tbuckley/cabot-search huggingface dataset:
Efficacy of four different regimens in 64 mantle-cell lymphoma cases: clinicopathologic comparison with 498 other non-Hodgkin's lymphoma subtypes. European Organization for the Research and Treatment of Cancer Lymphoma Cooperative Group.
Authors: I Teodorovic, S Pittaluga, J C Kluin-Nelemans, J H Meerwaldt, A Hagenbeek, M van Glabbeke, R Somers, L Bijnens, E M Noordijk, C D Peeters
Journal: Journal of Clinical Oncology (1995)

PURPOSE Before recognizing mantle-cell lymphoma (MCL) as a distinct entity, these patients were grouped into low-grade (LG) or intermediate-/high-grade categories (IGHG) according to the Working Formulation and received various therapies. This was a unique opportunity to evaluate characteristics, behavior, response to treatment, and outcome of patients with MCL from two phase III trials conducted by the European Organization for the Research and Treatment of Cancer (EORTC): EORTC 20855 IGHG and EORTC 20856 LG. PATIENTS AND METHODS After histologic review, 64 diagnosed MCL patients (29 IGHG and 35 LG) were compared with other patients in their respective trials. In the IGHG group, patients received cyclophosphamide, doxorubicin, teniposide (VM26), prednisone, vincristine, and bleomycin (CHVmP-VB) or modified doxorubicin, cyclophosphamide, etoposide (VP 16), mechlorethamine, vincristine, procarbazine, and prednisone (ProMACE-MOPP). In the LG group, after receiving cyclophosphamide, vincristine, and prednisone (CVP) induction, patients were randomized between maintenance treatment with interferon alfa-2a (IFN) or no further treatment. RESULTS MCL patients compared with IGHG subtypes showed a similar overall survival and response rate, but shorter duration of response and progression-free survival. Comparing with LG patients, their response rate, duration of response, and progression-free survival showed no difference, while their overall survival was nearly twice shorter. MCL patients treated with CHVmP-VB had the longest survival. No treatment showed any significant improvement in terms of progression-free survival. CONCLUSION These data confirm that MCL represents a clinicopathologic entity. In terms of survival, it behaves like IGHG subtypes, while in terms of progression-free survival, it behaves like LG lymphoma. It is still not clear which first-line treatment offers patients with MCL the best chance to obtain both a complete response (CR) and a long-term survival.
Clinical Activity and Safety of Medi4736, an Anti-Programmed Cell Death-Ligand 1 (Pd-L1) Antibody, in Patients with Non-Small Cell Lung Cancer
Authors: S. Antonia, S. Ou, S. Khleif, J.R. Brahmer, A. Blake-Haskins, P.B. Robbins, X. Li, J. Vasselli, N. Rizvi
Journal: Annals of Oncology (2014)
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
Authors: Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot
Journal: Genome biology (2015)

HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro .
Effect of Early Adult Patterns of Physical Activity and Television Viewing on Midlife Cognitive Function
Authors: Tina D. Hoang, Jared Reis, Na Zhu, David R. Jacobs, Lenore J. Launer, Rachel A. Whitmer, Stephen Sidney, Kristine Yaffe
Journal: JAMA Psychiatry (2015)

Sedentary behaviors and physical inactivity are not only increasing worldwide but also are critical risk factors for adverse health outcomes. Yet, few studies have examined the effects of sedentary behavior on cognition or the long-term role of either behavior in early to middle adulthood.
Pharmacokinetics of all-trans-retinoic acid administered on an intermittent schedule.
Authors: P C Adamson, J Bailey, J Pluda, D G Poplack, S Bauza, R F Murphy, R Yarchoan, F M Balis
Journal: Journal of Clinical Oncology (1995)

PURPOSE Administration of all-trans-retinoic acid (ATRA) on a continuous daily schedule results in a rapid and sustained decrease in plasma drug concentrations. This pharmacokinetic study was performed to determine if administration of ATRA on an intermittent schedule could overcome the rapid decrease in plasma drug concentration and provide repetitive periods of higher plasma drug exposure. MATERIALS AND METHODS ATRA was administered on repetitive cycles of 7 consecutive days of drug followed by 7 days without drug. On the days of pharmacokinetic monitoring, following an overnight fast, a fixed single oral dose of 40 mg/m2 was administered and frequent plasma samples were obtained over 8 hours. Patients had pharmacokinetic studies performed on the first and seventh days of the first week, and on the first day of the third and eleventh weeks. ATRA was measured in plasma with a reverse-phase high-performance liquid chromatography (HPLC) assay. RESULTS Plasma exposure to ATRA as measured by the area under the plasma concentration-time curve (AUC) decreased significantly during the first week of drug administration, from a mean of 145 +/- 26 mumol/L.min on day 1 to 18 +/- 4 mumol/L.min by day 7. Plasma ATRA concentrations at the start of weeks 3 and 11 of this every-other-week schedule were equivalent to those achieved on day 1 of treatment, with mean AUCs of 177 +/- 39 and 128 +/- 30 mumol/L.min, respectively. CONCLUSION An intermittent schedule of ATRA administration results in repetitive periods of exposure to concentrations of ATRA normally only observed on the first day of treatment. Phase II trials to evaluate the role of intermittent schedules of administration for ATRA are planned.
The Landscape of Prognostic Outlier Genes in High-Risk Prostate Cancer
Authors: Shuang G. Zhao, Joseph R. Evans, Vishal Kothari, Grace Sun, Ashley Larm, Victor Mondine, Edward M. Schaeffer, Ashley E. Ross, Eric A. Klein, Robert B. Den, Adam P. Dicker, R. Jeffrey Karnes, Nicholas Erho, Paul L. Nguyen, Elai Davicioni, Felix Y. Feng
Journal: Clinical Cancer Research (2015)

There is a clear need to improve risk stratification and to identify novel therapeutic targets in aggressive prostate cancer. The goal of this study was to investigate genes with outlier expression with prognostic association in high-risk prostate cancer patients as potential biomarkers and drug targets.We interrogated microarray gene expression data from prostatectomy samples from 545 high-risk prostate cancer patients with long-term follow-up (mean 13.4 years). Three independent clinical datasets totaling an additional 545 patients were used for validation. Novel prognostic outlier genes were interrogated for impact on oncogenic phenotypes in vitro using siRNA-based knockdown. Association with clinical outcomes and comparison with existing prognostic instruments was assessed with multivariable models using a prognostic outlier score.Analysis of the discovery cohort identified 20 prognostic outlier genes. Three top prognostic outlier genes were novel prostate cancer genes; NVL, SMC4, or SQLE knockdown reduced migration and/or invasion and outlier expression was significantly associated with poor prognosis. Increased prognostic outlier score was significantly associated with poor prognosis independent of standard clinicopathologic variables. Finally, the prognostic outlier score prognostic association is independent of, and adds to existing genomic and clinical tools for prognostication in prostate cancer (Decipher, the cell-cycle progression signature, and CAPRA-S).To our knowledge, this study represents the first unbiased high-throughput investigation of prognostic outlier genes in prostate cancer and demonstrates the potential biomarker and therapeutic importance of this previously unstudied class of cancer genes.
Pulse intravenous clomipramine for depressed adolescents: double-blind, controlled trial
Authors: F R Sallee, N S Vrindavanam, D Deas-Nesmith, S W Carson, G Sethuraman
Journal: American Journal of Psychiatry (1997)

Major depressive disorder in adolescents is characterized as treatment resistant, but a previous open-label trial of pulse intravenous clomipramine demonstrated rapid relief of depressive symptoms. In the present study a single intravenous dose of clomipramine (200 mg) was compared with saline placebo in a randomized controlled trial for depressed adolescents. The hypothesis was that adolescents who were treated with pulse clomipramine would exhibit lower scores on the Hamilton Depression Rating Scale at endpoint than would adolescents who received saline and that clomipramine would be superior to saline in terms of antidepressant response.Sixteen nonsuicidal outpatient adolescents (mean age = 16.2 years, SD = 1.0) who met the DSM-III-R criteria for major depression (score on 21-item Hamilton scale, > or = 18) were randomly assigned to receive either clomipramine (200 mg i.v., N = 8) or saline (N = 8). Assessments of depression severity were completed 36 hours and 6 days thereafter.The adolescents who received pulse clomipramine treatment demonstrated significant decreases in Hamilton depression scores from baseline at 6 days but not at 36 hours. A similar decrease from baseline was found in Clinical Global Impression severity at 6 days but not 36 hours. Seven of the clomipramine-treated patients and three of the saline-treated patients had drops of 50% or more from baseline in Hamilton depression score.Pulse clomipramine (200 mg i.v.) is associated with dramatic reduction in depressive symptoms at day 6 after infusion, which is significantly different from the effect of placebo.
Regulation of endothelial and mesothelial cell function by interleukin- 13: selective induction of vascular cell adhesion molecule-1 and amplification of interleukin-6 production
Authors: M Sironi, FL Sciacca, C Matteucci, M Conni, A Vecchi, S Bernasconi, A Minty, D Caput, P Ferrara, F Colotta
Journal: Blood (1994)
Prostaglandin E2 and other cyclic AMP elevating agents inhibit interleukin 2 gene transcription by counteracting calcineurin-dependent pathways.
Authors: F Paliogianni, R L Kincaid, D T Boumpas
Journal: The Journal of Experimental Medicine (1993)

We have previously shown that prostaglandin E2 and other cAMP elevating agents inhibit the nuclear transcription of the human IL-2 gene by interfering with a Ca(2+)-sensitive T cell signal transduction pathway. Calcineurin, a Ca2+/calmodulin-dependent 2B protein phosphatase, is an essential component of the T cell receptor signal transduction pathway leading to IL-2 gene expression. We have therefore tested the hypothesis that this phosphatase may be a target for the inhibitory effects of cAMP on IL-2 gene transcription. We report here that PGE2 markedly reduces the IL-2 promoter activity that is induced by a constitutively active form of calcineurin. In contrast to the complete inhibition of promoter activity produced by the immunosuppressants cyclosporin A and FK-506, this partial block suggests that PGE2 modulates downstream events needed for lymphokine gene activation. Overexpression of calcineurin in Jurkat cells decreases their apparent sensitivity to the inhibitory effects of PGE2 consistent with the fact that this enzyme plays a physiological role in dephosphorylating substrates of cAMP-dependent kinases in several tissues. These results provide evidence that cAMP-dependent pathways may antagonize calcineurin-regulated cascades for T cell activation in vivo, and suggest crosstalk between the Ca2+ and the cAMP signaling pathways during T cell activation.
Renal glomerular function and long-term lithium therapy
Authors: J R Depaulo, E I Correa, D G Sapir
Journal: American Journal of Psychiatry (1981)

Recently published studies vary widely in the quantitative assessment of glomerular filtration rate (GFR) in lithium-treated patients. Therefore, the authors tested 99 lithium-treated manic-depressive patients using several techniques to measure GFR. Ten of 86 patients who had no history of renal disease had mildly low creatinine clearance values. Significant correlations, which were not age-related, between the serum creatinine, Cockroft creatinine clearance, and duration of lithium therapy suggest a relationship between chronic lithium therapy and declining GFR. Since serum creatinine alone was insensitive, the authors recommend the use of duplicate classical creatinine clearances confirmed by Cockroft values to monitor GFR during lithium treatment.
Part 7: Adult Advanced Cardiovascular Life Support
Authors: Mark S. Link, Lauren C. Berkow, Peter J. Kudenchuk, Henry R. Halperin, Erik P. Hess, Vivek K. Moitra, Robert W. Neumar, Brian J. O’Neil, James H. Paxton, Scott M. Silvers, Roger D. White, Demetris Yannopoulos, Michael W. Donnino
Journal: Circulation (2015)
Long-term follow-up with ABDIC salvage chemotherapy of MOPP-resistant Hodgkin's disease.
Authors: N Tannir, F Hagemeister, W Velasquez, F Cabanillas
Journal: Journal of Clinical Oncology (1983)

Thirty-six consecutive patients with advanced recurrent Hodgkin's disease resistant to chemotherapy with mechlorethamine, vincristine, procarbazine, and prednisone (MOPP) were treated with doxorubicin (Adriamycin), bleomycin, (dacarbazine) DTIC, (lomustine) CCNU, and prednisone (ABDIC). Among the 34 patients evaluable for response, complete remission occurred in 35% and partial remission in 35%. The achievement of complete remission during primary MOPP induction was a statistically significant prognostic factor that predicted complete remission with ABDIC (p less than 0.01). The median time to complete remission was 2 months (range 1-11 mo). The median relapse-free survival time for complete responders is 47 months, and an estimated 53% of all patients who achieve complete remission are projected to be alive, free of disease off therapy at 3 years from initiation of ABDIC. The median survival of all patients is 24 months. The median survival of complete responders, partial responders, and nonresponders is 70, 17, and 4 months, respectively. The survival curve for complete responders is significantly different from that for partial responders (p less than 0.01); the survival curve for partial responders is also significantly different from that of nonresponders (p less than 0.01). Toxicity of ABDIC was acceptable; only one patient died from complications of myelosuppression. Our results indicate that ABDIC is a potentially curative regimen for a fraction of patients with MOPP-resistant Hodgkin's disease who achieve complete remission with prior MOPP therapy. It also prolongs the survival of patients who do not achieve complete remission with prior MOPP therapy.
Oral Rivaroxaban Versus Standard Therapy for the Treatment of Symptomatic Venous Thromboembolism in Patients with Cancer
Authors: M.H. Prins, T. Lensing, P. Prandoni, A.T. Cohen, B. Davidson, F. Misselwitz, Á. Pap, M. Trajanovic, S. Berkowitz, P. Wells
Journal: Annals of Oncology (2014)
A Supplemented High-Fat Low-Carbohydrate Diet for the Treatment of Glioblastoma
Authors: Regina T. Martuscello, Vinata Vedam-Mai, David J. McCarthy, Michael E. Schmoll, Musa A. Jundi, Christopher D. Louviere, Benjamin G. Griffith, Colby L. Skinner, Oleg Suslov, Loic P. Deleyrolle, Brent A. Reynolds
Journal: Clinical Cancer Research (2015)

Dysregulated energetics coupled with uncontrolled proliferation has become a hallmark of cancer, leading to increased interest in metabolic therapies. Glioblastoma (GB) is highly malignant, very metabolically active, and typically resistant to current therapies. Dietary treatment options based on glucose deprivation have been explored using a restrictive ketogenic diet (KD), with positive anticancer reports. However, negative side effects and a lack of palatability make the KD difficult to implement in an adult population. Hence, we developed a less stringent, supplemented high-fat low-carbohydrate (sHFLC) diet that mimics the metabolic and antitumor effects of the KD, maintains a stable nutritional profile, and presents an alternative clinical option for diverse patient populations.The dietary paradigm was tested in vitro and in vivo, utilizing multiple patient-derived gliomasphere lines. Cellular proliferation, clonogenic frequency, and tumor stem cell population effects were determined in vitro using the neurosphere assay (NSA). Antitumor efficacy was tested in vivo in preclinical xenograft models and mechanistic regulation via the mTOR pathway was explored.Reducing glucose in vitro to physiologic levels, coupled with ketone supplementation, inhibits proliferation of GB cells and reduces tumor stem cell expansion. In vivo, while maintaining animal health, the sHFLC diet significantly reduces the growth of tumor cells in a subcutaneous model of tumor progression and increases survival in an orthotopic xenograft model. Dietary-mediated anticancer effects correlate with the reduction of mTOR effector expression.We demonstrate that the sHFLC diet is a viable treatment alternative to the KD, and should be considered for clinical testing. Clin Cancer Res; 22(10); 2482-95. ©2015 AACR.
Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma
Authors: Shlomi Finkin, Detian Yuan, Ilan Stein, Koji Taniguchi, Achim Weber, Kristian Unger, Jeffrey L Browning, Nicolas Goossens, Shigeki Nakagawa, Ganesh Gunasekaran, Myron E Schwartz, Masahiro Kobayashi, Hiromitsu Kumada, Michael Berger, Orit Pappo, Klaus Rajewsky, Yujin Hoshida, Michael Karin, Mathias Heikenwalder, Yinon Ben-Neriah, Eli Pikarsky
Journal: Nature Immunology (2015)
A Comparison of Laparoscopically Assisted and Open Colectomy for Colon Cancer
Authors: Heidi Nelson, Daniel J Sargent, H Sam Wieand, James Fleshman, Mehran Anvari, Steven J Stryker, Robert W Beart, Michael Hellinger, Richard Flanagan, Walter Peters, David Ota
Journal: New England Journal of Medicine (2004)

Minimally invasive, laparoscopically assisted surgery was first considered in 1990 for patients undergoing colectomy for cancer. Concern that this approach would compromise survival by failing to achieve a proper oncologic resection or adequate staging or by altering patterns of recurrence (based on frequent reports of tumor recurrences within surgical wounds) prompted a controlled trial evaluation.
E-Waste and Harm to Vulnerable Populations: A Growing Global Problem
Authors: Michelle Heacock, Carol Bain Kelly, Kwadwo Ansong Asante, Linda S. Birnbaum, Åke Lennart Bergman, Marie-Noel Bruné, Irena Buka, David O. Carpenter, Aimin Chen, Xia Huo, Mostafa Kamel, Philip J. Landrigan, Federico Magalini, Fernando Diaz-Barriga, Maria Neira, Magdy Omar, Antonio Pascale, Mathuros Ruchirawat, Leith Sly, Peter D. Sly, Martin Van den Berg, William A. Suk
Journal: Environmental Health Perspectives (2015)

Background:Electronic waste (e-waste) is produced in staggering quantities, estimated globally to be 41.8 million tonnes in 2014. Informal e-waste recycling is a source of much-needed income in many low- to middle-income countries. However, its handling and disposal in underdeveloped countries is often unsafe and leads to contaminated environments. Rudimentary and uncontrolled processing methods often result in substantial harmful chemical exposures among vulnerable populations, including women and children. E-waste hazards have not yet received the attention they deserve in research and public health agendas.Objectives:We provide an overview of the scale and health risks. We review international efforts concerned with environmental hazards, especially affecting children, as a preface to presenting next steps in addressing health issues stemming from the global e-waste problem.Discussion:The e-waste problem has been building for decades. Increased observation of adverse health effects from e-waste sites calls for protecting human health and the environment from e-waste contamination. Even if e-waste exposure intervention and prevention efforts are implemented, legacy contamination will remain, necessitating increased awareness of e-waste as a major environmental health threat.Conclusion:Global, national, and local levels efforts must aim to create safe recycling operations that consider broad security issues for people who rely on e-waste processing for survival. Paramount to these efforts is reducing pregnant women and children’s e-waste exposures to mitigate harmful health effects. With human environmental health in mind, novel dismantling methods and remediation technologies and intervention practices are needed to protect communities.Citation:Heacock M, Kelly CB, Asante KA, Birnbaum LS, Bergman AL, Bruné MN, Buka I, Carpenter DO, Chen A, Huo X, Kamel M, Landrigan PJ, Magalini F, Diaz-Barriga F, Neira M, Omar M, Pascale A, Ruchirawat M, Sly L, Sly PD, Van den Berg M, Suk WA. 2016. E-waste and harm to vulnerable populations: a growing global problem. Environ Health Perspect 124:550–555; http://dx.doi.org/10.1289/ehp.1509699
A Randomized Phase II Trial of Biweekly S-1 with Paclitaxel (SPA) or Oxaliplatin (SOX) as First-Line Chemotherapy in advanced Gastric Cancer Patients: Preliminary Results
Authors: M. Haibo, W. Fang, Y. Zheng, P. Zhao, C. Mao, X. Zhang, J. Qian, H. Jiang, Y. Zheng, N. Xu
Journal: Annals of Oncology (2012)
Mutant mice without B lymphocyte follicles.
Authors: Y J Liu, J Banchereau
Journal: The Journal of Experimental Medicine (1996)

T he immune system requires the cognate interactions of T cells, B cells, and antigen-presenting cells to respond to invading antigens/pathogens.However, the peripheral lymphoid organs where immune responses occur are not simply made of a random mixture of T cells, B cells, and antigen-presenting cells.Rather they are organized into ruicroanatomic compartments that are composed mainly of T cell zones and B cell follicles.T cell zones are found in the paracortex of lymph nodes, the periarteriolar lymphoid sheaths (PALS) of spleen (Fig. 1) and the dome area of Peyer's patches.They contain both CD4 + and CD8 + T cells as well as interdigitating dendritic cells (IDC).B cell areas can be found in the form of either resting primary follicles or activated secondary follicles.A primary B cell follicle contains slgM+IgD + resting recirculating B cells and follicular dendritic cells (FDC) (Fig. 1).A secondary B cell follicle is composed of a follicular mantle containing slgM+IgD + resting B cells and a germinal center composed of centroblasts, centrocytes, activated CD4 + memory T cells, CD4 + CD1 lc+CD3 -germinal center dendritic cells (GCDCs) and FDC (1, 2).In addition, a third compartment, the marginal zone, observed in the spleen, contains a subset of nonrecirculating slgmhighIgDl~ B cells (Fig. 1) (3, 4), marginal macrophages as well as marginal metallophils (5-7).What are the functional advantages for peripheral lymphoid tissues to be structured into complex T and B cell zones?What are the molecular mechanisms underlying the segregation of T cell zones and B cell follicles?In this issue of Tke Journal of Experimental Medicine, Pasparakis et al. report that the spleens of TNFoL knock-out mice lack primary follicles and mature FDC (8).These mice display impaired humoral immune responses and are unable to form germinal centers in response to T cell-dependent antigens.This observation, together with other recent reports, highlights the fundamental role of members of the TNF-TNFR superfamily in the development of peripheral lymphoid organs and germinal centers.