tbuckley/cabot-search huggingface dataset:
Unraveling the clonal hierarchy of somatic genomic aberrations
Authors: Davide Prandi, Sylvan C Baca, Alessandro Romanel, Christopher E Barbieri, Juan-Miguel Mosquera, Jacqueline Fontugne, Himisha Beltran, Andrea Sboner, Levi A Garraway, Mark A Rubin, Francesca Demichelis
Journal: Genome biology (2014)

Abstract Defining the chronology of molecular alterations may identify milestones in carcinogenesis. To unravel the temporal evolution of aberrations from clinical tumors, we developed CLONET, which upon estimation of tumor admixture and ploidy infers the clonal hierarchy of genomic aberrations. Comparative analysis across 100 sequenced genomes from prostate, melanoma, and lung cancers established diverse evolutionary hierarchies, demonstrating the early disruption of tumor-specific pathways. The analyses highlight the diversity of clonal evolution within and across tumor types that might be informative for risk stratification and patient selection for targeted therapies. CLONET addresses heterogeneous clinical samples seen in the setting of precision medicine.
Privacy of Patient's Records
Authors: Hugh H. Hussey
Journal: JAMA (1973)

Transactions between physician and patient, as written in the patient's record or stored in the physician's mind, have traditionally enjoyed the utmost privacy. Indeed the<i>Oath of Hippocrates</i>states in part: "WHATEVER, in connection with my professional practice, or not in connection with it, I may see or hear in the lives of men which ought not to be spoken abroad I will not divulge, as reckoning that all such should be kept secret." And, in the<i>Daily Prayer of Maimonides</i>: "Grant that my patients may have confidence in me and my art..." True, there are certain legal processes that require a physician to depart from the principle of privacy—reporting of contagious diseases and gunshot or knife wounds—and the patient may waive the principle, for example, when it is to his advantage in a law suit. Recently, however, there have been reports of flagrant, unethical violations of a patient's privacy.
Abstract 844: No Clear Association Between Candidate Gene Variants and Outcomes in 3239 Patients with Chronic Heart Failure: Results from the CHARM Program
Authors: Christopher B Granger, Peter Sinnaeve, Olof Bengtsson, John J McMurray, Eric L Michelson, Marc A Pfeffer, Karl Swedberg, Salim Yusuf, Melissa Thornton, Martin Armstrong, Robert Roberts
Journal: Circulation (2008)
Neurodevelopmental Outcomes of Premature Infants Treated with Inhaled Nitric Oxide
Authors: Karen K.L. Mestan, Jeremy D. Marks, Kurt Hecox, Dezheng Huo, Michael D. Schreiber
Journal: New England Journal of Medicine (2005)

Chronic lung disease and severe intraventricular hemorrhage or periventricular leukomalacia in premature infants are associated with abnormal neurodevelopmental outcomes. In a previous randomized, controlled, single-center trial of premature infants with the respiratory distress syndrome, inhaled nitric oxide decreased the risk of death or chronic lung disease as well as severe intraventricular hemorrhage and periventricular leukomalacia. We hypothesized that infants treated with inhaled nitric oxide would also have improved neurodevelopmental outcomes.We conducted a prospective, longitudinal follow-up study of premature infants who had received inhaled nitric oxide or placebo to investigate neurodevelopmental outcomes at two years of corrected age. Neurologic examination, neurodevelopmental assessment, and anthropometric measurements were made by examiners who were unaware of the children's original treatment assignment.A total of 138 children (82 percent of survivors) were evaluated. In the group given inhaled nitric oxide, 17 of 70 children (24 percent) had abnormal neurodevelopmental outcomes, defined as either disability (cerebral palsy, bilateral blindness, or bilateral hearing loss) or delay (no disability, but one score of less than 70 on the Bayley Scales of Infant Development II), as compared with 31 of 68 children (46 percent) in the placebo group (relative risk, 0.53; 95 percent confidence interval, 0.33 to 0.87; P=0.01). This effect persisted after adjustment for birth weight and sex, as well as for the presence or absence of chronic lung disease and severe intraventricular hemorrhage or periventricular leukomalacia. The improvement in neurodevelopmental outcome in the group given inhaled nitric oxide was primarily due to a 47 percent decrease in the risk of cognitive impairment (defined by a score of less than 70 on the Bayley Mental Developmental Index) (P=0.03).Premature infants treated with inhaled nitric oxide have improved neurodevelopmental outcomes at two years of age.
Comparison of two high dose corticosteroid aerosol treatments, beclomethasone dipropionate (1500 micrograms/day) and budesonide (1600 micrograms/day), for chronic asthma.
Authors: P Ebden, A Jenkins, G Houston, B H Davies
Journal: Thorax (1986)

Twenty eight patients with chronic asthma took part in a double blind single crossover controlled trial of inhaled budesonide and inhaled beclomethasone dipropionate, using high doses of 1600 micrograms and 1500 micrograms daily respectively. Both drugs were administered by pressurised aerosol inhaler; the inhaler containing budesonide and its matching placebo were fitted with a collapsible spacer device. There was no significant difference in the control of asthma during the two six week treatment periods. There was no significant difference in FEV1 and forced vital capacity after four and six weeks of treatment or in mean morning and evening peak expiratory flow rates for the last 21 days of treatment. There was a small but statistically significant reduction in the daytime wheeze score while they were taking high dose budesonide but there was no difference for daytime activity, cough, and night symptoms. The mean basal cortisol concentrations were significantly lower after six weeks of high dose treatment than before treatment (budesonide p less than 0.01, beclomethasone p less than 0.05). There was no difference between mean basal cortisol values after six weeks of high dose treatment, and there was no effect on the rise of cortisol obtained after a short tetracosactrin test. High dose inhaled corticosteroids produced few side effects and were well tolerated.
Flawed interpretative strategies for lung function tests harm patients
Authors: P. Enright
Journal: European Respiratory Journal (2006)

To the Editors: 

“The devil's in the details” of the new American Thoracic Society (ATS)/European Respiratory Society (ERS) document regarding the interpretation of pulmonary function test (PFT) results 1. As a member of the Task Force, I was happy for the opportunity to help standardise the way in which clinically important PFTs are performed and interpreted. Unfortunately, the group spent almost all of the 3 yrs reaching an agreement (or compromise) on the mechanics of making accurate spirometry, diffusing capacity of the lung for carbon monoxide and lung volume measurements, but left inadequate time to thoroughly discuss the more important but controversial aspects of …
Nitrogen Versatility in Bats, Bears and Man
Authors: George F. Cahill
Journal: New England Journal of Medicine (1974)

The limits of nitrogen excretion and conservation by normal man continue to provoke interest for economic, anthropologic and medical reasons. Rudman et al.1 have recently shown that the maximum rate of urea synthesis is such that if man ate protein alone, he could barely meet his basal daily caloric needs, unless a chronic high protein intake induced an increase in urea synthetic capacity. Nuzum and Snodgrass2 have shown that such an increase occurs in protein-fed primates, and Snodgrass (personal communication) has suggested glucagon may be the inducer of the increase in urea-synthetic capacity. Normal man's relative rate of urea synthesis . . .
We need to address the issue of "mild troponinaemia"
Authors: M. S Parmar
Journal: BMJ (2009)

The new definition of myocardial infarction (MI) is timely but does not address the main issue of mild troponinaemia and overdiagnosis.1 2 Slight increases in troponin are often seen in patients with multiple comorbid conditions such as diabetes and heart or kidney failure who present with dyspnoea, infections such as pneumonia, exacerbation …
<i>HFE</i> Genotype, Particulate Air Pollution, and Heart Rate Variability
Authors: Sung Kyun Park, Marie S. O’Neill, Robert O. Wright, Howard Hu, Pantel S. Vokonas, David Sparrow, Helen Suh, Joel Schwartz
Journal: Circulation (2006)

Particulate air pollution has been associated with cardiovascular mortality and morbidity. Transition metals such as iron bound to the particles may be responsible for those associations. The protein product of the hemochromatosis (HFE) gene modulates uptake of iron and divalent cations from pulmonary sources and reduces their toxicity. Two HFE polymorphisms (C282Y and H63D) associated with increased iron uptake may modify the effect of metal-rich particles on the cardiovascular system.We investigated the association between particulate matter < or = 2.5 microm in aerodynamic diameter and heart rate variability in 518 older men from the Normative Aging Study who were examined between November 2000 and December 2004. Linear regression models were fit to evaluate interactions between HFE genotype and particulate matter < or = 2.5 microm in aerodynamic diameter in relation to heart rate variability, controlling for potential confounders. A 10-microg/m3 increase in particulate matter < or = 2.5 microm in aerodynamic diameter during the 48 hours before heart rate variability measurement was associated with a 31.7% (95% CI, 10.3% to 48.1%) decrease in the high-frequency component of heart rate variability in persons with the wild-type genotype, whereas no relationship in the high-frequency component was observed in persons with either HFE variant. The difference in effect of particulate matter < or = 2.5 microm in aerodynamic diameter on the high-frequency component between persons with and without HFE variants was significant (P for interaction=0.02).The effect of particles on cardiac autonomic function was shielded in subjects with at least 1 copy of an HFE variant compared with wild-type subjects. Transition metals, including iron, bound to ambient particles and the related oxidative stress may play an important role in cardiac toxicity of particles.
Bridging Antiplatelet Therapy With Cangrelor in Patients Undergoing Cardiac Surgery
Authors: Dominick J. Angiolillo, Michael S. Firstenberg, Matthew J. Price, Pradyumna E. Tummala, Martin Hutyra, Ian J. Welsby, Michele D. Voeltz, Harish Chandna, Chandrashekhar Ramaiah, Miroslav Brtko, Louis Cannon, Cornelius Dyke, Tiepu Liu, Gilles Montalescot, Steven V. Manoukian, Jayne Prats, Eric J. Topol, for the BRIDGE Investigators
Journal: JAMA (2012)

UAL ANTIPLATELET THERAPYwith aspirin and an oral P2Y 12 receptor inhibitor is the standard of care to prevent the short-and long-term risk of recurrent atherothrombotic events in high-risk settings, such as patients with an acute coronary syndrome (ACS) and those undergoing percutaneous coronary intervention (PCI). 1-4However, the ischemic benefit associated with more intense platelet blockade in these highrisk settings occurs at the expense of an increased risk of bleeding complications.Given that the risk of bleeding is significantly increased among
Clinicopathology of kidneys from brain-dead patients treated with vasopressin and epinephrine
Authors: Tomofumi Nagareda, Yoshihiro Kinoshita, Akira Tanaka, Masashi Takeda, Tsutomu Sakano, Kohei Yawata, Tsuyoshi Sugimoto, Yasuko Nishizawa, Nobuyuki Terada
Journal: Kidney International (1993)
Authors' reply to de Vries
Authors: M. Lund, B. Pasternak, J. Wohlfahrt, M. Melbye
Journal: BMJ (2014)

We thank de Vries for his valuable comments about our study.1 2 He states that the finding of an incidence rate ratio of 29.8 (95% confidence interval 16.4 to 54.1) for exposure from infant macrolide use during the first two weeks after birth is “either a very strong association or too good to be true.”

This association …
Antiretroviral therapy and the prevention of sexually transmitted HIV infection
Authors: G. W. Rutherford
Journal: BMJ (2011)

Early treatment in infected partners reduces transmission and improves clinical outcomes

Antiretroviral drugs have been used to prevent the transmission of HIV since the 1990s. The demonstration that zidovudine decreased the risk of HIV infection after percutaneous exposure,1 and success in prevention of mother to child transmission,2 have led to antiretrovirals being used for HIV prevention. However, transmission of HIV mostly occurs during sexual intercourse, and successes in this area have lagged behind. Prophylaxis after sexual exposure, although an established clinical practice,3 has not been evaluated in a randomised controlled trial. More recently, large well conducted trials demonstrated the effectiveness of pre-exposure prophylaxis of uninfected people, using tenofovir and emtricitabine or 1% tenofovir vaginal gel.4 5

Cohort studies suggested as early as 1994 that treating HIV infected patients with antiretroviral therapy (ART) would decrease the likelihood of them infecting their sexual partners. Seven cohort studies have examined this question in discordant couples, in which one sexual partner is infected with HIV and the other is not. A systematic review found that these studies had a pooled relative effect of 0.34 (95% confidence …
The Anatomic Atrial Connections Between Sinus and A-V Node
Authors: JOHN MERIDETH, JACK L. TITUS
Journal: Circulation (1968)

The morphology of the sinus and atrioventricular (A-V) nodes of human hearts was studied and connecting pathways between these nodes were sought. The cells of both nodes differed from ordinary atrial and ventricular myocardium in respect to size, shape, number, and arrangement of cytoplasmic organelles. Using the criteria of fiber-to-fiber connection, shown by means of serial histological sectioning, this study confirmed previous reports of three pathways between the sinus and A-V nodes in the human heart. It was not required that these pathways be composed of classic Purkinje-type fibers, though many of the fibers did possess some of the features of Purkinje fibers. While recent evidence reveals that specialized atrial pathways do demonstrate increased conduction velocity, their prime functional significance may be in the facilitation of orderly atrial depolarization, the maintenance of sinus node control of ventricular depolarization under various physiological conditions, and the provision of an orderly "input" into the A-V node, a tissue generally acknowledged to have a low margin of safety.
Trauma Surgeons: Primary Care Practitioners by Default
Authors: Charles C. Wiles
Journal: JAMA (1993)

<h3>To the Editor.</h3> —The current national government has redirected the focus of the American health care system to primary care. Preventive care and first-contact patient care characterize the primary care medical specialties including family practice, general internal medicine, obstetrics/gynecology, general pediatrics, emergency medicine, and occupational medicine. Trauma surgery should be considered as a primary care specialty as well. The main cause of death and disability for people between the ages of 1 and 39 years is trauma. Nearly every citizen of the United States will be involved in a serious trauma event within his or her individual lifetime. The geriatric age group is the fastest growing segment of the trauma population and for many adolescents and young and middle-aged adults, trauma provokes their only interface with the health care system. Trauma is their index illness. Trauma is a disease of nights and weekends. Three quarters of patients present to trauma
The Role of Exposure to Phthalates from Polyvinyl Chloride Products in the Development of Asthma and Allergies: A Systematic Review and Meta-analysis
Authors: Jouni J.K. Jaakkola, Trudy L. Knight
Journal: Environmental Health Perspectives (2008)

Phthalates from polyvinyl chloride (PVC) plastics may have adverse effects on airways and immunologic systems, but the evidence has not been reviewed systematically.We reviewed the evidence for the role of exposure to phthalates from PVC products in the development of asthma and allergies.We conducted a Medline database search (1950 through May 2007) for relevant studies on the respiratory and allergic effects of exposure to phthalates from PVC products.We based this review on 27 human and 14 laboratory toxicology studies. Two mouse inhalation experiments indicated that mono-2-ethylhexyl phthalate (MEHP) has the ability to modulate the immune response to exposure to a coallergen. The data suggested a no observed effect level of 30 microg MEHP/m3, calculated to be below the estimated level of human exposure in common environments. Case reports and series (n = 9) identified and verified cases of asthma that were very likely caused by fumes emitted from PVC film. Epidemiologic studies in adults (n = 10), mostly small studies in occupational settings, showed associations between heated PVC fumes and asthma and respiratory symptoms; studies in children (n = 5) showed an association between PVC surface materials in the home and the risk of asthma [fixed-effects model: summary odds ratio (OR), 1.55; 95% confidence interval (CI), 1.18-2.05; four studies] and allergies (OR, 1.32; 95% CI, 1.09-1.60; three studies).High levels of phthalates from PVC products can modulate the murine immune response to a coallergen. Heated PVC fumes possibly contribute to development of asthma in adults. Epidemiologic studies in children show associations between indicators of phthalate exposure in the home and risk of asthma and allergies. The lack of objective exposure information limits the epidemiologic data.
Experimental atrioventricular block without thoracotomy: a new instrument
Authors: I. Babotai, R. Brownlee
Journal: Cardiovascular Research (1971)

Journal Article Experimental atrioventricular block without thoracotomy: a new instrument Get access I. Babotai, I. Babotai From Surgical Clinic A, University of Zürich, Switzerland Search for other works by this author on: Oxford Academic PubMed Google Scholar R. Brownlee R. Brownlee 1 From Surgical Clinic A, University of Zürich, Switzerland 1McLaughlin Travelling Fellow. University of Alberta Medical Center, Edmonton 61, Alberta, Canada. Search for other works by this author on: Oxford Academic PubMed Google Scholar Cardiovascular Research, Volume 5, Issue 3, July 1971, Pages 416–418, https://doi.org/10.1093/cvr/5.3.416 Published: 01 July 1971
Case of Concealed Accidental Uterine Haemorrhage
Authors: J. Audland
Journal: BMJ (1857)

sent for to visit Mrs. -M., oged 4'2, who expected her tenth confinement in tl]ree or four weeks.I learned on that and subsequent visits, that on the previous Wednesday night, soon after getting into bed, she became very faint and cold, and had a severe fit
F-18 FDG Uptake in Breast Infection and Inflammation
Authors: SIEMA M. B. BAKHEET, JOHN POWE, ALAA KANDIL, ADNAN EZZAT, ASSEM ROSTOM, JOHN AMARTEY
Journal: Clinical Nuclear Medicine (2000)

Purpose Whole-body fluorine-18 fluorodeoxyglucose (F-18 FDG) positron emission tomography (PET) scanning has been useful in the management of breast cancer. However, F-18 FDG uptake sometimes has been associated with benign breast disease. Four cases are reported of F-18 FDG breast uptake caused by infectious or inflammatory mastitis that mimics malignant disease. Methods and Results Two women had F-18 FDG whole-body scans for the evaluation of a large breast mass after inconlusive results of ultrasonography. In both cases, intense focal F-18 FDG breast uptake was noted that mimicked breast cancer. Histologic examination showed, in one patient, chronic granulomatous infiltration that likely represented tuberculous mastitis, because she showed a good clinical response to empirical anti-tuberculous treatment. The second patient had lactational changes associated with acute inflammation, and the culture grew Staphylococcus aureus. The breast mass completely disappeared 3 weeks after a course of antibiotic treatment. The other two patients had staging F-18 FDG PET scans 1 and 12 months after lumpectomy for breast carcinoma to detect residual, recurrent, or metastatic disease. Both scans showed a ring-like uptake in the involved breast, with superimposed intense focal uptake suggesting tumor necrosis centrally and malignant foci peripherally. In both cases, histologic examination revealed hemorrhagic inflammation secondary to postsurgical hematomas and no evidence of malignancy. Conclusion Acute or chronic infectious mastitis and postsurgical hemorrhagic inflammatory mastitis should be considered in patients who have a breast mass, especially those with a history of tenderness or surgery.
Animals in Research: The American Medical Association's Position
Authors: Robert A. Petersen
Journal: JAMA (1990)

To the Editor.—  I am a full-time academic physician and I basically support the use of animals in research to benefit both other animals and humans. However, I think that the American Medical Association has gone too far in supporting all forms of animal experimentation and testing. An example of this extreme position that the American Medical Association seems to be taking is the article by Loeb et al. 1 There are many forms of animal experimentation and use of animals for testing that are a needless waste of life and cause of animal suffering. I think the interests of bona fide medical research using animals would be better served if the American Medical Association did not indiscriminately support all uses of animals, however cruel and useless. I can see an analogy between the American Medical Association's position on animal testing and the National Rifle Association's position on gun
If Only Grown-ups Would Pay Attention
Authors: Kelly Lauren Sloane
Journal: JAMA (2013)

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
Kennedy and colleagues' reply
Authors: B. P Kennedy, I. Kawachi, D. Prothrow-Stith
Journal: BMJ (1996)

In the present study, we analysed 44 formalin fixed paraffin embedded (FFPE) from different solid tumours by adopting two different next generation sequencing platforms: GeneReader (QIAGEN, Hilden, Germany) and Ion Torrent (Thermo Fisher Scientific, Waltham, Massachusetts, USA). We highlighted a 100% concordance between the platforms. In addition, focusing on variant detection, we evaluated a very good agreement between the two tests (Cohen’s kappa=0.84) and, when taking into account variant allele fraction value for each variant, a very high concordance was obtained (Pearson’s r=0.94). Our results underlined the high performance rate of GeneReader on FFPE samples and its suitability in routine molecular predictive practice.