tbuckley/cabot-search huggingface dataset:
Relationship of distinct B-cell receptor (BCR) isotype in diffuse large b-cell lymphoma (DLBCL) with ABC and GCB genetic signatures and association with signaling molecules of clinical significance.
Authors: Abid Qureshi, Ariz Akhter, Fahad Farooq, Joanne Luider, Douglas Allan Stewart, Adnan Mansoor
Journal: Journal of Clinical Oncology (2015)

8568 Background: DLBCL is a heterogeneous disease. Gene expression profile (GEP) based distinction into ABC and GCB sub-types, provides basis for risk stratification in DLBCL patients. GEP is an intricate platform, which is not routinely available in clinical laboratories. Hence, surrogate markers for distinction between ABC vs GCB subtypes of DLBCL are needed. Methods: We used Nanostring nCounter system for gene expression analysis, utilizing RNA from diagnostic biopsy tissues. We correlated, flow-cytometry based BCR-isotype (IgM/IgG) expression with mRNA levels in a series of ABC/GCB related genes (n = 54). We also investigated gene set (n = 48) related to TLR, NF-kB and JAK/STAT pathways to determine, if BCR- isotype expression has distinct influence on specific cell signaling pathways. Median expression for each gene was compared across two BCR isotype groups utilizing fisher’s exact test. Results: Our cohort (n = 44) comprised of IgG+ (n = 13; 30%) and IgM+ (n = 31; 70%) DLBCL patients. BCR-isotype expression showed significant association with specific molecular signature related to cell of origin. IgG expression was linked with GCB genetic profile and IgM expression allied with ABC related genes (P< 0.001), thus confirming a previous single report (Leukemia. 2011 Apr; 25 (4):681-8). IgM expression related well with higher median expression of BLNK, LYN, BCL10, CARD 11 (P< 0.001); while SYK/BTK expression showed no significant differences (P< 0.091). In NF-kB pathway, expression levels of p100, p52, IKKα were significantly higher in IgM+ DLBCL, compared to IgG+ DLBCL patients (P< 0.001); thus suggesting higher NF-kB activity. Genes related to TLR and PI3K/AKT pathway showed no significant differences between two BCR-isotype groups (P= 0.182). In relation to JAK/ERK/STAT signaling pathway, IgM+ DLBCL showed significantly higher expression of STAT3/JAK2 genes (P< 0.001). Conclusions: Our data stipulates some preliminary observations that BCR-isotype is distinct between ABC and GCB subtypes of DLBCL. We have also shown linkage of BCR-isotype with some critical pathways related to disease biology in DLBCL.
Efficacy of Eltrombopag in Adult East Asian and Non-East Asian Patients with Chronic Immune Thrombocytopenia (cITP): Results from the Extend Study
Authors: Raymond SM Wong, James B Bussel, Mansoor N. Saleh, Abderrahim Khelif, Balkis Meddeb, Ali El-Ali, Erhard Quebe-Fehling, Abdulgabar Salama
Journal: Blood (2016)
Cytotoxic activity of arsenic trioxides in ovarian cancer cell lines
Authors: Jeong-Yeol Park, Eun-Hye Hur, Yang-Kyun Kim, Dae-Yeon Kim, Hee-C Kim, Dae-Shik Suh, Jong-Hyeok Kim, Yong-Man Kim, Young-Tak Kim, Joo-Hyun Nam
Journal: Cancer Research (2008)

2297   Objectives; The aim of this study was to evaluate the cytotoxic effect of Arsenic trioxide (As 2 O 3 ) as a single agent and as a combination with cispaltin or paclitaxel in ovarian cancer cell lines.  Materials and methods; OVCAR-3 (adenocarcinoma), SKOV-3 (adenocarcinoma, malignant ascites), SNU-8 (adenocarcinoma) and SNU-119 (adenocarcinoma) were used as model cell lines for ovarian cancer and 293T (transformed primary embryonic kidney) was used as a normal tissue cell lines for comparison. A total of 96 well plates (1 x 10 4  cell/well) were treated with each cytotoxic agent alone [Cisplatin (5 ug/ml), taxol (1 uM) and As 2 O 3  (1,2,4,8 uM)] and combination of two agents [cisplatin (5 ug/ml) + taxol (1 uM), cisplatin (5 ug/ml) + As 2 O 3  (1,2,4,8 uM), and taxol (1 uM) + As 2 O 3  (1,2,4,8 uM)] for 72 hours. Cell viability were measured per 24 hours by MTS assay. The assay was done each two times by duplicate. To measure apoptosis of cells by each cytotoxic agent alone [Cisplatin (5 ug/ml), taxol (1 uM) and As 2 O 3  (1,2,4,8 uM)] and synergistic apoptosis by combination of two agents [cisplatin (5 ug/ml) + taxol (1 uM), cisplatin (5 ug/ml) + As 2 O 3  (1,2,4,8 uM), and taxol (1 uM) + As 2 O 3  (1,2,4,8 uM)], folw cytometric analysis and Dapi staining were used. Each cell line was served to Annexin V-FITC apoptosis detection kit (BD pharmingen). Each of cell lines was splited in 6 well plate (3 x 10 5  cell/well) and was incubated for overnight. After treatment of agents, apoptosis was measured in 24 hours interval for 72 hours. 293T was cultured in DMEM (Gibco) and ovarian cancer cell lines were cultured at RPMI 1640 (Gibco).  Results; In OVCAR-3 and SKOV-3 cell lines, As 2 O 3  alone showed no cytotoxic activity and also showed no synergistic effects in combination with taxol or cisplatin. But in SNU-8 and SNU-119, As 2 O 3  alone showed moderate cytotoxic activity and also showed synergistic effects in combination with taxol (As 2 O 3  2 uM vs. taxol + As 2 O 3  2 uM : 50.1% vs. 29% in SNU-8. As 2 O 3  2 uM vs. taxol + As 2 O 3  2 uM : 29.9% vs. 13.3% in SNU-119).  Conclusion; Cytotoxic effects of As 2 O 3  in the treatment of ovarian cancer cell lines were variable in each cell lines. But in some cell lines, especially in SNU-8, As 2 O 3  showed the potential role as an adjunct to known cytotoxic chemotherapeutic agents of ovarian cancer. Further study is needed to confirm the effects and adverse effects in animal models.
MiVideo: Personalized video visit summaries for cancer patients.
Authors: John C. Krauss, Vaibhav Sahai, Matthias A. Kirch, Diane M. Simeone, Lawrence C. An
Journal: Journal of Clinical Oncology (2015)

e20709 Background: Physicians providing oncologic care seek to cure or palliate patients by having them adhere to complicated treatment plans. However, patients and relatives are often overwhelmed during clinic consultation due to information overload which affects patient recall after visit. Furthermore, relatives who wish to participate in the care of their family member may have difficulty in obtaining needed medical information due to inability to attend a physician visit. In this pilot study, we explored the use of video visit summaries recorded by the patient’s physician as a novel tool to convey accurate and personalized information to patients and their relatives. Methods: After obtaining verbal consent, physicians recorded a 2-3 minute summary of the major findings and recommendations of the of the visit which was uploaded to a secure website. Patients were sent an email link to the secure website, and after logging on they could view and share the video with family and friends. The patients were asked to complete a 15 multiple choice question survey with 4 open ended questions. Results: Three physicians recorded and sent 56 MiVideo visit summaries to patients seen in their multidisciplinary pancreatic and colorectal cancer clinics. Forty patients logged into the secure site, and 37 viewed the videos. Fourteen patients shared their videos, inviting a total of 54 visitors. Forty-one visitors viewed the MiVideo. Average overall satisfaction with MiVideo was 9 on a 1-10 scale with 10 being most positive. The patients noted the videos were understandable, helped with recall of information about the visit, helped them tell friends and families about the visits, and would highly recommend the MiVideo program to a friend with cancer. Among the free form comments, the most notable were “provides details which may have been forgotten or misunderstood”; “a great synopsis of the current condition”; “it reviews what the doctor said at the appointment. Sometimes you forget what was said”. Conclusions: MiVideo visit summaries provide a personalized education tool that patients find highly useful, and incorporation into an electronic medical record should be explored to enhance patient understanding of their disease and treatment.
Yap/Taz regulate alveolar regeneration and resolution of lung inflammation
Authors: Ryan LaCanna, Daniela Liccardo, Peggy Zhang, Lauren Tragesser, Yan Wang, Tongtong Cao, Harold A. Chapman, Edward E. Morrisey, Hao Shen, Walter J. Koch, Beata Kosmider, Marla R. Wolfson, Ying Tian
Journal: Journal of Clinical Investigation (2019)

Alveolar epithelium plays a pivotal role in protecting the lungs from inhaled infectious agents. Therefore, the regenerative capacity of the alveolar epithelium is critical for recovery from these insults in order to rebuild the epithelial barrier and restore pulmonary functions. Here, we show that sublethal infection of mice with Streptococcus pneumoniae, the most common pathogen of community-acquired pneumonia, led to exclusive damage in lung alveoli, followed by alveolar epithelial regeneration and resolution of lung inflammation. We show that surfactant protein C–expressing (SPC-expressing) alveolar epithelial type II cells (AECIIs) underwent proliferation and differentiation after infection, which contributed to the newly formed alveolar epithelium. This increase in AECII activities was correlated with increased nuclear expression of Yap and Taz, the mediators of the Hippo pathway. Mice that lacked Yap/Taz in AECIIs exhibited prolonged inflammatory responses in the lung and were delayed in alveolar epithelial regeneration during bacterial pneumonia. This impaired alveolar epithelial regeneration was paralleled by a failure to upregulate IκBa, the molecule that terminates NF-κB–mediated inflammatory responses. These results demonstrate that signals governing resolution of lung inflammation were altered in Yap/Taz mutant mice, which prevented the development of a proper regenerative niche, delaying repair and regeneration of alveolar epithelium during bacterial pneumonia.
Characterization and Management of Arrhythmic Events in Young Patients With Brugada Syndrome
Authors: Yoav Michowitz, Anat Milman, Antoine Andorin, Georgia Sarquella-Brugada, M. Cecilia Gonzalez Corcia, Jean-Baptiste Gourraud, Giulio Conte, Frederic Sacher, Jimmy J.M. Juang, Sung-Hwan Kim, Eran Leshem, Philippe Mabo, Pieter G. Postema, Aviram Hochstadt, Yanushi D. Wijeyeratne, Isabelle Denjoy, Carla Giustetto, Yuka Mizusawa, Zhengrong Huang, Camilla H. Jespersen, Shingo Maeda, Yoshihide Takahashi, Tsukasa Kamakura, Takeshi Aiba, Elena Arbelo, Andrea Mazzanti, Giuseppe Allocca, Ramon Brugada, Ruben Casado-Arroyo, Jean Champagne, Silvia G. Priori, Christian Veltmann, Pietro Delise, Domenico Corrado, Josep Brugada, Kengo F. Kusano, Kenzo Hirao, Leonardo Calo, Masahiko Takagi, Jacob Tfelt-Hansen, Gan-Xin Yan, Fiorenzo Gaita, Antoine Leenhardt, Elijah R. Behr, Arthur A.M. Wilde, Gi-Byoung Nam, Pedro Brugada, Vincent Probst, Bernard Belhassen
Journal: Journal of the American College of Cardiology (2019)
Foxr2 promotes formation of CNS-embryonal tumors in a Trp53-deficient background
Authors: Boonmin Poh, Hideto Koso, Hiroyuki Momota, Takashi Komori, Yutaka Suzuki, Nobuaki Yoshida, Yasushi Ino, Tomoki Todo, Sumiko Watanabe
Journal: Neuro-Oncology (2019)

Abstract Background Embryonal tumors in the central nervous system (CNS) are primary, aggressive, and poorly differentiated pediatric brain tumors. We identified forkhead box R2 (Foxr2) as an oncogene for medulloblastoma through a transposon-based insertional mutagenesis screen. Foxr2 translocation has been identified in a subset of human embryonal tumors of the CNS, designated as CNS neuroblastoma with Foxr2 activation (CNS NB-Foxr2); however, the in vivo functions of Foxr2 remain elusive. Methods We analyzed the effect of Foxr2 overexpression in the mouse brain by generating a transgenic strain that expresses Foxr2 in the entire brain under a transformation related protein 53 (Trp53)–deficient background. We performed histological analysis of tumors and characterized tumor-derived sphere-forming cells. We investigated gene expression profiles of tumor-derived cells. Results Foxr2 and Trp53 loss promoted tumor formation in the olfactory bulb (OB) and brainstem (BS). The tumors showed the common morphological features of small round blue cell tumors, exhibiting divergent, mainly neuronal and glial, patterns of differentiation, which corresponds to the definition of CNS-embryonal tumors. Importantly, all mice developed CNS-embryonal tumors. In the OB, early proliferative lesions consisting of oligodendrocyte transcription factor 2 (Olig2+) cells were observed, indicating that Foxr2 expression expanded Olig2+ cells in the OB. Tumor-derived cells formed spheres in vitro and induced tumors that recapitulated the parental tumor upon transplantation, indicating the presence of tumor-initiating cells. Gene expression profiling revealed that OB and BS tumor cells were enriched for the expression of the genes specific to CNS NB-Foxr2. Conclusion Our data demonstrate that Foxr2 plays a causative role in the formation of CNS-embryonal tumors.
LBP-22-Outcome of 119 cirrhotic patients with splanchnic thrombosis: a single center real-life experience
Authors: Giuseppe Tarantino, Giorgia Micucci, Serena Rupoli, Gianluca Svegliati-Baroni, Alessandro Fiorentini, Alessio Ortolani, Laura Schiadà, Marco Marzioni, Massimo Offidani, Irene Federici, Attilio Olivieri, Antonio Benedetti
Journal: Journal of Hepatology (2019)
Broadening the Conversation About Intersectionality in Clinical Medicine
Authors: Yolonda Wilson, Amina White, Akilah Jefferson, Marion Danis
Journal: The American Journal of Bioethics (2019)

We found the commentaries for our recent article, “Intersectionality in Clinical Medicine: The Need for a Conceptual Framework” (Wilson et al. 2019) helpful in providing opportunities for us to cla...
Underlying liver disease and advanced stage liver cancer are associated with elevated neutrophil-lymphocyte ratio
Authors: Linda Wong, Kliment Bozhilov, Brenda Hernandez, Sandi Kwee, Owen Chan, Luke Ellis, Loic LeMarchand
Journal: Clinical and Molecular Hepatology (2019)

Inflammation-based scores, such as the neutrophil-to-lymphocyte ratio (NLR), have been associated with prognosis in hepatocellular carcinoma (HCC); but variable cut-off values and potential lack of specificity have limited the utility of NLR. This study evaluates NLR in a large cohort of HCC patients.We retrospectively reviewed 789 HCC cases (1993-2017) for demographics, tumor characteristics, treatment, and survival. NLR was stratified into NLR ≥1.5 and NLR ≥3 and analyzed for correlation with American Joint Committee on Cancer (AJCC) and Barcelona Clinic Liver Cancer (BCLC) stages. In 235 patients who underwent liver resection, survival and recurrence were evaluated by NLR.In 789 HCC cases, mean NLR was increased with advanced AJCC and BCLC stages. Hepatitis C patients were less likely to have NLR ≥1.5 and ≥3. Non-alcoholic steatohepatitis patients were more likely to have NLR ≥3. Patients with tumor size >5 cm, rupture, or macrovascular invasion were more likely to have NLR ≥3. In patients treated with resection, NLR ≥3 predicted early recurrence (odds ratio [OR] 4.14, P<0.01) and overall recurrence (OR 4.05, P<0.01). Mean NLR was 4.30 in those with recurrence and 2.75 in those without recurrence. Patients with NLR ≥3 showed significantly worse survival compared to those with NLR <3 (P<0.01 by log-rank test).Elevated NLR is associated with advanced cancer stage and aggressive tumor characteristics, such as large size, rupture, and invasion. NLR ≥3 was associated with early and overall recurrence after resection but varied with etiology. NLR may be a useful biomarker in predicting recurrence for HCC patients undergoing curative resection, but further studies are required to elucidate the effect of disease etiology.
Helen Salisbury: Who let the drug companies in?
Authors: Helen Salisbury
Journal: BMJ (2019)

In a recent BMJ article Tom Moberly brought our attention to joint working arrangements between the NHS and drug companies.1 Just such an arrangement is being rolled out in Oxford, in the form of an integrated multidisciplinary respiratory team, jointly funded by Boehringer Ingelheim and the local clinical commissioning group (CCG).

The project aims to improve care for patients with respiratory conditions and bring this care into the community. The team will include a respiratory consultant, GP, nurse, physiotherapist, psychologist, smoking cessation …
TCTAP C-018 The Nightmare During Percutaneous Coronary Intervention for Acute Coronary Syndrome
Authors: Wei-Chun Huang, Meitzu Wang, Cheng-Chung Hung, Chin-Chang Cheng, Feng Yu Kuo, Cheng-Hung Chiang, Guang-Yuan Mar, Chun-Peng Liu
Journal: Journal of the American College of Cardiology (2019)
THU-214-Annual average of integral FIB-4 index and HBV core-related antigen as an appropriate indicators for starting nucleoside analogues at an optimum timing
Authors: Shuhei Hige, Itaru Ozeki, Hirokazu Suii, Ryoji Tatsumi, Masakatsu Yamaguchi, Mutsuumi Kimura, Tomohiro Arakawa, Tomoaki Nakajima, Yasuaki Kuwata, Takumi Ohmura, Joji Toyota, Yoshiyasu Karino
Journal: Journal of Hepatology (2019)
Potential pharmacokinetic interactions affecting antitumor drug disposition in cancer patients
Authors: Dominique Leveque, Jihane Lemachatti, Laurence Beretz, Jean Pierre Bergerat
Journal: Cancer Research (2008)

220  Cancer patients are at high risk of drug-drug interactions since they take many medications (anticancer agents, drugs for supportive care and comorbidities, over-the counter products). In particular, anticancer agent activity may be altered by a co-administrated drug in relation with a pharmacokinetic interaction. The extent of potential pharmacokinetic drug-drug interactions affecting anticancer agent disposition has not specifically been investigated. We examined the prevalence of this type of interaction in adult ambulatory patients receiving systemic chemotherapy in our institution.  We prospectively collected the medication list in 200 consecutive cancer patients receiving intravenous chemotherapy by means of the prescriptions (chemotherapy, supportive care, medications for comorbidities) and a questionnaire (over-the counter products). Interacting drugs had to be taken in the previous 7 days. Data concerning the type of cancer and the nature of the comorbidities were also collected. Potential pharmacokinetic drug interactions affecting the anticancer agent disposition were identified using the French guide of drug interactions (Afssaps, june 2007) and the medical literature.  A total of 200 patients (mean age 60 years; range 17-96 years) entered the study and 73,5% were female. The most common cancer types were breast cancer (41%), non-Hodgkin9s lymphomas (17,5%), and gastrointestinal tumors (12,5%). The majority of the patients (58,5%) had a comorbid illness (cardiovascular diseases, hypothyroidism, diabete, depression). The median number of medications per patient was 4 (range 1-14). All patients received systemic chemotherapy but 29 (14,5%) also took anticancer drugs at home (hormonotherapy, capecitabine). We reported 9 potential pharmacokinetic interactions in 9 patients (frequency: 4,5%; 95% CI : 1,6-7,4%). Most of the interactions (7/9) involved fluconazole that may alter the metabolism of oxazaphosphorines or the elimination of bortezomib and paclitaxel. Five interactions were not associated with a published clinical effect. No potential interaction with an enzyme or drug transporter inducer (ie, rifampin, St John’s wort) was encountered.  The frequence of potential pharmacokinetic interactions affecting the disposition of antitumor drugs was low in our population of ambulatory adult cancer patients. Most of the potential pharmacokinetic interactions involved the antifungal agent fluconazole.
FRI-240-Comparison of Abbott RealTime HCV genotype II, Abbott HCV genotype plus RUO with Roche Cobas HCV genotyping assays for hepatitis C virus genotyping
Authors: Chen-Hua Liu, Tung-Hung Su, Chun-Jen Liu, Chun-Ming Hong, Hung-Chih Yang, Tai-Chung Tseng, Pei-Jer Chen, Ding-Shinn Chen, Jia-Horng Kao
Journal: Journal of Hepatology (2019)
Endoscopic ultrasound-guided gastrojejunostomy using a 2-cm lumen-apposing metal stent to treat benign afferent loop syndrome
Authors: Michael Lajin, Marc F. Catalano, Naser M. Khan, Issam Lajin
Journal: Endoscopy (2019)

Afferent loop obstruction is a complication of pancreaticoduodenectomy [1]. Traditionally, afferent loop obstruction is managed by surgical or percutaneous methods. We report on a case of afferent loop obstruction treated by endoscopic ultrasound (EUS)-guided gastrojejunostomy ([Video 1]).
FRI-245-Improvement in cognitive impairment following 12 weeks of aerobic exercise in individuals with non-cirrhotic, chronic hepatitis C
Authors: Philip O’gorman, Damien Ferguson, Orla Strahan, Ann Monaghan, Megan Kennedy, Colm Bergin, Susan Mckiernan, Robert Coen, Colin Doherty, Cuisle Forde, John Gormley, Suzanne Norris
Journal: Journal of Hepatology (2019)
Indoor Exposure and Sensitization to Formaldehyde among Inner-City Children with Increased Risk for Asthma and Rhinitis
Authors: Dong Keon Yon, Sohyun Hwang, Seung Won Lee, Hye Mi Jee, Youn Ho Sheen, Jeong Hee Kim, Dae Hyun Lim, Man Yong Han
Journal: American Journal of Respiratory and Critical Care Medicine (2019)
Reply to Amar U. Kishan, William Hall, and Daniel Spratt's Letter to the Editor re: Sebastian Berg, Alexander P. Cole, Marieke J. Krimphove, et al. Comparative Effectiveness of Radical Prostatectomy Versus External Beam Radiation Therapy Plus Brachytherapy in Patients with High-risk Localized Prostate Cancer. Eur Urol 2019;75:552–5 Comparing Apples to Oranges: A Self-fulfilling Prophecy?
Authors: Alexander P. Cole, Quoc-Dien Trinh
Journal: European Urology (2019)
SAT-486-Short- and long-term effects of transarterial chemoembolization on portal hypertension in patients with hepatocellular carcinoma
Authors: Bernhard Scheiner, Gregor Ulbrich, Mattias Mandorfer, Thomas Reiberger, Christian Müller, Fredrik Waneck, Michael Trauner, Claus Kölblinger, Prof. Dr. Arnulf Ferlitsch, Wolfgang Sieghart, Markus Peck, Matthias Pinter
Journal: Journal of Hepatology (2019)
Abstract 18309: Timing of Focused Cardiac Ultrasound During Resuscitation - A Prospective Clinical Study
Authors: Rasmus Aagaard, Bo Løfgren, Thorbjørn Grøfte, Erik Sloth, Roni R Nielsen, Christian A Frederiksen, Asger Granfeldt, Morten T Bøtker
Journal: Circulation (2017)

Introduction: Focused cardiac ultrasound (FoCUS) can potentially identify reversible causes of cardiac arrest during advanced cardiovascular life support (ACLS), but data on the timing of image acq...