tbuckley/cabot-search huggingface dataset:
Fecal microbial transplantation as a therapeutic option in patients colonized with antibiotic resistant organisms
Authors: Michael Laffin, Braden Millan, Karen L. Madsen
Journal: Gut Microbes (2017)

Despite increasing interest in fecal microbiota transplantation (FMT), its full therapeutic potential has yet to be determined. Since its increase in popularity, FMT has been shown to be highly effective in the treatment of both Clostridium difficile infection (CDI) and its recurrent form. Interest in FMT now expands well beyond the treatment of CDI to other processes with known associations to the microbiota such as antibiotic resistant infections, inflammatory bowel disease (IBD), hepatic encephalopathy, neuropsychiatric disorders, and metabolic disease. The rampant use and misuse of antibiotics in both medicine and agriculture has resulted in an increase in antibiotic resistant organisms which pose a significant risk to human health. The purpose of this commentary is to address the general issue of antibiotic resistance in the human microbiota and the restorative potential of FMT in this area.
S93 Novel biomarkers in prognostication and treatment monitoring of malignant pleural mesothelioma- a systematic review
Authors: DT Arnold, D De Fonseka, FW Hamilton, NA Maskell
Journal: Thorax (2016)

<h3>Introduction</h3> Pemetrexed with cisplatin is the only UK licensed treatment for malignant pleural mesothelioma (MPM) following an RCT that demonstrated a survival advantage of 2–3 months and response rate of 30–40% (Vogelzang, 2003). Radiological markers of treatment response and prognostication have significant limitations due to the morphology of the disease. Therefore, serum or pleural fluid biomarkers that could act as an adjunct to radiological assessment would be of significant value. The aim of this systematic review was to collate and summarise the literature relating to this topic. <h3>Methods</h3> The PubMed and EMBASE databases were interrogated using pre-defined search strings (with English language restrictions) up to 30 June 2016, with no early date limit applied. Two independent researchers (DA and FH) read the abstracts and, using the Quality in Prognostic Studies (QUIPS) tool, selected the studies to be included in the final review. <h3>Results</h3> From the 795 abstracts generated by the search strategy, 41 relevant studies were identified. Serum mesothelin was the most studied biomarker with 20 studies assessing its role in prognostication. A high serum mesothelin at baseline was thought to be an independent marker of poor prognosis in epithelioid MPM, however, recent studies suggest this is because levels increase with tumour stage and bulk. Six studies assessed serial serum mesothelin measurements during chemotherapy and all showed that it can be a proxy for treatment response and prognosis (see table). Pleural fluid mesothelin was not a useful prognostic biomarker in the 4 relevant studies. Serum Osetopontin (OPN) was the topic of 5 studies and appeared to offer prognostic information at baseline even after adjustment for covariates. Other serum or pleural fluid biomarkers such as fibulin-3, megakaryocyte-potentiating factor, hyaluronic acid and VEGF have shown prognostic utility in individual papers but are yet to be reproduced in large cohort studies. <h3>Discussion</h3> The literature suggests that a falling serum mesothelin following chemotherapy correlates with treatment response and improved overall survival. This could be of significant value to clinicians in deciding ongoing treatment, but a larger prospective study is required before its inclusion in routine clinical practice.
P2.01-087 Prognostic Significance of CA IX Overexpression in Stage III NSCLC Patients Received Neoadjuvant Treatment
Authors: Sezer Saglam, Kamuran Ibis, Esra Kaytan Saglam, Pınar Fırat, Dilek Yilmazbayhan, Alper Toker, Berker Ozkan, Veysel Hancer, Murat Buyukdogan, Rian Disci
Journal: Journal of Thoracic Oncology (2017)
Potentiated Activation of VLA-4 and VLA-5 Accelerates Proplatelet-Like Formation In Megakaryocytes.
Authors: Takuya Matsunaga, Fumio Fukai, Takuro Kameda, Kotaro Shide, Haruko Shimoda, Eri Torii, Yasuhiro Taniguchi, Tomonori Hidaka, Keiko Katayose, Yoko Kubuki, Kazuya Shimoda
Journal: Blood (2010)
The Unfulfilled Promise of ω-3 Fatty Acid Supplementation
Authors: Gregory Curfman
Journal: JAMA Internal Medicine (2017)

Ashley B. Irish, MD; Andrea K. Viecelli, MD; Carmel M. Hawley, MD, MMedSci; Lai-Seong Hooi, MD; Elaine M. Pascoe, MBiostat; Peta-Anne Paul-Brent, BSc; Sunil V. Badve, MD; Trevor A. Mori, PhD; Alan Cass, MD, PhD; Peter G. Kerr, MD, PhD; David Voss, MD; Loke-Meng Ong, MD; Kevan R. Polkinghorne, MD, PhD; for the Omega-3 Fatty Acids (Fish Oils) and Aspirin in Vascular Access Outcomes in Renal Disease (FAVOURED) Study Collaborative Group
FISH and SNP-Array Karyotyping Improve the Detection of Recurrent Chromosomal Defects Including Del(5q), Monosomy 7, Del(7q), Trisomy 8, and Del(20q) in Myelodysplastic Syndromes.
Authors: Hideki Makishima, Manjot Rataul, Lukasz P. Gondek, Jungwon Huh, James R. Cook, Karl S. Theil, Mikkael A Sekeres, Elizabeth Kuczkowski, Jaroslaw P. Maciejewski
Journal: Blood (2008)
Hemodynamic, Functional and Structural Markers of Vascular Involvement in Primary Systemic Light Chain (AL) Amyloidosis
Authors: Kimon Stamatelopoulos, Marita Lyka, Christos Papamichail, Maria Roussou, Maria Gavriatopoulou, Constantinos Pamboucas, Evangelos Terpos, Meletios A. Dimopoulos, Efstathios Kastritis
Journal: Blood (2014)
P2.04-013 Prognosis Factors and Survival Analysis in Thymic Epithelial Tumors
Authors: Luis Del Carpio, Margarita Majem, Laura López, Josep Belda, Elisabeth Martínez Tellez, Joan Carles Trujillo, Alfons Torrego, Virginia Pajares, Núria Farré, Enrique Lerma, Valle Camacho, Alejandro Fernandez, Ana Muñoz, Georgia Anguera
Journal: Journal of Thoracic Oncology (2017)
MA13.05 Nivolumab in Non-Small Cell Lung Cancer (NSCLC): The Real-Life Data
Authors: Elizabeth Dudnik, Mor Moskovitz, Sameh Daher, Sivan Shamai, Ekaterina Hanovich, Yelena Shechtman, Mahmoud Abu-Amna, Alona Zer, Mira Wollner, Jair Bar, Ofer Merimsky, Arnold Cyjon, Tzippy Shochat, Nir Peled
Journal: Journal of Thoracic Oncology (2017)
P1.04-028 Collection of ICHOM-Defined Patient-Reported Outcome Measures (PROMs) during Routine Lung Cancer Treatment: A Pilot Study
Authors: Jan Van Meerbeeck, Lesley De Backer, Annelies Janssens, Birgitta Hiddinga, Greetje Vanhoutte
Journal: Journal of Thoracic Oncology (2017)
MA04.05 P53 Non-Disruptive Mutation is a Negative Predictive Factor for OS and PFS in EGFR M+ NSCLC Treated with TKI
Authors: Julia Roeper, Maria Netchaeva, Anne Lueers, Prenzel Regina, Douglas Sriba, Kay Willborn, Ursula Stropiep, Cora Hallas, Markus Tiemann, Nicole Neemann, Lukas Heukamp, Frank Griesinger, Markus Falk
Journal: Journal of Thoracic Oncology (2017)
Potassium channels of T lymphocytes take center stage in the fight against cancer
Authors: Laura Conforti
Journal: Journal for ImmunoTherapy of Cancer (2017)

A recent study by Eil at al. published in Nature in September 2016 provides evidence that alterations of the K<sup>+</sup> homeostasis of tumor infiltrating lymphocytes (TILs) in necrotic areas of the tumor microenvironment (TME) suppress the function of effector T cells. Furthermore, they establish that overexpression of K<sup>+</sup> channels in T lymphocytes counterbalances this negative effect of the TME and restores the ability of TILs to function, ultimately leading to increased survival of tumor bearing mice. Thus, K<sup>+</sup> channels in T lymphocytes become interesting new targets for novel immunotherapies in cancer. This Commentary discusses Eil's finding in the context of the central role that K<sup>+</sup> channels play in the suppressed state of TILs as they mediate the immunosuppressive effects of multiple conditions of the TME including hypoxia and adenosine.
P3.02b-113 Clinical Course of NSCLC Patients with EGFR Mutation Undergoing Rebiopsy and Osimertinib Therapy
Authors: Kenichiro Hirai, Hiroshi Yokouchi, Tatsuhiko Koizumi, Hiroyuki Minemura, Kana Watanabe, Tatsuro Fukuhara, Kenya Kanazawa, Makoto Maemondo, Yoshinori Tanino, Mitsuru Munakata
Journal: Journal of Thoracic Oncology (2017)
P33 Patients with pulmonary arteriovenous malformations and hereditary haemorrhagic telangiectasia report forced expiratory manoeuvres during pulmonary function tests provoke nosebleeds and migraines
Authors: HC Tighe, H McKernan, JT Springett, L Babawale, J Perks, T Patel, CL Shovlin
Journal: Thorax (2016)

<h3>Introduction and objectives</h3> Forced expiratory manoeuvres during lung function testing produce major pressure swings that are often overlooked by referring clinicians. Standard tests use a noseclip to prevent air leakage through the nose. Our goal was to examine how often the tests caused clinical sequelae such as nosebleeds in people with abnormal nasal and pulmonary vasculature due to hereditary haemorrhagic telangiectasia (HHT). <h3>Methods</h3> With ethical approval, self-reported migraine features and exacerbations were examined in HHT subjects with and without pulmonary AVMs, for a series of noninvasive and invasive investigations, using an unbiased online survey. <h3>Results</h3> Of 677 HHT-affected participants, 284 reported performing forced expiratory manoeuvres either with or without a noseclip in place. The median age was 54 years (interqurtile range 44–62) and the majority were female. All described nosebleeds: 130 (46%) experienced these at least daily, and a further 95 (33%) at least once per week. Only 1 of 253 (0.4%) reported nosebleeds were worse after finger oximetry measurements, compared to 53/282 (18.8%) after “blowing out hard without a noseclip” (chi-squared p &lt; 0.0001). A higher proportion still reported nosebleeds were worse when a noseclip was used (66/192 (34.3%, p = 0.0003)). Similarly, migraine headaches (which are more frequent in people with HHT), were reported to be worse after forced expiratory manoeuvres both with (10/85 (11.7%) and without (11/105 (10.5%)) a noseclip, but not after oximetry or being weighed. <h3>Conclusion</h3> Noseclip use should be restricted in people already experiencing regular nosebleeds, and further pretest information may be required.
Analysis of Genetic Alterations In 843 Korean Acute Leukemia Patients by Multiplex RT-PCR Assay (HemaVision) and Karyotyping
Authors: Jihyang Lim, Myungshin Kim, Yonggoo Kim, Kyungja Han, Hee-Je Kim, Seok Lee, Woo-Sung Min, Nak-Gyun Chung, Bin Cho, Hack-Ki Kim
Journal: Blood (2010)
Methylenetetrahydrofolate Reductase (MTHFR) Polymorphisms of Both Donor and Recipient Can Modify the Rate of Recurrence in Allogeneic Hematopoietic Stem Cell Transplantation.
Authors: So Yeon Oh, Hye Jin Kim, Hyeon Gyu Yi, Jin Won Kim, Cheng Zhe Piao, Chongwon Chang, Eunsoon Shin, Inho Kim, Sung-Soo Yoon, Seonyang Park, Byoung Kook Kim
Journal: Blood (2007)
S89 The use of tuberculosis chemoprophylaxis in patients of renal replacement therapy
Authors: N Ahern, H Jarvis, R Charif, OM Kon
Journal: Thorax (2016)

<h3>Introduction</h3> Individuals with end stage renal disease (ESRD) undergoing renal replacement therapy (RRT) are at increased risk of tuberculosis (TB). Timely identification and treatment of latent TB infection (LTBI) reduces the risk of progression to active disease. Diagnosing LTBI is challenging in ESRD as standard tests, such as the tuberculin skin test (TST) and Interferon Gamma Release Assay (IGRA) are less reliable. Although TB guidelines exist for ESRD they acknowledge a lack of evidence base and are limited in their scope. This study aimed to establish the current LTBI screening and treatment practice in patients of RRT in a central London teaching hospital with the hypothesis that there would be a varied approach with overall low levels of screening. <h3>Methods</h3> New starters on haemodialysis (HD) in the year 2010 were identified from computerised renal databases and information collected on; demographics, renal diagnosis, co-morbidities, dialysis attributes, TB risk factors, screening methods and LTBI treatment. All patients were followed for a period of 5 years to establish the rate of active TB after commencing RRT. Screening was considered to have taken place if any of the following were performed irrespective of symptoms of active disease; TST, IGRA, radiography specifically to investigate for TB or documented risk stratification. <h3>Results</h3> Of the 331 eligible patients only 77 (23.2%) received screening. In those who were screened, 13 (16.9%) were diagnosed with active TB equating to an incidence of 3927/100,000, 37 (48.1%) with latent TB and 27 (35.1%) with neither. Risk factor stratification was the commonest modality of LTBI identification although there were a wide variety of approaches. Chemoprophylactic treatment regimes were non-standardised and often based on clinical experience rather than guidelines. Of those with active infection, disease developed most commonly within the first year of starting HD. <h3>Conclusion</h3> High rates of active TB occur mainly within the first year of RRT. There is a lack of a uniform approach to detecting and treating LTBI in this population currently. Risk stratification and the use of immunological tests may offer the most sensitive approach to screening ESRD and within the first year of RRT.
MA01.03 The Non-Invasive LuCED® Test for Detection of Early Stage Lung Cancer
Authors: Michael Meyer, Timothy Bell, Daniel Sussman, David Wilbur, Chris Presley, Jon Hayenga, Frances Lakers, Jonus Reyna, Michael Davies, John Field, Gregory Yang, Christy Lancaster, Javier Zulueta, Alan Nelson
Journal: Journal of Thoracic Oncology (2017)
The Genetic Landscape Of Mantle Cell Lymphoma and The Epigenetic Origins Of Lineage Specific Mutations
Authors: Jenny Zhang, Dereje Jima, Qingquan Liu, Andrea Moffitt, Magdalena Czader, Eric D. Hsi, Yuri Fedirow, Kristy L. Richards, Javed Gill, Zhen Sun, Cassandra L Love, Paula B. Scotland, Eric Lock, Shawn Levy, David Dunson, Sandeep Dave
Journal: Blood (2013)
P2.04-019 A Peripheral Immune Signature Associated with Clinical Activity of Sunitinib in Thymic Carcinoma
Authors: Yusuke Tomita, Anish Thomas, Sunmin Lee, Min-Jung Lee, Chul Kim, Arlene Berman, Udayan Guha, Giuseppe Giaccone, Patrick Loehrer, Arun Rajan, Jane Trepel
Journal: Journal of Thoracic Oncology (2017)
MA08.03 Osimertinib vs Platinum-Pemetrexed for T790M-Mutation Positive Advanced NSCLC (AURA3): Plasma ctDNA Analysis
Authors: Yi Long Wu, Suzanne Jenkins, Suresh Ramalingam, Ji-Youn Han, Angelo Delmonte, Te-Chun Hsia, Janessa Laskin, Sang-We Kim, Yong He, Sabina Patel, Rachel Hodge, Marcelo Marotti, Vassiliki Papadimitrakopoulou, Tony Mok
Journal: Journal of Thoracic Oncology (2017)
Results of the AIEOP AML 2002/01 Study for Treatment of Children with Acute Myeloid Leukemia.
Authors: Andrea Pession, C. Rizzari, Maria Caterina Putti, Riccardo Masetti, Fiorina Casale, Franca Fagioli, Luca Lo Nigro, Matteo Luciani, Concetta Micalizzi, Giuseppe Menna, Nicola Santoro, Anna Maria Testi, Roberto Rondelli, Andrea Biondi, Giuseppe Basso, Franco Locatelli
Journal: Blood (2009)
Simplifying the WHO ‘how to hand rub’ technique: three steps are as effective as six—results from an experimental randomized crossover trial
Authors: S. Tschudin-Sutter, M.L. Rotter, R. Frei, D. Nogarth, P. Häusermann, A. Stranden, D. Pittet, A.F. Widmer
Journal: Clinical Microbiology and Infection (2017)
Specific Gamma Delta T Cells for Cellular Immunotherapy of EBV-Associated Diseases after Allo-HSCT By T-Cell Receptor Gene Modification
Authors: Xiuli Wu, Xinyu Wang, Zhenyi Jin, Ling Xu, Shaohua Chen, Lijian Yang, Piotr Grabarczyk, Grzegorz K. Przybylski, Christian A Schmidt, Yangqiu Li
Journal: Blood (2014)
S51 MTOR regulates TGF-β induced pro-fibrotic gene expression in primary human lung fibroblasts
Authors: HV Woodcock, JD Eley, C Nanthakumar, TM Maher, PF Mercer, RC Chambers
Journal: Thorax (2016)

<h3>Introduction</h3> TGF-β is a major pro-fibrotic cytokine with a critical role in the pathogenesis of idiopathic pulmonary fibrosis (IPF). TGF-β drives fibroblast to myofibroblast differentiation and extracellular matrix synthesis. mTOR plays a critical role in regulating protein translation and is the catalytic subunit of two functionally distinct complexes, mTORC1 and mTORC2, which have differential sensitivities to rapamycin. The aim of this study was to delineate mTOR signalling in response to TGF-β in human lung fibroblasts and investigate the role of the mTOR pathway in TGF-β mediated myofibroblast differentiation and collagen synthesis. <h3>Methods</h3> All human samples were obtained with informed, signed consent and with research ethics committee approval. Primary human lung fibroblasts (pHLFs) were grown from explant cultures. Cells were pre-incubated with varying concentrations of inhibitor before stimulation with TGF-β 1ng/ml. Collagen biosynthesis and αSMA expression were measured by a high-content imaging based molecular crowding assay. Gene expression was measured by qPCR. Western blots were performed to assess mTOR substrate phosphorylation. <h3>Results</h3> TGF-β was found to stimulate the delayed and sustained induction of mTOR signalling in pHLFs and this signalling pathway was critical for mediating the late peak in TGF-β induced pro-fibrotic gene expression. Accordingly, active-site mTOR inhibition exerted pronounced inhibitory effects on pHLF collagen biosynthesis and myofibroblast differentiation. The induction of mTOR signalling in response to TGF-β was dependent on the canonical Smad pathway. In addition, potent and selective pharmacological agents demonstrated that TGF-β induced mTOR signalling was independent of PI3K/Akt activity, suggesting that mTOR is not activated through the prototypical linear PI3K/Akt axis downstream of TGF-β. Moreover, rapamycin-resistant mTOR signalling was found to be critical for TGF-β induced pro-fibrotic gene expression in pHLFs. <h3>Conclusion</h3> mTOR is a an important pro-fibrotic signalling node downstream of TGF-β and a potential target for therapeutic intervention in IPF.
Race is associated with differences in airway inflammation in patients with asthma
Authors: Sharmilee M. Nyenhuis, Jerry A. Krishnan, Alalia Berry, William J. Calhoun, Vernon M. Chinchilli, Linda Engle, Nicole Grossman, Fernando Holguin, Elliot Israel, Rick A. Kittles, Monica Kraft, Stephen C. Lazarus, Erik B. Lehman, David T. Mauger, James N. Moy, Stephen P. Peters, Wanda Phipatanakul, Lewis J. Smith, Kaharu Sumino, Stanley J. Szefler, Michael E. Wechsler, Sally Wenzel, Steven R. White, Steven J. Ackerman
Journal: Journal of Allergy and Clinical Immunology (2017)
Analysis of IgVH, BCL-6, PIM, RHO/TTF and PAX5 Mutational Status in Splenic and Nodal Marginal Zone B Cell Lymphoma Suggests a Particular B Cell Origin.
Authors: Alexandra Traverse-Glehen, Aurelie Verney, Lucille Baseggio, Pascale Felman, Evelyne Callet-Bauchu, Catherine Thieblemont, Bertrand Coiffier, Francoise Berger, Gilles Salles
Journal: Blood (2005)
Release of Alkaline Phosphatase Caused by PIGV Mutations In Patients with Hyperphosphatasia-Mental Retardation Syndrome (HPMR), a Recently Found Second Inherited GPI Anchor Deficiency.
Authors: Yoshiko Murakami, Peter M Krawitz, Peter N Robinson, Stefan Mundlos, Yusuke Maeda, Taroh Kinoshita
Journal: Blood (2010)
M6 Improving follow-up in patients attending and discharged from accident and emergency with asthma exacerbations
Authors: WJ Newman, O Lamont
Journal: Thorax (2016)

<h3>Introduction</h3> The Respiratory and Accident and Emergency (A&amp;E) departments in Forth Valley audited asthma care in the emergency department over the past years. Shortcomings in a number of areas have been identified and quality improvement measures undertaken. One area was the failure to organise follow-up for patients following attendance at A&amp;E, (24% in 2009, 47% in 2012). As a result a new system was introduced. <h3>Methods</h3> Forth Valley Health Board serves a population of 310,000 and has one acute hospital with 860 beds. The Respiratory Service comprises of 6 Consultants and 5.5 Respiratory Nurses. There are specialist asthma clinics run by the physicians/nurses. Patients with an asthma exacerbation discharged from the A&amp;E department are identified by interrogating the A&amp;E patient management system daily and clinical and contact details obtained. The Respiratory nurses contact any patient to obtain further information (standardised questionnaire) and make a management plan with the patient. Their case is then discussed with the on-call Respiratory physician and further recommendations instituted. <h3>Results</h3> 88 cases ( 27 (30%) male, 61 (70%) female) were identified as having attended with an exacerbation of their asthma and discharged from A&amp;E during 2015. Median age 36 (range 17–78), 46 (58%) presented at weekends or outwith working hours (0800–1800), 70 (80%) were discharged home with oral steroids. Of the 88 patients one had no telephone/one lived outside the UK. 26 (30%) patients did not reply and the GP practice was contacted to advise of the attendance. Following discussion with the consultant it was recommended that 11 (42%) continued to be managed in primary care (follow-up attendance unknown), and 15 (58%) be reviewed by the Respiratory Service. 13 (86%) attended the appointment. 62 (70%) were contactable, one was a nursing home resident (Respiratory nurses subsequently visited), one declined to answer questions. 35 (39%) had already made an appointment to see their general practitioner. Following discussion one patient was re-admitted (same day), 30 (48%) patients continued to be managed in primary care (follow-up attendance unknown) and 31 (50%) were reviewed by the Respiratory service. 27 (87%) attended the appointment. <h3>Conclusions</h3> The introduction of a telephone conversation/management plan improves follow-up of patients with asthma exacerbations discharged from A&amp;E.
Inhibition of Elastase or SDF-1/CXCR4 Axis Promotes Differentiation of Human AML Cells.
Authors: Sigal Tavor, Jasmine Jacob-Hirsch, Manny Eisenbach, Sigi Kay, Shoshana Baron, Ninette Amariglio, Elizabeth Naparstek, Gideon Rechavi
Journal: Blood (2006)
P1.05-007 Analysis of RNA Sequencing Data along with PET SUV-max Can Discover Novel Gene Sets Which Can Predict Surgical Outcome of NSCLC
Authors: Yoohwa Hwang, Yoo Jin Jung, Sae Bom Lee, Yoon Ho Kim, Kwanyong Hyun, Samina Park, Hyun Joo Lee, In Kyu Park, Chang Hyun Kang, Young Tae Kim
Journal: Journal of Thoracic Oncology (2017)
Interleukin-15 Is a Proto-Oncogene In Acute Large Granular Lymphocyte Leukemia
Authors: Anjali Mishra, Shujun Liu, Gregory H Sams, Douglas P Curphey, Ramasamy Santhanam, Laura J Rush, Deanna Schaefer, Lauren G Falkenberg, Laura Sullivan, Laura Jaroncyk, Xunchang Zou, Harold Fisk, Jadwiga Labanowska, Enrico Caserta, Lai-Chu Wu, Heiko Becker, Sebastian Schwind, Jason C. Chandler, Yue-Zhong Wu, Nyla A. Heerema, Pierluigi Porcu, Ramiro Garzon, Guido Marcucci, Michael A. Caligiuri
Journal: Blood (2010)
Targeting Menin-MLL Interaction to Inhibit MLL Fusion Oncoproteins in Leukemia
Authors: Jolanta Grembecka, Shihan He, Aibin Shi, Trupta Purohit, Andrew G. Muntean, Xiaoqin Li, Thomas Hartley, Duxin Sun, Jay L. Hess, Tomasz Cierpicki
Journal: Blood (2011)