tbuckley/cabot-search huggingface dataset:
Abstract B1-12: RNA Architect: High performance tools to exhaustively detect cancer-specific structural events in RNA sequencing data
Authors: Roland Chrisitian Arnold, Andrej Rosic, Reid JP Hayes, Adam Shlien
Journal: Cancer Research (2015)

Abstract The transcriptomes of cancer cells differ structurally and numerically from normal tissue and between different types of cancer. However, a comprehensive large-scale analysis of structural transcriptomic events has been intractable so far due to computational limitations and the lack of an integrative software tool to detect a complete list of events. We developed an optimized computation pipeline, named RNA Architect, which enables the detection of such events from RNA sequencing data for thousands of cancer samples. RNA Architect detects events by discordant read pair and split-read analysis down to the resolution of individual breakpoints. Beside different kinds of fusion events (as in-frame, out of frame, fusions to intergenic regions), it reports a comprehensive overview of other transcriptional events including specific and novel splice-forms, inversions, cryptic and alternative splice sites, exon skips, exon re-usages, and early polyadenylation sites. In this poster, we describe the individual steps of the algorithm as well as our latest benchmarking results on a compilation of literature curated gene fusions: the approach shows a high sensitivity and recovers 92% of known fusion events. We also describe the post-processing of the data, which enables us to delineate relevant events from non-cancer specific ones and noise. We especially discuss optimizations implemented to run the software efficiently on a state of the art compute cluster. These optimizations enable the computation of a large amount of samples in a reasonable time frame (~ 8h on a 100 CPU system for the core split-read algorithm and ~3 hours for the discordant pair analysis on a 50 CPU system per sample). The high performance of the pipeline allows generating a comprehensive catalogue of all transcriptional events from large sets of cancer samples. RNA Architect is also fast enough to be used in time critical clinical settings as a potential diagnostic tool. Citation Format: Roland Chrisitian Arnold, Andrej Rosic, Reid JP Hayes, Adam Shlien. RNA Architect: High performance tools to exhaustively detect cancer-specific structural events in RNA sequencing data. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-12.
Post-transplant cyclophosphamide-based haplo-identical transplantation as alternative to matched sibling or unrelated donor transplantation for non-Hodgkin lymphoma: a registry study by the European society for blood and marrow transplantation
Authors: S Dietrich, H Finel, C Martinez, J Tischer, D Blaise, P Chevallier, L Castagna, N Milpied, A Bacigalupo, P Corradini, M Mohty, M Sanz, A Hausmann, S Montoto, S Robinson, A Boumendil, A Sureda, P Dreger
Journal: Leukemia (2016)
Syncope Following Orthotopic Heart Transplant
Authors: Jennifer M. Wright, Michael E. Field
Journal: JAMA Internal Medicine (2016)

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 Internal Medicine HomeNew OnlineCurrent IssueFor Authors Podcast 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) 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 Internal Medicine journal
Folliculocentric and Octagonal Scaly Papules
Authors: Justin P. Bandino, Michael C. Royer, Walter L. Rush
Journal: JAMA Dermatology (2016)

A woman in her early 50s presented with a 1- to 2-year history of outbreaks of mildly pruritic “flowers” on her skin occurring in crops of 3 to 4 on arms, legs, trunk, and buttocks that would last a few months before spontaneously resolving without scarring. What is your diagnosis?
English acute care trusts earned nearly £0.5bn from private patients in 2014-15
Authors: Gareth Iacobucci
Journal: BMJ (2015)

NHS hospital trusts in England earned almost £0.5bn (€0.7bn; $0.8bn) from treating private patients last year, a new analysis by The BMJ has found. But although the analysis found that the total amount of private income earned by hospital trusts in England has risen by around £50m in the past two years, it shows that this has remained broadly static as a proportion of trusts’ income from treating patients, at around 1.2%.

For the analysis The BMJ examined the annual accounts for 2014-15 of 129 foundation and non-foundation trusts. In total, these 129 trusts earned £498.9m from private patients in 2014-15, representing around 1.2% of their overall income from treating patients of £42.8bn.

This compared with a total of £474.1m from private patients in 2013-14 (also 1.2% of the total of £40.4bn) and £451.9m from private patients in 2012-13 (again 1.2% of the total of £38.5bn).

The static proportion of overall NHS income derived from private patients comes despite the Health and Social Care Act 2012 removing the previous cap that restricted most NHS foundation trusts from deriving …
Outbreak of norovirus infection in a hotel in Oslo, Norway, January 2011
Authors: B Guzman-Herrador, B  T Heier, E J Osborg, V H Nguyen, L Vold
Journal: Eurosurveillance (2011)

A total of 56 people were affected with gastroenteritis after attending a one-day meeting in a high-quality hotel in the centre of Oslo, Norway, at the end of January 2011. A complete outbreak investigation was carried out. The microbiological investigation confirmed that the outbreak was caused by norovirus. All participants at the meeting were invited by email to complete an online questionnaire asking for information on demographic data, symptoms and food consumption. The results of the epidemiological investigation of the food items served were inconclusive and the source and transmission route of this outbreak remains unclear. However, the environmental investigation highlighted several irregularities in the kitchen that may have enabled the spread of the virus. Specific cleaning procedures and rules were set up for the kitchen staff. As a consequence of this outbreak investigation, the hotel is planning to change its internal routine protocols, for example, samples of food items served at every meal during an event will be stored.
Endobronchial Pseudolymphoma associated with Sjögren's Syndrome
Authors: N Miyazaki, M Kido, A Kajiki, H Yamazaki, S Yoashihara, A Kuroiwa
Journal: Endoscopy (1989)

A case of pseudolymphoma occurring in a patient with Sjögren's syndrome is described. The lesion, which gave rise to intraluminal tumor masses in the airway, grew progressively, resulting in severe dyspnea. Treatment with prednisolone brought relief.
Treating Hypercholesterolemia
Authors: A S Brett
Journal: New England Journal of Medicine (1989)

AN unprecedented wave of enthusiasm for treating patients who have hypercholesterolemia has followed the publication of the findings of the Lipid Research Clinics trial and the Helsinki Heart Study.1 , 2 These studies have demonstrated that therapy with lipidlowering drugs plus attention to diet may reduce the incidence of some cardiovascular end points when asymptomatic middle-aged men with markedly elevated serum cholesterol levels are treated for five years or more. Because these results are congruent with the epidemiologic and experimental evidence that the serum cholesterol level is a coronary risk factor, many authorities consider the benefits of drug therapy to be unequivocal. . . .
Further Analysis of the Detailed Structure of Type B and C Particles<xref ref-type="fn" rid="FN1">1</xref>
Authors: Albert J. Dalton
Journal: JNCI Journal of the National Cancer Institute (1972)

The mouse mammary-tumor-virus (MTV) virion appears to develop in two different ways: by incorporation of an intracytoplasmic A particle into the forming bud, or by simultaneous development of the two layers of the nucleoid just under the plasma membrane during bud formation. In both ways free virions are produced that possess identical morphologic features: a centrally located nucleoid with an electron-lucent center, a distinct intermediate layer, and an outer envelope with spikes. Later changes, such as the development of pleomorphic forms, an apparent increase in fluid between the envelope and the intermediate layer, and increased density and condensation of the nucleoid with its displacement from the center of the virion, are considered to be aging phenomena. These phenomena may or may not be related to a loss of infectivity. Type-C virus virions usually develop at the surface of an infected cell by the simultaneous appearance of the two layers of the nucleoid in crescentic form under a bulging plasma membrane. From the beginning the substance of the inner part of the nucleoid of type-C viruses is more electron dense than that of the MTV and more electron dense than the intermediate layers of both types of viruses. Differences in the thickness and position of the intermediate layer make is possible to distinguish between the virions of Moloney leukemia virus (MLV) and ESP-I. Intermediate layers of the Rauscher leukemia-virus virion that grows in human embryonic kidney and Rauscher leukemia-virus virion grown in a mouse line (MLV-Rauscher in JLSV-5) appear to be identical and different from ESP-I. These results support the hypothesis that the intermediate layer of type-C viruses is virus specific, as is the capsid of DNA viruses and naked RNA viruses such as Reo, and is viral-genome not host-cell directed in its formation and structure.
Abstract IA24: Developing and deploying experimental models systems towards novel drug discovery in ovarian cancer.
Authors: Ronny Drapkin, Anna Budina, Yi Feng, Kai Doberstein
Journal: Clinical Cancer Research (2016)

Abstract Ovarian cancer carries significant mortality in the absence of effective methods for prevention and screening. Preventive salpingo-oophorectomy is currently the only method known to reduce the risk of ovarian cancer-related death. Histopathological analyses of these surgical specimens indicate that a high proportion of ovarian cancers in women at high risk and in the general population arise from the fallopian tube. This paradigm shift in our understanding of the cell of origin for the most common subtype of ovarian cancer, high-grade serous carcinoma, has sparked a major effort within the research community to develop new and robust model systems to study the fallopian tube epithelium, it susceptibility to neoplastic transformation, and opportunities for therapeutic intervention. These models include primary cell line cultures, fallopian tube-derived lines, epithelial-stromal co-cultures, genetically-engineered mouse models, and patient-derived tumor xenografts or ‘avatars’. There has also been a re-evaluation of the fidelity of established ovarian cancer cell lines and the need to develop new lines that represent the human disease. Critical to this effort is the need to go beyond genomics and critically evaluate the functional utility of new cell lines. The deploying of these new models is already have a profound effect on our ability to identify unique susceptibilities in ovarian cancer through genetic screens, chemical screens, and targeted approaches. In addition, the search for novel biomarkers that can play a role in early detection or prognostication is being re-defined by looking at the fallopian tube fimbria as the source. Citation Format: Ronny Drapkin, Anna Budina, Yi Feng, Kai Doberstein. Developing and deploying experimental models systems towards novel drug discovery in ovarian cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr IA24.
Benign Recurrent Intrahepatic Cholestasis
Authors: C J Liu, J H Kao, P J Chen, M Y Lai, T L Mao, T H Wang, D S Chen
Journal: JAMA (1963)

Benign recurrent intrahepatic cholestasis is a rare disorder of unknown etiology and has not yet been reported in Taiwan. We report a case with a typical clinical course. A 17-year-old Taiwanese boy had three episodes of pruritus and jaundice from February 1993 to July 1995, each lasting 3 to 4 months. Jaundice spontaneously subsided and he was symptom-free during periods of remission. A fourth episode of pruritus began in July 1995, with jaundice developing later and lasting for 3 months. Laboratory tests revealed direct hyperbilirubinemia. Endoscopic retrograde cholangiopancreatography showed normal intra- and extrahepatic biliary trees. Light microscopy of a liver biopsy sample revealed hepatocellular and canalicular cholestasis with bile retention in the Kupffer cells. Benign recurrent intrahepatic cholestasis was diagnosed after exclusion of other possible causes of jaundice. The patient made an uneventful recovery.
Possible Role of the Immune Response in the Stem Cell Depression Produced by Melphalan2
Authors: C. D. R. Dunn
Journal: JNCI Journal of the National Cancer Institute (1974)

Journal Article Possible Role of the Immune Response in the Stem Cell Depression Produced by Melphalan Get access C. D. R. Dunn, Ph. D. C. D. R. Dunn, Ph. D. Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 52, Issue 1, January 1974, Pages 181–188, https://doi.org/10.1093/jnci/52.1.181 Published: 01 January 1974 Article history Received: 09 July 1973 Accepted: 14 September 1973 Published: 01 January 1974
Basophilic differentiation in transient abnormal myelopoiesis
Authors: Barbara J. Bain
Journal: American Journal of Hematology (2016)

Differentiation in transient abnormal myelopoiesis of Down syndrome is variable from case to case. Often multiple lineages are involved. Megakaryocytic differentiation is often prominent and sometimes also erythroid. This baby was unusual in having prominent basophilic as well as neutrophilic differentiation.
DNA Repair by ERCC1 in Non–Small-Cell Lung Cancer
Authors: Jane E Wilcox
Journal: New England Journal of Medicine (2006)

To the Editor: Olaussen and colleagues (Sept. 7 issue)1 report a survival benefit associated with the absence of the excision repair cross-complementation group 1 (ERCC1) protein in patients with completely resected non–small-cell lung cancer who received adjuvant cisplatin-based chemotherapy. Most of the operative specimens of ERCC1positive tumors examined were squamous-cell carcinoma, whereas the ERCC1-negative tumors were almost evenly divided between squamouscell carcinoma and adenocarcinoma.1 Does this skewed distribution reflect a selection bias? Originally, the International Adjuvant Lung Cancer Trial (IALT) showed a difference in survival of 2.3 percentage points for patients with squamous-cell tumors who received cisplatin (as compared with those in the control group who did not receive cisplatin-based chemotherapy). Among patients with adenocarcinoma who received cisplatin, the survival difference was 4.9 percentage points. The absolute 5-year survival benefit was 4.1 percentage points.2 Does this difference fail to differentiate between the two histologic types? Lower expression of ERCC1 is correlated with adenocarcinoma,1 decreased survival,3 and the most benefit from adjuvant cisplatin-based therapy.1 ERCC1 expression in squamous-cell carcinoma may be more useful than the histologic type as a guide to chemotherapy.
Is Annual Influenza Immunization Worthwhile in Industry?
Authors: G H COLLINGS
Journal: JAMA (1963)

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
Permanent prostate brachytherapy: Outcome in the community/HMO setting
Authors: D. E. Linstadt, D. Stickney, M. Logsdon, S. Workman, D. Chabra, M. Russo, L. Goldman
Journal: Journal of Clinical Oncology (2005)

4707 Background: Ultrasound-guided 125I permanent prostate brachytherapy (PPB) has proven to be a safe, effective treatment for prostate cancer when performed by pioneering specialized centers of excellence. However, given the demanding and complex nature of PPB, can similar success can be achieved when PPB is adopted into the general medical community/HMO setting? Methods: Between January 1998 and November 2001, 473 consecutive previously untreated prostate cancer patients underwent pre-planned 125I PPB in a start-up community/HMO-based program. Patients had low or intermediate risk disease (low risk=cT1C-T2A,Gleason Sum (GS) ≤6,PSA ≤10.0; intermediate-risk=cT1C-T2A,GS=7,PSA ≤10.0 or cT1C-T2A,GS≤6,PSA 10.1–20.0). The prescribed radiation dose was 144–145 Gy; median implant activity was 37.8 mCi (range 27.0–53.7 mCi). 100 patients (21%) received hormonal downsizing with leuprolide for 4–12 months prior to PPB. No patient received external beam radiotherapy or post-implant adjuvant hormonal therapy. Median post-implant CT dosimetry (day 30) values were V-100=95%, V-150=60%, and D-90=160 Gy. Successful PSA biochemical outcome (bNED) was defined using the ASTRO consensus definition. Median follow-up was 43 months; 96 patients have follow-up in excess of 5 years. Actuarial results were calculated using the Kaplan-Meier method. Results: The 5-year bNED rate was 95%. 2 patients developed biopsy-proven local recurrence; the 5-year local control rate was 99%. There were no deaths from prostate cancer, and the 5-year overall survival rate was 97%. 7 patients received salvage treatment after PPB (all with androgen deprivation); the 5-year freedom from salvage treatment was 97%. One patient (0.2%) developed a rectourethral fistula requiring colostomy and urinary diversion; one (0.2%) required Ar laser plasma coagulation for rectal bleeding. 4 patients (0.8%) required TURP/TUIP for chronic urinary retention. Conclusions: The 5-year results reported in this series compare favorably with those reported from specialized pioneering centers. Despite its complex, technically demanding nature, these results confirm that 125I PPB can be successfully performed on a large scale in newly developed community/HMO programs. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Bard, Mentor
Still Malignant Diphtheria?
Authors: H OTTO
Journal: JAMA (1963)

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
DSM-III in Botswana: a field trial in a developing country
Authors: D I Ben-Tovim
Journal: American Journal of Psychiatry (1985)

The author found that DSM-III criteria were generally applicable to the diagnoses of a series of new and repeat outpatients studied under field conditions in Botswana, a developing African country. Some problems were encountered, however, with axis II, which was not commonly used. Other clinical aspects of the patients are commented on, including the rarity of acute psychoses and culture-bound syndromes.
Case 6-1984
Authors: Nancy L. Sprince, Eugene J. Mark
Journal: New England Journal of Medicine (1984)

Presentation of CaseA 20-year-old woman was admitted to the hospital because of pulmonary densities.She was in vigorous health until four months earlier, when a cough developed and subsequently increased in severity. Three months before admission she coughed up blood-tinged sputum on two occasions. Two months before entry she coughed up gross blood with clots and came to this hospital. Physical examination was negative. X-ray films of the chest (Fig. 1) showed a cavitary lesion, 1.5 cm, in the right upper lobe; there were irregular nodular densities in the remainder of the posterior segment of the right upper lobe; . . .
Inhibitory Activity of Human Lactoferrin and Its Peptide on Chondroitin Sulfate A-, CD36-, and Thrombospondin-Mediated Cytoadherence ofPlasmodium falciparum–Infected Erythrocytes
Authors: Shigetoshi Eda, Keiko Eda, Jacques G. Prudhomme, Irwin W. Sherman
Journal: Blood (1999)
The effects of caffeine on reaction time in hyperkinetic and normal children
Authors: C C Reichard, S T Elder
Journal: American Journal of Psychiatry (1977)

Using a double-blind design, the authors investigated 1) caffeine's effect in hyperkinetic children on a choice reaction time task, 2) whether caffeine has different effects on simple reaction time and choice reaction time, and 3) whether its effects in the hyperkinetic compared with the normal group of children are best described by the law of initial values or as a "paradoxical effect." The results indicate that caffeine produced an increase in the accuracy of stimulus identification and processing and a decrease in lapses of attention for the hyperkinetic group. The law of initial values best represented the phenomena observed.