tbuckley/cabot-search huggingface dataset:
Coevolution between Stop Codon Usage and Release Factors in Bacterial Species
Authors: Yulong Wei, Juan Wang, Xuhua Xia
Journal: Molecular Biology and Evolution (2016)

Three stop codons in bacteria represent different translation termination signals, and their usage is expected to depend on their differences in translation termination efficiency, mutation bias, and relative abundance of release factors (RF1 decoding UAA and UAG, and RF2 decoding UAA and UGA). In 14 bacterial species (covering Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria and Spirochetes) with cellular RF1 and RF2 quantified, UAA is consistently over-represented in highly expressed genes (HEGs) relative to lowly expressed genes (LEGs), whereas UGA usage is the opposite even in species where RF2 is far more abundant than RF1. UGA usage relative to UAG increases significantly with PRF2 [=RF2/(RF1 + RF2)] as expected from adaptation between stop codons and their decoders. PRF2 is > 0.5 over a wide range of AT content (measured by PAT3 as the proportion of AT at third codon sites), but decreases rapidly toward zero at the high range of PAT3 This explains why bacterial lineages with high PAT3 often have UGA reassigned because of low RF2. There is no indication that UAG is a minor stop codon in bacteria as claimed in a recent publication. The claim is invalid because of the failure to apply the two key criteria in identifying a minor codon: (1) it is least preferred by HEGs (or most preferred by LEGs) and (2) it corresponds to the least abundant decoder. Our results suggest a more plausible explanation for why UAA usage increases, and UGA usage decreases, with PAT3, but UAG usage remains low over the entire PAT3 range.
A calcium- and calpain-dependent pathway determines the response to lenalidomide in myelodysplastic syndromes
Authors: Jing Fang, Xiaona Liu, Lyndsey Bolanos, Brenden Barker, Carmela Rigolino, Agostino Cortelezzi, Esther N Oliva, Maria Cuzzola, H Leighton Grimes, Celia Fontanillo, Kakajan Komurov, Kyle MacBeth, Daniel T Starczynowski
Journal: Nature Medicine (2016)
HG-11BRAF V600E MUTATION IN PEDIATRIC ASTROBLASTOMAS
Authors: Manila Antonelli, Paolo Nizza, Marina P. Gardiman, Francesca R. Buttarelli, Michele Cerati, Claudia Milanaccio, Antonella Coli, Maura Massimino, Bianca Pollo, Loredana Moi, Manuela Badiali, Felice Giangaspero
Journal: Neuro-Oncology (2016)
Therapy-related leukemia: what is the role of 4-epi-doxorubicin?
Authors: M Riggi, A Riva
Journal: Journal of Clinical Oncology (1993)

Article Tools Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.1993.11.7.1430 Journal of Clinical Oncology - published online before print September 21, 2016 PMID: 8315440 Therapy-related leukemia: what is the role of 4-epi-doxorubicin? M RiggixM RiggiSearch for articles by this author , A RivaxA RivaSearch for articles by this author https://doi.org/10.1200/JCO.1993.11.7.1430 PDF "Therapy-related leukemia: what is the role of 4-epi-doxorubicin?." Journal of Clinical Oncology, 11(7), pp. 1430–1431© 1993 by American Society of Clinical Oncology
Case 5-1968
Authors: Vincent P. Perlo, Martin H. Flax, Jay P. Mohr
Journal: New England Journal of Medicine (1968)

Presentation of Case First admission. A thirty-four-year-old woman was admitted to the hospital because of weakness and difficulty in swallowing.Ten years previously she had had an episode of hematuria associated with the development of an erythematous, macular and papular rash over the arms. Intermittent proteinuria was detected; a Wassermann test and repeated L.E.-cell tests were positive. Five years before entry ptosis of the eyelids and diplopia occurred. A year before admission there was the onset of intermittent left-sided pleuritic pain and recurrent polyarthralgia, accompanied by difficulty in swallowing and talking and marked myasthenia. The myasthenia increased in severity despite . . .
Sexual transmission of Zika virus in an entirely asymptomatic couple returning from a Zika epidemic area, France, April 2016
Authors: Thomas Fréour, Sophie Mirallié, Bruno Hubert, Carole Splingart, Paul Barrière, Marianne Maquart, Isabelle Leparc-Goffart
Journal: Eurosurveillance (2016)

The current Zika virus outbreak and its potential severe health consequences, especially congenital fetal syndrome, have led to increased concern about sexual transmission, especially in pregnant women and women of reproductive age. Here we report a case of Zika virus sexual transmission, likely male-to-female, in a totally asymptomatic couple.
E-cadherin and APC expression in normal-appearing rectal mucosa between cases of incident, sporadic colorectal adenomatous polyps and healthy controls in the Markers of Adenomatous Polyp II (MAPII) case-control study
Authors: Ahearn Thomas, Aasma Shaukat-Bhatti, Chiranjeev Dash, Roberd Bostick
Journal: Cancer Research (2007)

1711   Colorectal cancer is the second leading cause of cancer deaths in the United States. Despite advances in screening methods and treatments, mortality attributed to the disease has declined minimally over the last 30 years. There are no accepted biomarkers of risk for colorectal cancer even though the molecular basis of the disease is becoming clearer. E-cadherin, a calcium-dependent cell-cell adhesion transmembrane glycoprotein, is essential for maintaining cellular organization. APC gene mutation has been repeatedly shown to be one of the earliest events in colon carcinogenesis. E-cadherin and APC are suspected of being able to modulate each other by competing for binding to β-catenin. In a colonoscopy-based, pilot case-control study (n = 49 cases, 154 controls) to investigate E-cadherin and APC expression as possible biomarkers of risk for colorectal cancer, biopsies from normal-appearing mucosa from a random selection of 22 cases and 22 controls were immunohistochemically processed for E-cadherin and APC. The expression of E-cadherin and APC as assessed by staining intensity was quantified using a novel image analysis program. Mean overall expression of neither APC nor E-cadherin differed substantially between cases and controls (-0.5%, [p = 0.81], and -4.6% [p = 0.40], respectively). The ratio of E-cadherin/APC expression was 12.5% higher in cases than controls (p = 0.26). The crude odds ratios (OR) for the associations of E-cadherin, APC, and the E-cadherin/APC ratio with adenomas were 1.44 (95% confidence interval [CI] 0.44 - 4.76), 0.38 (CI 0.11 - 1.32), and 4.50 (CI 1.15 - 17.68), respectively. The association of the E-cadherin/APC ratio with adenomas, controlling for sex, family history of colorectal cancer, and fiber intake was 16.67 (CI 2.36 - 117.97, p = 0.005). Among persons with a higher fat intake, the E-cadherin/APC ratio was greater in cases (OR 8.88; CI 1.92 - 41.05; p = 0.005). Although the expression of either E-cadherin or APC alone may be insufficient as biomarkers of risk for colorectal cancer, our preliminary data suggest that the ratio of E-cadherin/APC expression may be a valid indicator of risk and needs further investigation.
HG-41OUTCOMES FOR PATIENTS WITH RECURRENT MALIGNANT GLIOMA ENROLLED ON PHASE II CLINICAL TRIALS: AN ANALYSIS OF CONTEMPORARY CHILDREN'S ONCOLOGY GROUP (COG) AND PEDIATRIC BRAIN TUMOR CONSORTIUM (PBTC) TRIALS
Authors: Eugene Hwang, Catherine Billups, Arzu Onar-Thomas, Sridharan Gururangan, Katherine Warren, Oren Beaty, Anne Warwick, Tobey Macdonald, Roger Packer, Amar Gajjar, Maryam Fouladi
Journal: Neuro-Oncology (2016)
SUDDEN AND UNEXPECTED DEATH
Authors: A K Mant
Journal: JAMA (1935)

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
Carcinogenicity of drinking coffee, mate, and very hot beverages
Authors: Dana Loomis, Kathryn Z Guyton, Yann Grosse, Béatrice Lauby-Secretan, Fatiha El Ghissassi, Véronique Bouvard, Lamia Benbrahim-Tallaa, Neela Guha, Heidi Mattock, Kurt Straif
Journal: The Lancet Oncology (2016)
Case 59-1964
Authors: Edwin W. Salzman, Benjamin Castleman
Journal: New England Journal of Medicine (1964)

Presentation of Case First admission. An eighty-eight-year-old woman was admitted to the hospital because of abdominal pain.Three weeks previously she experienced the onset of nausea, anorexia and pain that was vaguely localized to the epigastrium and the right upper quadrant of the abdomen. Two days before admission chilliness occurred. She had recently lost an unknown amount of weight.Eight years before entry she was given digitalis because of congestive heart failure. Three years later her physician advised her to omit fatty foods because of abdominal pain after meals. There was no history of vomiting, change in bowel habit, melena, . . .
Extrapyramidal side effects in lithium maintenance therapy
Authors: M H Branchey, J Charles, G M Simpson
Journal: American Journal of Psychiatry (1976)

The authors neurologically examined 36 patients who had been maintained on lithium therapy for periods ranging from 6 months to 7 years to determine the presence of parkinson-like side effects. Only a few patients demonstrated rigidity, including cogweel rigidity, and this was at a low level of severity. These results do not support the previously reported frequent occurrence of cogwheel rigidity in patients on lithium maintenance.
Reduction of distress in hyperprolactinemia with bromocriptine
Authors: M T Buckman, R Kellner
Journal: American Journal of Psychiatry (1985)

In a double-blind placebo-controlled crossover study of bromocriptine in eight hyperprolactinemic patients, self-rated distress decreased and well-being increased parallel with the fall in prolactin levels; for the majority of measures the differences were significant.
Host Influence on Homoplastic Skin Grafts in Inbred Mice&lt;xref ref-type="fn" rid="FN1"&gt;2&lt;/xref&gt;&lt;xref ref-type="fn" rid="FN2"&gt;3&lt;/xref&gt;
Authors: A G LIEBELT
Journal: JNCI Journal of the National Cancer Institute (1957)

Journal Article Host Influence on Homoplastic Skin Grafts in Inbred Mice Get access Annabel G. Liebelt Annabel G. Liebelt Departments of Anatomy, Baylor University College of Medicine, Texas Medical Center, Houston, Texas, and University of Illinois College of Medicine, Chicago, Illinois Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 18, Issue 2, February 1957, Pages 209–215, https://doi.org/10.1093/jnci/18.2.209 Published: 01 February 1957 Article history Received: 03 July 1956 Published: 01 February 1957
MB-16NOTCH1 PROMOTES GROUP 3 MEDULLOBLASTOMA METASTASIS, INITIATION AND SELF-RENEWAL
Authors: Suzana Assad Kahn, Xin Wang, Ryan Nitta, Sharareh Gholamin, Vijay Ramaswamy, Tej Azad, Debashis Sahoo, Rogelio Esparza, Pauline Chu, Paul Fisher, Hannes Vogel, Gordon Li, Yoon-Jae Cho, Michael Taylor, Siddhartha Mitra, Irving Weissman, Samuel Cheshier
Journal: Neuro-Oncology (2016)
The Appearance and Disappearance of Antibodies to Rous Virus in Normal Chickens&lt;xref ref-type="fn" rid="FN1"&gt;2&lt;/xref&gt;
Authors: F. B. Bang, R. Haley
Journal: JNCI Journal of the National Cancer Institute (1958)

The Appearance and Disappearance of Antibodies to Rous Virus in Normal Chickens Get access F. B. Bang, F. B. Bang Department of Patho-biology, The Johns Hopkins University School of Hygiene and Public Health, Baltimore, Maryland Search for other works by this author on: Oxford Academic PubMed Google Scholar R. Haley R. Haley Department of Patho-biology, The Johns Hopkins University School of Hygiene and Public Health, Baltimore, Maryland Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 20, Issue 2, February 1958, Pages 329–338, https://doi.org/10.1093/jnci/20.2.329 Published: 01 February 1958 Article history Received: 19 July 1957 Published: 01 February 1958
Epidemic Neuromyasthenia
Authors: Alexis Shelokov, Karl Habel, Elizabeth Verder, William Welsh
Journal: New England Journal of Medicine (1957)

IN July, 1953, a sharp outbreak of a disease, which at first was thought to be poliomyelitis, occurred among student and supervisor nurses of a private psychiatric hospital near Washington, D. C. In a typical severe case the early manifestations included localized muscular weakness, stiffness of the neck and back, headache, diarrhea and temperature elevation. Within a few days it became apparent that the epidemiologic features and the course of the illness were not compatible with poliomyelitis and that we were dealing with an entity unknown to us. Before the few additional cases occurred in September among the newly arrived . . .
Ventricular enlargement in child psychiatric patients: a controlled study with planimetric measurements
Authors: D Reiss, C Feinstein, D R Weinberger, R King, R J Wyatt, D Brallier
Journal: American Journal of Psychiatry (1983)

Data from adult schizophrenic patients suggest that patients with enlarged ventricles have a poorer premorbid history and may have an earlier onset of their illness than patients with ventricles of normal size. The authors examined a group of child psychiatric patients to discover whether these children at risk for major psychopathology had enlarged ventricles. Twenty psychiatric patients showed significantly enlarged ventricles compared with 19 control patients. There were no clear relationships between the children's psychiatric diagnosis and ventricular size.
Trainee doctors could be taken out of London hospital emergency department
Authors: Clare Dyer
Journal: BMJ (2016)

A London hospital’s accident and emergency unit is being threatened with closure on safety grounds by the bodies responsible for approving and organising junior doctors’ training, for the first time in NHS history.

The General Medical Council is so worried about the risk to the safety of patients from the shortage of senior and middle grade emergency doctors at North Middlesex Hospital in north London that it has used its powers for the first time to issue a “pre-statutory letter,” warning that it could withdraw approval for junior doctors to be trained at the unit.

The letter was sent on 21 May to Health Education England, which arranges training posts. In the …
Prescription of Long-Acting Opioids and Mortality in Patients With Chronic Noncancer Pain
Authors: Wayne A. Ray, Cecilia P. Chung, Katherine T. Murray, Kathi Hall, C. Michael Stein
Journal: JAMA (2016)

<h3>Importance</h3> Long-acting opioids increase the risk of unintentional overdose deaths but also may increase mortality from cardiorespiratory and other causes. <h3>Objective</h3> To compare all-cause mortality for patients with chronic noncancer pain who were prescribed either long-acting opioids or alternative medications for moderate to severe chronic pain. <h3>Design, Setting, and Participants</h3> Retrospective cohort study between 1999 and 2012 of Tennessee Medicaid patients with chronic noncancer pain and no evidence of palliative or end-of-life care. <h3>Exposures</h3> Propensity score–matched new episodes of prescribed therapy for long-acting opioids or either analgesic anticonvulsants or low-dose cyclic antidepressants (control medications). <h3>Main Outcomes and Measures</h3> Total and cause-specific mortality as determined from death certificates. Adjusted hazard ratios (HRs) and risk differences (difference in incidence of death) were calculated for long-acting opioid therapy vs control medication. <h3>Results</h3> There were 22 912 new episodes of prescribed therapy for both long-acting opioids and control medications (mean [SD] age, 48 [11] years; 60% women). The long-acting opioid group was followed up for a mean 176 days and had 185 deaths and the control treatment group was followed up for a mean 128 days and had 87 deaths. The HR for total mortality was 1.64 (95% CI, 1.26-2.12) with a risk difference of 68.5 excess deaths (95% CI, 28.2-120.7) per 10 000 person-years. Increased risk was due to out-of-hospital deaths (154 long-acting opioid, 60 control deaths; HR, 1.90; 95% CI, 1.40-2.58; risk difference, 67.1; 95% CI, 30.1-117.3) excess deaths per 10 000 person-years. For out-of-hospital deaths other than unintentional overdose (120 long-acting opioid, 53 control deaths), the HR was 1.72 (95% CI, 1.24-2.39) with a risk difference of 47.4 excess deaths (95% CI, 15.7-91.4) per 10 000 person-years. The HR for cardiovascular deaths (79 long-acting opioid, 36 control deaths) was 1.65 (95% CI, 1.10-2.46) with a risk difference of 28.9 excess deaths (95% CI, 4.6-65.3) per 10 000 person-years. The HR during the first 30 days of therapy (53 long-acting opioid, 13 control deaths) was 4.16 (95% CI, 2.27-7.63) with a risk difference of 200 excess deaths (95% CI, 80-420) per 10 000 person-years. <h3>Conclusions and Relevance</h3> Prescription of long-acting opioids for chronic noncancer pain, compared with anticonvulsants or cyclic antidepressants, was associated with a significantly increased risk of all-cause mortality, including deaths from causes other than overdose, with a modest absolute risk difference. These findings should be considered when evaluating harms and benefits of treatment.
The Sharing of Loss
Authors: Ranjana Srivastava
Journal: New England Journal of Medicine (2016)

Just as the Friday evening efflux of staff begins, a patient with cancer whom I saw only days ago is reported to be not quite right. She may not think so, but I have always liked her. At her first consult, she flatly refused to mention her weight in front of her husband, causing me to wonder if she feared he would leave her. Far from it — though she was significantly overweight, he said, “I love her just the way she is,” and I was touched by his ability to support her in the way she needed, then and . . .
Living Better or Living Longer? Perceptions of Patients (Pts) and Health Care Professionals (Hcp) in Oncology
Authors: D.A. Toloi, G. Critchi, A. Mangabeira, P.M. Hoff, F. Matsushita, E.D. Saad, R.P. Riechelmann
Journal: Annals of Oncology (2014)
Affective flattening and the criteria for schizophrenia
Authors: N C Andreasen
Journal: American Journal of Psychiatry (1979)

The author used a scale that emphasizes objective behavioral signs to evaluate affective flattening and to rate affect in 69 patients suffering from schizophrenia (N = 30), mania (N = 19), and depression (N = 20). Raters were blind to the patient's diagnosis. Interrater reliability was assessed and found to be adequate to good for most items on the scale and for a global rating. The affective flattening was found to be common, but not omnipresent, in schizophrenia; it was also common among the depressed patients. The author recommends that affective flattening be considered as an important criterion for schizophrenia and that future research explore its frequency and prognostic significance.
TB-20PRELIMINARY EXPERIENCE WITH WHOLE EXOME SEQUENCING FOR CHILDREN WITH CNS TUMORS
Authors: James Garvin, Richard Anderson, Neil Feldstein, Eileen Stark, Julia Glade Bender, Jennifer Oberg, Danielle Pendrick Denney, Peter Canoll, Mahesh Mansukhani, Andrew Kung
Journal: Neuro-Oncology (2016)

INTRODUCTION:The Precision in Pediatric Sequencing (PiPSeq) program at Columbia University was initiated in 2014, offering genomic sequencing for children with high-risk or recurrent cancers, including primary CNS tumors, the subject of this report.METHODS: After obtaining informed Overall survival
Mathematical Modeling of Cancer Immunotherapy and Its Synergy with Radiotherapy
Authors: Raphael Serre, Sebastien Benzekry, Laetitia Padovani, Christophe Meille, Nicolas André, Joseph Ciccolini, Fabrice Barlesi, Xavier Muracciole, Dominique Barbolosi
Journal: Cancer Research (2016)

Combining radiotherapy with immune checkpoint blockade may offer considerable therapeutic impact if the immunosuppressive nature of the tumor microenvironment (TME) can be relieved. In this study, we used mathematical models, which can illustrate the potential synergism between immune checkpoint inhibitors and radiotherapy. A discrete-time pharmacodynamic model of the combination of radiotherapy with inhibitors of the PD1-PDL1 axis and/or the CTLA4 pathway is described. This mathematical framework describes how a growing tumor first elicits and then inhibits an antitumor immune response. This antitumor immune response is described by a primary and a secondary (or memory) response. The primary immune response appears first and is inhibited by the PD1-PDL1 axis, whereas the secondary immune response happens next and is inhibited by the CTLA4 pathway. The effects of irradiation are described by a modified version of the linear-quadratic model. This modeling offers an explanation for the reported biphasic relationship between the size of a tumor and its immunogenicity, as measured by the abscopal effect (an off-target immune response). Furthermore, it explains why discontinuing immunotherapy may result in either tumor recurrence or a durably sustained response. Finally, it describes how synchronizing immunotherapy and radiotherapy can produce synergies. The ability of the model to forecast pharmacodynamic endpoints was validated retrospectively by checking that it could describe data from experimental studies, which investigated the combination of radiotherapy with immune checkpoint inhibitors. In summary, a model such as this could be further used as a simulation tool to facilitate decision making about optimal scheduling of immunotherapy with radiotherapy and perhaps other types of anticancer therapies. Cancer Res; 76(17); 4931-40. ©2016 AACR.