity Influence on Outcome in EGFRmut+ NSCLC Patients Treated at a Single Canadian Institution
Authors: Roxana Tudor, Karen Kopciuk, Darren Brenner, Alain Tremblay, Paul Maceachern, Don Morris, D. Gwyn Bebb
Journal: Journal of Thoracic Oncology (2017)
P197 Medium term impacts of ecmo on adult survivors
Authors: MM Abdelaziz, J Fowles, A Vulysteke, K Valchanov, K Sulankey, J Parmar
Journal: Thorax (2016)

<h3></h3> Veno-venous Extra-Corporeal Membrane Oxygenation (VV-ECMO) is an established support for severe adult respiratory distress. Previous studies have showed improvement in survival over conventional treatment for ARDS, however little is known about the medium term impact of ECMO on patients, lung physiology and quality of life (QoL). This study investigates these factors in a cohort of patients post-ECMO. All VV-ECMO survivors at a national cardiothoracic centre were offered follow-up six months post-discharge. Thirty-four patients were followed over a three-year period. We examined lung physiology, six-minute walk distance, chest X-rays and change in BMI. QoL subjective measures included mobility, self-care, psychological state and pain scores. Mean duration of ECMO support was 14.5 days (± 10.2; range = 3–40 days). Indications were infective (22/34), embolic (4/34), bronchospasm (4/34), trauma (3/34) and drug overdose (1/34). There was insignificant correlation between indication/ECMO duration and lung physiology at six months, with good recovery in all lung physiology parameters (%FEV1 mean = 88.0% ± 16.9; %FVC mean = 93.1% ± 16.2) with the exception of TLCO%predicted (mean = 76.6% ± 16.6). This however didn’t translate into a measureable difference in exercise physiology, with no correlation between six-minute walk distance and ECMO duration (R2 = 0.0022, mean = 424 m ± 82.5). Seventy-nine percent of 29 X-rays assessed were normal. Mean BMI change during ECMO admission was -6.87% ± 11.99 with greater BMI decline alongside longer ECMO support. Interestingly, post-discharge men regained most weight by follow-up whereas females continued to lose (Figure 1). No significant correlations were seen between ECMO length, indication, and QoL measures. Qualitative analysis suggests worsening anxiety/depression amongst 13 (6 M 7F) patients/family members post-ECMO; four patients giving unprompted mention of flashbacks/nightmares. ECMO offers undoubted short term improvement in ARDS mortality. In this cohort, recovery of lung physiology, chest radiology and QoL is good. The isolated transfer factor reduction probably relates to a loss of functioning alveolar units but doesn’t appear to impact exercise physiology or QoL. The main lasting impact appears to be psychological. In the absence of a control group, the impact of critical illness is difficult to separate from that of ECMO, however in this uncontrolled single centre observational study much reassurance can be gained about medium term impact of ECMO.
Predictors of failure after single faecal microbiota transplantation in patients with recurrent Clostridium difficile infection: results from a 3-year, single-centre cohort study
Authors: G. Ianiro, L. Valerio, L. Masucci, S. Pecere, S. Bibbò, G. Quaranta, B. Posteraro, D. Currò, M. Sanguinetti, A. Gasbarrini, G. Cammarota
Journal: Clinical Microbiology and Infection (2017)
P1.02-019 Complex Mutation of Epidermal Growth Factor Receptor (EGFR) in Patients with Non-Small Lung Cancer
Authors: Hiromasa Arai, Michihiko Tajiri, Junya Morita, Yohei Kameda, Kimihisa Shiino, Koji Okudela, Munetaka Masuda
Journal: Journal of Thoracic Oncology (2017)
Clinical Significance of the Presence of Occult CNS Involvement Assessed by Cytofluorometry in Patients with Non Hodgkin’s Lymphoma and High Risk of CNS Relapse
Authors: Juan-Manuel Sancho, Alberto Orfao, Olga García, Carlos Panizo, Elena Pérez, Mireia Morgades, Antonio Salar, José-Antonio García-Vela, Natalia Alonso, Eva González-Barca, Josefa Plaza, Dolores Caballero, Mariano Provencio, Miguel Marin, Teresa Molero, Josep-Maria Ribera
Journal: Blood (2008)
Outcomes of Unrelated Cord Blood Transplantation for Non-Malignant Diseases in Children Are Not Associated with KIR-Ligand Matching Between Donor and Recipient: a Study On Behalf of Eurocord.
Authors: Annalisa Ruggeri, Duncan Purtill, Michel Gerard, Pascale Loiseau, Marc B Bierings, Andrew Cant, Guillermo Sanz, Yves Bertrand, Fabienne Pouthier, Marta Torrabadella, Gerard Socie, Cristina Navarrete, Gesine Koegler, Eliane Gluckman, Roelof Willemze, Vanderson Rocha
Journal: Blood (2009)
Allogeneic Stem Cell Immunotherapy for Advanced Metastatic Breast Cancer: Lessons from Experience
Authors: Didier Blaise, Anthony Goncalves, Sabine Furst, Jacques-Olivier Bay, Catherine Faucher, Mauricette Michallet, Reza Tabrizi, Jean-Yves Cahn, Anne Sirvent, Mohamad Mohty, Christian Chabannon, Gwenaelle Gravis, Benjamin Esterni, Jean-Marc Extra, Patrice Viens
Journal: Blood (2008)
The Chromosomal Pattern 14q-Translocation Plus 13q-Deletion Is Characteristic for Multiple Myeloma after a Preceding Monoclonal Gammopathy of Undetermined Significance.
Authors: Johannes Drach, Jutta Ackermann, Catrin Baldia, Hannes Kaufmann, Thomas Noesslinger, Heinz Gisslinger, Sonja Seidl, Verena Sagaster, Andrea Keck, Heinz Ludwig, Ulrich Jaeger, Christoph Zielinski
Journal: Blood (2004)
P2.06-016 Phase 2 Study of Ramucirumab plus Weekly Docetaxel in Stage IV NSCLC Following Progression after Platinum-Based Chemotherapy
Authors: Martin Sebastian, Santiago Ponce, Petros Nikolinakos, Rocio Varea, Bo Chao, Annamaria Zimmermann, Ekaterine Alexandris, Pablo Lee, Frederico Cappuzzo
Journal: Journal of Thoracic Oncology (2017)
Propranolol as first‐line treatment for life‐threatening diffuse infantile hepatic hemangioma: A case report
Authors: Giulia Varrasso, Amalia Schiavetti, Silvia Lanciotti, Maria Sapio, Eva Ferrara, Alessandra De Grazia, Anna Clerico
Journal: Hepatology (2017)

Varrasso, Giulia; Schiavetti, Amalia; Lanciotti, Silvia; Sapio, Maria; Ferrara, Eva; De Grazia, Alessandra; Clerico, Anna Author Information
The mitochondrial-targeted peptide, SS-31, improves glomerular architecture in mice of advanced age
Authors: Mariya T. Sweetwyne, Jeffrey W. Pippin, Diana G. Eng, Kelly L. Hudkins, Ying Ann Chiao, Matthew D. Campbell, David J. Marcinek, Charles E. Alpers, Hazel H. Szeto, Peter S. Rabinovitch, Stuart J. Shankland
Journal: Kidney International (2017)
P1.02-068 The Impact of TP53 Overexpression on EMT and the Prognosis in Lung Adenocarcinoma Harboring Driver Mutations
Authors: Shigeto Nishikawa, Toshi Menju, Terumasa Soawa, Koji Takahashi, Ryo Miyata, Hiroyuki Cho, Shinya Neri, Takao Nakanishi, Masatsugu Hamaji, Hideki Motoyama, Kyoko Hijiya, Akihiro Aoyama, Toshihiko Sato, Fengshi Chen, Makoto Sonobe, Hiroshi Date
Journal: Journal of Thoracic Oncology (2017)
Unique Pharmacokinetic Self-Potentiation of Idarubicin through Induction of Carbonyl Reducing Enzymes in Contrast to Other Anthracyclines, Pharmacologic and Clinical Study
Authors: Shinji Kishi, Taro Yamashita, Toshihiro Fukushima, Yoshimasa Urasaki, Tamami Seo, Toru Nakamura, Toshihiro Haba, Ken-ichi Kamiya, Jun Murakami, Mikio Ueda, Shinji Nakao, Takanori Ueda
Journal: Blood (2008)
P3.02c-055 Incidence and Grade of Pneumonitis in Advanced Non-Small Cell Lung Cancer (NSCLC) Patients Treated with Anti-PD-1 Antibodies
Authors: Andrew Yam, Megan Barnet, Anthony Mersiades, Bo Gao, Steven Kao, Michael Boyer, Rina Hui, Adnan Nagrial
Journal: Journal of Thoracic Oncology (2017)
P3.04-020 Segmentectomy in Patients with Pulmonary Malignancies Using 3D-CT Reconstruction and Bronchovascular Separation
Authors: Oleg Pikin, Andrey Ryabov, Ali Amiraliev, Nataliya Rubtsova, Alexander Khalimon, Konstantin Kolbanov, Vladimir Bagrov, Vitaliy Barmin, Nikolay Epifanov
Journal: Journal of Thoracic Oncology (2017)
Overall health status (HS) in patients (pts) with advanced (adv) non-squamous (NSQ) NSCLC treated with nivolumab (nivo) or docetaxel (doc) in CheckMate 057
Authors: M. Reck, J.R. Brahmer, B. Bennett, F. Taylor, J.R. Penrod, M. Derosa, H. Dastani, R. Gralla
Journal: Annals of Oncology (2016)
P123 What causes occupational asthma in cleaners?
Authors: VC Moore, PS Burge, AS Robertson, ED Parkes, GI Walters
Journal: Thorax (2016)

Domestic cleaners show a consistently raised risk of developing asthma in population-based epidemiological studies. The main risks appear to be the use of bleach and sprayed cleaning agents. These risks are now found in other occupations, such as healthcare due to the requirement for disinfection of clinical areas. Since 2000, there has been 26 cleaners and healthcare workers with occupational asthma (OA) reported to Shield (West Midlands registry for OA) thought to be due to cleaning agents. The majority of these were using chlorine-releasing substances containing dichloro-isocyanurate for disinfection purposes. We have carried out 8 specific inhalation challenge tests to chlorine-releasing tablets mixed with cold water but none of these have elicited an asthmatic reaction despite the workers previously showing work-related changes on serial peak flows when exposed. In a separate worker, a positive reaction was seen when challenged to a washing up liquid containing triclosan (another chlorine based substance). Due to the negative nature of the majority of tests, we considered the possibility that the chlorine itself may not be the provoking factor, but that chlorine-releasing formulations have the potential to react with amines from urine or bodily fluids when they are being used to disinfect clinical areas. We report a 48 year-old health-care assistant for the elderly exposed to Haztabs (a chlorine-based cleaner) at work who had clear evidence of occupational asthma from serial peak expiratory flow records (Oasys score 3.44, ABC score 40 L/min/hr, 5 positive timepoints), but negative tests to Haztab exposure when mixed with cold water. Adding urine (5%) to the Haztab mixture resulted in a dual immediate and late asthmatic reaction (Figure 1). She showed mild airway hyper-reactivity pre challenge which was not repeated post challenge due to a continued low FEV1 of 39% predicted. <h3>Conclusions</h3> The SIC results suggested that chloramines were the cause of her asthma, similar to the agents causing occupational asthma in workers exposed to indoor swimming pool vapours/mists.
Experimental study of virus myocarditis in culture.
Authors: S. Yoneda, K. Senda, K. Hayashi
Journal: Circulation (1979)

In this present paper, the authors would like to present here two points of results from the experimental study concerning virus myocarditis in culture. One is the direct delicate features of heart cells affected with Coxsackie B3 (Cox. B3) virus viewed through both light microscope and electron microscope. The other is the fact that marked proliferation of fibroblastic cells take place to replace the heart cells impaired by the virus suggesting to us the possibility of one of the genesisses, revealing fibroblastic involvement in the Idiopathic Cardiomyopathy (ICM) which could be followed by the residual of the virus myocarditis.
P3 Thoracic ultrasound experiences amongst respiratory trainees – a national survey
Authors: P Sivakumar, M Kamalanathan, A Collett, L Ahmed
Journal: Thorax (2016)

<h3>Introduction</h3> Level 1 proficiency in thoracic ultrasound is a mandatory curriculum requirement for respiratory speciality trainees in the UK. Guidance on attaining and maintaining this competency is outlined by The Royal College of Radiologists (RCR).<sup>1</sup> This has been a focus of the GMC survey specialty specific questions. <h3>Aims</h3> To further evaluate thoracic ultrasound competencies and training experiences amongst respiratory registrars in England. <h3>Methods</h3> We invited all respiratory trainees in England to complete an online survey. Responses were collected between October 2015 and June 2016. <h3>Results</h3> 202 (of approximately 600) respiratory trainees completed the survey from 14 deaneries. 65.8% (131/199) trainees are level 1 accredited with 20.6% (22/107) of these performing fewer than 20 ultrasounds in the past year. Figure 1 illustrates the self-reported confidence in identifying pathology. 59% (107/171) of all respondents are never or rarely supervised. 60% (102/169) of queries are answered by real time evaluation or review of stored media. The remaining 40% reported that advice was based on verbal descriptions. 29.2% (50/171) of trainees reported that access to an ultrasonographer for advice was either “not easy” or “impossible”. 9% (15/167) reported that there were no level 1 or level 2 accredited consultants at their current hospital. <h3>Conclusion</h3> Most trainees are level 1 accredited, but many do not perform the minimum 20 scans/year to maintain their competency.<sup>1</sup> Access to supervision is also limited. Though not a requirement, trainees are less confident in identifying pathology pertinent to acute and respiratory medicine, particularly pulmonary oedema and pneumothorax. Encouragingly ultrasound training has evolved considerably in recent years, but ongoing work needs to focus on improving supervision and training. There is a case for reviewing current guidance and to consider tailoring training and expectations to align with the specific needs of respiratory registrars. <h3>Reference</h3> The Royal College of Radiologists. Ultrasound training recommendations for medical and surgical specialties. 2nd edn. London: The Royal College of Radiologists, 2012.
A phase I trial of the addition of the CDK 4/6 inhibitor palbociclib to cetuximab in patients with incurable head and neck squamous cell carcinoma (HNSCC).
Authors: Loren S. Michel, Jessica C. Ley, Tanya Marya Wildes, Kathryn Trinkaus, Douglas Adkins
Journal: Journal of Clinical Oncology (2015)

6043 Background: Overexpression of cyclin D1 and inactivation of p16 occur in the majority ( > 90%) of HPV-unrelated HNSCC. Resistance to cetuximab and cisplatin, the two most effective systemic agents in HNSCC, is in part attributable to cyclin D1 overexpression which can be targeted with inhibitors of the cyclin D axis. Palbociclib is a selective inhibitor of CDK4/6. Methods: A phase I trial was performed to determine the maximum tolerated dose (MTD) of palbociclib added to cetuximab. Palbociclib was given orally q.d. on days 1-21 of each 28 day cycle and cetuximab was given weekly (400 mg/m2, then 250 mg/m2). Palbociclib was given at 100 mg/d (level 1) or 125 mg/d (level 2: max dose). Fibonacci (3+3) design was utilized. Eligible patients (pts) had incurable HNSCC (p16 -or +) and adequate organ function. Correlative studies included total and p- Rb (IHC), p16 (IHC), and PK analysis of palbociclib. Tumor response assessment using RECIST criteria 1.1 was performed every 2 cycles. Results: Nine pts were enrolled (5 platin and cetuximab-resistant and 1 cetuximab-resistant ; 5 p16- and 4 p16+): 3 pts on dose level 1 and 6 pts on dose level 2. Mild (grade 1/2) neutropenia and thrombocytopenia occurred in 2 pts on dose level 1 and in 4 and 3 pts, respectively, on dose level 2. The MTD was not reached as there were no dose limiting toxicities and no AE-related treatment discontinuations. Tumor response assessment following cycle 2 showed partial response in 2 pts (both at dose level 2; both p16 – HNSCC; one with cetuximab- and platin-resistant disease), stable disease in 5 pts (one with cetuximab-resistant disease with an 18% decrease in target lesions), progression in 1 pt, and not yet evaluable in 1 pt. Median time-to-progression was 112 (range: 28-182) days. Conclusions: The MTD of palbociclib was not reached during the phase I study; 125 mg/d given on days 1-21 of a 28 day cycle when added to cetuximab, was determined as the recommended phase II dose. Impressively, tumor responses occurred in pts with cetuximab- and platin-resistant HNSCC. Phase II of the trial is enrolling pts with p16-/Rb+ HNSCC on Arm 1 (platin-resistant disease) and Arm 2 (cetuximab-resistant disease). Clinical trial information: NCT02101034.
P31 PHA-UK living with pulmonary hypertension 2016 survey
Authors: I Armstrong, CG Billings, C Harries, J Yorke
Journal: Thorax (2016)

<h3>Background</h3> Pulmonary Hypertension Association UK (PHA-UK) is the only charity in the UK especially for people affected by pulmonary hypertension (PH). To gain information on the patient journey and how PH impacts on daily living, surveys have been conducted by PAH-UK in 2007, 2010 and more recently in 2016. This paper reports the 2016 survey and provides comparisons with previous survey results. <h3>Method</h3> A quantitative survey consisting of 4 sections regarding diagnosis, management, ongoing quality-of-life and treatment was available to complete online via PHA-UK’s website or by hard copy sent to PHA-UK members and to patients on PH-specific targeted therapy. <h3>Results</h3> 551 responses were received. Participant mean age was 58.3 ± 16.6 years and age at diagnosis was 52.3 ± 18.8 years. 49% of patients had symptoms for &gt;6 months before going to see a doctor and 22% were seen by 4 or more doctors before diagnosis. Time from first symptoms to diagnosis was &gt;1 year in 49% with 31% of patients admitted as an emergency because of their symptoms. After diagnosis, 48% see a specialist at least every 6 months, 87% at least every 12 months. 62% think the support they receive is excellent and 26% good. 90% thought it was better to travel to a Specialist PH Centre rather than to be under the care of a non-PH specialist at a more local hospital. <h3>Discussion</h3> This survey found that care of patients with PH is generally good or excellent and patients were keen to travel to Specialist PH Centres for their care. The early symptoms of pulmonary hypertension can be mild and are common to many diseases so it is often a lengthy process to arrive at the diagnosis. Compared with the previous survey the percentage of patients seeing &gt;4 doctors before diagnosis was reduced (22% <i>vs </i>47%) suggesting an increasing awareness of pulmonary hypertension amongst physicians. However, 49% of patients had symptoms for &gt;6 months before presenting, which has not improved since previous surveys. As earlier diagnosis of patients results in better long-term survival, further work should be undertaken to continue to raise awareness in the UK of pulmonary hypertension.
Lineage Fingerprints: The Transcriptome of the Hematopoietic System.
Authors: Stuart M. Chambers, Nathan C. Boles, Kuan-Yin K. Lin, Akil A. Merchant, David C. Weksberg, Teresa A. Venezia, Steven B. Bradfute, Alice J. Chen, Margaret A. Goodell
Journal: Blood (2005)
P3.02b-072 A Multicenter Phase II Study of Gefitinib in Squamous NSCLC Patients Who Failed First-Line Chemotherapy
Authors: Hae Su Kim, Tae Kyu Lim, Seung-Hyun Nam, Yoon Hee Choi, Young-Woong Won, Hoon-Gu Kim, Jong-Mu Sun, Jung Hye Kwon, Ki-Hyang Kim, Joung Soon Jang, Jin Hyoung Kang, Bong-Seog Kim
Journal: Journal of Thoracic Oncology (2017)
OA15.02 Survival Outcomes in Sublobar Resection for Clinical T1N0M0 Non-Small Cell Lung Cancer: Wedge Resection or Segmentectomy
Authors: Aki Kobayashi, Renta Ishikawa, Motoshi Takao, Akira Shimamoto, Atsushi Ito, Hideto Shimpo
Journal: Journal of Thoracic Oncology (2017)
Studies on Heart Failure in Old Age (Part 1) : Clinical and Hemodynamic Characteristics in Elderly Patients with Heart Failure
Authors: Junichiro Mifune
Journal: Circulation (1978)

Hemodynamic characteristics were examined in elderly patients with heart failure. The results obtained are as follows: 1. Most of the underlying causes of heart failure in elderly patients were heart diseases which were commonly found in middle or od age. The onset of clinical manifestations of heart failure were in old age in most cases. 2. It was supposed that main factors which cause clinical manifestations were low cardiac output and low arterial oxygen tension rather than congestion in mild heart failure in old age. 3. In moderate or severe heart failure, cardiac output and arterial oxygen tension were markedly reduced, while venous pressure and total circulating blood volume were moderately increased. 4. Blood pressure was maintained due to elevation in total peripheral resistance in all stages of heart failure. 5. Aging changes contributed markedly to the hemodynamic changes in elderly patients with heart failure.