tbuckley/cabot-search huggingface dataset:
Use of a novel patient-specific model of glioma growth kinetics to elucidate underlying biology as measured by gene expression microarray.
Authors: Andrew Daniel Trister, Brian Bot, Andrea Hawkins-Daarud, Kellie Fontes, Carly Bridge, Anne Baldock, Russ Rockne, Erich Huang, Kristin Swanson
Journal: Journal of Clinical Oncology (2012)

71 Background: Gliomas are heterogeneous diseases with a wide distribution of growth kinetics that can be estimated prior to treatment and that are prognostic for patient outcome after treatment. Coherent molecular data sets have been made available through cooperative projects such as REMBRANDT and TCGA. We apply our novel patient specific method of measuring the net proliferation and diffusion rate from routinely available preoperative MRI sequences on patients included in these publicly available data sets to assess the underlying biology with imaging. Methods: The normalized microarray data from REMBRANDT (n=475) was used to discover a set of genes differentially expressed among GBM patients when compared with lower grade gliomas (n=853). 647 of these genes were also assessed with probesets in TCGA (n=466). Of these 466 patients, 84 also had preoperative MRI imaging available through The Cancer Imaging Archive (TCIA), for which net diffusion (D) proliferation (ρ) were estimated. Differential gene expression comparing these patients was performed. Results: 37 genes were differentially expressed with D. Genes implicated in cell adhesion, ECM maintenance and the production of focal adhesions are negatively correlated with D. Genes positively correlated with D are related to cell motility and pseudopodia formation. When considering ρ, 20 genes were found to be differentially expressed. A subset of these genes is related to hypoxia and therapy resistance. Some genes are also increased after radiation in cell-lines. Clustering on these genes revealed two classes; one with a survival advantage (p=0.0002). Conclusions: This work demonstrates the potential to assess underlying differences in biology in a heterogeneous disease through patient specific assessment of routinely available imaging. We find that more diffuse tumors will under-express genes involved in focal-adhesions and production of ECM, while they express genes in pathways related to motility and pseudopodia formation. Furthermore, tumors with high ρ are seen to express genes related to treatment resistance, which may explain worse survival in these patients. Future work will verify these markers in model organisms.
MR signal-fat-fraction analysis and T2* weighted imaging measure BAT reliably on humans without cold exposure
Authors: Milja Holstila, Marko Pesola, Teemu Saari, Kalle Koskensalo, Juho Raiko, Ronald J.H. Borra, Pirjo Nuutila, Riitta Parkkola, Kirsi A. Virtanen
Journal: Metabolism (2017)
Individual patient data meta-analysis of the impact of treatment expertise on the outcome of head and neck cancer patients treated within 6 randomized trials
Authors: P. Bossi, R. Miceli, M. Benasso, R. Corvò, A. Bacigalupo, G. Sanguineti, C. Fallai, M.C. Merlano, G. Infante, C. Dani, V. Di Giannantonio, L. Licitra
Journal: Annals of Oncology (2016)
Very Poor Outcome and Chemoresistance of Acute Myeloid Leukemia Patients with TP53 Mutations: Correlation with Complex Karyotype and Clinical Outcome
Authors: Cristina Papayannidis, Anna Ferrari, Stefania Paolini, Carmen Baldazzi, Chiara Sartor, Abbenante maria Chiara, Giovanni Marconi, Sarah Parisi, Francesca Volpato, Ilaria Iacobucci, Antonella Padella, Viviana Guadagnuolo, Margherita Perricone, Valentina Robustelli, Claudia Venturi, Giorgia Simonetti, Alberto Conficoni, Katia Mancuso, Beatrice Zannetti, Emanuela Ottaviani, Elisa Zuffa, Eugenia Franchini, Nicoletta Testoni, Michele Cavo, Giovanni Martinelli
Journal: Blood (2014)
Smoking: Lung and Bladder Cancer: Reply
Authors: Richard G. Stevens, Suresh H. Moolgavkar
Journal: JNCI Journal of the National Cancer Institute (1980)

Journal Article Smoking: Lung and Bladder Cancer: Reply Get access Richard G. Stevens, Richard G. Stevens Institute for Cancer Research Philadelphia, Pennsylvania 19111 Search for other works by this author on: Oxford Academic PubMed Google Scholar Suresh H. Moolgavkar Suresh H. Moolgavkar Institute for Cancer Research Philadelphia, Pennsylvania 19111 Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 65, Issue 4, October 1980, Pages 667–668, https://doi.org/10.1093/jnci/65.4.667-a Published: 01 October 1980
A study of allelic diversity underlying flowering-time adaptation in maize landraces
Authors: J Alberto Romero Navarro, Martha Willcox, Juan Burgueño, Cinta Romay, Kelly Swarts, Samuel Trachsel, Ernesto Preciado, Arturo Terron, Humberto Vallejo Delgado, Victor Vidal, Alejandro Ortega, Armando Espinoza Banda, Noel Orlando Gómez Montiel, Ivan Ortiz-Monasterio, Félix San Vicente, Armando Guadarrama Espinoza, Gary Atlin, Peter Wenzl, Sarah Hearne, Edward S Buckler
Journal: Nature Genetics (2017)
OnabotulinumtoxinA vs Sacral Neuromodulation for Urgency Incontinence—Reply
Authors: Cindy L. Amundsen, Holly E. Richter, Dennis Wallace
Journal: JAMA (2017)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
High Microbiome Diversity and IgA Responses in Breast Milk of Old Order Mennonites with a Low Prevalence of Allergic Diseases
Authors: Antti E. Seppo, Sade Fridy, John Varrone, Steven R. Gill, Alex Grier, Jeanne M. Lomas, Camille Martina, Richard J. Looney, Kirsi M. Jarvinen-Seppo
Journal: Journal of Allergy and Clinical Immunology (2017)
Chemotherapy in cancer patients undergoing hemodialysis: A multicenter study
Authors: T. Funakoshi, T. Horimatsu, M. Nakamura, K. Suyama, T. Mizukami, S. Arita, Y. Ozaki, H. Yasui, H. Satake, M. Toyoda, S. Yazumi, T. Kirishima, A. Nozaki, A. Yoshioka, T. Matsubara, M. Yanagita, S. Fukuhara, M. Muto
Journal: Annals of Oncology (2016)
NIMG-40. TUMOR PROGRESSION BETWEEN SURGERY AND INITIATION OF ADJUVANT CONCURRENT CHEMORADIATION IN NEWLY DIAGNOSED GLIOBLASTOMA PATIENTS
Authors: Seunggu Han, Javier Villanueva-Meyer, Jennie Taylor, Jennifer Clarke, Nancy Ann Oberheim-Bush, Susan Chang, Sarah Nelson, Mitchel S. Berger, Soonmee Cha, Nicholas Butowski
Journal: Neuro-Oncology (2016)

Glioblastoma remains a challenge due to its propensity for recurrence. Timely initiation of adjuvant chemoradiation after surgery has been encouraged due to fear of interval tumor progression. To characterize the incidence and clinical significance of tumor growth/progression between resection and chemoradiation, MRIs of 106 patients with newly diagnosed glioblastoma, enrolled on successive upfront trials at UCSF with similar eligibility, were analyzed by neuroradiology at three different time points: prior to surgical resection, after surgery, and prior to initiation of chemoradiation. The pre-chemoradiation images were compared to the postsurgical diffusion weighted imaging (DWI) to differentiate postsurgical infarct from increased enhancement attributable to tumor progression. New or increased contrast enhancement (CE) was seen on pre-chemoradiation scan in 66 patients. In 18 patients, new CE was seen only in the diffusion restricted areas seen on post-operative scan, while in 48 patients, the CE was indicative of tumor growth/progression. Median survival was 15.5 months for patients who had interval tumor progression and 21.7 months for patients who did not. A greater proportion of patients who suffered interval tumor growth had received less than gross total resection at time of surgery (75% vs. 34%, respectively). Interestingly, there was no significant difference in the time interval between surgery and initiation of chemoradiation between patients who had and did not have early interval tumor growth after surgery (29 and 32 days respectively). Increased CE indicative of tumor growth between surgery and chemoradiation is seen in nearly half of patients with newly diagnosed glioblastoma, and it appears associated with worse survival outcomes. Achieving gross total resection is associated with a lower likelihood early interval tumor growth prior to chemoradiation, however it remains unclear whether earlier initiation of chemoradiation would be beneficial. Relationship to other variables such as age, KPS, extent of resection etc. also will be discussed.
KW-2449, a Novel Multi-Kinase Inhibitor Against FLT3, Abl, FGFR1 and Aurora, Suppresses the Growth of AML Both In Vitro and In Vivo.
Authors: Yukimasa Shiotsu, Hitoshi Kiyoi, Kazutaka Ozeki, Hiroshi Umehara, Makiko Shimizu, Shiro Akinaga, Tomoki Naoe
Journal: Blood (2007)
TMIC-16. TUMOR-INFILTRATING MYELOID CELLS MEDIATE ADAPTIVE IMMUNE RESISTANCE IN GLIOBLASTOMA
Authors: Joseph Antonios, Horacio Soto, Richard Everson, Joey Orpilla, Namjo Shin, Diana Moughon, Shaina Sedighim, Janet Treger, Sylvia Odesa, Alexander Tucker, William Yong, Timothy Cloughesy, Robert Prins, Linda Liau
Journal: Neuro-Oncology (2016)

Adaptive immune resistance in the tumor microenvironment appears to mitigate immunotherapeutic targeting of glioblastoma (GBM) in preclinical models. We have previously shown that the programmed death-1/ligand-1 (PD-1/PD-L1) signaling mechanism is a dominant mediator of the immune response generated by tumor lysate-pulsed dendritic cell (DC) vaccine treatment. In this study, we identified a tumor-infiltrating Ly6-C+ CD11b+ myeloid (TIM) cell population that expands in response to DC vaccine treatment and significantly expresses PD-L1 in both our murine model and patient GBM samples. We hypothesized that this cell population is dominantly responsible for mitigating the immune response. To evaluate this, we administered tumor lysate-pulsed DC vaccine treatment to mice bearing intracranial murine GL261 tumor. Mice were randomized into treatment groups receiving PD-1 mAb, Ly6-C depleting mAb, or both. Following treatments, we euthanized mice and harvested tumor-bearing brain hemisphere for analysis. We noted that the TIL population was significantly activated in mice that had received PD-1 mAb or Ly6-C depleting mAb. There was no additional activation in groups receiving both treatments. These results were recapitulated in an in vitro cytotoxicity assay, with TIM inhibition of TIL cytolysis of tumor cells significantly reduced with PD-1 mAb blockade. To target TIMs in vivo with a clinically-relevant treatment, we next evaluated the use of colony stimulating factor-1 receptor inhibitor (CSF-1Ri, PLX3397), a drug already in clinical trials, instead of Ly6-C depleting mAb. Treatment with PLX3397 reduced the TIM population and promoted expression of key chemotactic factors associated with increased TIL infiltration in remaining TIMs. When combined with PD-1 mAb blockade, PLX3397 resulted in increased the number of TILs and their activation in both murine in vivo studies as well as in ex vivo GBM patient studies. Together, these findings demonstrated that TIMs restrict the immune response and are the dominant mediators of the PD-1/PD-L1 mechanism in GBM.
TCT-754 Instent-restenosis after interventional treatment of carotid artery stenoses - a long term follow-up of a single center cohort
Authors: Jürgen Kammler, Hermann Blessberger, Klaus Kerschner, Michael Lichtenauer, Thomas Lambert, Karim Saleh, Stefan Schwarz, Alexander Nahler, Alexander Kypta, Clemens Steinwender
Journal: Journal of the American College of Cardiology (2015)
NAVIGATE I: A Randomized Double-Blind Trial of a Fluticasone Propionate Exhalation Delivery System (FLU-EDS) for Treatment of Chronic Rhinosinusitis with Nasal Polyps (CRSwNP)
Authors: Daniel F. Soteres, John Messina, Jennifer Carothers, Ramy Mahmoud, Per G. Djupesland
Journal: Journal of Allergy and Clinical Immunology (2017)
MPTH-15. WHO GRADING IS NOT PROGNOSTIC IN 1p/19q-CODELETED OLIGODENDROGLIAL TUMORS, WHEN TREATED UNIFORMLY WITH ONLY CHEMOTHERAPY WITHOUT IRRADIATION
Authors: Tomoo Matsutani
Journal: Neuro-Oncology (2016)

The 2016 WHO classification widely include genotyping to categorize gliomas, but histological grading is still assigned to predict the biological behavior. Although several recent publications have revealed similar survival period in both grade II and III gliomas with 1p/19q-codeletion, an initial irradiation is generally preferred for grade IIII, and postponed for grade II. Indeed, the prognostic impact of WHO grading under the uniform treatment is not clarified well. In our institute, oligodendroglioma with 1p/19q-codeletion was consecutively treated with only PAV (Procarbazine, ACNU and Vincristine) without the initial irradiation regardless of its WHO grading since 2006, and survival data were retrospectively analyzed. Of sixty-seven oligodendroglial tumors, 38 were classified with 1p/19q-codeleted tumors by FISH analysis. Twenty-one of 38 were histopathologically diagnosed as grade II, and seventeen as grade III. None of the patients received any irradiation initially, and 32 of 38 received PAV chemotherapy in the following-period. Progression-free survival (PFS) and Overall survival (OS) is not significantly different between grade II and III. 5-year OS and 10-year OS are 100% and 90.9% in grade II, and 85.6% and 76.1% in grade III, respectively. WHO grading has no survival impact on uniformly-treated 1p19q-codelted oligodendroglioma without initial irradiation.
Discovery and Preclinical Characterization of a Novel Hepcidin Antagonist with Tunable PK/PD Properties for the Treatment of Anemia in Different Patient Populations
Authors: Andreas M Hohlbaum, Stefan Trentman, Hendrik Gille, Andrea Allersdorfer, Rachida Siham Belaiba, Martin Huelsmeyer, Juergen Christian, Thomas Sandal, Gabriele Matschiner, Kristian Jensen, Arne Skerra, Laurent P Audoly
Journal: Blood (2011)
A new paradigm for patient-centered breast cancer care.
Authors: Kristina M Diaz, Edward Paul, Gregory John C. Yang, Shirley Phillips, John Bowles, Trudie Milner
Journal: Journal of Clinical Oncology (2016)

46 Background: The active role of a primary care physician has been shown to improve outcomes for patients in all areas of health management. Cancer care is rapidly evolving as a result of major advances in cancer genomics and the production of new, mostly oral, chemotherapeutic agents targeted to specific patients. The estimated number of cancer survivors is expected to dramatically increase in the next decade. One good example of a new model of cancer care that relies upon the steady presence and involvement of the primary care physician is the care of patients with non-metastatic breast cancer. The current model of breast cancer care includes the primary physician identifying a lesion, obtaining required imaging, making a preliminary diagnosis of presumptive breast cancer, referring to the surgeon and/or oncologist, then resuming care of the patient post survivorship. In the new model of care described here, oncologists play a peripheral role and once therapy is initiated, care by the primary care physician in an integrated, team-oriented, system becomes ideal. Methods: Via a shared care model in which the primary physician is trained to provide direct oncologic care for the patient. They will thereafter initiate a survivor plan that will allow the patient to return to their own medical ecosystem with the least delay and compromise. The primary physician is anticipated to actively direct care for the cancer patient including prescribing recommended cancer treatment, managing medication side effects, and making appropriate referrals when necessary. Results: see below Conclusions: There is good evidence that outcomes by a primary care physician throughout the entire breast cancer treatment phase are comparable to care provided by oncologists in the current model. When the primary care physician is given the right tools and empowered to lead the care for the patient, improved compliance, improved psychosocial quality, and appropriate survivorship follow up can be achieved. With the ability to care for all aspects of their patient’s needs, both biomedical and emotional, the primary physician can, and should, start taking a more active and holistic role in providing care for their patients. Never was this more true then now.
Comparison of FDG-PET and Ga-67 Scintigraphy in the Evaluation of Lymphoma and Its Relationship to the Pathologic Diagnosis Using WHO Classification System.
Authors: Norifumi Tsukamoto, Uchiumi Hideki, Takafumi Matsushima, Masamitsu Karasawa, Hirokazu Murakami, Masaru Kojima, Yoshihisa Nojima
Journal: Blood (2004)
Hematopoietic Regeneration Is Suppressed by the GvHD Condition in a Haplo-Identical Bone Marrow Transplant Model.
Authors: Xiaoxia Hu, Xiaomeng Zhuang, Weiwei Zhang, Chongmei Huang, Shenglan Gong, Hui Cheng, Tao Cheng, Jianmin Wang
Journal: Blood (2009)
Predisposing germline mutations in high grade ER+HER2- breast cancer (BC) patients diagnosed (Dx).
Authors: Judy Ellen Garber, Nadine M. Tung, Eric P. Elkin, Brian Allen, Anne-Renee Hartman, Nanda Singh, Richard J. Wenstrup, Eric P. Winer, Nancy U. Lin
Journal: Journal of Clinical Oncology (2015)

1503 Background: Evaluation of women with triple negative BC for germline BRCA1/2 mutations has become standard of care due to its impact on management and 11% mutation prevalence. Approximately 70% of BRCA2-associated BC is high grade ER+/HER2-, but the prevalence of BRCA1/2 mutations has not been assessed. Methods: Blood samples from BC patients age <50 at the Dana-Farber Cancer Institute with grade III ER+/HER2- invasive BC who consented to research were identified in the Dana-Farber/Harvard SPORE biobank. DNA mutations in 25 cancer genes were identified using a next generation sequencing based panel. Germline sequence variations and large rearrangements were classified for pathogenicity. Results: 104 samples from eligible subjects were included. Mutations were found in 11 (10.6%) women [95% CI 5.4-18.1%]). BRCA1/2 mutations were found in 6.7% [95% CI 2.7-13.4%]. Mutation frequencies were higher among Ashkenazim (p=0.02), women with PR negative tumors (p<0.01) and women who had undergone prior clinical testing (p=0.01). 3/11 mutation carriers had BC age 45-49. Family hx of BC/ovarian cancer (OC) in 1st or 2nd degree relatives (FDR/SDR) was not associated with mutation status. Among 49 women with no FDR/SDR with BC/OC, 5 (10.2%) had a mutation. Two mutations (1 BRCA2, 1 PALB2) were found in 56 women who had not undergone previous clinical testing. Conclusions: Approximately 10% of women with high grade BC ER+/HER2- diagnosed age <50 carry a germline mutation in a BC-associated gene. The frequency of BRCA1 mutations is notable. Expanded testing in women with Grade III ER+/HER2- BC age <50 will find mutation carriers, which can impact management decisions. Examination of women diagnosed age >50 will be important. Gene Frequency Percent BC Dx Age Ashkenazim Family Hx** BRCA1 4 3.85% 28,38,41,46 Y,Y,N,N Y,Y,Y,Y BRCA2 3* 2.88% 37,39*,42 Y,N,N Y,N,N PALB2 2 1.92% 25,43 N,N N,N CHEK2 1 0.96% 49 N Y ATM 2* 1.92% 39*,47 N,N N,N *1 patient with BRCA2 and ATM. **FDR or SDR with BC or OC.
Improving patient safety: Factors leading to radiation therapy events in a large academic institution.
Authors: Gary V. Walker, Jennifer Johnson, Timothy Edwards, Sandra E. Hayden, Beverly A. Riley, Dean F. Sittig, Michael Gillin, Geoffrey Ibbott, Thomas A. Buchholz, Prajnan Das
Journal: Journal of Clinical Oncology (2013)

224 Background: The purpose of this study was to elucidate the factors associated with radiation therapy (RT) treatment events and near misses at a large academic institution. Methods: All RT patient events and near misses/good catches were prospectively collected using an electronic incident reporting system from April 1, 2011-April 30, 2013. The event origin was categorized according to the step in the treatment process (simulation, physician prescription, dosimetry/physics, treatment delivery and other). The incident database was linked to the RT delivery (record and verify) database which contains date of treatment, radiation beam duration, number of fractions, and type of treatment. A treatment record was defined as a unique site description and date/time. Results: There were 224 reported RT events or near misses/good catches analyzed, of which there were 59 RT treatment delivery events associated with 105 treatment records, including 0 level I (most severe), 18 level II, 35 level III (least severe), and 6 level IV (near misses/good catches) among the 13,899 patients and 468,489 treatments. The remaining 165 RT events occurred at the other steps of the treatment process. The overall rate of RT events and near misses was 161.2 per 10,000 patients. The rate of RT treatment delivery events and near misses was 42.4 per 10,000 patients and 2.2 per 10,000 treatment records. Logistical multivariate analysis showed that treatment on Tuesday (Odds Ratio = 2.50, 95% CI 1.67-3.73, p&lt;0.001), first day of treatment (5.16, 95% CI 3.32-8.02, p&lt;0.001), number of fractions (continuous) (0.98, 95% CI 0.96-0.997, p&lt;0.03), intensity modulated radiation therapy (IMRT) (2.87, 95% CI 1.44-5.74, p=0.003), electron only fields (2.00, 95% CI 1.27-3.14, p=0.003), and radiation beam duration (continuous minutes) (1.03, 95% CI 1.02-1.04, p&lt;0.001), were associated with RT treatment events and near misses, while age, proton treatment, number of fields and after hours treatment were not. Conclusions: Treatments delivered on Tuesdays, on the first day of treatment, with fewer fractions, with IMRT, with electron only fields, and with longer radiation beam duration were associated with an increased risk of RT treatment events.