tbuckley/cabot-search huggingface dataset:
Analyses of Prognostic Factors for Survival in East African Patients with AIDS-Related Non-Hodgkin’s Lymphoma (AR-NHL) Treated with Dose Modified Oral Chemotherapy.
Authors: Vivek Subbiah, O.W. Mwanda, Jackson Orem, P. Fu, C. Banura, J. Kakembo, A. Ness, J. Johnson, J. Bako, E. Katongole-Mbidde, Scot Remick
Journal: Blood (2006)
Assessing the Impact of Smoking Status and Number of Comorbidities on Improvement in Asthma Knowledge in Patients Receiving the Algorithmic Software Tool to Help Manage Asthma (ASTHMA)-Educator and Nurse-delivered Asthma Education
Authors: Taha Keskin, Joshua Grossman, Sunit P. Jariwala
Journal: Journal of Allergy and Clinical Immunology (2017)
Chemotherapy in elderly lung cancer patients: A retrospective analysis
Authors: L. Zhang, C. Zhou
Journal: Journal of Clinical Oncology (2008)

20630 Background: Elderly patients with non-small-cell lung cancer (NSCLC) have been habitually underrepresented in clinical trials. Therapeutic neglect and legitimate concerns about toxicity are responsible. Case control study showed that elderly age alone should not preclude patients from receiving platinum-based chemotherapy, since it seems well tolerated and effective in non-small-cell lung cancer among elderly patients. But patients enrolled into this study were over 70 years old. Whether elderly patients, who were over 75 years old, tolerate chemotherapy and derive the same survival advantage is unknown. This retrospective study evaluated the influence of age on survival, chemotherapy delivery and toxicity. Methods: Pretreatment characteristics, follow up data and survival benefit from treatment were collected. Chemotherapy delivery, toxicity, 1-year survival and disease control rate (DCR) were compared for 291 treated patients. Results: There were 291 elderly patients who were over 75 years. Clinical characteistics were listed in table 1. 135 patients completed 1 cycle chemotherapy, 75 for 2 cycles, 35 for 3 cycles, 38 for 4 cycles, 3 for 5 cycles and 5 for 6 cycles. There were 25 received second line chemotherapy. There were 150 patients to evaluate response and 162 patients to calculate 1-year survival rate. Overall DCR for general was 90%, that for monotherapy, two-drug and three-drug were 93%, 91% and 67%, respectively. Median survival time was 8, 7, 8, 7 months, respectively. 1-year survival rate was 26%, 33%, 28% and 20%, respectively. Toxicities were evaluated for all the patients. The toxicity was tolerable. Conclusions: Chemotherapy improves overall survival in patients aged >75 with acceptable toxicity. Chemotherapy should not be withheld from elderly patients. Total (n = 291) Male (n = 240) Female (n = 51) Age 75–80 268 217 51 ≥80 23 23 0 Pathology Squamous 93 88 5 Adenocarcinoma 118 80 38 Adeno-squamous 9 9 0 NSCLC 19 14 5 SCLC 34 33 1 Un-typed 18 16 2 Clinical stage Ia 3 2 1 Ib 7 4 3 IIa 2 2 0 IIb 13 11 2 IIIa 39 37 2 IIIIb 88 78 10 IV 139 108 31 Bone 61 46 15 Brain 17 17 7 Liver 13 9 4 Lung 55 43 12 Adrenal gland 2 2 0 ECOG performance status 0 10 9 1 1 255 212 43 2 26 19 7 Chemotherapy Monotherapy (94) Gemcitabine 55 9 Vinorelbine 26 5 Taxel 12 3 Double 184 25 Triple 13 2 Second-line 25 6 No significant financial relationships to disclose.
Sexual function of long-term rectal cancer survivors.
Authors: Carmit K. McMullen, Marcia Grant, Christopher Wendel, Joanna E Bulkley, Virginia Sun, Lisa J. Herrinton, Mark C. Hornbrook, Robert S. Krouse
Journal: Journal of Clinical Oncology (2016)

209 Background: Many rectal cancer survivors report problems with intimacy and sexual function after surgery. The extent of these problems is not well known. Methods: Long-term rectal cancer survivors (5+ years post-diagnosis) who were members of Kaiser Permanente with permanent ostomy (n = 183) or sphincter-sparing surgery (N = 394) completed a mailed survey. Participants were identified through tumor registries and health plan data. Items from the City of Hope Quality of Life Colorectal Cancer scale assessed disruption to intimate relationships due to the surgery on a scale of 0-10, with 10 indicating the least disruption. Other items assessed current experiences of and satisfaction with sexual function as well as comfort being undressed in front of a partner. Results: Survey response rate was 60.5% (N = 577). Respondents’ average age was 73 years, 41% were female, 63% were married or partnered at the time of survey, and 30% reported being sexually active. Fifteen percent of those who were not sexually active feared resuming sexual activity. Thirty-five percent of all respondents found their sexual activity unsatisfying. Of the 236 female respondents, 24% reported current problems with vaginal dryness, 12% with vaginal stricture, and 9% with vaginal pain. Of the 341 male respondents, 64% reported current problems getting an erection and 65% with maintaining one. Survivors with ostomy vs. sphincter-sparing surgery reported more interference with personal relationships (6.4 vs. 8.3, p &lt; .001) and less ability to be intimate (5.1 vs. 7.0, p &lt; .0001). A higher percentage with ostomy also reported discomfort being undressed in front of their partner (40.6% vs. 10.6%, p &lt; .001). Conclusions: Many rectal cancer survivors were unsatisfied with their sexual activity. One in ten women reported vaginal stricture, which can be mitigated by early intervention. Nearly 1/4 reported problems (dryness, pain) that can be addressed at any phase of survivorship. Two thirds of men reported trouble with getting an erection and with maintaining one, indicating a significant opportunity for intervention in this cohort. Sexual function did not differ significantly between surgery groups. In line with previous reports, survivors with ostomy had more intimacy and body image problems.
Progesterone to improve neurocognitive outcomes following cranial irradiation.
Authors: Derick Okwan-Duodu, Fahim Atif, David S. Yu, Seema Yousuf, Deborah Bruner, Walter John Curran, Donald G Stein
Journal: Journal of Clinical Oncology (2016)

128 Background: Neurocognitive functional decline is a common sequalae of cranial irradiation (CI) that significantly impacts quality of life. Preclinical studies and randomized clinical trials show that following traumatic brain injury and cerebrovascular accidents, premenopausal women demonstrate decreased mortality and improved neurocognitive function, with these benefits presumed to be derived from progesterone. We hypothesized that progesterone may serve similar role in neuroprotection following cranial irradiation. Methods: Adult non-tumor bearing wild type C57BL/6 male mice were treated with two separate fractionated radiation therapy regimen (9 Gy and 15 Gy) to the brain. Cohorts of these mice were administered progesterone (16mg/kg daily) as a pretreatment for 3 days and concurrent with the radiotherapy for a total of 14 days with tapering during the last two days. The animals were then tested using different behavioral measures for cognitive function including morris water maze (MWM) for assessing spatial and related forms of learning and memory, elevated plus maze (EPM), , and spontaneous locomotor activity (SLA) tests. Mice were tested for cognitive function on day 10 and after 30 days of treatment for short and long-term effects of (CI) on memory function. Results: All irradiated mice showed statistically significant decline in MWM, EPM, and SLA measures. There were no significant differences in the 9 Gy versus 15 Gy cohorts. Progesterone administration produced a statistically significant group effect (F (4, 25) = 8.553; P&lt;0.001) in the improvement of long-term memory function over 5 days of learning process. Progesterone administration also demonstrated a significant group effect (F (4, 25) = 8.613; P&lt;0.001) in the probe trial, and a significant beneficial effect (F (4, 25) = 7.993; P&lt;0.001) in short-term memory functional latency to reach the platform. Conclusions: The preclinical data show that progesterone improves radiation-induced deficits in short-and long-term memory functions in adult mice. Further work is required to show if progesterone may show similar clinical benefit in neuroprotection for adults undergoing prophylactic CI or definitive CI for brain metastases or benign intracranial processes such as AVM.
455P Population-level impact of EGFR mutation testing in nonsquamous NSCLC
Authors: M.J. McKeage, J.M. Elwood, S. Tin Tin, P. Khwaounjoo, P. Aye, A. Li, P. Shepherd, G. Laking, N. Kingston, C. Lewis, D. Love
Journal: Annals of Oncology (2016)
RTHP-02. TOWARDS THERAPEUTIC OPTIMISM – INCREASING RADIATION THERAPY UTILIZATION IN PATIENTS WITH GLIOBLASTOMA
Authors: Derek Johnson, Timothy Kaufmann, Jonathan Ashman, Alyx Porter
Journal: Neuro-Oncology (2016)

Despite extensive data demonstrating the efficacy of radiation therapy (RT) in glioblastoma, previous studies have found declining RT utilization over time, likely related to therapeutic nihilism. The impact of recent advances in glioblastoma care upon this trend is unknown. Adult patients with glioblastoma diagnosed from 1992 to 2013 were identified in the population-based Surveillance, Epidemiology, and End Results (SEER) database. Trends in radiation use over this period were analyzed using permutation testing in SEER Joinpoint regression software. Predictors of RT utilization in recent years (2010-2013) were identified with logistic regression. 44,357 patients met criteria for inclusion in this analysis. Between 1992 and 2002, the previously described trend of decreasing RT utilization continued, with an annual percent change (APC) of -0.57% (p<0.05). This trend reversed in 2002, with a positive APC of 0.70% for the 2002 to 2013 period (p<0.05). The trend reversal was observed in both elderly and non-elderly patient populations. In the subset of 11,685 patients diagnosed from 2010 to 2013, positive predictors of RT utilization included younger age, marital status (married>unmarried), and surgical status (resection>biopsy>none); all p<0.0001. The rate of RT utilization is increasing, in contrast to a previous trend of declining use. In the absence of significant new data for RT, this change is likely due to a shift toward greater therapeutic optimism in light of other advances in the field.
Single-Cell Pharmacodynamic Monitoring of Ribosomal Protein S6 Phosphorylation During AC220 Therapy Demonstrates in Vivo FLT3 Inhibition in Circulating Leukemic Blasts and Accurately Detects the Development of AC220 Resistance.
Authors: Alexander E Perl, Grace R Jeschke, Catherine C Smith, James K. Mangan, Selina M. Luger, Martin Carroll
Journal: Blood (2012)
Impact of humoral immune response against p53 on clinical outcome of High-Grade Serous Ovarian Cancer (HGSOC) patients
Authors: M. Garziera, E. Cecchin, M. Montico, R. Roncato, S. Gagno, E. De Mattia, R. Sorio, S. Scalone, E. Poletto, G. Toffoli
Journal: Annals of Oncology (2016)
Racial disparities in prostate cancer outcome among prostate-specific antigen screening eligible populations in the United States
Authors: B.A. Mahal, Y.-W. Chen, V. Muralidhar, A.R. Mahal, T.K. Choueiri, K.E. Hoffman, J.C. Hu, C.J. Sweeney, J.B. Yu, F.Y. Feng, S.P. Kim, C.J. Beard, N.E. Martin, Q.-D. Trinh, P.L. Nguyen
Journal: Annals of Oncology (2017)
Inhibition of IL-6 Release in Vitro by in Vivo Administration of an IKK Inhibitor in Mice with Lung Fibrosis Induced by Poly I:C
Authors: KarryAnne Karin Belanger, Bing Tian, Allan R. Brasier, Bill T. Ameredes
Journal: Journal of Allergy and Clinical Immunology (2017)

Interleukin(IL)-6 is known to act as a growth factor that promotes epithelial-to-mesenchymal transition (EMT) and fibrosis, and is upregulated in acute animal models of airway injury with Polyinosinic:polycytidylic acid (Poly (I:C)), a viral mRNA analog. Previously, we demonstrated that Poly (I:C) results in leukocyte priming for IL-6 release that is maintained beyond the early and late phases of chronic airway inflammation. To establish mechanism, we investigated the relevance of the NF-κB pathway in this response, by in vivo treatment with an IKK inhibitor. C57Bl6 mice were administered intranasal Poly (I:C) (500 mcg; n=5/group) daily, over 21 days. A subset was pre-treated with an IKK inhibitor BMS345541 (BMS; 10mg/kg body weight, i.p.) 1 day before each poly (I:C) challenge. One week after last challenge, bronchoalveolar lavage (BAL) fluid and leukocytes were collected, and cells were cultured (72 hr), with and without LPS (1000 ng/ml). IL-6 in the culture media was measured by ELISA; data were compared by t-tests. As compared to PBS-treated controls, BAL total cell counts (in 104 cells/ml) were slightly elevated with Poly (I:C) (4.5 vs. 3.1; P<0.05), and not different with Poly (I:C)+BMS (3.3, n.s.). Spontaneous IL-6 release from cultured leukocytes was undetectable, whereas with LPS stimulation, it was significantly increased with Poly (I:C) (495 pg/ml, P<0.05), and significantly reduced with BMS (27 pg/ml), to levels not different from PBS controls (13 pg/ml). We conclude that the NF-κB pathway is essential in the Poly (I:C)-dependent priming response of airway leukocytes to produce and release IL-6 within the airway.
246P The association of plasma soluble major histocompatibility complex class I polypeptide-related sequence A (sMICA) level with the pathological complete response (pCR) in locally advanced esophageal squamous cell carcinoma (ESCC)
Authors: H.-Y. Kuo, Y.-C. Lin, J.-C. Guo, T.-C. Huang, C.-C. Lin, K.-H. Yeh, A.-L. Cheng, C.-H. Hsu, C.-C. Chang
Journal: Annals of Oncology (2016)
Design of a phase II trial comparing tepotinib + gefitinib with cisplatin + pemetrexed in EGFR inhibitor-resistant, c-Met+ NSCLC
Authors: Y.-L. Wu, K. Park, D.-W. Kim, R. Soo, U. Stammberger, W. Chen, G. Locatelli, J. Yang
Journal: Annals of Oncology (2016)
Standardisation and application of the single-breath determination of nitric oxide uptake in the lung
Authors: Gerald S. Zavorsky, Connie C.W. Hsia, J. Michael B. Hughes, Colin D.R. Borland, Hervé Guénard, Ivo van der Lee, Irene Steenbruggen, Robert Naeije, Jiguo Cao, Anh Tuan Dinh-Xuan
Journal: European Respiratory Journal (2017)

Diffusing capacity of the lung for nitric oxide ( D LNO ), otherwise known as the transfer factor, was first measured in 1983. This document standardises the technique and application of single-breath D LNO . This panel agrees that 1) pulmonary function systems should allow for mixing and measurement of both nitric oxide (NO) and carbon monoxide (CO) gases directly from an inspiratory reservoir just before use, with expired concentrations measured from an alveolar “collection” or continuously sampled via rapid gas analysers; 2) breath-hold time should be 10 s with chemiluminescence NO analysers, or 4–6 s to accommodate the smaller detection range of the NO electrochemical cell; 3) inspired NO and oxygen concentrations should be 40–60 ppm and close to 21%, respectively; 4) the alveolar oxygen tension ( P AO 2 ) should be measured by sampling the expired gas; 5) a finite specific conductance in the blood for NO (θNO) should be assumed as 4.5 mL·min -1 ·mmHg -1 ·mL -1 of blood; 6) the equation for 1/θCO should be (0.0062· P AO 2 +1.16)·(ideal haemoglobin/measured haemoglobin) based on breath-holding P AO 2 and adjusted to an average haemoglobin concentration (male 14.6 g·dL −1 , female 13.4 g·dL −1 ); 7) a membrane diffusing capacity ratio ( D MNO / D MCO ) should be 1.97, based on tissue diffusivity.
P06.18 DNA methylation distance score in lower-grade gliomas has prognostic value: a POLA network study
Authors: A. Alentorn, A. Kamoun, F. Ducray, C. Dehais, K. Mokhtari, E. Uro-Coste, D. Figarella-Branger, J. Delattre, A. Idbaih, M. Sanson
Journal: Neuro-Oncology (2016)

AbstractBackground:CpG Island Methylator Phenotype (CIMP) is strongly associated with IDH1/2 mutations that are frequently found in lower-grade gliomas (LGG: WHO grade II and WHO grade III). In addition, LGG have been recently divided in three histomolecular subgroups with clinical relevance: (i) IDH wild type, (ii) IDH mutated without 1p/19q co-deletion and (iii) IDH mutated with 1p/19q co-deletion. However, the study of intra-tumor methylation heterogeneity in LGG has not been fully elucidated, so far.Objectives:We sought to study the intra-tumor methylation heterogeneity in LGG.Material and methods:108 LGG from the POLA network, as the discovery cohort, were included in the present study. 273 lower grade gliomas from the TCGA dataset, were used as the validation cohort. Methylation analysis was performed using Infinium Human Methylation 450 Illumina BeadChip arrays in both cohorts. We have also used methylation dataset of adult normal brain publicly available (GSE36278). A phylogenetic methylation score was calculated comparing normal brain to the different molecular subgroups of LGG. Overall survivals (OS) were compared using log-rank test in univariate analysis. All covariates with p-value < 0.2 were included in a Cox’s proportional hazard ratio model for multivariate analysis. Statistical tests were two-sided and p-values < 0.05 were interpreted as statistically significant.Results:Mean promoter-level methylation was strongly correlated with the different molecular subgroups of LGG. Interestingly, we have identified a subgroup of 1p/19q co-deleted LGG harboring a significantly higher level of CIMP (hCIMP). In parallel, this particular subgroup of hCIMP exhibits the highest intra-tumor methylation level heterogeneity.Finally, using a phylogenetic clustering approach, we have identified a methylation heterogeneity score derived from distances of the methylation pattern of each tumor that is associated with poor prognosis in Cox’s proportional hazard model after adjusting by age, WHO grade, IDH1/2 mutation and 1p/19q co-deletion. These findings were validated in the TCGA dataset.Conclusion:We have identified a subgroup of 1p19q co-deleted LGG with hCIMP and higher intra-tumor methylation heterogeneity. In addition, a phylogenetic methylation score is a potential new prognostic biomarker in LGG.Acknowledgements: The results shown here are in whole or part based upon data generated by the TCGA Research Network: http://cancergenome.nih.gov/. La Ligue Nationale Contre La Cancer. The Institut Universitaire de Cancerologie (IUC). The program Investissements d’avenir” ANR-10-IAIHU-06. POLA network is supported by Institut National du Cancer.
High Resolution Genomic Analysis In CLL Demonstrates Genomic Stability In Untreated Patients and Novel Markers of Progression In Treated Patients
Authors: Jennifer R Brown, Megan Hanna, Bethany Tesar, Lillian Werner, Hazel Reynolds, Stacey M Fernandes, Laura Macconaill, Yaoyu Wang, Mick Correll, Donna Neuberg, Arnold S. Freedman
Journal: Blood (2010)
Enhancement Of Assay Specificity By Allergenic Components In The Diagnosis Of Hazelnut Allergy In Children: A Systematic Literature Review And Meta-Analysis
Authors: Sigrid Sjolander, Barbara Mascialino, Donna Fountain, Kevin Cadwell, Chrysanthi Papageorgakopoulou, Malin Berthold, Robert G. Hamilton
Journal: Journal of Allergy and Clinical Immunology (2017)
Grafts From HLA-Identical Siblings Versus HLA-Allelic-Matched Unrelated Donors (10/10) In Patients Undergoing Allogeneic Stem Cell Transplantation Following Reduced-Intensity Conditioning Regimen
Authors: Eva De Berranger, Mathieu Wemeau, Charles Herbaux, Cracco Pascale, Jean-Pierre Jouet, Ibrahim Yakoub-Agha
Journal: Blood (2010)
Fludarabine, Cyclophosphamide, Rituximab (FCR) and Vorinostat Followed By Rituximab and Vorinostat Maintenance Therapy in Patients with Previously Untreated Chronic Lymphocytic Leukemia (CLL) or Small Lymphocytic Leukemia (SLL) - Final Results of a Phase I/II Study
Authors: Mazyar Shadman, Ajay K Gopal, Oliver Press, David G. Maloney, Raya Mawad, Troy Wadsworth, Trevor W. Dennie, Karl Schultheiss, Kiarash Kojouri, Britt E Kammerer, John M. Pagel
Journal: Blood (2016)
TMIC-14. TUMOR EVOLUTION OF GLIOMA INTRINSIC GENE EXPRESSION SUBTYPE ASSOCIATES WITH IMMUNOLOGICAL CHANGES IN THE MICROENVIRONMENT
Authors: Qianghu Wang, Xin Hu, Florian Muller, Hoon Kim, Massimo Squatrito, Tom Mikkelsen, Lisa Scarpace, Floris Barthel, Yu-Hsi Lin, Nikunj Satani, Emmanuel Martinez-Ledesma, Edward Chang, Adriana Olar, Baoli Hu, Ana deCarvalho, Eskil Eskilsson, Siyuan Zheng, Amy Heimberger, Erik Sulman, Do-Hyun Nam, Roel Verhaak
Journal: Neuro-Oncology (2016)

GBM tumor cells along with the tumor microenvironment create a complex milieu that ultimately promotes tumor cell plasticity and disease progression. Here, we explored the properties of the microenvironment in different GBM expression subtypes and characterized the transition between molecular subtypes before and after therapeutic intervention. We improved the robustness of expression subtype classification system by leveraging IDH wild type glioblastomas (GBM) and derivative neurosphere models to define three tumor-intrinsic mRNA transcription phenotype amongst IDH wild type GBMs. We observed 34/369 samples activated more than one transcriptional subtype. Subclonal mutation rate was significantly higher (p-value=0.024) in samples with multiple subtypes, suggesting that increased intratumoral heterogeneity associates with increased transcriptional heterogeneity. We used an in-silico cytometry method to evaluate the cellular components of the tumor microenvironment and demonstrated that M2 macrophages/microglia are the most frequent type of immune cells in the glioma microenvironment, followed by CD4+ T lymphocytes. The M2 macrophage signature also showed a greater association with the MES subtype (13.4%) relative to the PN (4.6%) and CL (6.0%). There was also a significantly higher fraction of MES samples that expressed M1 macrophage (p-value=3.20E-5) and neutrophil (p-value=1.30E-9) signatures. In contrast, the activated natural killer T-cell signature (p–value=4.91E-2) was significantly reduced in the MES and resting memory CD4+ T cells (p-value=5.40E-7) were less frequently expressed in the PN. Longitudinal transcriptome analysis of 124 pairs of primary and recurrent glioma showed expression subtype is retained in 53% of cases with no proneural to mesenchymal transition being apparent. The MES subtype was most stable (64%) while the CL (47%) and PN (43%) phenotypes were less frequently retained. Inference of the tumor microenvironment through gene signatures revealed a decrease in invading monocytes but a subtype dependent increase in M2 macrophages/microglia cells after disease recurrence. Our longitudinal expression dataset can be accessed at http://recur.bioinfo.cnio.es/.
Validation of the European Leukemia Net (ELN) Genetic Classification of Acute Myeloid Leukemia: Inclusion of Monosomal Karyotype Improves Prognostic Discrimination
Authors: Montserrat Hoyos, Salut Brunet, Josep F. Nomdedeu, Jordi Esteve, Rafael F. Duarte, Josep-Maria Ribera, Mar Tormo, Andreu Llorente, Ramon Guardia, M. Paz Queipo, Javier Bueno, Juan Besalduch, Pio Torres, Inmaculada Heras, Carmen Pedro, Josep M. Martí-Tutusaus, Antoni Garcia, Joan Bargay, Llorenç Font, Antonia Sampol, Olga Salamero, David Gallardo, Lourdes Escoda, Marisa Calabuig, Montserrat Arnan, Marta Pratcorona, Jorge Sierra
Journal: Blood (2010)
Improved Management For Children With Asthma And Anaphylaxis Via A Web-based Quality Improvement Project
Authors: Irum Noor, Randy Alevi, Jennifer Theriot, Ratika Gupta, Mark A. Davis-Lorton, Marcella Aquino, Luz S. Fonacier, David R. Stukus, Ruth Gubernick
Journal: Journal of Allergy and Clinical Immunology (2017)