tbuckley/cabot-search huggingface dataset:
Abstract 2198: Exome and transcriptome sequencing of human tumors and tumor-derived cell lines
Authors: Michael L. Nickerson, Kate McGee, Bert Gold, Cindy Lawley, Bao Tran, Claudia Stewart, Tim Harkins, Fred Waldman, Berton Zbar, Lee Moore, Mike Dean
Journal: Cancer Research (2010)

Abstract Insight into the cancer genome has recently increased in an unprecedented way due to high throughput (HT) sequencing technology to examine the genome, exome, and transcriptome. We sought new genetic biomarkers for cancer by using HT sequencing to examine highly characterized primary sporadic tumors and tumor-derived cell lines. Several tumors/cell lines represented the most common subtype of kidney cancer, clear cell renal cell carcinoma, as well as NCI-60 panel cell lines from breast (MCF7) and prostate (PC3). Incorporation of NCI-60 panel cell lines was advantageous due to extensive prior characterization of these reagents, including gene expression, comparative genome hybridization, SNPs, and drug cytotoxicity. The study was performed using three major platforms (454, Illumina, ABI) to compare sequencing quality, cost, quantity, and computational amenability. Different methodologies were examined including exome, transcriptome, and whole genome sequencing. Alignment of sequence to a consensus genome (hg 18) allowed identification of novel and previously documented genomic variants. Various filters were implemented to sort the large number of variants detected, including dbSNP, personal genome variants, and 1000 genomes data. An average of 65 million 35-50 base pair sequences were generated from transcriptomes of two primary clear cell RCC tumors. Over 2 million 375 base pair sequences were generated from each of four cell line exomes. Differences were observed in extent and depth of coverage of a given target region by various experimental approaches. SNP array genotyping showed 1% discordance with sequencing. Previously characterized mutations were confirmed in HT sequences. We identified multiple regions of homozygosity at an unprecedented resolution. For example, in the clear cell renal cancer cell line, 786-0, a known mutation in VHL (311delG) was identified, and LOH at SNP positions across the entire length of chromosome 3 was confirmed. Alignment to a reference genome (hg 18) permitted identification of 2583-5307 genomic sequence variants, including 92-297 novel non-synonymous variants in the exomes of each cell line. Variants include frameshift and nonsense mutations. Novel non-synonymous variants were identified in cancer-related genes and these are being examined in additional tumors. Potential functions of newly identified mutated genetic loci suggest perturbation of signaling pathways and are candidates for targeted therapy. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2198.
TWO FATAL CASES OF SNAKE-BITE: WITH REMARKS
Authors: R. H. Powell
Journal: BMJ (1853)

ISM.O3IG!AL COMMUNICA1IONS.778 brothwn and site have, from a cause, all died;or have orig y come out a pthishl, andhve lived free from all tubercular mplait.Auguxt 18A.* It may be smsed that the treatment pursued subsequently to the ex- hibition of depressing astiragents proved too active for a system laboung under the sedative influenoe ot a virulent poison.The latter part of the tratment was, however, judicious; and in such canse little room is left ibr critical rearks, from their all but universal fatality.v. L P.
Mexico! It's Marlboro Country
Authors: Joanne Cornbleet
Journal: JAMA (1992)

<h3>To the Editor.</h3> —The tobacco industry claims not to advertise or promote their product to children. However, recent articles in<i>JAMA</i>suggest active efforts of tobacco companies to encourage name recognition among children.<sup>1-3</sup>I saw visual evidence of this while traveling in Mexico in 1990, as shown in the photograph of a young boy wearing a jacket obviously made only for a child (Figure). In the absence of legal restrictions, it is apparent that corporate "moral responsibility" stops at the international boundary.
Clinical response and pharmacokinetics from a phase 1 study of an active dosing schedule of flavopiridol in relapsed chronic lymphocytic leukemia
Authors: Mitch A. Phelps, Thomas S. Lin, Amy J. Johnson, Eunju Hurh, Darlene M. Rozewski, Katherine L. Farley, Di Wu, Kristie A. Blum, Beth Fischer, Sarah M. Mitchell, Mollie E. Moran, Michelle Brooker-McEldowney, Nyla A. Heerema, David Jarjoura, Larry J. Schaaf, John C. Byrd, Michael R. Grever, James T. Dalton
Journal: Blood (2008)
Computers in Medicine
Authors: Beverly J. Montgomery
Journal: JAMA (1978)

Computers now can be used in diagnostic cytological examinations, in the differential diagnosis of abdominal pain, in predicting the probability that patients with appendicitis have gangrene or perforation, and in maintaining patient charts and billing records. In fact, computers these days are found throughout hospitals in laboratories, radiology departments, emergency rooms, and nursing stations. They are a crucial part of ECG and EEG monitoring systems. In addition, they serve as a core of instructional techniques in many medical schools, both for basic medical sciences and for simulations of clinical situations. As the importance of this technology to medicine has grown, some computer uses are particularly noteworthy: At Seattle's Harborview Medical Center, a computer automatically adjusts the amounts of fluids administered intravenously to burn patients. Such variables as blood pressure, urine output, and arterial and central venous pressures are computer monitored to determine when more or less fluids may be
Molecular Classification of Gastric Cancer: A New Paradigm
Authors: Manish A. Shah, Raya Khanin, Laura Tang, Yelena Y. Janjigian, David S. Klimstra, Hans Gerdes, David P. Kelsen
Journal: Clinical Cancer Research (2011)

Abstract Purpose: Gastric cancer may be subdivided into 3 distinct subtypes—proximal, diffuse, and distal gastric cancer—based on histopathologic and anatomic criteria. Each subtype is associated with unique epidemiology. Our aim is to test the hypothesis that these distinct gastric cancer subtypes may also be distinguished by gene expression analysis. Experimental Design: Patients with localized gastric adenocarcinoma being screened for a phase II preoperative clinical trial (National Cancer Institute, NCI #5917) underwent endoscopic biopsy for fresh tumor procurement. Four to 6 targeted biopsies of the primary tumor were obtained. Macrodissection was carried out to ensure more than 80% carcinoma in the sample. HG-U133A GeneChip (Affymetrix) was used for cDNA expression analysis, and all arrays were processed and analyzed using the Bioconductor R-package. Results: Between November 2003 and January 2006, 57 patients were screened to identify 36 patients with localized gastric cancer who had adequate RNA for expression analysis. Using supervised analysis, we built a classifier to distinguish the 3 gastric cancer subtypes, successfully classifying each into tightly grouped clusters. Leave-one-out cross-validation error was 0.14, suggesting that more than 85% of samples were classified correctly. Gene set analysis with the false discovery rate set at 0.25 identified several pathways that were differentially regulated when comparing each gastric cancer subtype to adjacent normal stomach. Conclusions: Subtypes of gastric cancer that have epidemiologic and histologic distinctions are also distinguished by gene expression data. These preliminary data suggest a new classification of gastric cancer with implications for improving our understanding of disease biology and identification of unique molecular drivers for each gastric cancer subtype. Clin Cancer Res; 17(9); 2693–701. ©2011 AACR.
Peroral endoscopic myotomy (POEM) for esophageal achalasia
Authors: H. Inoue, H. Minami, Y. Kobayashi, Y. Sato, M. Kaga, M. Suzuki, H. Satodate, N. Odaka, H. Itoh, S. Kudo
Journal: Endoscopy (2010)

See also: Commentaire de travail de H. Inoue et al., pp. 265Endoscopy 2010; 42(04): 350-350DOI: 10.1055/s-0031-1291851 Referred to by: Peroral endoscopic myotomy (POEM) opens the door of third-space endoscopyEndoscopy 2019; 51(11): 1010-1012DOI: 10.1055/a-1019-1865
Hookah pipes are associated with young people starting smoking, study finds
Authors: J. Wise
Journal: BMJ (2014)

Hookah pipes and the smokeless tobacco product snus may serve as a gateway to cigarette smoking, researchers say.

A longitudinal analysis, published online by JAMA Pediatrics , found that smoking waterpipe tobacco from hookahs and using snus were associated with starting cigarette smoking among previously non-smoking teenagers and young adults.1

The research included 1596 young people aged 15 to 23, who completed a survey at the start of the study and again two years later. Two thirds …
Atypical moles in a patient undergoing chemotherapy with oral 5-fluorouracil prodrug
Authors: S. Fukushima, N. Hatta
Journal: British Journal of Dermatology (2004)

We present a patient with multiple pigmented lesions on the palms, soles, oral mucosa and nails after chemotherapy with oral 5‐fluorouracil (5‐FU) prodrug. Dermoscopically, most of the macules showed similar features, with pigmentation present predominantly on the crista superficialis, while a large, dark macule also showed pigmentation along the sulcus superficialis with irregular hyperpigmentation and depigmentation, suggesting malignancy. However, histologically, both types of lesion showed basal hyperpigmentation and the presence of a small number of large atypical melanocytes. We diagnosed these lesions as pigment flecks induced by 5‐FU, and the pigmented lesions gradually diminished after the cessation of chemotherapy. Our findings suggested that immunosuppression and 5‐FU led to the development of the atypical pigmented lesions.
Importance of Aspirin as a Cause of Anaemia and Peptic Ulcer in Rheumatoid Arthritis
Authors: F. D. Baragar, J. J. R. Duthie
Journal: BMJ (1960)

Few would question the value of aspirin (acetylsalicylic acid) in the treatment of rheumatoid arthritis.Carefully controlled trials (Empire Rheumatism Council, 1957; Medical Research Council and Nuffield Foundation, 1957) have shown little difference between the therapeutic effect of aspirin and cortisone in the long-term manage- ment of this disease.A number of reports have been published which suggest that aspirin may be an important cause of gastro- intestinal bleeding.Douthwaite and Lintott (1938) reported that aspirin can cause anaemia, and showed by gastroscopy that it had an irritant action on the gastric mucosa.
Private companies are appointed to provide support to commissioning groups
Authors: G. Iacobucci
Journal: BMJ (2015)

A host of private companies have been appointed to provide up to £5bn (€6.7bn; $7.6bn) of commissioning support services to the NHS in England.

Capita Business Services, the business services company Mouchel, and Optum (part of United Health) are among the firms appointed by NHS England to its “lead provider framework for commissioning support services.”1

NHS clinical commissioning groups (CCGs) will …
All the Cs
Authors: Fiona Godlee
Journal: BMJ (2008)

It’s a trivial point, but many of the words that describe what makes a good doctor begin with the letter C. A cohort of UK doctors that has been tracked by the BMA since they qualified in 1995 has twice been asked to rank a list of core professional values (www.bma.org.uk/ap.nsf/Content/profval~values). Competence scores highest on both occasions, but caring, compassion, and commitment are all up there in the top six.

It’s right that competence is seen as a professional value and not as something to be assumed. Perhaps doctors have always taken responsibility for ensuring their own competence, but I find it …
Small-for-size liver transplanted into larger recipient: A model of hepatic regeneration
Authors: Antonio Francavilla, Qihua Zeng, Lorenzo Polimeno, Brian I. Carr, Dantong Sun, Kendrick A. Porter, David H. van Thiel, Thomas E. Starzl
Journal: Hepatology (1994)

Orthotopic liver transplantation was performed in 60 recipient rats weighing 200 to 250 gm. Sixty rats of the same strain were used as liver donors, 30 weighing 100 to 140 gm (small for size) and the other 30 weighing 200 to 250 gm (same size). After 1, 2, 3, 4, 7 and 14 days (n = 5 each) DNA synthesis, nuclear thymidine labeling and mitoses were increased in both the small-for-size and same-size groups, but significantly more in the former. These changes were maximal after 48 to 72 hr, similar to but later than the well-known regeneration response after partial hepatectomy, which peaks at 24 hr in rats. Indirect indexes of regeneration of the transplanted livers also were measured: plasma or serum ornithine decarboxylase; insulin and glucagon serum levels; estradiol and testosterone serum levels (and their nuclear and cytosolic receptors); and transforming growth factor-beta, c-Ha-ras and c-jun mRNA expressions. With the small-for-size transplantation, these followed the same delayed pattern as the direct regeneration parameters. The small livers gradually increased in size over the course of 1 to 2 wk and achieved a volume equal to that of the liver originally present in the recipient. In contrast, no significant liver weight gain occurred in the transplanted livers from same-size donors despite the evidence of regeneration by direct indexes, but not by most of the surrogate parameters, including ornithine decarboxylase.
The Infant Health and Development Program: Results at 8 Years-Reply
Authors: Cecelia M. McCarton
Journal: JAMA (1997)

<h3>In Reply.</h3> —The analyses of Drs Baumeister and Bacharach as reported in<i>Intelligence</i><sup>1</sup>are flawed by their use of correlational analyses to draw inferences regarding causality and by selectively analyzing smaller, post-hoc subgroups to support their conclusions. Their current criticism of the 3-year, 5-year, and 8-year data is based on a conclusion derived from a correlational analysis of a selected cohort of the combined intervention and follow-up groups drawn from data deposited with NAPS. This approach violates the design of the study as a multisite randomized trial, ignores the specific characteristics of each assessment point, and biases their sample by including only those children seen at all time points. At each age, we followed the intention-to-treat principle used in randomized controlled trials to minimize bias: every available randomized child was analyzed without any post-hoc exclusions. As seen in Table 2 in our article, the sample seen at 8 years was nearly
The Effects of Acid Perfusion of the Esophagus on Ventilation and Respiratory Sensation
Authors: STEPHEN K. FIELD, JOHN A. EVANS, LORNE M. PRICE
Journal: American Journal of Respiratory and Critical Care Medicine (1998)

The relationship between gastroesophageal reflux (GER) and asthma remains controversial. Asthma symptoms worsen with GER, but are not consistently related to changes in lung function. The purpose of this study was to determine whether acid perfusion (AP) of the esophagus alters ventilation and causes respiratory symptoms. Nonasthmatic patients with normal lung function and esophageal disease (16 females and nine males, FEV1 %predicted = 99 ± 9.6), underwent a Bernstein test after motility testing. Airflow, rib cage (Vrc), and abdominal (Vab) tidal volumes, esophageal (Pes) and gastric (Pga) pressure, and surface (Es) and esophageal (Edi) diaphragm electromyographic (EMG) signals were measured. Throat, swallowing, chest, and stomach discomfort and respiratory sensation were estimated with the Borg scale. Minute ventilation (V˙ e) increased during AP and declined during recovery with saline perfusion of the esophagus (7.1 ± 1.5 to 8.5 ± 2.4 to 7.3 ± 2.1 L/min; n = 25; p = 0.0002). Respiratory rate (RR) went from 13.6 ± 2.6 to 15.8 ± 3.4 to 15.3 ± 3.1 breaths/min (n = 25; p = 0.0002) during AP. V˙ e was greater in the Bernstein-positive patients during AP. Tidal volume (Vt), Vrc, Vab, Pes, Pga, Es, and Edi did not change during AP. Chest discomfort (D) correlated with ventilation (V˙ e = 0.7 + 0.8 D; r = 0.67; p < 0.001) and respiratory effort sensation (B) (B = 0.2 + 0.4 V˙ e; r = 0.70; p < 0.001) during AP. AP did not inhibit diaphragm activity. Increased V˙ e may explain the paradox of GER worsening respiratory symptoms without changing lung function.
CONSERVATIVE TREATMENT OF WOUNDS OF THE EYE-BALL.Read in the Section on Ophthalmology, at the Forty-fifth Annual Meeting of the American Medical Association, held at San Francisco. June 5-8, 1894.
Authors: LEWIS H. TAYLOR
Journal: JAMA (1894)

I do not propose to weary the members of the Section by attempting to discuss the subject of wounds of the eye-ball in all of the phases which that subject might present, nor will I even enumerate the varieties and grades of these injuries, but will confine my remarks briefly to a consideration of some of the more serious forms, such as penetrating and lacerated wounds involving the iris and lens. Living as some of us do, either in mining or manufacturing districts, we are frequently confronted with eye injuries of all grades, from the small cinder lodged upon the cornea, which in its effects is oftentimes by no means small, to the severe laceration of cornea, lens, iris and sclera. The important question that at once arises is, to what extent shall I interfere with this eye? and how far dare I trust to the recuperative powers of nature
Effect Of Desloratadine On The Bronchial Reactivity During Allergen Provocation Tests In Rhinitics Allergic To Grass Pollen
Authors: A. Purohit, C. Donnay, A. Casset, M. Kopferschmitt, I. Dreyfus, F. Sevenier, F. de Blay
Journal: Journal of Allergy and Clinical Immunology (2007)
Dendritic cells induce antigen-specific regulatory T cells that prevent graft versus host disease and persist in mice
Authors: Uri Sela, Peter Olds, Andrew Park, Sarah J. Schlesinger, Ralph M. Steinman
Journal: The Journal of Experimental Medicine (2011)

Foxp3+ regulatory T cells (T reg cells) effectively suppress immunity, but it is not determined if antigen-induced T reg cells (iT reg cells) are able to persist under conditions of inflammation and to stably express the transcription factor Foxp3. We used spleen cells to stimulate the mixed leukocyte reaction (MLR) in the presence of transforming growth factor β (TGF-β) and retinoic acid. We found that the CD11chigh dendritic cell fraction was the most potent at inducing high numbers of alloreactive Foxp3+ cells. The induced CD4+CD25+Foxp3+ cells appeared after extensive proliferation. When purified from the MLR, iT reg cells suppressed both primary and secondary MLR in vitro in an antigen-specific manner. After transfer into allogeneic mice, iT reg cells persisted for 6 mo and prevented graft versus host disease (GVHD) caused by co-transferred CD45RBhi T cells. Similar findings were made when iT reg cells were transferred after onset of GVHD. The CNS2 intronic sequence of the Foxp3 gene in the persisting iT reg cells was as demethylated as the corresponding sequence of naturally occurring T reg cells. These results indicate that induced Foxp3+ T reg cells, after proliferating and differentiating into antigen-specific suppressive T cells, can persist for long periods while suppressing a powerful inflammatory disease.
Mass Media and Medicine: Challenges and Opportunities
Authors: Julie Suzumi Young
Journal: JAMA (2002)

IN 1959, A RURAL COUPLE TOOK THEIR 9-MONTH-OLD SON, “JOHN,” TO BE tested for something they had never heard of before, hemophilia. They had just read an article about the disease in Reader’s Digest and wondered if John’s bruising and listlessness could be explained by the unfamiliar bleeding disorder. Soon thereafter, John was diagnosed with hemophilia A, a coagulation defect that required countless doctor visits and painful bleeding crises throughout his childhood. While John was in his 20s, the first report about an unusual disease affecting homosexual men appeared in the scientific literature. Later identified as the disease caused by the human immunodeficiency virus (HIV), AIDS has since received tremendous mass media coverage. Perhaps partly as a result of how AIDS was depicted in the press, patients with hemophilia and other groups associated with HIV became modern-day pariahs among some members of the public, who responded with fear and discrimination against them. John, who eventually tested positive for HIV, entertained the idea of submitting a more detailed account of his experiences for this issue of MSJAMA. However, 20 years after AIDS first hit the press, John decided that publishing his story would invite unwelcome scrutiny of him and his family, especially by those in his community who still live in irrational fear and ignorance of the transmissibility of HIV. This true story illustrates the enormous impact—both positive and negative—that magazines, television, radio stations, daily newspapers, and other communication entities that comprise the “mass media” can have on an individual’s health and life. Every day, physicians face the myriad effects of the mass media on their patients’ perceptions of health care and medical science. This issue of MSJAMA explores some challenges and opportunities that arise as a result of disseminating scientific and medical information to the public. To better understand how the mass media shapes the public’s perception of medicine, it is important to quantify the public’s response to media coverage and critically analyze the contents of this coverage. Gail Geller, Barbara A. Bernhardt, and Neil A. Holtzman discuss the mass media’s role in influencing the public’s perception of genetics research. Lisa Schwartz and Steven Woloshin lend a critical eye to the health claims made in some medical advertisements. While misrepresentation of medical information by mass media can have negative consequences, the use of mass media to educate the public about medicine has an enormous potential to do good. Physician and reporter Miriam Shuchman discusses examples of good reporting that has resulted in positive changes in the health care field.
Selecting the Best Candidates for Lung Cancer Screening
Authors: Tanner Caverly
Journal: JAMA Internal Medicine (2015)

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