tbuckley/cabot-search huggingface dataset:
YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens
Authors: Darren A Abbey, Jason Funt, Mor N Lurie-Weinberger, Dawn A Thompson, Aviv Regev, Chad L Myers, Judith Berman
Journal: Genome Medicine (2014)

Abstract The design of effective antimicrobial therapies for serious eukaryotic pathogens requires a clear understanding of their highly variable genomes. To facilitate analysis of copy number variations, single nucleotide polymorphisms and loss of heterozygosity events in these pathogens, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains of Candida albicans , the most prevalent human fungal pathogen. The Y MAP pipeline ( http://lovelace.cs.umn.edu/Ymap/ ) automatically illustrates genome-wide information in a single intuitive figure and is readily modified for the analysis of other pathogens with small genomes.
Expression profiling of the schizont and trophozoite stages of Plasmodium falciparumwith a long-oligonucleotide microarray
Authors: Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam, Joseph L DeRisi
Journal: Genome biology (2003)

The worldwide persistence of drug-resistant Plasmodium falciparum, the most lethal variety of human malaria, is a global health concern. The P. falciparum sequencing project has brought new opportunities for identifying molecular targets for antimalarial drug and vaccine development. We developed a software package, ArrayOligoSelector, to design an open reading frame (ORF)-specific DNA microarray using the publicly available P. falciparum genome sequence. Each gene was represented by one or more long 70 mer oligonucleotides selected on the basis of uniqueness within the genome, exclusion of low-complexity sequence, balanced base composition and proximity to the 3' end. A first-generation microarray representing approximately 6,000 ORFs of the P. falciparum genome was constructed. Array performance was evaluated through the use of control oligonucleotide sets with increasing levels of introduced mutations, as well as traditional northern blotting. Using this array, we extensively characterized the gene-expression profile of the intraerythrocytic trophozoite and schizont stages of P. falciparum. The results revealed extensive transcriptional regulation of genes specialized for processes specific to these two stages. DNA microarrays based on long oligonucleotides are powerful tools for the functional annotation and exploration of the P. falciparum genome. Expression profiling of trophozoites and schizonts revealed genes associated with stage-specific processes and may serve as the basis for future drug targets and vaccine development.
The Eradication of Rubella
Authors: Stanley A. Plotkin
Journal: JAMA (1999)

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
Emergency ambulance dispatch: is there a case for triage?
Authors: S Thakore, E A McGugan, W Morrison
Journal: Journal of the Royal Society of Medicine (2002)

Emergency telephone calls for an ambulance (999 calls) are usually dealt with first-come first-served. We have devised and assessed criteria that ambulance dispatch might use to prioritize responses. Data were collected retrospectively on consecutive patients presenting to an accident and emergency (A&E) department after a 999 call. An unblinded researcher abstracted data including age, date, time, caller, location, reason for call and A&E diagnosis and each case was examined for ten predetermined criteria necessitating an immediate ambulance response—namely, cardiac arrest; chest pain; shortness of breath; altered mental status/seizure; abdominal/loin pain >65 years old; fresh haematemesis; fall > 2 m; stabbing; major burns. 471 patients were recruited, 55% male, median age 50 years. 406 calls came from bystanders or the patients themselves, 36 from general practitioners, 8 from other hospitals and 21 from the police. 52% of patients were admitted. 44% met at least one of the above criteria. Most patients did not meet the criteria for an immediate ambulance response but might nonetheless be suitable for an urgent response. The criteria used in this study have the advantage of being based on the history provided by the caller. The introduction of a priority-based dispatch system could reduce response times to those who are seriously ill, and also improve road safety.
Sampling of exhaled nitric oxide in children: end-expiratory plateau, balloon and tidal breathing methods compared
Authors: Q Jobsis, SL Schellekens, A Kroesbergen, WC Hop, JC de Jongste
Journal: European Respiratory Journal (1999)

The aim of this study was to compare exhaled nitric oxide concentrations obtained during controlled slow exhalation, presently considered as the method of choice, with two sampling methods that are easily performed by children: blowing air into a balloon and tidal breathing through a mouthpiece. One hundred and one well controlled, stable allergic asthmatic children (median age 11.7 yrs) performed the following tasks in duplicate: 1) exhalation from total lung capacity through a mouthpiece against a resistor with a standardized flow rate of 20% of the subject's vital capacity per second, using a biofeedback system; 2) a single deep exhalation into an NO-impermeable mylar balloon; and 3) tidal breathing through a low resistance mouthpiece over 2 min. NO was measured using a chemiluminescence analyser. Twenty-nine children (29%) were not able to perform a constant-flow exhalation of at least 3 s. All children performed the balloon and tidal breathing methods without difficulty. NO concentrations (means +/-SEM) were 5.3+/-0.2 parts per billion (ppb) at the end-expiratory plateau, 5.2+/-0.3 ppb in balloons (intraclass correlation coefficient (r(i)) = 0.73) and 8.0+/-0.4 ppb during tidal breathing (p&lt;0.001, r(i) = 0.53 compared to plateau values). Mean values of NO during tidal breathing increased significantly with time, suggesting increasing contamination with nasal air. It was concluded that, in asthmatic children, the end-expiratory plateau concentration of nitric oxide during exhalation at 20% of the vital capacity per second is similar to the values obtained with the balloon method, with satisfactory agreement, but differs from values obtained during tidal breathing. The balloon method is cheap, simple and offers the interesting possibility to study exhaled nitric oxide in young children independently of the presence of a nitric oxide analyser.
Hospital versus Home Practice
Authors: J. M. Duncan
Journal: BMJ (1869)

the vitreous humour.It was pear-shaped in form, and barely altered its position after the patient had moved the eye quickly up and down, and from side to side.It appeared to be attached by its pointed extre- mity somewhat firmly, the base floating in the vitreous humour immediately behind the lens.It was impossible to get a glimpse of the disk.The opacity was extremely dense, resembling a piece of thick crape.There were not any vessels near it.Now and again, as the film moved slightly, a retinal vessel could be seen.The retina and choroid ap- peared healthy, and the eye was free from pain.There was no history of syphilis.The heart was healthy, the urine was normal, and there was no suspicion of brain-mischief Vision was limited to shadows.Mercury had no effect; for, after mildly keeping up its specific action for a fortnight, the film remained unaltered in character, and vision had not improved.Iodide of potassium, given in increasing doses, produced a marked change.Vision in a few days so far improved that fingers could be counted.Unfortunately, at this stage she ceased to attend.Some months afterwards, I accidentally heard that she recovered a fair amount of vision.CASE II.-A healthy-looking young man, by trade a mechanic, assured me that he had enjoyed good vision.On April 25th last, he accom- panied a militia regiment from their barracks to a church at some considerable distance.The sun was shining brightly at the time, and the red cloth of the soldiers' tunics sadly dazzled his eyes.As he continued to stare at the soldiers, the left eye suddenly "went quite dark."He had no pain in the head, nor any other distressing symptom at the time,
Echocardiographically Documented Mitral-Valve Prolapse
Authors: Rick A. Nishimura, Michael D. McGoon, Clarence Shub, Fletcher A. Miller, Duane M. Ilstrup, A.Jamil Tajik
Journal: New England Journal of Medicine (1985)

We determined the long-term prognosis for patients with mitral-valve prolapse documented by echocardiography by following 237 minimally symptomatic or asymptomatic patients for a mean of 6.2 years (range, 1 to 10.4). The actuarial eight-year probability of survival was 88 per cent, which is not significantly different from that for a matched control population. An initial left ventricular diastolic dimension exceeding 60 mm was the best echocardiographic predictor of the subsequent need for mitral-valve replacement (17 patients). Of the 97 patients with redundant mitral-valve leaflets identified echocardiographically, 10 (10.3 per cent) had sudden death, infective endocarditis, or a cerebral embolic event; in contrast, of the 140 patients with nonredundant valves, only 1 (0.7 per cent) had such complications (P<0.001). Most patients with echocardiographic evidence of mitral-valve prolapse have a benign course, but subsets at high risk for the development of progressive mitral regurgitation, sudden death, cerebral embolic events, or infective endocarditis can be identified by echocardiography. (N Engl J Med 1985; 313:1305–9.)
Human biliary epithelial cells secrete and respond to cytokines and hepatocyte growth factors in vitro: Interleukin-6, hepatocyte growth factor and epidermal growth factor promote DNA synthesis in vitro
Authors: Koshi Matsumoto, Hiroaki Fujii, George Michalopoulos, John J. Fung, Anthony J. Demetris
Journal: Hepatology (1994)

Recombinant growth factors and proinflammatory cytokines were added to primary cultures of human intrahepatic biliary duct epithelia to test for their ability to stimulate DNA synthesis and elicit cytokine production. Interleukin-6 and hepatocyte and epidermal growth factors were found to increase the DNA labeling index of biliary duct epithelium from fourfold to sixfold 24 hr after their addition to primary biliary duct epithelium cultures maintained in serum-free medium. The proliferative responses to all three biliary duct epithelium mitogens peaked within 24 hr, and hepatocyte growth factor was effective over a concentration range of 1.0 to 50 ng/ml, whereas interleukin-6 was effective from 1 to 1,000 U/ml. Insulin-like growth factor, phorbol myristate acetate, interleukin-1 beta and platelet-derived growth factor BB showed mild stimulatory effects, whereas interleukin-4, gamma-interferon, phytohemagglutinin and platelet-derived growth factors AA and AB did not increase DNA synthesis in biliary duct epithelium. Interleukin-1 beta and phorbol myristate acetate were also shown to induce in a dose-dependent fashion a threefold to fivefold increase of interleukin-6 production as measured by enzyme-linked immunosorbent assay in human primary biliary duct epithelium cultures, when compared with hepatocyte growth factor, epidermal growth factor, insulin-like growth factor, phytohemagglutinin, tumor necrosis factor-alpha or platelet-derived growth factor. These results show that interleukin-6 participates in growth regulation of human biliary duct epithelium. This could be exerted in a paracrine or autocrine manner.(ABSTRACT TRUNCATED AT 250 WORDS)
Corrigendum to “Analysis of IL-10, IL-4 and TNF-α polymorphisms in drug-induced liver injury (DILI) and its outcome” [J Hepatol 49 (2008) 107–114]
Authors: Ketevan Pachkoria, M. Isabel Lucena, Esperanza Crespo, Francisco Ruiz-Cabello, Susana Lopez-Ortega, Ma. Carmen Fernandez, Manuel Romero-Gomez, Ana Madrazo, Jose Antonio Durán, Ana Malcon de Dios, Yolanda Borraz, Jose Maria Navarro, Raúl J. Andrade
Journal: Journal of Hepatology (2009)
Activation of the Estrogen-Signaling Pathway by p21WAF1/CIP1 in Estrogen Receptor-Negative Breast Cancer Cells
Authors: Xiaomei Chen, Christopher Danes, Michael Lowe, Thaddeus W. Herliczek, Khandan Keyomarsi
Journal: JNCI Journal of the National Cancer Institute (2000)

Background: Estrogen stimulates the proliferation of cells in normal mammary glands and most estrogen receptor (ER)-positive mammary carcinomas by binding to the ER and promoting the transcription of ER-responsive genes. In cells with functional ERs, estrogen mediates the transition of cells from the G1 to S phase of the cell cycle. Several cell cycle regulatory proteins have been implicated in the ER-signaling pathway involved in estrogen-mediated growth stimulation and antiestrogen-mediated growth arrest. We sought to determine whether p21, a cyclin-dependent kinase inhibitor, is a component of this pathway and, if so, whether it can mediate estrogen's action in ER-negative breast cancer cells. Methods: We overexpressed p21 with a tetracycline-inducible system in ER-negative, p21-negative breast cancer cells. Activity of the ER-signaling pathway was monitored in transient transfection assays by using constructs in which the ER promoter or the estrogen-response element (ERE) controls Luciferase expression. The growth-modulating effects of estradiol and antiestrogens on p21-overexpressing clones were assessed. All P values are from two-sided tests. Results: A strong positive association was found between the expression of p21 and ER in nine breast cancer cell lines and in tumor samples from 60 patients with breast cancer (P<.001). Overexpression of p21 in a p21-negative, ER-negative cell line induced both the ER and ERE promoters in an estrogen-responsive manner. Last, stable p21 clones that also lack the expression of wild-type ER were responsive to the growth-inhibitory effects of ICI 182,780, a potent antiestrogen, and the growth-stimulatory effects of 17β-estradiol. Conclusion: The ability of p21 to mediate the activation of the estrogen-signaling pathway in ER-negative tumor cells suggests that p21 plays a novel role in this pathway, a finding that also has important clinical implications.
AXL Is an Essential Factor and Therapeutic Target for Metastatic Ovarian Cancer
Authors: Erinn B. Rankin, Katherine C. Fuh, Tiffany E. Taylor, Adam J. Krieg, Margaret Musser, Jenny Yuan, Kevin Wei, Calvin J. Kuo, Teri A. Longacre, Amato J. Giaccia
Journal: Cancer Research (2010)

The receptor tyrosine kinase AXL is thought to play a role in metastasis; however, the therapeutic efficacy of an AXL-targeting agent remains largely untested in metastatic disease. In this study, we defined AXL as a therapeutic target for metastatic ovarian cancer. AXL is primarily expressed in metastases and advanced-stage human ovarian tumors but not in normal ovarian epithelium. Genetic inhibition of AXL in human metastatic ovarian tumor cells is sufficient to prevent the initiation of metastatic disease in vivo. Mechanistically, inhibition of AXL signaling in animals with metastatic disease results in decreased invasion and matrix metalloproteinase activity. Most importantly, soluble human AXL receptors that imposed a specific blockade of the GAS6/AXL pathway had a profound inhibitory effect on progression of established metastatic ovarian cancer without normal tissue toxicity. These results offer the first genetic validation of GAS6/AXL targeting as an effective strategy for inhibition of metastatic tumor progression in vivo. Furthermore, this study defines the soluble AXL receptor as a therapeutic candidate agent for treatment of metastatic ovarian cancer, for which current therapies are ineffective.
Phase I Trial of a Glypican-3–Derived Peptide Vaccine for Advanced Hepatocellular Carcinoma: Immunologic Evidence and Potential for Improving Overall Survival
Authors: Yu Sawada, Toshiaki Yoshikawa, Daisuke Nobuoka, Hirofumi Shirakawa, Toshimitsu Kuronuma, Yutaka Motomura, Shoichi Mizuno, Hiroshi Ishii, Kohei Nakachi, Masaru Konishi, Toshio Nakagohri, Shinichiro Takahashi, Naoto Gotohda, Tadatoshi Takayama, Kenji Yamao, Katsuhiko Uesaka, Junji Furuse, Taira Kinoshita, Tetsuya Nakatsura
Journal: Clinical Cancer Research (2012)

The carcinoembryonic antigen glypican-3 (GPC3) is an ideal target of anticancer immunotherapy against hepatocellular carcinoma (HCC). In this nonrandomized, open-label, phase I clinical trial, we analyzed the safety and efficacy of GPC3 peptide vaccination in patients with advanced HCC.Thirty-three patients with advanced HCC underwent GPC3 peptide vaccination (intradermal injections on days 1, 15, and 29 with dose escalation). The primary endpoint was the safety of GPC3 peptide vaccination. The secondary endpoints were immune response, as measured by IFN-γ ELISPOT assay, and the clinical outcomes tumor response, time to tumor progression, and overall survival (OS).GPC3 vaccination was well-tolerated. One patient showed a partial response, and 19 patients showed stable disease 2 months after initiation of treatment. Four of the 19 patients with stable disease had tumor necrosis or regression that did not meet the criteria for a partial response. Levels of the tumor markers α-fetoprotein and/or des-γ-carboxy prothrombin temporarily decreased in nine patients. The GPC3 peptide vaccine induced a GPC3-specific CTL response in 30 patients. Furthermore, GPC3-specific CTL frequency after vaccination correlated with OS. OS was significantly longer in patients with high GPC3-specific CTL frequencies (N = 15) than in those with low frequencies (N = 18; P = 0.033).GPC3-derived peptide vaccination was well-tolerated, and measurable immune responses and antitumor efficacy were noted. This is the first study to show that peptide-specific CTL frequency can be a predictive marker of OS in patients with HCC receiving peptide vaccination.
Cry j 2, a major allergen of Japanese cedar pollen, shows polymethylgalacturonase activity
Authors: T. Ohtsuki, Y. Taniauchi, K. Kohno, S. Fukuda, M. Usui, M. Kurimoto
Journal: Allergy (1995)

We examined Cry j 2, a major allergen of Japanese cedar (Cryptomeria japonica) pollen, for polygalacturonase enzyme activity, since a nucleotide sequence of cDNA of Cry j 2 showed a significant homology with that of tomato polygalacturonase. Polygalacturonase is well known to depolymerize preferentially polygalacturonic acid (PGA) by hydrolysis. However, Cry j 2 did not act on PGA, but was found to depolymerize pectin and methylesterified PGA in a dose-dependent manner. The substrate specificity of Cry j 2 was different from that of polygalacturonase derived from Aspergillus niger. The depolymerizing activity of Cry j 2 reached a maximum at 50%-60% of methylesterification of PGA. In contrast, polygalacturonase showed its maximum activity of PGA, and the activity decreased as the degree of methylesterification increased. Interestingly, the pectin-depolymerizing activity of Cry j 2 was due to a hydrolysis, but not a lyase, activity which splits the glycosidic bonds by beta-elimination, since no unsaturated uronides were found by measurement of absorbance at 235 nm in the reaction mixture. The enzyme activity was markedly inhibited by anti-Cry j 2 antibodies. These results indicate that Cry j 2 probably has polymethylgalacturonase enzyme activity, as postulated by von Neukom in 1963, although existence of this activity has not yet been proven.
Benefits and Costs of Interventions to Improve Breast Cancer Outcomes in African American Women
Authors: Jeanne S. Mandelblatt, Clyde B. Schechter, K. Robin Yabroff, William Lawrence, James Dignam, Peter Muennig, Yoko Chavez, Jennifer Cullen, Marianne Fahs
Journal: Journal of Clinical Oncology (2004)

Purpose Historically, African American women have experienced higher breast cancer mortality than white women, despite lower incidence. Our objective was to evaluate whether costs of increasing rates of screening or application of intensive treatment will be off-set by survival benefits for African American women. Methods We use a stochastic simulation model of the natural history of breast cancer to evaluate the incremental societal costs and benefits of status quo versus targeted biennial screening or treatment improvements among African Americans 40 years of age and older. Main outcome measures were number of mammograms, stage, all-cause mortality, and discounted costs per life year saved (LYS). Results At the current screening rate of 76%, there is little incremental benefit associated with further increasing screening, and the costs are high: $124,053 and $124,217 per LYS for lay health worker and patient reminder interventions, respectively, compared with the status quo. Using reminders would cost $51,537 per LYS if targeted to virtually unscreened women or $78,130 per LYS if targeted to women with a two-fold increase in baseline risk. If all patients received the most intensive treatment recommended, costs increase but deaths decrease, for a cost of $52,678 per LYS. Investments of up to $6,000 per breast cancer patient could be used to enhance treatment and still yield cost-effectiveness ratios of less than $75,000 per LYS. Conclusion Except in pockets of unscreened or high-risk women, further investments in interventions to increase screening are unlikely to be an efficient use of resources. Ensuring that African American women receive intensive treatment seems to be the most cost-effective approach to decreasing the disproportionate mortality experienced by this population.