tbuckley/cabot-search huggingface dataset:
Abstract B2-43: Bioinformatics analysis of TCGA tumors to identify cancer associated epigenetic regulators
Authors: Florian Gnad, Zemin Zhang
Journal: Cancer Research (2015)

Abstract Many cancer cells show distorted epigenetic landscapes. The Cancer Genome Atlas (TCGA) project profiles thousands of tumors, allowing the discovery of somatic alterations in the epigenetic machinery and the identification of potential cancer drivers among members of epigenetic protein families. We integrated mutation, expression, and copy number data from thousands of tumors from major cancer types to train a classification model that predicts the likelihood of being an oncogene (OG), tumor suppressor (TSG) or neutral gene (NG). Using classical driver genes to train an OG/TSG predictor, we determined mutation parameters as the most predictive features. We applied this predictor to epigenetic regulator genes (ERGs), and used differential expression and correlation network analysis to identify dysregulated ERGs along with co-expressed cancer genes. Mutation-based classifiers uncovered the TSG-like profiles for several ERGs, but did not detect any OG-like profile. Differential gene expression and correlation network analyses revealed that EZH2 is the most significantly over-expressed ERG in cancer and is co-regulated with a cell cycle network. Furthermore we quantified global proteomic changes by mass spectrometry after EZH2 inhibition. Proteomic analysis showed that EZH2 inhibition induced down-regulation of cell cycle regulators in lymphoma cells. We have now expanded our analysis to other types of proteins including kinases and secreted proteins. Note: This abstract was not presented at the conference. Citation Format: Florian Gnad, Zemin Zhang. Bioinformatics analysis of TCGA tumors to identify cancer associated epigenetic regulators. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-43.
HbA1c-Based Classification Reveals Epidemic of Diabetes and Prediabetes in Vietnam
Authors: Lan T. Ho-Pham, Thanh T. Do, Lesley V. Campbell, Tuan V. Nguyen
Journal: Diabetes Care (2016)

The Asia Pacific region, with its rapid economic development and changes in lifestyles, has been identified as an epicenter of diabetes. However, the prevalence of diabetes in this region has not been well documented. Glycated hemoglobin (HbA1c) has been introduced as a new diagnostic test for diabetes, but its impact on disease prevalence is unknown. In this study, we sought to estimate the prevalence of undiagnosed diabetes in an urban population in Vietnam by using new HbA1c diagnostic criteria.

The study was designed as a population-based investigation that involved 1,339 individuals (973 women) randomly sampled from Ho Chi Minh City, Vietnam. All individuals were aged 30 years and above (average age ∼53 years, no significant difference between women and men). Blood samples were collected after overnight fasting and analyzed within 24 h after collection. HbA1c was measured with high-performance liquid chromatography (ARKRAY, …
Gene amplification in drug resistance: of mice and men.
Authors: G A Curt, K H Cowan, B A Chabner
Journal: Journal of Clinical Oncology (1984)

Article Tools Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.1984.2.1.62 Journal of Clinical Oncology - published online before print September 22, 2016 PMID: 6699659 Gene amplification in drug resistance: of mice and men. G A CurtxG A CurtSearch for articles by this author , K H CowanxK H CowanSearch for articles by this author , B A ChabnerxB A ChabnerSearch for articles by this author https://doi.org/10.1200/JCO.1984.2.1.62 First Page PDF © 1984 by American Society of Clinical Oncology
Further Observations on the Effects of Cancer Chemotherapeutic Agents on the &lt;italic&gt;in Vitro&lt;/italic&gt; Dehydrogenase Activity of Cancer Tissue&lt;xref ref-type="fn" rid="fn1"&gt;2&lt;/xref&gt;
Authors: Maurice M. Black, M.D., Francis D. Speer, M.D.
Journal: JNCI Journal of the National Cancer Institute (1954)

Journal Article Further Observations on the Effects of Cancer Chemotherapeutic Agents on the in Vitro Dehydrogenase Activity of Cancer Tissue Get access Maurice M. Black, M.D., Maurice M. Black, M.D. Department of Pathology, New York Medical College, Flower and Fifth Avenue Hospitals, New York, N. Y. Search for other works by this author on: Oxford Academic PubMed Google Scholar Francis D. Speer, M.D. Francis D. Speer, M.D. Department of Pathology, New York Medical College, Flower and Fifth Avenue Hospitals, New York, N. Y. Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 14, Issue 5, April 1954, Pages 1147–1158, https://doi.org/10.1093/jnci/14.5.1147 Published: 01 April 1954 Article history Received: 06 November 1953 Published: 01 April 1954
Deletion of the multidrug resistance protein MRP1 gene in acute myeloid leukemia: the impact on MRP activity
Authors: Dorina M. van der Kolk, Edo Vellenga, Anneke Y. van der Veen, Leonore Noordhoek, Hetty Timmer-Bosscha, Gert J. Ossenkoppele, Reinier A. Raymakers, Michael Müller, Eva van den Berg, Elisabeth G. E. de Vries
Journal: Blood (2000)
A high-throughput screening assay for eukaryotic elongation factor 2 kinase inhibitors
Authors: Ting Xiao, Rui Liu, Christopher G. Proud, Ming-Wei Wang
Journal: Acta Pharmaceutica Sinica B (2016)

Eukaryotic elongation factor 2 kinase (eEF2K) inhibitors may aid in the development of new therapeutic agents to combat cancer. Purified human eEF2K was obtained from an Escherichia coli expression system and a luminescence-based high-throughput screening (HTS) assay was developed using MH-1 peptide as the substrate. The luminescent readouts correlated with the amount of adenosine triphosphate remaining in the kinase reaction. This method was applied to a large-scale screening campaign against a diverse compound library and subsequent confirmation studies. Nine initial hits showing inhibitory activities on eEF2K were identified from 56,000 synthetic compounds during the HTS campaign, of which, five were chosen to test their effects in cancer cell lines.
Lymphoid Reconstitution After Autologous PBSC Transplantation With FACS-Sorted CD34+ Hematopoietic Progenitors
Authors: Catherine Bomberger, Meeta Singh-Jairam, Glenn Rodey, Anastasia Guerriero, Andrew M. Yeager, William H. Fleming, H. Kent Holland, Edmund K. Waller
Journal: Blood (1998)
Abstract P6-04-03: Transcriptome profiling reveals enrichment of luminal feature in aged basal cell population in murine mammary gland
Authors: X Gu, H Gao, A Wu, A Bandyopadhyay, Q Dong, L-Z Sun
Journal: Cancer Research (2016)

Abstract Aging is the number one risk factor for breast cancer development. Increasing evidence suggests the potential of mammary stem cells (MaSCs) and their progenitors to generate certain types of breast cancers through neoplastic transformation. Our previous study has shown increased percentage of MaSC-enriched basal cell population (Lin-CD49fhighCD24med) and increased MaSC frequency during aging in murine models. On the other hand, a recent study from another group showed an increased frequency of CD49fhigh cells in the human luminal population (CD227+) during aging, indicating possible aberrant expression of CD49f in the aged luminal cells. However, how these age-related luminal cells with basal markers are generated and how they contribute to potential breast cancer development remains unknown. Here we apply bioinformatics analysis on Next Generation Whole Transcriptome Sequencing data of MaSC-enriched basal cell population (Lin-CD49fhighCD24med) and luminal progenitor-enriched cell population (Lin-CD49flowCD24high) of both young (4 to 6 months) and old (26 to 31 months) mouse mammary gland to test the hypothesis that age-associated increase of basal cell population and MaSCs may be due to the gain of basal cell markers and features by luminal cells. By Gene Set Enrichment Analysis (GSEA) we found a significant loss of basal cell and basal mammosphere signatures and a significant enrichment of luminal cell and luminal mammosphere signature in the old basal cell population and mammospheres in comparison with the young basal cell population and mammospheres. The core enrichment luminal genes from GSEA are able to cluster the old MaSC-enriched basal cell population as well as mammospheres closer to the cluster of luminal population than to the young basal population. These analyses indicate that aging may be associated with an expansion of aberrant MaSCs with both basal and luminal markers in mice, which may be the precursors of certain types of breast cancer. We are now studying the potential function of the basal-like luminal cells in the aged basal population. Citation Format: Gu X, Gao H, Wu A, Bandyopadhyay A, Dong Q, Sun L-Z. Transcriptome profiling reveals enrichment of luminal feature in aged basal cell population in murine mammary gland. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-04-03.
The Communicant
Authors: M Therese Southgate
Journal: JAMA (2005)

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 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) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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
Jumping the nuclear envelope barrier: Improving polyplex-mediated gene transfection efficiency by a selective CDK1 inhibitor RO-3306
Authors: Xuefei Zhou, Xiangrui Liu, Bingxiang Zhao, Xin Liu, Dingcheng Zhu, Nasha Qiu, Quan Zhou, Ying Piao, Zhuxian Zhou, Jianbin Tang, Youqing Shen
Journal: Journal of Controlled Release (2016)
ANATOMY OF THE CENTRAL NERVOUS SYSTEM
Journal: BMJ (1939)

In an anatomical investigation of the central nervous system of the terrestrial isopod Armadillidium vulgare (Latreille), some specimens were dissected; others were sectioned and stained for light microscopical study. The brain, consisting of protocerebral, deutocerebral, and tritocerebral divisions, is situated ventrally in the extreme anterior region of the cephalothorax. The protocerebrum is bilobed and divided dorsally by a deep, median cleft. Each lobe (=optic lobe) tapers to form a large optic nerve. A pseudofrontal organ is suspended ventrally from the distal extremity of each optic lobe. A pair of accessory lobes extends ventrally beneath the main lobes of the protocerebrum. The deutocerebrum is much reduced in size, reflecting an apparent adaptive trend among terrestrial isopods (and amphipods) toward reduction of the antennules and associated loss of olfactory function. The well-developed lobes of the tritocerebrum extend laterally and continue as the circumesophageal connectives, completing encirclement of the esophagus to form a paired connective that unites with the subesophageal mass. The subesophageal mass is a fusion of the mandibular, maxillulary, maxillary, and maxillipedal ganglia. The ventral nerve cord, for most of its length, consists of seven pereionic ganglia joined by paired longitudinal connectives and smaller, single, median intermediate connectives. Six pairs of pleonic ganglia are fused into a single pleonic mass. Characteristic groupings of nerve cell bodies occur on the surfaces of the brain and ventral nerve cord. Distinctive, small, and densely packed glomerular cells occupy the surfaces of the optic lobes. Neuropiles and fiber tracts form conducting pathways, although those of the ventral cord are not so distinct morphologically as are some in the brain. Strong tagmatization is suggested by fusion to form a single pleonic mass.
Abstract 17: The Comparison of Adipose Derived Regenerative Cells and Bone Marrow Mononuclear Cells as Transplanted Cells for Therapeutic Angiogenesis
Authors: Satoshi Shintani, Changning Hao, Yuuki Shimizu, Kazuhisa Kondo, Toyoaki Murohara
Journal: Circulation Research (2014)

Background: Transplantation of adipose-derived regenerative cells (ADRCs) enhances ischemia-induced angiogenesis, but the underlying mechanism remains unknown. Here, we compared the efficacy of ADRC transplantation with bone marrow mononuclear cell (BM-MNC) treatment using a hindlimb ischemia (HLI) rabbit model, and examined if the anti-inflammatory phenotypic polarization of macrophages regulates postnatal neovascularization. Methods and Results: ADRCs and BM-MNCs were isolated from New Zealand White (NZW) rabbits and C57BL/6J mice. In the rabbit studies, ADRCs were incorporated into the existing vascular formation in vitro and in vivo. ADRC-conditioned media (CM) and BM-MNC-CM similarly enhanced the migratory ability and prevented apoptosis induction in human umbilical vein endothelial cells. Four weeks after treatment, NZW rabbits administered with either ADRCs or BM-MNCs revealed enhanced collateral vessel formation and functional blood flow recovery. In mice, lipopolysaccharide and/or hypoxic stress increased the level of prostaglandin E2 (PGE2), and led to the polarization of M2 macrophages in cultured ADRCs. Gene expressions of several angiogenic cytokines were amplified in macrophages cultured in ADRC-CM rather than BM-MNC-CM. The expression of interleukin (IL)-10 was increased in ischemic muscles of mice treated with ADRCs compared with those from BM-MNC- treated and control groups. The blockade of IL-10 using a neutralizing antibody attenuated ischemia-induced angiogenesis in vivo. Conclusions: The therapeutic angiogenesis potential of ADRCs was comparable with those of BM-MNCs in healthy animals. Anti-inflammatory phenotypic polarization of macrophages plays an important role in the regenerative action of ADRCs through the PGE2-EP2/4 axis.
Proliferative Lesions Resembling Chordoma Following Puncture of the Nucleus Pulposus in Rabbits
Authors: Congdon, Charles C.
Journal: JNCI Journal of the National Cancer Institute (1952)

Journal Article Proliferative Lesions Resembling Chordoma Following Puncture of the Nucleus Pulposus in Rabbits Get access Charles C. Congdon, M. D. Charles C. Congdon, M. D. Department of Pathology, University of Michigan, Ann Arbor, Mich. Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 12, Issue 4, February 1952, Pages 893–907, https://doi.org/10.1093/jnci/12.4.893 Published: 01 February 1952 Article history Received: 09 November 1951 Published: 01 February 1952
Studies on Marek's Disease. I. Experimental Transmission
Authors: P. M. Biggs, L. N. Payne
Journal: JNCI Journal of the National Cancer Institute (1967)

A strain of infectious agent, HPRS-B14, was isolated from a case of Marek's disease and maintained through 40 serial passages. This agent produced a disease characterized by neural involvement and, in some affected chickens, lymphoid tumors principally involving the ovary. This disease conformed to the description of the classical form of Marek's disease. This disease is contagious, spreading to chickens by direct and indirect contact with infected chickens. Females were more susceptible to the disease than males. Treatment with female and male sex hormones had no significant effect on the incidence of Marek's disease. Lines of chicken also differed in their susceptibility to disease produced by the HPRS-B14 agent, and it is concluded that these differences are due to the genetic constitution of the chicken. Chickens of a susceptible line inoculated with HPRS-B14 at 50 days of age were more resistant to the development of Marek's disease than chicks of the same line inoculated at 1 day of age. Blood and other organs and tissues of chickens, clinically affected with Marek's disease produced by HPRS-B14, were infective. Infectivity was associated with cell-containing fractions of blood and kidney tissue. It is concluded that infectivity of blood and other organs is due to an infectious agent, but we have insufficient evidence at present to classify the HPRS-B14 agent of Marek's disease.
Influences of body size phenotype on the incidence of gestational diabetes needing prescription; analysis by Korea National Health Insurance (KNHI) claims and the National Health Screening Examination (NHSE) database
Authors: Hye Jin Yoo, Kyung Mook Choi, Sei Hyun Baik, Jong Heon Park, Soon-Ae Shin, Soon-Cheol Hong, Min-Jeong Oh, Hai-Joong Kim, Geum Joon Cho
Journal: Metabolism (2016)
Abstract B05: MicroRNA-206 drives rhabdomyosarcoma differentiation through downregulation of PAX7
Authors: Jason A. Hanna, Matthew R. Garcia, Jonathan C. Go, David Finkelstein, Kiran Kodali, Vishwajeeth Pagala, Eric N. Olson, Junmin Peng, Mark E. Hatley
Journal: Cancer Research (2016)

Abstract The goal of this work is to understand the mechanism of microRNA-206 (miR-206) induced differentiation in rhabdomyosarcoma (RMS). RMS is the most common soft tissue sarcoma of childhood with both histology and gene expression suggestive that RMS tumor cells resemble a developmental arrest of skeletal muscle. miR-206 is a skeletal muscle specific miRNA expression increases through normal muscle development and has decreased levels in RMS compared to normal skeletal muscle. Exogneous miR-206 replacement drives differentiation and cell cycle exit of RMS. However, the target genes responsible for the relief of the development arrest are largely unknown. Using a combinatorial approach with mRNA microarrays and tandem mass tag (TMT) proteome profiling we identified 165 mRNAs and 272 proteins downregulated in miR-206 mimic transfected RMS cells. Potential targets were validated with 3'UTR reporter assays as well as real-time PCR and immunoblot from miR-206 mimic transfected cells. Further analysis with genetic rescue identified the key targets responsible for the RMS differentiation block as PAX7, PAX3, CCND2, and NOTCH3. However, siRNA knockdown of these targets alone and in a pooled combination failed to induce differentiation to the same extent as miR-206 despite knockdown levels comparable to miR-206. Thus, target identification collectively is key to understanding the mechanism of miR-206 function in RMS, suggesting the one miRNA-one target model to be insufficient for the complex phenotype of miR-206 induced differentiation. Genetic deletion of miR-206 in a mouse model of RMS accelerated and exacerbated tumor development indicating that both in vitro and in vivo miR-206 possesses tumor suppressive properties. In addition, Notch3 and Pax7 levels were increased in knockout tumors compared to wild type, providing further evidence for these genes as key targets of miR-206 in RMS. These results illustrate that miR-206 relieves the differentiation arrest in RMS and suggests that miR-206 replacement therapy could be a potential therapeutic strategy. Citation Format: Jason A. Hanna, Matthew R. Garcia, Jonathan C. Go, David Finkelstein, Kiran Kodali, Vishwajeeth Pagala, Eric N. Olson, Junmin Peng, Mark E. Hatley. MicroRNA-206 drives rhabdomyosarcoma differentiation through downregulation of PAX7. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr B05.
Sixty seconds on . . . psilocybin
Authors: Nigel Hawkes
Journal: BMJ (2016)

Not so fast. There’s a long way to go. But a study in London has shown that the active ingredient in magic mushrooms, psilocybin, may be effective against treatment resistant depression. Its effects were quick—within a week—and more than 40% of the patients treated were still in remission three months later.1

Yes, as far as it goes. These were people whose depression had …
Mixed Epidermal Cell-Lymphocyte Reaction in Prediction of Acute Graft-Versus-Host Disease in Bone Marrow Recipients&lt;xref ref-type="fn" rid="FN1"&gt;1&lt;/xref&gt;
Authors: M Bagot, C Cordonnier, J P Vernant, L Dubertret, H Rochant, J P Levy
Journal: JNCI Journal of the National Cancer Institute (1986)

Peripheral blood lymphocytes (PBL) and epidermal cells (EC) of 44 patients to be grafted with bone marrow from an HLA-identical sibling have been used as stimulator cells in primary cultures with effector PBL of one or several potential donors. Proliferative responses against PBL did not differ from those obtained with effector cells cultured in medium alone, whereas EC induced clearly positive proliferation in 21/53 (40%) of the pairs tested. Evaluation of 30 patients followed for more than 3 months after the graft shows that a high level of response in the mixed epidermal cell lymphocyte reaction is directly correlated with the incidence of acute graft-versus-host disease.
Decay of ccc-DNA marks persistence of intrahepatic viral DNA synthesis under tenofovir in HIV-HBV co-infected patients
Authors: Anders Boyd, Karine Lacombe, Fabien Lavocat, Sarah Maylin, Patrick Miailhes, Caroline Lascoux-Combe, Constance Delaugerre, Pierre-Marie Girard, Fabien Zoulim
Journal: Journal of Hepatology (2016)
Empirical Studies About Attendance at Religious Services and Health
Authors: Dan German Blazer
Journal: JAMA Internal Medicine (2016)

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 Internal Medicine HomeNew OnlineCurrent IssueFor Authors Podcast 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 Internal Medicine journal