tbuckley/cabot-search huggingface dataset:
Abstract 2902: Global bioinformatic analysis for transcription factor genomic binding sites from ChIP-sequencing.
Authors: Junjiang Fu
Journal: Cancer Research (2013)

Abstract The technique for Chromatin Immunoprecipitation (ChIP) combining with high-throughput DNA sequencing (ChIP-seq), is better than the ChIP-on-chip, which might reveal interactions between proteins and DNAs by the new generation sequencing technology. ChIP-seq can accurately reveal all possible binding sites in the whole cellular genome of the transcription factors or interesting proteins. TWIST, an important transcription factor which has a highly conserved, basic helix - loop - helix (bHLH) domain, can bind with DNA motif CANNTG (E-box). However, ChIP-seq will generate millions of data and the exactly E-boxes of TWIST in the whole genome is unknown. In this study, we performed the global bioinformatic analysis for transcription factor TWIST genomic binding sites from ChIP-seq result in cell lines. MACS software was used to identify TWIST binding sites from ChIP-seq data. MEME, a motif discovery tool, was used to search for statistically over-represented motifs in and near TWIST-occupied regions. There are 26,229 binding sites and 90,659 E-boxes in whole genome, and 42,390 E-boxes within the peak of 100bp in the binding sites. The majority of ChIP-seq signals could be parsimoniously explained by a CABVTG motif within ±200bp of ChIP summit and, of these, CAGCTG is most prevalent. Specifically, the characteristics of E-box mainly are CACATG, CATATG, CAGATG, CAGCTG and CACCTG. The CAGCTG is most prevalent E-box with 9% in total, and most E-boxes located within ±200bp of ChIP summit with more than 70% in total. Additionally, further analysis in chromosome 6 revealed 1936 binding sites and 6,437 E-boxes. We defined 88 genes in which binding sites located at promoter region in chromosome 6. Through gene function prediction, they are divided into three clusters. Some genes from the clusters function as tumor development and necrosis, which will provide us the clues for studying TWIST net work regulation and signal pathways in cancer biology. Therefore, our results showed that bioinformatics analysis from high resolution ChIP-seq data may be used to drive effective discovery and dissect all of binding sites for transcript factors, including TWIST, in silico. This work was supported by NSFC (30371493, 81172049). We thank Drs. R Chen, J Xu and Ms. J Cheng. Citation Format: Junjiang Fu. Global bioinformatic analysis for transcription factor genomic binding sites from ChIP-sequencing. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2902. doi:10.1158/1538-7445.AM2013-2902 Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.
Phylogenetic Discordance at the Species Boundary: Comparative Gene Genealogies Among Rapidly Radiating Heliconius Butterflies
Authors: Margarita Beltrán, Chris D. Jiggins, Vanessa Bull, Mauricio Linares, James Mallet, W. Owen McMillan, Eldredge Bermingham
Journal: Molecular Biology and Evolution (2002)

Recent adaptive radiations provide excellent model systems for understanding speciation, but rapid diversification can cause problems for phylogenetic inference. Here we use gene genealogies to investigate the phylogeny of recent speciation in the heliconiine butterflies. We sequenced three gene regions, intron 3 (≈550 bp) of sex-linked triose-phosphate isomerase (Tpi), intron 3 (≈450 bp) of autosomal mannose-phosphate isomerase (Mpi), and 1,603 bp of mitochondrial cytochrome oxidase subunits I and II (COI and COII), for 37 individuals from 25 species of Heliconius and related genera. The nuclear intron sequences evolved at rates similar to those of mitochondrial coding sequences, but the phylogenetic utility of introns was restricted to closely related geographic populations and species due to high levels of indel variation. For two sister species pairs, Heliconius erato-Heliconius himera and Heliconius melpomene-Heliconius cydno, there was highly significant discordance between the three genes. At mtDNA and Tpi, the hypotheses of reciprocal monophyly and paraphyly of at least one species with respect to its sister could not be distinguished. In contrast alleles sampled from the third locus, Mpi, showed polyphyletic relationships between both species pairs. In all cases, recent coalescence of mtDNA lineages within species suggests that polyphyly of nuclear genes is not unexpected. In addition, very similar alleles were shared between melpomene and cydno, implying recent gene flow. Our finding of discordant genealogies between genes is consistent with models of adaptive speciation with ongoing gene flow and highlights the need for multiple locus comparisons to resolve phylogeny among closely related species.
Crisis in General Practice
Authors: Robert Siekert
Journal: JAMA (1964)

<h3>To the Editor:—</h3> This is an excellent statement on a problem that not only general practitioners but physicians in general face. Members of the Board of Trustees and officers of the Association should be familiar with it and attempt to solve the problem that Dr. Foster describes so well. As aJournalreader who has an interest in the total practice of medicine, I wish to thank you for publishing such a worthwhile contribution.
A case of Acinetobacter calcoaceticus pneumonia.
Authors: H Bilgic, E S Akin, Y Tasan, K Ekiz, O Seber
Journal: Thorax (1995)

Abstract A case of community acquired pneumonia with Acinetobacter calcoaceticus is presented. Acinetobacter must be considered in the differential diagnosis of Gram negative coccobacillary pneumonia.
Risa Lavizzo-Mourey, MD, MBA
Authors: M.J. Friedrich
Journal: JAMA (2003)

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
Randomized study of reduced-intensity chemotherapy combined with imatinib in adults with Ph-positive acute lymphoblastic leukemia
Authors: Yves Chalandon, Xavier Thomas, Sandrine Hayette, Jean-Michel Cayuela, Claire Abbal, Françoise Huguet, Emmanuel Raffoux, Thibaut Leguay, Philippe Rousselot, Stéphane Lepretre, Martine Escoffre-Barbe, Sébastien Maury, Céline Berthon, Emmanuelle Tavernier, Jean-François Lambert, Marina Lafage-Pochitaloff, Véronique Lhéritier, Sylvie Chevret, Norbert Ifrah, Hervé Dombret
Journal: Blood (2015)
STUDIES OF THE VENTILATION-PERFUSION RELATIONSHIPS IN THE LUNGS OF SUBJECTS WITH CHRONIC PULMONARY EMPHYSEMA, FOLLOWING A SINGLE INTRAVENOUS INJECTION OF RADIOACTIVE KRYPTON (Kr85). I. PRESENTATION AND VALIDATION OF A THEORETICAL MODEL *
Authors: H. P. Gurtner, W. A. Briscoe, A. Cournand
Journal: Journal of Clinical Investigation (1960)
AN INTERNATIONAL MEDICAL COUNCIL FOR THE RECONSTRUCTIVE PERIOD
Authors: J. M. Anders
Journal: JAMA (1918)

To the Editor:  —With the termination of actual hostilities, new problems will confront the medical profession in three main directions: (1) physical fitness; (2) the increased incidence of certain infective diseases, and (3) the insanitary, pestilential conditions resulting from the war.  The ideal method of preparing for this vitally important work would be by the creation of an international medical council to be composed of two or three representatives from each nation belonging to the Allies. The aims of such a body would be multiple, as follows: 1. To promote unity of purpose and action and to maintain friendly relations during postbellum days or the reconstruction period. 2. To exchange information bearing on the conditions, situations and methods, both medical and sanitary, of individual nations, and in this way facilitate the immense work to be done in combating disease, and in hygiene, sanitation and physical reconstruction. 3. Direct assistance could
Polycystic-Ovary Syndrome — What Is It?
Authors: Judith L. Vaitukaitis
Journal: New England Journal of Medicine (1983)

THE term "polycystic-ovary syndrome" is best reserved for describing a clinical but not a specific pathophysiologic syndrome, since the cause of the disorder encompasses several different abnormalities with similar clinical presentations.1 , 2 The syndrome is probably the most common endocrinologic disorder among women during their reproductive years.Almost 50 years ago, Stein and Leventhal described a syndrome consisting of obesity, hirsutism, and amenorrhea in women with bilaterally enlarged polycystic ovaries.3 Since then, however, many women have been described who do not have amenorrhea, hirsutism, or obesity, but who have Normal-Sized or enlarged ovaries containing fluid-filled follicular cysts and have other characteristic . . .
The Experimental Biology of Brain Tumors
Authors: H. M. Zimmerman
Journal: JAMA (1972)

Kirsch and the Paolettis have compiled and edited an invaluable book by 35 contributors on the pathogenesis, diagnosis, and therapy of brain tumors. The contributions that experimental tumorigenesis has made to an understanding of human intracranial neoplasia are emphasized. The book is divided into five sections, the first two of which deal mainly with experimental glioma production in animals by means of chemical carcinogens and viruses and with the intermediary metabolism of brain tumors. The third section summarizes the effects of drugs and physical agents on brain tumor metabolism. In the fourth section there is a chapter on environmental factors in the structure, metabolism, and growth of glial tumors, and one on the permeability of the brain adjacent to gliomas. The purpose of these sections is to supply theoretical and practical suggestions for any therapeutic attempts that may be made on human gliomas. The very diversity of the subject matter
Folate status and requirement in pregnancy.
Authors: I. Chanarin, D. Rothman, A. Ward, J. Perry
Journal: BMJ (1968)

Some controversial aspects of rheumatic heart disease are discussed in the light of personal experience in Edinburgh.Symptoms are not always a reliable guide to severity, and the correct time for surgical treatment should be based on an objective assessment.Dangers of delay include progressive damage to the pulmonary circulation, lungs, right ventricle, and liver, and the risks of systemic embolism, pulmonary oedema, and pulmonary infarction.The New York Heart Association classification of disability is unreliable and a potentially dangerous guide.The concepts of the pliant valve, critical stenosis, areas of auscultation, and the ejection murmur are criticized.No relation has been found between the size of the left auricle or atrium and the incidence of embolism.There is reason to doubt the value of anticoagulants.In relation to mitral valvotomy factors influencing operative mortality, complications, traumatic mitral incompetence, sys- temic embolism, and restenosis are discussed, and also the influence of calcification and of associated aortic valvular disease.Reference is also made to the place of open heart surgery.I am grateful to my colleagues, Andrew Logan, with whom I have been so closely associated since he carried out our first valvotomy in 1950 and later introduced the transventricular approach to the mitral valve and, for many years now, Arthur Kitchin, who as a clinician is also in charge of our laboratory, for innumerable discussions and for their advice on the subject matter of this paper.
Incidence, risk factors and clinical outcome of leukemia relapses with loss of the mismatched HLA after partially incompatible hematopoietic stem cell transplantation
Authors: L Crucitti, R Crocchiolo, C Toffalori, B Mazzi, R Greco, A Signori, F Sizzano, L Chiesa, E Zino, M T Lupo Stanghellini, A Assanelli, M G Carrabba, S Marktel, M Marcatti, C Bordignon, C Corti, M Bernardi, J Peccatori, C Bonini, K Fleischhauer, F Ciceri, L Vago
Journal: Leukemia (2014)
Reticulum-Cell Sarcoma of Host Origin Arising in a Transplanted Kidney
Authors: ROBERT S. BROWN
Journal: Annals of Internal Medicine (1974)

A reticulum-cell sarcoma, involving the transplanted kidney and the skin of the abdominal wall, developed 22 months after renal transplantation in a 47-year-old woman. A comparison of the malignant tumor cells with donor and recipient lymphocytes, by histocompatibility serotyping, clearly showed that the reticulum sarcoma cells were identical to the recipient's lymphocytes, distinctly different from the donor's lymphocytes, and therefore must have arisen from the host. It has been assumed that the malignant lymphomas in transplant patients have arisen de novo in the recipients, but this study confirms a host-cell etiology, despite involvement of the allograft. In-vitro studies showed lymphocyte-mediated cytotoxicity of tumor cells and the presence of "blocking factors." Immunosuppression may have encouraged origination of the tumor, but inappropriate blocking factors probably fostered its growth. In addition, viral infection with hepatitis-associated antigen (HB Ag) and subacute hepatic necrosis, with the development of tuberculin anergy, were temporally related to tumor development.
C-reactive protein: A potential new molecular link between inflammation, thrombosis and vascular cell proliferation?
Authors: A PANDOLFI
Journal: Cardiovascular Research (2005)

C-reactive protein (CRP), a pentraxin synthesized in the liver, is a highly conserved pentameric plasma protein that participates in the systemic response to inflammation.In humans, plasma levels of CRP may rise rapidly and markedly (> 1000-fold) after an acute inflammatory stimulus and presumably contribute to host defence [1].On the other hand, although CRP may exert pleiotropic effects, both ''proinflammatory'' [2] and ''anti-inflammatory'' (reviewed in Ref. [1]), a large number of studies have demonstrated an association between slightly elevated CRP plasma levels (3 -10 Ag/ml) and increased risk of developing cardiovascular disease in apparently healthy individuals [2].This suggests that CRP might be not only a simple downstream marker of inflammation but may have a direct role in atherothrombosis.Accumulating evidence suggests that CRP may directly elicit a variety of pro-atherogenic effects in vascular tissue.In particular, it has been reported that CRP stimulates production of interleukin-8 (IL-8), monocyte chemoattractant protein-1 (MCP-1), plasminogen activator inhibitor-1 (PAI-1), intercellular cell adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1) and E-selectin in vascular endothelial cells [3].Also, CRP attenuates endothelial progenitor cell survival, differentiation, and function via inhibition of nitric oxide (NO) [4].Vascular smooth muscle cells (vSMC) may be also a target of the pro-inflammatory and pro-atherogenic actions of CRP.In fact, it increases angiotensin II-induced vSMC proliferation, migration and reactive oxygen species (ROS) production.In addition, CRP
Muscle fibrosis and contractures in a pethidine addict.
Authors: F L Mastaglia, D Gardner-Medwin, P Hudgson
Journal: BMJ (1971)

Myopathy complicating intramuscular administration of some drugs is well recognized. The repeated intramuscular injection of chloroquine, for example, induces intense necrosis and phagocytosis at the injection site (Aguayo and Hudgson, 1970). Pethidine is usually injected intramuscularly, and it is perhaps surprising that there has been only one report of  myopathy developing in those addicted to it (Aberfeld et al., 1968). We believe that the case described here was of this kind.
Massachusetts Medical Society
Authors: John Figgis Jewett
Journal: New England Journal of Medicine (1977)

First delivered uneventfully of a 3740-g infant at 19 years of age, an unmarried patient reported for prenatal care at 31 weeks' gestation in her second pregnancy about a year later. At the three prenatal visits all findings were normal, but at 36 weeks, abruptio placentae resulted in a stillbirth followed by post-partum hemorrhage and disseminated intravascular coagulopathy. Nine units of blood and 4 g of fibrinogen were required. At autopsy that infant showed small adrenal and thymus glands, a hypoplastic heart and increased erythropoiesis.Four years later, now 24 years of age, the patient reported for prenatal care at . . .
Effects of dietary cholesterol and fatty acids on plasma lipoproteins.
Authors: G Schonfeld, W Patsch, L L Rudel, C Nelson, M Epstein, R E Olson
Journal: Journal of Clinical Investigation (1982)

The effects of dietary cholesterol and fatty acids on low density and high density lipoproteins (LDL and HDL) were studied in 20 young men. After 2-3 wk of evaluations on ad lib. diets, basal diets, which consisted of 15% protein, 45% carbohydrates, 40% fat, and 300 mg/day of cholesterol, were given for 4-5 wk (Basal). The ratio of dietary polyunsaturated to saturated fatty acids (P/S) for different groups of subjects were 0.25, 0.4, 0.8, or 2.5. 750 and 1,500 mg/d of cholesterol were added to the basal diets as 3 and 6 eggs, respectively. Total cholesterol and LDL cholesterol were lower in all subjects on the basal diets than on the ad lib. diets. Addition of 750 mg cholesterol to the diet with P/S = 0.25-0.4 raised LDL cholesterol by 16 +/- 14 mg/dl to 115% of basal diet values (n = 11, P less than 0.01); 1,500 mg increased LDL cholesterol by 25 +/- 19 mg/dl to 125% (n = 9, P less than 0.01). On the diet with P/S = 0.8, 750 mg produced insignificant increases in LDL cholesterol, but 1,500 mg produced increases of 17 +/- 22 mg/dl to 115% of basal (n = 6, P less than 0.02). On the P/S = 2.5 diet, neither 750 nor 1,500 mg produced significant changes. Thus, both the cholesterol contents and P/S ratios of diets were important in determining LDL levels. The lipid and apoprotein compositions, flotation rates, molecular weights, and binding by cellular receptors of LDL were virtually unchanged by the addition of cholesterol to the diets high in saturated fat. These diets, therefore, caused an increase in the number of LDL particles of virtually unchanged physical and biological properties. On the diet with low P/S ratio, HDL2 rose, whereas this effect was absent on diets with high P/S ratios. The response of LDL to dietary manipulations is consonant with epidemiologic data relating diets high in cholesterol and saturated fat to atherogenesis. The response of HDL2, however, is opposite to that of its putative role as a negative risk factor. Further work is needed to clarify this interesting paradox.
Effect of Aspirin on Renal Clearance of 125I-Diatrizoate
Authors: L. Beeley, M. J. Kendall
Journal: BMJ (1971)

Glomerular filtration rate was measured from the plasma disappearance curve after a single injection of sodium <sup>125</sup>I-diatrizoate. A therapeutic dose of aspirin in 13 subjects produced a mean fall in glomerular filtration rate of 10·5%.
Activation-induced cytidine deaminase links bile duct inflammation to human cholangiocarcinoma
Authors: Junji Komori, Hiroyuki Marusawa, Takafumi Machimoto, Yoko Endo, Kazuo Kinoshita, Tadayuki Kou, Hironori Haga, Iwao Ikai, Shinji Uemoto, Tsutomu Chiba
Journal: Hepatology (2008)

Chronic inflammation plays a critical role in oncogenesis in various human organs. Epidemiological studies have demonstrated that patients with primary sclerosing cholangitis have a predisposition to develop cholangiocarcinoma (CC). However, the molecular mechanisms that account for the development of bile duct carcinomas are not well defined. We recently provided evidence that activation-induced cytidine deaminase (AID), a member of the DNA/RNA editing enzyme family, is implicated in human tumorigenesis via its mutagenic activity. We found here that ectopic AID production is induced in response to tumor necrosis factor-α (TNF-α) stimulation via the IkappaB kinase-dependent nuclear factor-κB (NF-κB) activation pathway in human cholangiocarcinoma-derived cells. Aberrant expression of AID in biliary cells resulted in the generation of somatic mutations in tumor-related genes, including p53 , c - myc , and the promoter region of the INK4A / p16 sequences. In human tissue specimens, real-time reverse transcription polymerase chain reaction (RT-PCR) analyses revealed that AID was increased significantly in 28 of 30 CC tissues (93%), whereas only trace amounts of AID were detected in the normal liver. Immunohistochemistry showed that all of the CC tissue samples examined showed overproduction of endogenous AID protein in cancer cells. Moreover, immunostaining for AID was detectable in 16 of 20 bile epithelia in the tissues underlying primary sclerosing cholangitis. Conclusion: The proinflammatory cytokine-induced aberrant production of AID might link bile duct inflammation to an enhanced genetic susceptibility to mutagenesis, leading to cholangiocarcinogenesis.