tbuckley/cabot-search huggingface dataset:
Abstract 2957: Characterization of oral tumors by massively parallel ligation sequencing
Authors: Rebecca R. Laborde, Brian B. Tuch, Kerry D. Olsen, Jan L. Kasperbauer, Eric J. Moore, Melissa A. Barker, Francisco M. De La Vega, David I. Smith
Journal: Cancer Research (2010)

Abstract Cancers of the head and neck rank as the 6th most commonly observed cancers worldwide with an average 5-year survival rate of only 50% for advanced disease. Nearly 95% of head and neck cancers are squamous cell carcinomas (SSC) and these are frequently highly invasive metastatic tumors. The newly developing technologies of Next Generation Sequencing have allowed for the most comprehensive genetic analysis of these cancers to date. We have taken 3 tumor/normal pairs from patients with oral squamous cell carcinoma and performed full transcriptome and mate-pair DNA sequencing analysis using the AB SOLiD system. These runs generated 129-256 million 50bp long sequence reads per sample, with 21 to 56 million reads per sample uniquely aligning to human genome sequence. Analysis of these samples has revealed pathways with aberrant expression in tumor versus normal tissue. Our results show up-regulation of some metalloproteinase genes, HGMA2, which is a prognostic marker for oral carcinoma, and extracellular matrix, adhesion, and motility gene classes in tumors. Our functional analysis also indicates extensive down-regulation, in the tumors, of genes functioning in epidermal development. We were also able to measure allelic specific expression for the 50% most highly expressed genes and detect examples of allelic imbalance linked to pathways with dysregulated gene expression. Additionally, the depth of sequencing that was achieved (5-16X coverage of RefSeq Exons) also allowed us to detect mutations occurring in the transcripts. We have also detected evidence of RNA editing associated with point mutations, which we are validating in a larger group of samples. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2957.
Diagnosis of Cavernous Sinus Artenovenous Fistula by Measurement of Ocular Pulse Amplitude
Authors: Karl C. Golnik, Neil R. Miller
Journal: Ophthalmology (1992)

The ocular pulse amplitude (OPA), the difference between the maximum and minimum intraocular pressure (IOP) during the cardiac cycle, has been reported to be elevated in the eye ipsilateral to a cavernous sinus arteriovenous fistula.The OPA was measured with a pneumotonometer in three groups of patients. Patients in group 1 had no orbital disease (n = 50), patients in group 2 had either unilateral or asymmetric orbital disease (n = 30), and patients in group 3 had angiographically proven cavernous sinus arteriovenous fistulas (n = 15).Patients in group 3 had a higher OPA than patients in either group 1 (P less than 0.001) or group 2 (P less than 0.001). The difference in OPA between an individual's eyes (delta OPA) also was higher in patients with cavernous sinus arteriovenous fistulas than in patients without fistulas (P less than 0.0001).A delta OPA of more than 1.6 mmHg was 100% sensitive and 93% specific in identifying patients with cavernous sinus arteriovenous fistulas. There was no difference in delta OPA between direct and dural cavernous sinus arteriovenous fistulas. Successful transvascular embolization of the cavernous sinus arteriovenous fistula normalized the delta OPA by reducing the OPA on the affected side.
Impaired Synthesis of Polyclonal (Non-Paraprotein) Immunoglobulins by Circulating Lymphocytes from Patients with Multiple Myeloma
Authors: Samuel Broder, Richard Humphrey, Mary Durm, Marcia Blackman, Bruce Meade, Carolyn Goldman, Warren Strober, Thomas Waldmann
Journal: New England Journal of Medicine (1975)

Since patients with myeloma have serious abnormalities of humoral immunity, we applied an in vitro assay to determine the capacity of B lymphocytes to mature into immunoglobulin-secreting cells. In peripheral blood lymphocytes from 22 normal persons, geometric mean immunoglobulin synthesis was 4910 ng for IgM, 1270 ng for IgA and 1625 ng for IgG. The synthesis rates of peripheral blood lymphocytes of 22 patients with myeloma were 458 ng for IgM, 321 ng for IgA and 218 ng for IgG. Circulating mononuclear cells from three of six patients tested suppressed polyclonal immunoglobulin synthesis by cocultured normal lymphocytes. Suppressive activity was not mediated by purified T cells alone. Removal of phagocytic mononuclear cells from lymphocyte populations of one patient nullified suppressive activity. Removal of phagocytic mononuclear cells from lymphocyte populations of a second patient led to a nearly 10-fold increase in polyclonal immunoglobulin synthesis. Therefore, host suppressor cells may play a part in the decreased capacity of B lymphocytes to secret immunoglobulin in certain patients with myeloma.
Effect of Menstruation on Schoolgirls' Weekly Work
Authors: K. Dalton
Journal: BMJ (1960)

ORAa long time, even though the gut was washed repeatedly with fresh Tyrode solution.The contraction caused by 1 ml. of C.D. could be antagonized completely by mepyramine maleate (0.02 y/ml. in the bath).We have thus obtained some evidence that our C.D. contained a histamine liberator, and we should like to advance the hypothesis that some of the symptoms of byssinosis are caused by a histamine liberator in the cotton dust inhaled by card-room workers.Our evidence indicates that the histamine release can take place without a preceding antigen-antibody reaction. SummaryInhalation of an extract of cotton dust caused a delay in the clearance of nitrogen from the lungs during oxygen-breathing.This effect, which presumably is due to bronchial obstruction, was obtained in two men who had not previously been exposed to the dust in cotton-mills.The effect was not caused by histamine present in the extract.The results of our experiments, as well as some of the symptoms of byssinosis, may be explained by the assumption that the cotton dust contains a histamine liberator.Some evidence was obtained, from animal prepara- tions, that the cotton-dust extract used here contained a substance capable of releasing histamine.This exceedingly rare bone anomaly is related to prenatal factors arising during the early phase of foetal development which prevent the laying down of certain parts of the osseous system.The cranial vault, the vertebral arches, and the pelvic and shoulder girdles may likewise manifest serious structural deficiencies.Short references to phocomelia have been made by Church and Peterson (1911( ), Aschoff (1928)), and Kaufmann (1929), but the most descriptive record, with
Independent risk factors for atrial fibrillation in a population-based cohort. The Framingham Heart Study
Authors: E. J. Benjamin
Journal: JAMA (1994)

To determine the independent risk factors for atrial fibrillation.Cohort study.The Framingham Heart Study.A total of 2090 men and 2641 women members of the original cohort, free of a history of atrial fibrillation, between the ages of 55 and 94 years.Sex-specific multiple logistic regression models to identify independent risk factors for atrial fibrillation, including age, smoking, diabetes, electrocardiographic left ventricular hypertrophy, hypertension, myocardial infarction, congestive heart failure, and valve disease.During up to 38 years of follow-up, 264 men and 298 women developed atrial fibrillation. After adjusting for age and other risk factors for atrial fibrillation, men had a 1.5 times greater risk of developing atrial fibrillation than women. In the full multivariable model, the odds ratio (OR) of atrial fibrillation for each decade of advancing age was 2.1 for men and 2.2 for women (P < .0001). In addition, after multivariable adjustment, diabetes (OR, 1.4 for men and 1.6 for women), hypertension (OR, 1.5 for men and 1.4 for women), congestive heart failure (OR, 4.5 for men and 5.9 for women), and valve disease (OR, 1.8 for men and 3.4 for women) were significantly associated with risk for atrial fibrillation in both sexes. Myocardial infarction (OR, 1.4) was significantly associated with the development of atrial fibrillation in men. Women were significantly more likely than men to have valvular heart disease as a risk factor for atrial fibrillation. The multivariable models were largely unchanged after eliminating subjects with valvular heart disease.In addition to intrinsic cardiac causes such as valve disease and congestive heart failure, risk factors for cardiovascular disease also predispose to atrial fibrillation. Modification of risk factors for cardiovascular disease may have the added benefit of diminishing the incidence of atrial fibrillation.
PEST Domain Mutations in Notch Receptors Comprise an Oncogenic Driver Segment in Triple-Negative Breast Cancer Sensitive to a γ-Secretase Inhibitor
Authors: Kai Wang, Qin Zhang, Danan Li, Keith Ching, Cathy Zhang, Xianxian Zheng, Mark Ozeck, Stephanie Shi, Xiaorong Li, Hui Wang, Paul Rejto, James Christensen, Peter Olson
Journal: Clinical Cancer Research (2015)

To identify and characterize novel, activating mutations in Notch receptors in breast cancer and to determine response to the gamma secretase inhibitor (GSI) PF-03084014.We used several computational approaches, including novel algorithms, to analyze next-generation sequencing data and related omic datasets from The Cancer Genome Atlas (TCGA) breast cancer cohort. Patient-derived xenograft (PDX) models were sequenced, and Notch-mutant models were treated with PF-03084014. Gene-expression and functional analyses were performed to study the mechanism of activation through mutation and inhibition by PF-03084014.We identified mutations within and upstream of the PEST domains of NOTCH1, NOTCH2, and NOTCH3 in the TCGA dataset. Mutations occurred via several genetic mechanisms and compromised the function of the PEST domain, a negative regulatory domain commonly mutated in other cancers. Focal amplifications of NOTCH2 and NOTCH3 were also observed, as were heterodimerization or extracellular domain mutations at lower incidence. Mutations and amplifications often activated the Notch pathway as evidenced by increased expression of canonical Notch target genes, and functional mutations were significantly enriched in the triple-negative breast cancer subtype (TNBC). PDX models were also identified that harbored PEST domain mutations, and these models were highly sensitive to PF-03084014.This work suggests that Notch-altered breast cancer constitutes a bona fide oncogenic driver segment with the most common alteration being PEST domain mutations present in multiple Notch receptors. Importantly, functional studies suggest that this newly identified class can be targeted with Notch inhibitors, including GSIs.
Review: Antiplatelet therapies are more effective in smokers than nonsmokers
Authors: Debabrata Mukherjee
Journal: Annals of Internal Medicine (2014)

Source Citation Gagne JJ, Bykov K, Choudhry NK, et al. Effect of smoking on comparative efficacy of antiplatelet agents: systematic review, meta-analysis, and indirect comparison. BMJ. 2013;347:f5307. 24046285
Renal transplantation in polycystic renal disease. Decrease in size of the cystic kidneys and erythremia
Authors: D. C. Martin
Journal: JAMA (1967)

A 37-year-old man with apparent familial polycystic renal disease reached a terminal phase of uremia in 1964. Renal transplantation was carried out from the patient's mother in July of the same year. The recipient enjoys good renal function more than three years following transplantation. This patient's polycystic kidneys were left in at the time of transplantation and have since been observed to be shrinking in size. The patient also has an erythremia (polycythemia vera) following transplantation, which persists more than three years postoperatively.
Serum Ferritin Levels Lack Diagnostic Accuracy for Liver Fibrosis in Patients With Nonalcoholic Fatty Liver Disease
Authors: Paul Angulo, Jacob George, Christopher P. Day, Ester Vanni, Lee Russell, Anna C. De la Cruz, Hammad Liaquat, Lavinia Mezzabotta, Eun Lee, Elisabetta Bugianesi
Journal: Clinical Gastroenterology and Hepatology (2013)
Management of Tuberculosis
Authors: Seymour Krevsky
Journal: JAMA (1976)

To the Editor.—  In their article on the management of tuberculosis in the mid-1970s, Drs Mc Conville and Rapoport (235:172, 1976) state that, according to some evidence, patients discharged on a regimen of chemotherapy, even those with sputum positive for the infecting organism, do not constitute an important risk of infection to their contacts. The authors quote a study by Brooks et al, of 21 patients with positive sputum; this may represent an encouraging study, yet it would seem that these patients with positive sputum specimens still represent a very highly contagious group for tuberculin-negative contacts.  While they state that there was no tuberculin conversion among their contacts who initially had negative skin test reactions and who continued close association with the index patient, it should be recognized that all these contacts were receiving chemoprophylaxis in the home environment, and this may have delayed the establishment of a positive skin
Cellulitis Due to<i>Haemophilus influenzae</i>Type B
Authors: Murray Feingold, Sydney S. Gellis
Journal: New England Journal of Medicine (1965)

IN 1957 Green and Fousek1 reported 6 cases of cellulitis due to Haemophilus influenzae Type B, in 4 of which blood cultures were positive. In a review of the literature two years later Thilenius and Carter2 could find only 3 other cases and added 1 of their own. To the best of our knowledge, these 10 cases are the only ones mentioned in the literature.Since 1957, 7 patients with cellulitis due to H. influenzae Type B, with positive blood cultures, and 2 others with probable cases were admitted to the Pediatric Service of the Boston City Hospital. Because of . . .
Regulation of transcription of the human T cell antigen receptor delta chain gene. A T lineage-specific enhancer element is located in the J delta 3-C delta intron.
Authors: J C Bories, P Loiseau, L d'Auriol, C Gontier, A Bensussan, L Degos, F Sigaux
Journal: The Journal of Experimental Medicine (1990)

We have defined transcriptional enhancing sequences inside the TCR-delta gene locus, using transient transfections with constructs containing DNA fragments cloned upstream to a reporter gene fused to a heterologous promoter. A 14-kb DNA region extending from the J delta 3 segment to 6 kb 3' to C delta was analyzed. We show the presence of positive regulatory sequences inside the J delta 3-C delta intron and have localized these sequences to two DNA fragments of approximately 300 and 258 bp. Analysis of cell specificity of the activation of such sequences demonstrates a T cell pattern for one of the two fragments. The nucleotide sequence of the T cell-specific element shows motifs sharing homology with previously described core enhancers.
A gene mutated in X–linked myotubular myopathy defines a new putative tyrosine phosphatase family conserved in yeast
Authors: Jocelyn Laporte, Ling Jia Hu, Christine Kretz, Jean-Louis Mandel, Petra Kioschis, Johannes F. Coy, Sabine M. Klauck, Annemarie Poustka, Niklas Dahl
Journal: Nature Genetics (1996)
Differential in situ cytokine gene expression in acute versus chronic atopic dermatitis.
Authors: Q Hamid, M Boguniewicz, D Y Leung
Journal: Journal of Clinical Investigation (1994)

The mechanisms involved in the initiation and maintenance of skin inflammation in atopic dermatitis (AD) are poorly understood. Recent data suggest that the pattern of cytokines expressed locally plays a critical role in modulating the nature of tissue inflammation. In this study, we used in situ hybridization to investigate the expression of interleukin 4 (IL-4), IL-5, and interferon-gamma (IFN-gamma) messenger RNA (mRNA) in skin biopsies from acute and chronic skin lesions of patients with AD. As compared with normal control skin or uninvolved skin of patients with AD, acute and chronic skin lesions had significantly greater numbers of cells that were positive for mRNA, IL-4 (P < 0.01), and IL-5 (P < 0.01), but not for IFN-gamma mRNA expressing cells. However, as compared with acute AD skin lesions, chronic AD skin lesions had significantly fewer IL-4 mRNA-expressing cells (P < 0.01), but significantly greater IL-5 mRNA (P < 0.01). T cells constituted the majority of IL-5-expressing cells in acute and chronic AD lesions. Chronic lesions also expressed significantly greater numbers of activated EG2+ eosinophils than acute lesions (P < 0.01). These data indicate that although acute and chronic AD lesions are associated with increased activation of IL-4 and IL-5 genes, initiation of acute skin inflammation in AD is associated with a predominance of IL-4 expression whereas maintenance of chronic inflammation is predominantly associated with increased IL-5 expression and eosinophil infiltration.
Strategy Against Obesity?
Authors: Tracy Hampton
Journal: JAMA (2012)

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
Defective Antitumor Function of Monocyte-Derived Macrophages from Epithelial Ovarian Cancer Patients
Authors: Ilyssa O. Gordon, Ralph S. Freedman
Journal: Clinical Cancer Research (2006)

Abstract Purpose: Monocytes/macrophages (MO/MA) are an important but heterogeneous population of immune inflammatory cells that have diverse effector functions. We examined and compared these differences in peripheral blood and ascites of epithelial ovarian cancer patients with peripheral blood of normal donors. Experimental Design: Comparisons were made of cell surface subsets, cytokine production, and FcR-dependent cytotoxicity of CD14+ MO/MA and the CD14brightCD16−HLA-DR+ MO/MA subset in normal donor peripheral blood and peripheral blood and ascites from epithelial ovarian cancer patients. Studies were done on monocyte-derived macrophages cultured with macrophage colony-stimulating factor and activated with lipopolysaccharide or a combination of lipopolysaccharide plus recombinant IFN-γ. Results: We determined that MO/MA or its subset from epithelial ovarian cancer patients had altered morphology and significantly less antibody-dependent cell-mediated cytotoxicity and phagocytic activity than did MO/MA from normal donors. Our findings also showed that monocyte-derived macrophages from both epithelial ovarian cancer patients and normal donors produce macrophage colony-stimulating factor–stimulated cytokines, including interleukin-8, tumor necrosis factor-α, and interleukin-6. Conclusions: These findings highlight for the first time the defective antibody-dependent cell-mediated cytotoxicity and phagocyte functions of epithelial ovarian cancer–associated MO/MA, which could have implications for immunobiotherapeutic strategies.
Parametric statistical tests for independent groups: numerical data
Authors: P. Sedgwick
Journal: BMJ (2012)

Researchers investigated whether a school based educational programme aimed at reducing consumption of carbonated drinks prevented excessive weight gain in children. A cluster randomised controlled trial study design was used. The intervention, which was delivered over one school year, included focused education promoting a healthy diet together with discouragement of carbonated drink consumption. The control group received no intervention. Children were followed for three years from baseline.1

The main outcome measures included body mass index (BMI) converted to age and sex specific z scores. A total of 644 children aged between 7 and 11 years from six schools were recruited. Measurements were obtained from 434 children three years after baseline. Distributional assumptions of normality in the BMI z scores were verified. At follow-up the age and sex specific BMI z scores had increased in the control group by a mean of 0.1 (SD 0.53) but decreased in the intervention group by 0.01 (SD 0.58). The mean difference between treatment groups was not significant (0.1 (95% confidence interval 0 to 0.21); P=0.06).

Which one of the following statistical tests was most likely used to compare treatment groups in the mean difference in the mean change in BMI z score over three years from baseline?

Student’s t test (answer b ) would most likely have been used to compare the …
The role of plants and plant/microbial systems in the reduction of exposure.
Authors: J R Shann
Journal: Environmental Health Perspectives (1995)

The activities of plants and plant/microbial associations may offer a viable means of accomplishing the in situ remediation of contaminated soils. Two uses of plants for phytoremediation are reported here. In one set of studies, the ability of plants to foster degradative microorganisms was investigated. Results indicated that the degradation of several chlorinated pesticides increased in rhizosphere soil and that this same increase occurred when unplanted soils were given materials released from plant roots. In current investigations, the potential for plants to remove and accumulate metals from their environment is being considered. This work employs a unique testing system, the target-neighbor method, that allows evaluation of how planting density influences metal uptake. Results of these studies could provide the information needed to manipulate plant density for optimization of metal removal (remediation of metal-contaminated soil) or minimization of the amount of toxic metals in important crops (reduction of human exposure).
Studies in General Physiology.
Authors: Jacques Loeb
Journal: JAMA (1905)

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