tbuckley/cabot-search huggingface dataset:
A new gene expression-based diagnostic test to predict prognosis of gliomas for the support of histopathologic diagnosis.
Authors: K. Kato, M. Shirahata, S. Kawarazaki, R. Matoba, J. Takahashi
Journal: Journal of Clinical Oncology (2010)

2085 Background: Histopathologic classification of gliomas is often clinically inadequate due to the diversity of tumors that fall within the same class. Based on the strong correlation between malignancy and gene expression profile in gliomas, we constructed a diagnostic test to predict the prognosis of glioma patients. Methods: As the first step, we performed gene expression profiling with 152 gliomas (100 glioblastomas, 21 anaplastic astrocytomas, 19 diffuse astrocytomas, and 12 anaplastic oligodendrogliomas) using the high-throughput RT-PCR technique named adaptor-tagged competitive PCR (ATAC-PCR), and constructed a prognostic predictor. As the second step, we transferred this prognosis predictor into that based on real-time PCR, a more widespread technology. Results: (The first step) Using 110 gliomas as a learning set, we constructed a prognosis predictor based on the expression profile of 58 genes. The predictor was confirmed with an additional 42 gliomas as a test set: it classified all the samples as well as 23 glioblastomas out of the 42 into two prognostic groups (progression-free survival, p = 0.0001 and p = 0.05, respectively). Multivariate Cox analysis revealed that the gene expression profile was a strong and independent prognostic parameter. (The second step) We obtained stable real-time PCR amplification with 30 of the 58 genes. We utilized linear correlation between the Ct value of real-time PCR and the logarithmically converted expression level measured with microarray or ATAC- PCR. Using linear regression with data obtained from the learning set, we constructed a formula to calculate the diagnostic score of the above predictor directly from Ct values of the 30 genes. This new predictor successfully classified 16 samples from the above test set into the same group as the first predictor did. The new predictor classified 37 new samples into two prognostic groups with performance better than grade classification (p = 0.003; grade classification, p = 0.04). Conclusions: After confirmation with a larger cohort, this method should be useful as a new diagnostic test to support the histopathological diagnosis. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration DNA Chip Research Inc. DNA Chip Research Inc.
Geographic Correlations Between Cancer Mortality Rates and Alcohol-Tobacco Consumption in the United States 2
Authors: Norman E. Breslow, James E. Enstrom
Journal: JNCI Journal of the National Cancer Institute (1974)

Average annual age-adjusted cancer mortality rates for 1950-67 were correlated with per-capita consumption of cigarettes, spirits, wine, and beer as estimated from tax receipts in 41 States of the United States in 1960. These correlations were made for cancers of 19 sites for white males and of 20 sites for white females. Multiple regression analyses were used to estimate the simultaneous effects on cancer mortality of State-to-State variation in the urban component of the population and in the consumption of spirits, beer, and cigarettes. Respiratory cancers were related to cigarette consumption, certain cancers of the upper alimentary tract to consumption of spirits, and cancers of the stomach, large bowel, kidney, bladder (for men), and breast (for women) to consumption of beer. The strongest single association was between rectal cancer and beer consumption, a result found also with similar data for 24 other countries. The hazards of attempting to draw sound scientific inferences from such data are acknowledged.
Single administration of pegylated filgrastim once per cycle compared to daily filgrastim in patients with primary breast cancer receiving neoadjuvant chemotherapy
Authors: C. Wenzel, R. Bartsch, D. Hussian, U. Pluschnig, G. J. Locker, U. Sevelda, C. C. Zielinski, G. G. Steger
Journal: Journal of Clinical Oncology (2005)

8206 Background: Neutropenia is common in patients with cancer who receive myelosuppressive chemotherapy (CT) and contributes to therapy induced morbidity and mortality. In regimens with known high rates of febrile neutropenia granulocyte-colony stimulating factors are necessary to reduce therapy induced mortality and to maintain dose intensity. This retrospective clinical evaluation was designed to determine wether a single subcutaneous administration of pegfilgrastim is as safe and effective as daily filgrastim in patients with primary breast cancer. Methods: 90 patients received epidoxorubicin 75 mg/m2 and docetaxel 75 mg/m2 on day 1 plus subcutaneous injection of filgrastim on day 3–10, q 21 (ET + F). Filgrastim was dosed according to body weight with 30 MioIE < 60 kg and 48 MioIE > 60 kg. To the other 20 patients pegfilgrastim was applied on day 2 of the respective therapy regimen subcutaneously and was dosed independently to body weight with 6 mg in all patients. 16 patients received ET + P and the other 4 a combination therapy consisting of oral capecitabine, 1000 mg/m2, twice daily on days 1–14 in combination with the previously mentioned regimen on day 1 of each treatment cycle, q 21 (TEX + P). Since our group has already demonstrated the introduction of capecitabine into the ET regimen does not increase hematological toxicities. Results: Patients received 441 cycles with CT + F and 110 cycles with CT + P. One dose of pegfilgrastim per CT cycle was comparable to daily subcutaneous injection of filgrastim with regard to the occurrence of febrile neutropenia (CT + F: 8/441, 1,8%; CT + P: 1/110, 0,9%) and the need for hospitalization (CT + F: 8/441, 0,45%; CT P: 1/110, 0%). Conclusions: Both treatment groups had an identically adverse event profile. We conclude that single dose application of pegfilgrastim has a good safety profile and offering more convenience to patient and staff in the neoadjuvant treatment for patients with primary breast cancer receiving the ET or TEX regimen respectively. No significant financial relationships to disclose.
Potential role of Tc<sup>99M</sup> - MIBI scan for detecting bone marrow metastasis in childhood solid tumors
Authors: R. Kebudi, K. Berberoglu, S. Unal, I. Ayan, C. Turkmen, Ö. Görgün
Journal: Journal of Clinical Oncology (2004)

8570 Background: The aim of this study is to evaluate the role of Tc99m - MIBI for detecting bone marrow metastases in childhood solid tumors including lymphomas. Methods: In this prospective study; 22 children (16 M, 6F) with biopsy proven solid tumors and a mean age of 8.2±5.4 years were enrolled. The diagnosis were neuroblastoma (N) (7), Hodgkin's disease (HD) (4), non-Hodgkin's lymphoma (NHL) (2), Ewing sarcoma (ES) (3), Langerhans cell histiocytosis (LCH) (4), rhabdomyosarcoma (R) (1) and germ cell tumor (GCT) (1). Bone marrow aspiration and/or biopsy was done in all children at diagnosis. Tc99m - MIBI and Tc99m bone scans were obtained at diagnosis. One patient had pretheraphy and postthreaphy MIBI scans. The Tc99m - MIBI scans were classified as normal, diffuse, focal and combined patterns. MIBI scans with diffuse patterns were scored semiquantitatively according to the extension and intensity of tracer uptake and >2/6 scores in diffuse pattern scans and all scans with focal patterns were considered as abnormal, thus positive for bone marrow involvement. The correlation of bone marrow involvement in Tc99m - MIBI scans and microscopic bone marrow involvement was assessed. Results: Tc99m - MIBI scans showed normal patterns in 15 patients and diffuse patterns in 7. The score in 4/7 patients showing diffuse pattern were ≤2 and interpreted as normal. Only 3/7 patients with diffuse patterns had scores >2, thus were considered as positive for bone marrow involvement. All of these three were neuroblastoma patients. Bone marrow cytology revealed bone marrow metastases in all 3 patients which showed abnormal Tc99m - MIBI uptake. The remaining 19 patients with normal MIBI scans had negative bone marrow cytology(p= 0.0006, Fisher's exact test). One of three patients who had abnormal MIBI scan had normal MIBI scan and negative bone marrow cytology after four courses of chemotherapy. Conclusions: Noninvasive Tc99m -MIBI imaging appears promising for evaluating bone marrow metastases in children with solid tumors. This value of this method is worth to be investigated in larger series. No significant financial relationships to disclose.
Preferential Dissemination of B-Cell Gastric Mucosa-Associated Lymphoid Tissue (MALT) Lymphoma to the Splenic Marginal Zone
Authors: Ming-Qing Du, Huai-Zheng Peng, Ahmet Dogan, Tim C. Diss, Haiqun Liu, Lang-Xing Pan, Robin P. Moseley, Michael J. Briskin, John K.C. Chan, Peter G. Isaacson
Journal: Blood (1997)
Epigenetic regulation of IFN-α2b in multiple myeloma by a hydroxamic acid histone deacetylase (HDAC) inhibitor (SAHA) and a non-hydroxamic acid HDAC inhibitor (A-423378)
Authors: V. Cheriyath, K. B. Glaser, C. Healan-Greenberg, J. F. Waring, M. Kalaycio, E. C. Borden
Journal: Journal of Clinical Oncology (2007)

14048 Background: Full clinical potential of IFN-a2b is yet to be achieved in multiple myeloma. Although IFN-a2b leads to the induction of pro-apoptotic interferon stimulated genes (ISGs) (&gt;100 fold) in myeloma cells, &lt;20% of cells underwent apoptosis. Thus, we hypothesized that epigenetic silencing of ISGs may be responsible for the sub-optimal cellular response of myeloma to IFNs. Re-expression of suppressed ISGs by inhibiting HDACs could enhance IFNs effects. Methods: Myeloma cell lines NCI H929, RPMI 8266 and U266 treated for 96 hr with increasing concentrations of SAHA (Suberoyl Anilide Hydroxamic Acid) or A-423378, were assessed with alamar blue to determine IC 50 , and synergy between IFN-a2b and HDAC inhibitors (HDACi). Microarray analysis was performed to determine the effects on gene expression. Results: Both SAHA and A-423378 inhibited myeloma cell growth (IC 50 100–400 ?M). Combinations of IFN-a2b and sub-IC 50 concentrations of A-423378 or SAHA synergistically reduced the viability of NCI H929 and RPMI 8266. Treatments at their IC 50 did not increase the expression of p21, p27 or p16, known mediators of HDACi. To identify target genes mediating cellular effects, RNA from RPMI 8266 cells treated for 18 or 72 hr with IFN-a2b, A-423378, SAHA or their combinations were hybridized to Affymetrix human genome U133A array. A-423378 had a greater effect on global gene expression (3228 genes) than SAHA (2249 genes) at 18 hr. But, at 72 hr SAHA (1344 genes) had more persistent effect on gene modulation than A-423378 (1091 genes). IFN-a2b altered the expression of 2072 genes at 18 hr and 1374 genes at 72 hr. Combination of IFN-a2b with A-423378 further altered the gene expression (IFN-a2b plus A-423378 3589 genes, IFN-a2b plus SAHA 2017 genes at 18 hr). RARRES3, a tumor suppressor gene was synergistically induced (34 fold) by IFN-a2b and HDACi combinations. Conclusions: A-423378 had a greater effect on global gene expression at early time points whereas SAHA had a more persistent effect. HDACi of different classes enhanced anti-viability effects of IFN- a2b. RARRES3, a tumor suppressor gene, may mediate antiproliferative effects of HDACi and IFN-a2b. No significant financial relationships to disclose.
Outcomes in Patients With Transcatheter Aortic Valve Replacement and Left Main Stenting
Authors: Tarun Chakravarty, Rahul Sharma, Yigal Abramowitz, Samir Kapadia, Azeem Latib, Hasan Jilaihawi, Kanhaiya Lal Poddar, Gennaro Giustino, Henrique B. Ribeiro, Didier Tchetche, Benoit Monteil, Luca Testa, Giuseppe Tarantini, Michela Facchin, Thierry Lefèvre, Brian R. Lindman, Babak Hariri, Jigar Patel, Nobuyuki Takahashi, George Matar, James Mirocha, Wen Cheng, Murat E. Tuzcu, Horst Sievert, Josep Rodés-Cabau, Antonio Colombo, Ariel Finkelstein, Jean Fajadet, Raj R. Makkar
Journal: Journal of the American College of Cardiology (2016)
Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents.
Authors: J Sullivan, K E Holsinger, C Simon
Journal: Molecular Biology and Evolution (1995)

We analyze sequences from two mitochondrial genes, cytochrome b (cyt b) and 12S rRNA (12S), for a group of sigmodontine rodents among which phylogenetic relationships are well understood based on concordance of morphological, chromosomal, allozyme, and other DNA data sets. Because these two genes are physically linked on the nonrecombining mitochondrial genome, they necessarily share the same history. Phylogenetic analysis of the cyt b gene recovers the well-corroborated relationships, generally with strong support. None of the methods that we employed, including variously weighted parsimony, neighbor joining on both single-rate and gamma-corrected distances, and maximum likelihood, were able to recover these relationships for the 12S gene. Parsimony analyses of the 12S data resulted in a relatively strongly supported placement of Peromyscus eremicus that conflicts with that suggested by cyt b and all other data. There is extreme among-site rate variation in the 12S sequences and moderate levels in the cyt b sequences. This highly skewed distribution of rates in the 12S gene makes phylogenetic analyses of these sequences particularly susceptible to the misleading effects of nonindependence and other nonrandom noise, suggesting that phylogenetic analyses of data sets that contain a great deal of among-site rate variation be interpreted with caution.
Neurolymphomatosis on 18F-FDG PET/CT
Authors: Pieterjan Gykiere, Lennart Jans, Bert Degrieck, Ingeborg Goethals
Journal: Clinical Nuclear Medicine (2015)

Neurolymphomatosis represents a peripheral lymphomatous neural infiltration and is a relatively rare condition. Histopathologically, most patients are demonstrated to have non-Hodgkin lymphoma. A 27-year-old man with a history of HLA-B27-positive ankylosing spondylitis and diffuse large B-cell lymphoma was referred for the investigation of a severe neuropathic pain radiating down his right hip and posterior thigh for 1 month. This report describes the diagnosis and therapy response assessment in a relapsing aggressive non-Hodgkin lymphoma on an F-FDG PET scan.
Clonal Abundance of Tumor-Specific CD4 + T Cells Potentiates Efficacy and Alters Susceptibility to Exhaustion
Authors: Nicole Malandro, Sadna Budhu, Nicholas F. Kuhn, Cailian Liu, Judith T. Murphy, Czrina Cortez, Hong Zhong, Xia Yang, Gabrielle Rizzuto, Grégoire Altan-Bonnet, Taha Merghoub, Jedd D. Wolchok
Journal: Immunity (2016)
Gadolinium-Based Nanoparticles and Radiation Therapy for Multiple Brain Melanoma Metastases: Proof of Concept before Phase I Trial
Authors: Shady Kotb, Alexandre Detappe, François Lux, Florence Appaix, Emmanuel L. Barbier, Vu-Long Tran, Marie Plissonneau, Hélène Gehan, Florence Lefranc, Claire Rodriguez-Lafrasse, Camille Verry, Ross Berbeco, Olivier Tillement, Lucie Sancey
Journal: Theranostics (2016)

from teaching and research institutions in France or abroad, or from public or private research centers.L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
A neonate with respiratory distress and unilateral pulmonary hyperinflation
Authors: Abdullah Yousef, Ella Sugo, Bruce Currie, Pamela Palasanthiran, Adam Jaffe
Journal: European Respiratory Journal (2011)

Introduction:  Bronchial atresia is characterized by a mucus-filled bronchocoele in a blind-ending segmental or lobar bronchus, with hyperinflation of the obstructed segment of lung.We report a case of bronchial atresia in a neonate with Congenital Cytomegalovirus infection.   Case report:  A 9-day old boy presented with history of increased work of breathing and cyanosis. Antenatal ultrasound at 22 weeks of gestation demonstrated hyper-echoic changes in the thorax and abdomen which did not progress throughout pregnancy. At presentation to hospital he was in moderate respiratory distress and was commenced initially on CPAP but he required mechanical ventilation in the 2nd week of life. He had a normal white cell count,C-reactive protein & negative blood cultures. CMV was detected by PCR in urine and blood, and in endotracheal aspirate samples. Blood samples from newborn screen taken on day 2 of life was also positive for CMV by PCR, CMV IgM antibody was also positive. A chest CT scan was performed (Figure A, B & C).  The child had a right middle lobectomy & pathology revealed a bronchocoele with an 11mm mucus plug (Figure D) in a sub-segmental bronchus of the right middle lobe. CMV inclusions with minimal surrounding inflammation were noted on microscopy of the peripheral lung. In summary, this is the first reported case of bronchial atresia occurring with cCMV infection which may give further insight into the pathogenesis of this rare condition.
Sentinel Lymph Node Biopsy in Pelvic Tumors
Authors: Marco Maccauro, Alice Lorenzoni, Flavio Crippa, Gianpiero Manca, Sotirios Chondrogiannis, Francesco Giammarile, Patrick M. Colletti, Gary J. Cook, Domenico Rubello
Journal: Clinical Nuclear Medicine (2016)

Sentinel lymph node (SLN) sampling is an attractive alternative to complete lymphadenectomy. Based on the identification and sampling of the first LN draining a primary tumor, SLN biopsy is the most accurate and the only reliable method for microscopic nodal staging for solid tumors including breast cancer and melanoma. Lymph node status in pelvic tumors remains the most important prognostic factor for recurrence and survival and a major decision criterion for adjuvant therapy. We review the clinical indications, controversies, and perspective of SLN biopsy in male and female pelvic cancers.
A phase I trial investigating a twice weekly administration of the oral taxane BMS-275183 in patients with advanced solid tumors
Authors: L. E. Broker, R. Ruyter, M. Voi, M. Woo, L. Astier, E. Heath, P. M. Lorusso, G. Giaccone
Journal: Journal of Clinical Oncology (2005)

2040 Background: BMS-275183, a novel oral taxane, had peripheral neuropathy as the main side effect on a weekly regimen with the recommended phase II dose being 200 mg/m2. Considerable anti-tumor activity was observed in non-small cell lung cancer and other tumor types (Bröker et al., ASCO 2004, #2029). In the current phase I trial, we evaluated the safety, dose limiting toxicity (DLT), pharmacokinetics (PK) and possible anti-tumor activity of BMS-275183 given on a twice weekly schedule, in an effort to reduce its neurotoxicity. Methods: BMS-275183 was given on a continuous twice weekly regimen to adult patients with advanced solid tumors refractory to standard therapy. Plasma samples were collected on week 1 and 3 for 72 h after drug administration and analyzed using an LC/MS/MS assay. Results: To date, 16 patients have been treated at escalating dose levels of 60 (n=3), 80 (n=10) and 100 mg/m2 (n=3). At the 80 mg/m2 dose level, 2 DLTs have been observed consisting a grade (gr) 3 fatigue and a dose-omission due to gr 2 peripheral neuropathy, respectively. No DLTs have been observed in the first 3 patients treated at 100 mg/m2. Other side effects in the first 10 patients treated at 60 (n=3) and 80 mg/m2 (n=7) have included gr 1–2 fatigue (n=5), peripheral neuropathy (n=3), diarrhea (n=6), anorexia (n=5), taste disturbance (n=4), nausea (n=3), vomiting (n=2), stomatitis (n=1), epistaxis (n=3), neutropenia (n=1), myalgia (n=1), skin rash (n=1) and alopecia (n=2). PK analysis at the 80 mg/m2 dose level (n=7), revealed a rapid uptake with a median Tmax of 1 h and a mean T½ of 23 h. The mean AUC was 1264 ng.h/mL with an interpatient variability of 39%. These PK parameters are comparable to those obtained when BMS-275183 is administered once weekly at similar dose levels. One confirmed PSA-response has been observed in a patient with prostate carcinoma treated at 80 mg/m2 with a duration of 5+ months. Conclusions: Neurotoxicity appears to occur less frequently and to be less severe on a twice weekly regimen of BMS-275183 than on a weekly schedule. At present, the 100 mg/m2 dose level is being explored further to better define the safety of a dose to be recommended in phase II trials. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Bristol-Myers Squibb Bristol-Myers Squibb Bristol-Myers Squibb Bristol-Myers Squibb
Phase-2 study of imatinib in metastasized medullary thyroid carcinoma
Authors: B. A. Zonnenberg, T. Links, P. Quarles van Uffort, C. Lips, J. De Groot, E. Voest
Journal: Journal of Clinical Oncology (2006)

15500 Background: Medullary thyroid carcinoma (MTC) is a relatively rare tumor that metastasizes to regional lymph nodes, lung, liver and bone. When surgery is no longer a curative treatment option, no effective systemic therapy is currently available. In most cases a (somatic or germline) mutation in the RET (REarranged during Transfection) gene is considered to be an essential step in the pathogenesis of MTC. Imatinib is an oral inhibitor of several protein-tyrosine kinases including RET kinase. It has shown to be an effective drug in chronic myeloid leukemia and gastrointestinal stromal tumors. Methods: A two-step open label phase-2 study was initiated using 600 mg imatinib daily with a scheduled dose increase to 800 mg in case of minimal toxicity. Standard RECIST criteria were used for response evaluation using CT/MRI scans every 2 months. The two-step design allowed no further inclusion in the absence of objective responses in 15 patients. Results: 15 patients with metastasized MTC were included. No objective responses were observed but long term stable disease over 18 months was noted in 4 patients. However, toxicity was considerable. Emergency tracheotomy had to be performed in 2 cases due to mucosal swelling in patients with laryngeal nerve palsy and a narrow vocal cleft. In 3 cases the dose of Imatinib had to be decreased because of unacceptable toxicity (malaise, mucosal swelling (2) and fatigue). In 7 patients with a history of a thyreoidectomy, the dose of thyroxine had to be increased considerably to avoid serious hypothyroidism due to an incompletely understood interaction. Conclusion: Treatment with Imatinib yielded no objective responses and considerable toxicity in patients with MTC. Long-term stabilization of the disease was observed in only a minority of the patients. Patients with hypothyroidism and with laryngeal nerve palsy are at risk for serious adverse events and need special attention when treated with Imatinib. No significant financial relationships to disclose.