tbuckley/cabot-search huggingface dataset:
De-Novo Diffuse Large B Cell Lymphoma (DLBCL) Treated with Rituximab (R)-CHOP: Definition and Validation of a Prognostic Score Model Based on MYC, BCL2 and BCL6 Expression By Immunohistochemistry (IHC)
Authors: Barbara Botto, Alessia Castellino, Annalisa Chiappella, Mattia Novo, Luigi Zattera, Federica Cavallo, Paola Ghione, Andrea Evangelista, Chiara Ciochetto, Giovannino Ciccone, Maria Stella Scalzo, Roberto Chiarle, Domenico Novero, Umberto Vitolo
Journal: Blood (2015)
Comparison of DRPM and MEPM as the first-line therapy in FN patients with acute leukemia: A randomized, controlled trial
Authors: Tatsuo Oyake, Yuka Fujisawa, Norifumi Sugawara, Takahiro Mine, Yasuhiko Tsukushi, Ichiro Hanamura, Yusei Aoki, Shugo Kowata, Shigeki Ito, Yoji Ishida
Journal: Annals of Oncology (2016)
Treatment of Burns.
Authors: C. E. Tennant
Journal: JAMA (1907)

Denver, Oct. 24, 1907. <h3>To the Editor:</h3> —In reading the article inThe Journal, September 7, page 863, on "Treatment of Burns," my attention was called to the number of picric acid formulas recommended. I was also reminded of my own personal experience with the use of this compound after a severe bromin burn and the excruciating pain it caused me to suffer. After several dressings of picric acid solution on gauze strips, with as many periods of torture thereby induced, I decided to use some agent which was both antiseptic and anesthetic. Carbolic acid was, of course, one of the first to be thought of, but discarded because of its tendency to produce gangrene. It was then that liquor cresolis comp. was tried with the most gratifying results. Since then, some twelve years past, I have had many occasions to employ it, and whether the burn was due to
Monocyte Chemotactic Response in Cancer Patients: A Discussion 01 Statistical Evaluation: Reply
Authors: David A. Boetcher
Journal: JNCI Journal of the National Cancer Institute (1975)

Journal Article Monocyte Chemotactic Response in Cancer Patients: A Discussion 01 Statistical Evaluation: Reply Get access David A. Boetcher, M. D. David A. Boetcher, M. D. Wheaton, Maryland 20902 Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 54, Issue 4, April 1975, Page 1015, https://doi.org/10.1093/jnci/54.4.1015-b Published: 01 April 1975
Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations
Authors: Rafal Mostowy, Nicholas J. Croucher, Cheryl P. Andam, Jukka Corander, William P. Hanage, Pekka Marttinen
Journal: Molecular Biology and Evolution (2017)

Prokaryotic evolution is affected by horizontal transfer of genetic material through recombination. Inference of an evolutionary tree of bacteria thus relies on accurate identification of the population genetic structure and recombination-derived mosaicism. Rapidly growing databases represent a challenge for computational methods to detect recombinations in bacterial genomes. We introduce a novel algorithm called fastGEAR which identifies lineages in diverse microbial alignments, and recombinations between them and from external origins. The algorithm detects both recent recombinations (affecting a few isolates) and ancestral recombinations between detected lineages (affecting entire lineages), thus providing insight into recombinations affecting deep branches of the phylogenetic tree. In simulations, fastGEAR had comparable power to detect recent recombinations and outstanding power to detect the ancestral ones, compared with state-of-the-art methods, often with a fraction of computational cost. We demonstrate the utility of the method by analyzing a collection of 616 whole-genomes of a recombinogenic pathogen Streptococcus pneumoniae, for which the method provided a high-resolution view of recombination across the genome. We examined in detail the penicillin-binding genes across the Streptococcus genus, demonstrating previously undetected genetic exchanges between different species at these three loci. Hence, fastGEAR can be readily applied to investigate mosaicism in bacterial genes across multiple species. Finally, fastGEAR correctly identified many known recombination hotspots and pointed to potential new ones. Matlab code and Linux/Windows executables are available at https://users.ics.aalto.fi/~pemartti/fastGEAR/ (last accessed February 6, 2017).
CBIO-14. EXPLORING THE OTX2 REGULATORY NETWORK: TARGETING THE “GROW AND GO” ARMS OF THE MOST AGGRESSIVE MEDULLOBLASTOMAS
Authors: Margaret Stromecki, Ravinder Kaur, Nazanin Tatari, Ludivine Morrison, Patryk Skowron, Michael Taylor, Tamra Werbowetski-Ogilvie
Journal: Neuro-Oncology (2016)

Medulloblastoma (MB) is a highly heterogeneous primary malignant pediatric brain cancer. Despite improved 5-year survival rates, MB is frequently accompanied by metastatic dissemination and poor long-term prognosis. The most aggressive tumors are refractory to conventional chemotherapy and radiation. Our goal is to identify new signaling pathways that regulate the treatment-resistant MB cellular phenotypes, namely the stem cells and metastatic or highly motile cells. To this end, we have discovered that the OTX2 gene, which is amplified or overexpressed in the majority of aggressive MBs, is a central regulator of both stem cell function or self-renewal and cell migration in these tumors. However, the molecular mechanisms by which OTX2 regulates these functions are still unknown. Here, we employed complementary bioinformatics approaches to characterize the OTX2 regulatory network and have discovered a novel relationship between OTX2 and neurodevelopmental genes associated with axon guidance signaling in Group 3 and Group 4 MB stem/progenitor cells. Following OTX2 knockdown, transcripts associated with semaphorin, netrin, ephrin and slit signaling were mostly upregulated. ChIP-sequencing identified putative OTX2 DNA binding sites and revealed statistically significant associations between OTX2 and these axon guidance pathway genes, with the presence of 1 or more OTX2 binding peaks within the transcription start site. Further, Group 3 and 4 MB patient samples were evaluated for correlations between expression of axon guidance pathway genes, OTX2 and survival. Semaphorin signaling was the most overrepresented pathway across all datasets with expression of all pathway genes being upregulated following OTX2 KD. Moreover, one semaphorin gene was identified as a novel prognostic biomarker. We anticipate that delineation of the OTX2 network will identify molecular regulators of both self-renewal and motility, and that these genes will serve as better targets for development of novel therapeutics to effectively eradicate both the “grow and go” arms of the most aggressive MB.
NTOX-11. RECURRENT EPISODES OF STROKE-LIKE MIGRAINE ATTACKS AFTER RADIATION THERAPY (SMART) SYNDROME IN ADULTS
Authors: Alexander Mohler, B.K. Kleinschmidt-DeMasters, Denise Damek
Journal: Neuro-Oncology (2016)

Stroke-like migraine attacks after radiation therapy (SMART) syndrome is a rare late complication of cranial irradiation. SMART syndrome is characterized by abrupt, stroke-like onset of neurological deficits referable to a defined cortical region, headaches, and corresponding MRI findings of gyriform enhancement and cortical swelling within the previously irradiated field. To date, reported SMART syndrome cases reflect a single self-limited syndrome that lasts for several weeks before complete or partial resolution. Recurrence has only rarely been reported in pediatric, but not adult patients. We report two cases of multiply-recurrent SMART syndrome, one autopsy-documented. Case 1 is a 46 year old woman with an atypical meningioma treated with resection and radiation who presented sixteen months after completion of radiation with sudden onset hemiparesis and dysarthria. Brain MRI showed the typical gyriform enhancement seen in SMART syndrome. No other attributable disorders were found on extensive workup, and both symptoms and radiographic abnormalities resolved over several weeks without further therapies. Six months later she again presented with identical symptoms and MRI findings. Incomplete resolution of neurological deficits occurred after this second episode, albeit with resolution of gyriform enhancement. Case 2 was a 43 year old man who had been treated for acute lymphocytic leukemia at the age of four years with chemotherapy and prophylactic cranial irradiation who presented decades after treatment with multiple (n=4) recurrent episodes of sudden onset weakness, seizures, and severe headaches with near complete resolution prior to the next episode. Each event met diagnostic criteria for SMART syndrome and was accompanied by recurrent MRI findings of gyriform enhancement and cortical swelling. Tumor absence and histological features of SMART syndrome were confirmed at autopsy. These two cases expand the clinical presentation of SMART syndrome, as to our knowledge, this is the first report of multiply-recurrent SMART syndrome in adults.
Vitamin D supplementation does cut respiratory infections, new study suggests
Authors: Gareth Iacobucci
Journal: BMJ (2017)

The debate over whether patients should be encouraged to supplement their diet has reignited after a study found that vitamin D supplementation can help reduce the risk of acute respiratory tract infections.

Researchers from Queen Mary University of London argued that their findings, published in The BMJ ,1 support the introduction of food fortification in the UK.

But in a linked editorial other academics, who recently questioned the evidence using vitamin D supplements to prevent disease, said that a clinically useful effect remains uncertain and requires confirmation in further “well designed, adequately powered” randomised controlled trials.2

After setting out to determine the overall effect of vitamin D supplements on the risk of acute respiratory tract infection the researchers conducted …
Relative Efficacy of Steroid Therapy in Ameliorating Autoimmune Thrombocytopenia Mediated by Anti-Platelet GPIIbIIIa Versus GPIbα Antibodies.
Authors: Lili Tao, Jing Bao, Lingyan Zhu, Huawei Miao, Mingzhen Yang, Lingjie Zhang, Ruixiang Xia, Qingshu Zeng, Heyu Ni
Journal: Blood (2009)
CBIO-07. IDH1 MUTATIONS TRIGGER ENHANCEMENT OF ENDOCYTOSIS VIA Rac1
Authors: Yang Liu, Yanxin Lu, Chunzhang Yang
Journal: Neuro-Oncology (2017)

Mutations in isocitrate dehydrogenase (IDH1/2) are common early genetic abnormalities in low grade gliomas including WHO grade II and III astrocytomas and oligodendrogliomas. Although these IDH mutations have profound effects on the tricarboxylic acid cycle, little is known about the impact of IDH mutations on the adaptive changes in cellular biology and tumor characteristics such as cell migration. In the present study, we report that IDH1 mutations result in fundamental changes in endocytosis and cellular motility, through the activation of a small GTPase Rac1. We established a series of U251 cell lines with stable expression of IDH1 Wildtype, R132C or R132H variant. Endocytosis was analyzed using electron microscopy, optical imaging and uptake assays. Changes in molecular signaling were further analyzed by quantitative PCR, western blots, immunostaining and GTPase activation assays. Introduction of IDH1 mutations led to marked changes in the plasma membrane, which was demonstrated by increased membrane ruffling, lamellipodia formation, enhancement in endocytosis (>27x increase endocytosis index) and cellular migration (>2x increase in travel distance). Up-regulation of endocytosis/endosomal markers further demonstrated that several mechanisms of endocytosis were activated, such as caveolin, clathrin, Rab5 and EEA1 (over 1.9x, 14x, 5.0x and 4.3x increase, respectively). In addition, the endocytosis was related to the activation of Rac1, as Rac1 phosphorylation increased by 1.5x in mutant cells. Furthermore, inhibition on Rac1 pathway extensively limited endocytosis (>89% reduction as endocytosis index) in IDH1 mutant cells. Our study identified a novel molecular mechanism that is possibly involved in IDH1-associated oncogenesis. We observed enhanced endocytosis and cellular motility, suggesting this as a potential mechanism related to a more infiltrative and possibly more aggressive phenotype during cancer progression. The unexpected finding of Rac1 activation may provide a novel therapeutic target for glioma treatment.
Cord Blood NK Cytotoxic Activity Can Be Selelctively Modulated by Accessory.
Authors: Dongxia Xing, Sufang Li, Robinson N. Simon, Decker William, Yang Hong, Steiner David, Thomas Michael, Richard E. Champlin, John D. McMannis, Marcelo F. Vina, Laurence J.N. Cooper, Paul J. Simmons, Patrick A. Zweidler-Mckay, Elizabeth J. Shpall
Journal: Blood (2007)
Nab-paclitaxel/gemcitabine first line therapy in patients with metastatic pancreatic carcinoma and high-bilirubin values - Data from the German QoliXane pancreatic cancer registry
Authors: Gzur Hausen, O. Waidmann, M.A. Woerns, H.G. Hoeffkes, S. Doerfel, M.O. Zahn, A. Aldaoud, M. Stauch, C. Springfeld, N. Haertel, A. Reichart, T.O. Goetze, S. Schwarz, C. Pauligk, J. Roemmler-Zehrer, R.D. Hofheinz, S.-E. Al-Batran
Journal: Annals of Oncology (2016)
High Definition Contrast-Enhanced MR Imaging in Paroxysmal Nocturnal Hemoglobinuria (PNH) Suggests a High Frequency of Subclinical Thrombosis.
Authors: Anita Hill, Scott A. Reid, Russell P. Rother, Mark T. Gladwin, Paul O. Collinson, David C. Gaze, Angela Lowe, Ashley Guthrie, Mohan U. Sivananthan, Peter Hillmen
Journal: Blood (2006)
Anti-Myeloma Activity of Two Novel N-Substituted and Tetraflourinated Thalidomide Analogues.
Authors: Shaji Kumar, Noopur Raje, Teru Hideshima, Kenji Ishitsuka, Aldo Roccaro, Norihiko Shiraishi, Makoto Hamasaki, Hiroshi Yasui, Nikhil C. Munshi, William D. Figg, Kenneth C. Anderson
Journal: Blood (2004)
Erratum: Corrigendum: Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue
Authors: Colin S Cooper, Rosalind Eeles, David C Wedge, Peter Van Loo, Gunes Gundem, Ludmil B Alexandrov, Barbara Kremeyer, Adam Butler, Andrew G Lynch, Niedzica Camacho, Charlie E Massie, Jonathan Kay, Hayley J Luxton, Sandra Edwards, Zsofia Kote-Jarai, Nening Dennis, Sue Merson, Daniel Leongamornlert, Jorge Zamora, Cathy Corbishley, Sarah Thomas, Serena Nik-Zainal, Manasa Ramakrishna, Sarah O'Meara, Lucy Matthews, Jeremy Clark, Rachel Hurst, Richard Mithen, Robert G Bristow, Paul C Boutros, Michael Fraser, Susanna Cooke, Keiran Raine, David Jones, Andrew Menzies, Lucy Stebbings, Jon Hinton, Jon Teague, Stuart McLaren, Laura Mudie, Claire Hardy, Elizabeth Anderson, Olivia Joseph, Victoria Goody, Ben Robinson, Mark Maddison, Stephen Gamble, Christopher Greenman, Dan Berney, Steven Hazell, Naomi Livni, Cyril Fisher, Christopher Ogden, Pardeep Kumar, Alan Thompson, Christopher Woodhouse, David Nicol, Erik Mayer, Tim Dudderidge, Nimish C Shah, Vincent Gnanapragasam, Thierry Voet, Peter Campbell, Andrew Futreal, Douglas Easton, Anne Y Warren, Christopher S Foster, Michael R Stratton, Hayley C Whitaker, Ultan McDermott, Daniel S Brewer, David E Neal
Journal: Nature Genetics (2015)
Immunosurveillance and therapy of multiple myeloma are CD226 dependent
Authors: Camille Guillerey, Lucas Ferrari de Andrade, Slavica Vuckovic, Kim Miles, Shin Foong Ngiow, Michelle C.R. Yong, Michele W.L. Teng, Marco Colonna, David S. Ritchie, Marta Chesi, P. Leif Bergsagel, Geoffrey R. Hill, Mark J. Smyth, Ludovic Martinet
Journal: Journal of Clinical Investigation (2015)
Comparative Clinical and Biological Features of Primary Mediastinal B-Cell Lymphoma (PMBL) and Mediastinal Grey Zone Lymphoma (MGZL).
Authors: Kieron Dunleavy, Stefania Pittaluga, Kevin Tay, Nicole Grant, Clara C Chen, Margaret Shovlin, Seth Steinberg, Louis M Staudt, Elaine S Jaffe, John E Janik, Wyndham H Wilson
Journal: Blood (2009)
“Back-up” Stem Cell Harvest Is Beneficial for Patients Receiving Unrelated Donor Allogeneic Hematopoietic Cell Transplantation.
Authors: Huarui Fu, Yamin Tan, Yi Luo, Yanlong Zheng, Jimin Shi, Jingsong He, Wenjun Wu, Jie Sun, Li Li, Xiaoyan Han, Xiaoli Zhu, Shuiyun Chen, Zhen Cai, Xiujin Ye, Wanzhou Xie, Jie Zhang, Maofang Lin, He Huang
Journal: Blood (2010)
Nivolumab in patients with previously treated advanced NSCLC in clinical practice and correlation with immunological characteristics
Authors: F. Vitiello, B. Casale, M. Gilli, A. Tortoriello, M. Hengeller, A. Bianco, R. Maffucci, P. Gaglione, R. Manzo, F. Piantedosi
Journal: Annals of Oncology (2016)
PDTM-05. CD271 (p75NTR) AS A NOVEL DIAGNOSTIC MARKER AND THERAPEUTIC TARGET FOR SHH MEDULLOBLASTOMA
Authors: Lisa Liang, Ludivine Morrison, Nazanin Tatari, Vijay Ramaswamy, Marc Del Bigio, Michael Taylor, Cynthia Hawkins, Jennifer A Chan, Tamra Werbowetski-Ogilvie
Journal: Neuro-Oncology (2017)

The extensive heterogeneity within the medulloblastoma (MB) molecular variants has revealed a critical need for subtype-specific biomarkers and therapeutic strategies. Using a high throughput flow cytometry screen and gain/loss of function studies, we previously identified CD271/p75NTR as a candidate stem/progenitor cell marker specifically in SHH MB. Here, we performed immunohistochemical analysis to evaluate expression levels of CD271 across the MB subtypes as well as OTX2, which is not expressed in SHH tumors. Our data demonstrated that SHH tumors are associated with high CD271 and negligible OTX2 levels. In support of these findings, transcriptome analysis of CD271 and OTX2 in 763 MB patient samples revealed a striking pattern of high CD271 expression with correspondingly low OTX2 across all SHH tumors, but particularly in older patients exhibiting TERT mutations. We further characterized the heterogeneity within SHH tumors and showed that CD271+ and CD271- subpopulations are distinct and co-existing cellular subsets. RNA sequencing analysis revealed that genes/pathways associated with cell survival, proliferation and motility were downregulated, whereas genes associated with the MYC pathway and a proneural signature were upregulated in CD271- vs. CD271+ subpopulations. Inhibition of pathways that are upregulated in CD271+ cells such as polo-like kinase (PLK1) and ERK1/2 resulted in significant decreases in proliferation and survival of SHH MB stem-like cells, while inhibition of pathways upregulated in CD271- subpopulation such as cytosolic phospholipase A2 (cPLA2) and SHH signaling had no significant effect. Importantly, combinatory treatments targeting both CD271- and CD271+ cells resulted in an additive inhibitory effect on tumorsphere size and cell survival. Our study demonstrates that CD271+/OTX2- IHC staining may be effectively utilized as a combinatory diagnostic tool for SHH MB. In addition, our results show that the CD271- and CD271+ subpopulations are molecularly distinct and must be concomitantly targeted for more effective treatment of SHH MB tumors.
A phase I / II trial of pemetrexed plus radiation therapy in elderly patients with locally advanced NSCLC
Authors: S. Atagi, A. Tamiya, S. Fukuda, Y. Naoki, M. Morimoto, T. Ibe, K. Okishio, H. Goto, A. Yoshii, T. Kita, Y. Tomizawa, N. Nogami, Y. Fujita
Journal: Annals of Oncology (2016)
Evaluation of the interindividual variability in plasma nivolumab level in non-small-lung cancer outpatients: preliminary results
Authors: A. Puszkiel, G. Noé, P. Boudou-Rouquette, C. Le Cossec, J. Arrondeau, J.S. Giraud, J. Alexandre, M. Vidal, F. Goldwasser, B. Blanchet
Journal: Annals of Oncology (2016)
Impact of Myeloablative and Reduced Intensity Conditioning On Outcomes After Unrelated Cord Blood Transplantation for Adults with Acute Lymphoblastic Leukemia.
Authors: Luciana Tucunduva, Annalisa Ruggeri, Guillermo Sanz, Sabine Furst, Bernard Rio, Gerard Socie, William Arcese, Mauricette Michallet, Ibrahim Yakoub-Agha, Jan J Cornelissen, Miguel Angel Sanz, Pau Montesinos, Duncan Purtill, Eliane Gluckman, Vanderson Rocha
Journal: Blood (2012)
The impact of staging by positron emission tomography (PET) on overall survival (OS) and progression-free survival (PFS) in the phase III PROCLAIM study
Authors: N. Iscoe, R. Govindan, A.M. Hossain, B. San Antonio, N. Chouaki, M. Koczywas, E. Vokes, S. Senan
Journal: Annals of Oncology (2016)
DDIS-13. IDENTIFICATION OF INDIVIDUALIZED THERAPY OPTIONS IN PATIENTS WITH GLIOBLASTOMA BY HIGH-THROUGHPUT DRUG SCREENING
Authors: Erlend Skaga, Evgeny Kulesskiy, Cecilie Jonsgar Sandberg, Artem Fayzullin, Aija Kyttälä, Iver Arne Langmoen, Aki Laakso, Emília Gaál-Paavola, Markus Perola, Krister Wennerberg, Einar Osland Vik-Mo
Journal: Neuro-Oncology (2016)

Glioblastoma (GBM) remains rapidly fatal and identification of new treatments has proven difficult due to patient specific characteristics of the tumor. Patient-derived GBM cell cultures enriched for tumor stem cells under serum-free, growth factor-enriched conditions are able to recapitulate the human disease upon xenotransplantation. We hypothesized that patient-derived GBM cultures display patient specific drug sensitivity patterns. We cultured 12 primary GBMs and evaluated viability and cytotoxicity to 470 anticancer drugs in a 5-point dose-response curve using high-throughput screening. The drug collection consisted of both approved and investigational drugs. Screening results were verified in 5 of the screened samples to 4 effective drugs and to temozolomide, the standard of care, across assays measuring viability, cytotoxicity, sphere-forming capability and invasion. We found that inhibition of survivin by an investigational drug was lethal in all samples and effective across all assays. Furthermore, several FDA approved drugs were potent across many samples such as two proteasome inhibitors, a protein synthesis inhibitor and a RNA-/DNA-synthesis inhibitor. Several investigational drugs in clinical phases were potent in many samples, such as a Chk1/Cdk2–, a combined HDAC-/PIK3- and two HSP90 inhibitors. Interestingly, temozolomide was ineffective in all samples except one. In 9 of the screened samples a patient specific drug response was identified. We were able to reproduce the effect of potent drugs and the resistance to temozolomide in our verification set up measuring viability, cytotoxicity and sphere-forming capability. However, the effect on invasion was limited. The high-throughput screening of patient-derived GBM samples creates a drug sensitivity and resistance profile to each patient and leads to identification of possible new effective treatments. By reproducing the screening results in our verification set up we are able to reliably identify preclinical effective therapeutic options on a patient specific level with the possibility to translate preclinical data into a clinical setting.
Evidence for Selective Benefit of Sequential Treatment with Azanucleosides in Patients with Myelodysplastic Syndromes (MDS)
Authors: Susmitha Apuri, Jeffrey E Lancet, Najla H Al Ali, Eric Padron, Viet Q. Ho, Javier Pinilla-Ibarz, Alan F. List, Rami S. Komrokji
Journal: Blood (2012)
Impact of prior therapies on everolimus treatment in the subgroup of patients with advanced lung neuroendocrine tumors (NET) in the RADIANT-4 trial
Authors: R. Buzzoni, G.D. Fave, J. Strosberg, M. Voi, A. Ridolfi, L. Bubuteishvili-Pacaud, F. Herbst, E. Wolin, N. Fazio
Journal: Annals of Oncology (2016)