tbuckley/cabot-search huggingface dataset:
Birth and Death of Orphan Genes in Rickettsia
Authors: H. Amiri
Journal: Molecular Biology and Evolution (2003)

The origin and evolution of the thousands of species-specific genes with unknown functions, the so-called orphan genes, has been a mystery. Here, we have studied the rates and patterns of orphan sequence evolution, using the Rickettsia as our reference system. Of the Rickettsia conorii orphans examined in this study, 80% were found to be short gene fragments or fusions of short segments from neighboring genes. We reconstructed the putative sequences of the full-length genes from which the short orphan fragments are thought to have originated. One of the genes thus reconstructed displays weak similarity to the ankyrin-repeat protein family, an identification that is strongly supported by comparative molecular modeling. Studies of the patterns of gene fragmentation underscore the importance of short repeated sequences as targets for recombination events that result in sequence loss and the formation of short, transient open reading frames. Our analysis demonstrates that gene sequences present in the common ancestor can be inferred even in cases when no full-length open reading frame is present in any of the contemporary species. Such reconstructions support the identification of lost protein functions and hint at important lifestyle changes.
Abstract 4974: Allele-specific mRNA and protein expression on genetic variants of CCNE1 associated with risk of bladder cancer
Authors: Indu Kohaar, Yi-Ping Fu, Wei Tang, McAnthony Tarway, Brian Muchmore, Patricia Porter-Gill, Ludmila Prokunina-Olsson
Journal: Cancer Research (2011)

Abstract A single nucleotide polymorphism (SNP), rs8102137, located 6 Kb upstream from the cyclin E1 gene (CCNE1) on chromosome 19q12, has recently been identified as a risk factor for bladder cancer (OR, p=1.7×10-11, Rothman et al, Nat Gen, 2010). We found a higher expression of CCNE1 mRNA in cDNA samples from bladder tumors (n=42) compared to adjacent normal bladder tissue (n=41, 3.7 fold, p=2.7×10-12). However, the expression did not correlate with genotypes of rs8102137. We also performed allelic expression imbalance (AEI) using a coding synonymous variation in the last exon (rs7257694, Ser390Ser) that is in high LD with the GWAS rs8102137 (normal bladder tissue samples, n = 41, D’=1.0, r2=0.815 and in HapMap CEU samples, n=60, D’=0.95, r2=0.68). In normal and tumor tissue samples heterozygous for both SNPs, the risk variant of rs8102137 was associated with lower expression of allele T of rs7257694 (p=2.2×10-4 in normal samples and 1.11×10-10 in tumor samples). Western blot protein analysis with bladder tissue and prostate cell lines lysates showed that this allele-specific difference in mRNA expression is likely to be related to two protein isoforms that showed a differential pattern of expression dependent on rs8102137 and rs7257694 genotypes. CCNE1 regulates cell cycle G1/S transition, and alternative protein forms may have differential functions in cell cycle regulation, thereby affecting the risk of cancer. Alternative splicing forms of CCNE1 have been cloned and their functional analysis is ongoing. In conclusion, our results suggest that bladder cancer associated genetic variants within the CCNE1 gene may affect mRNA splicing and protein structure of the gene, contributing to altered regulation of cell cycle and risk of bladder and other cancers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4974. doi:10.1158/1538-7445.AM2011-4974
Clinical Management of Chronic Obstructive Pulmonary Disease
Authors: Warren Summer
Journal: Annals of Internal Medicine (2002)

Medical Writings: Book Notes15 October 2002Clinical Management of Chronic Obstructive Pulmonary DiseaseWarren Summer, MDWarren Summer, MDLousiana State University Health Science Center, New Orleans, Louisiana.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-137-8-200210150-00038 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Similowski T, Whitelaw WA, and Derenne JP, eds. 1072 pages. New York: Marcel Dekker; 2002. $250.00. ISBN 0824706102. Order phone 212-696-9000.Field of medicine: Pulmonary medicine.Format: Hardcover book.Audience: Pulmonary specialists, internal medicine physicians, or general practitioners with a desire for a comprehensive knowledge of management of chronic obstructive pulmonary disease (COPD).Purpose: To inform the clinician on current COPD management, including several chapters providing an international perspective.Content: Multiauthored book comprising 45 chapters. The first chapter, by Snider, gives a panoramic view on what we have learned about COPD and where the future challenges lie with this complex ... Author, Article, and Disclosure InformationAffiliations: Lousiana State University Health Science Center, New Orleans, Louisiana. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 15 October 2002Volume 137, Issue 8Page: 706KeywordsChronic obstructive pulmonary diseaseForecastingLungsPulmonary medicineQuality of lifeSleep disordersSoftware toolsSteroidsTracheostomyVentilators ePublished: 15 October 2002 Issue Published: 15 October 2002 Copyright & PermissionsCopyright © 2002 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
A LIQUID SYNTHETIC MEDIUM SUITABLE FOR THE DIFFERENTIATION OF MICROSPORUM AUDOUINI GRUBY 1843, AND OF MICROSPORUM CANIS BODIN 1902
Authors: J. W. HUGHES
Journal: British Journal of Dermatology (1952)

Journal Article A LIQUID SYNTHETIC MEDIUM SUITABLE FOR THE DIFFERENTIATION OF MICROSPORUM AUDOUINI GRUBY 1843, AND OF MICROSPORUM CANIS BODIN 1902 Get access J. W. HUGHES J. W. HUGHES Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 64, Issue 9, 1 September 1952, Pages 334–338, https://doi.org/10.1111/j.1365-2133.1952.tb15816.x Published: 01 September 1952
Evolution of anaerobic ciliates from the gastrointestinal tract: phylogenetic analysis of the ribosomal repeat from Nyctotherus ovalis and its relatives
Authors: A. H. van Hoek, T. A. van Alen, V. S. Sprakel, J. H. Hackstein, G. D. Vogels
Journal: Molecular Biology and Evolution (1998)

The 18S and 5.8S rDNA genes and the internal transcribed spacers ITS-1 and ITS-2 of ciliates living in the hindgut of frogs, millipedes, and cockroaches were analyzed in order to study the evolution of intestinal protists. All ciliates studied here belong to the genus Nycrotherus. Phylogenetic analysis revealed that these ciliates from a monophyletic group that includes the distantly related anaerobic free-living heterotrichous ciliates Metopus palaeformis and Metopus contortus. The intestinal ciliates from the different vertebrate and invertebrate hosts are clearly divergent at the level of their rDNA repeats. This argues for the antiquity of the associations and a predominantly vertical transmission. This mode of transmission seems to be controlled primarily by the behavior of the host. The different degrees of divergence between ciliates living in different strains of one and the same cockroach species most likely reflect the different geographical origins of the hosts. In addition, host switches must have occurred during the evolution of cockroaches, since identical ciliates were found only in distantly related hosts. These phenomena prevent the reconstruction of potential cospeciation events.
Counteracting Alcohol's 'Glamour Image'
Authors: Charles Marwick
Journal: JAMA (1992)

ALCOHOL-RELATED injuries cost the nation an estimated $47.5 billion a year.  In more personal terms, such injuries cost every man, woman, and child in the United States about $190 a year, says Lewis Eigen, PhD, president, Science and Health Services, a Rockville, Md, communications firm.  Eigen spoke at a national conference on alcohol-related injuries, sponsored by a number of federal departments including Health and Human Services, Education, Housing and Urban Development, Labor, and Transportation.  Surgeon General's Call  Conferees heard Antonia Novello, MD, surgeon general of the Public Health Service, call for a broad, society-wide approach to dealing with alcohol abuse. She says this approach cannot remain solely in the hands of the police and the legal system.  The conferees drew up a series of recommendations that they hope will prevent or at least reduce injuries related to excessive alcohol consumption, ineluding the following:   Reducing availability of alcohol, through increased taxes;
New Tests to Assess Lung Function
Authors: Peter T. Macklem, A. Sonia Buist
Journal: New England Journal of Medicine (1975)

FOWLER, who described the single-breath nitrogen test in 1949, proposed it as a useful test for abnormal intrapulmonary gas mixing and uneven ventilation.1 Since then, it has been used quite extensively both clinically and in several large epidemiologic studies. Recently, there has been renewed interest in the procedure because it offers promise of being able to detect airways obstruction at a potentially reversible stage and because it has become useful in clinical and epidemiologic research. The test as currently used2 is a modification of Fowler's technic and extends the scope of the original test considerably so that total lung capacity, . . .
Doctors like emailing patients but want to be paid for it, study finds
Authors: M. McCarthy
Journal: BMJ (2013)

Doctors who regularly use email find that it is an effective way to communicate with patients but that it adds to their workload without adding to their income, a study has found.

Tara Bishop and her colleagues at Weill Cornell Medical College, New York City, interviewed leaders of 21 US medical groups that used electronic communication extensively. 

They then followed up with interviews with providers and staff working in …
No H pylori: less dyspepsia?
Authors: K E L McCOLL
Journal: Gut (2000)

See article on page 473 

Functional dyspepsia is a common disorder of heterogeneous aetiology for which there is no clearly effective treatment. In this issue of Gut , Blum and colleagues1 report their large controlled clinical trial assessing the effectiveness of antisecretory medication in functional dyspepsia (see page 473). Patients with and without evidence of Helicobacter pylori infection were recruited into the study.

The study found symptomatic benefit over placebo at the end of two weeks' treatment with omeprazole 20 mg per day in H pylori positive patients but no significant benefit in primary outcome with the same treatment in H pylori negative patients. The therapeutic gain over placebo for omeprazole 20 mg in the H pylori positive patients was 17.6% (95% confidence intervals 4.2–31%; p<0.014). There was no significant benefit over placebo following omeprazole 10 mg or ranitidine 150 mg in H pylori positive patients or following any of the three treatments in the H pylori negative subjects. The superior benefit from omeprazole 20 mg in the H pylori positive versus negative subjects was also apparent with respect to improvement in quality of life.

The reason for symptomatic benefit over placebo with powerful acid suppression being confined to the H pylori infected subjects in this study is unclear and needs to be addressed. An earlier large study …
Abstract A53: Effect of an ERβ agonist in the gerbil senile prostate: Novel treatment for age related disorders?
Authors: Sabrina S. Rochel-Maia, Sebastião R. Taboga, Margaret Warner, Jan-Åke Gustafsson
Journal: Cancer Research (2012)

Abstract This study evaluated the effect of a selective estrogen receptor beta (ERβ) agonist in the prostate of the aging Mongolian gerbil. The gerbil is a rodent known for spontaneous development of prostatic lesions such as prostatic intraepithelial neoplasias (PIN), adenocarcinomas and micro invasive carcinomas as they become old. This representative feature makes the gerbil interesting for testing the role of novel targets to prevent or treat prostate cancer. ERβ is known to have anti-proliferative and pro-apoptotic effects in the prostate epithelium, and therefore is a potential target for treatment of prostatic disorders. ERβ agonist and vehicle pellets were implanted subcutaneously in 12-month-old male gerbils (n=5) and the ventral prostates were harvested after 3 and 7 consecutive days of treatment. The tissue was processed for light microscopy and stained for H&amp;E for morphological analysis. Expression of the nuclear receptors AR, ERα and ERβ, as well as markers of proliferation and apoptosis were examined by immunohistochemistry. Anatomically, the prostates of gerbils treated with vehicle pellets were smaller and more compact than those treated for 3 days with the ERβ agonist. The change was due to increased volume of the ducts and return of the ductal epithelium to a single organized layer. Histologically, the slides stained with H&amp;E showed a hyperplastic and inflamed epithelium with a dense stroma in the vehicle treated groups, as typical of senile gerbil prostates. However, the treatment with the ERβ agonist promoted a reorganization of the prostatic epithelium. Ducts became lined in single layer of cubic/columnar cells, with enlarged lumen, full of secretion. The hyperplastic phenotype had normalized. These effects were more prominent after 3 days than after 7 days and were confirmed by a decreased expression of the proliferation marker ki67. In addition, ERβ expression, which is usually very weak or undetectable in the prostate of 12-month-old gerbils, was fully recovered after 3 days of treatment while expression of ERα and AR remained the same, indicating the effects occurred via ERβ signaling exclusively. Upon 7 days of continuous exposure to the ERβ agonist, ERβ expression was down-regulated. Therefore, the results found so far are promising as they indicate the ERβ as a novel and effective target for the treatment of prostatic disorders. However, the route and regimen of drug delivery remains to be carefully worked out. Citation Format: Sabrina S. Rochel-Maia, Sebastião R. Taboga, Margaret Warner, Jan-Åke Gustafsson. Effect of an ERβ agonist in the gerbil senile prostate: Novel treatment for age related disorders? [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr A53.
Blunted feedback suppression of SREBP processing by dietary cholesterol in transgenic mice expressing sterol-resistant SCAP(D443N).
Authors: B S Korn, I Shimomura, Y Bashmakov, R E Hammer, J D Horton, J L Goldstein, M S Brown
Journal: Journal of Clinical Investigation (1998)

Feedback regulation of cholesterol biosynthesis is mediated by membrane-bound transcription factors designated sterol regulatory element-binding proteins (SREBP)-1 and -2. In sterol-deprived cultured cells, SREBPs are released from membranes by a proteolytic process that is stimulated by SREBP cleavage-activating protein (SCAP), a membrane protein containing a sterol-sensing domain. Sterols suppress SREBP cleavage by blocking the action of SCAP, thereby decreasing cholesterol synthesis. A point mutation in SCAP(D443N) causes resistance to sterol suppression. In this article, we produced transgenic mice that express mutant SCAP(D443N) in liver. In these livers the nuclear content of SREBP-1 and -2 was increased, mRNAs encoding proteins involved in uptake and synthesis of cholesterol and fatty acids were elevated, and the livers were engorged with cholesteryl esters and triglycerides enriched in monounsaturated fatty acids. When the mice were challenged with a high cholesterol diet, cleavage of SREBP-1 and -2 was reduced in wild-type livers and less so in transgenic livers. We conclude that SCAP(D443N) stimulates proteolytic processing of native SREBPs in liver and decreases the normal sterol-mediated feedback regulation of SREBP cleavage, suggesting a central role for SCAP as a sterol sensor in liver.
Voluntary Organ Donation: Autonomy... Tragedy-Reply
Authors: Stuart J. Youngner
Journal: JAMA (1993)

<h3>In Reply.</h3> —While Dr Iserson urges us to "stop dancing around society's ethical constraints on organ donation," Dr Kunin's moving story demonstrates just how complex and subtle those "constraints" can be. Iserson fails to recognize that autonomy is not the only value patients, their families, and health professionals deem important. Family authority over the fate of the newly dead, about to be dead, or probably dead bodies of their children, parents, and spouses (even if they have previously expressed a wish to be donors) is a cultural value that will be difficult to obliterate by government regulation. Ignoring these issues increases the likelihood that passage of new regulations, such as presumed consent and mandated choice, will backfire and alienate more persons from the process. If our experience with required request serves as an example, pressuring people to do things about which they are uncomfortable simply doesn't work.<sup>1</sup> There are
RAPID RESPONSES FROM BMJ.COM
Authors: Godfrey Oakley
Journal: BMJ (2004)

Randomized controlled trials are not the usual way serious, uncommon adverse effects of a new drug are discovered. They are usually discovered in observational studies, often case-control studies. I think there is danger in using RCTs to find adverse effects. It would feed on the current vogue from trialists that the only data that count are those from RCTs. By this standard, we would …
Floating Mobile Mass That Is Probably Thrombus
Authors: Chuwa Tei, Fletcher A. Miller
Journal: Circulation (1998)

A 52-year-old woman presented with palpitations, pro- gressive shortness of breath, and transient dizziness during the week preceding this echocardiographic study.Physical examination was typical for mitral stenosis, with an irregular heart rate of 78 bpm, accentuated first heart sound, opening snap, and apical diastolic rumble.The ECG demonstrated atrial fibrillation.Two-dimensional (2D) echocardiographic images from the parasternal and apical positions are shown in the upper and lower panels of the Figure respectively, and an M-mode recording through the mitral valve and left atrium is also shown in the lower panel.The mitral
Forward-Viewing Endoscope or Side-Viewing Duodenoscope for ERCP in Patients after Billroth II Gastrectomy?
Authors: S. Mosca, G. Uomo, A. Ascione
Journal: Endoscopy (1998)

See also: Reply to the letter by Mosca et al.Endoscopy 1998; 30(01): 52-52DOI: 10.1055/s-2007-993511 See also: Is It Always True That ERCP Cannot Be Carried out in Patients with Roux-en-Y Gastrojejunostomy?Endoscopy 1998; 30(09): 870-870DOI: 10.1055/s-2007-1001426 See also: Endoscopic Retrograde Cholangiopancreatography and Needle-Knife Sphincterotomy in Patients with Billroth II Gastrectomy: A Comparative Study of the Forward-viewing Endoscope and the Side-viewing DuodenoscopeEndoscopy 1997; 29(02): 82-85DOI: 10.1055/s-2007-1004080
TCT-773 The Prognostic Significance of Changes in B-type Naturetic Peptide (BNP) after Transcatheter Aortic Valve Replacement (TAVR): THE PARTNER I EXPERIENCE
Authors: Mayra Guerrero, Brian O'Neill, Vinod Thourani, Susheel Kodali, Mathew Williams, Vasilis Babaliaros, Tom McAndrew, Howard C. Herrmann, Augusto Pichard, Michael Mack, Martin Leon, William W O'Neill
Journal: Journal of the American College of Cardiology (2013)
Thyroid Transcription Factor-1 Amplification and Expressions in Lung Adenocarcinoma Tissues and Pleural Effusions Predict Patient Survival and Prognosis
Authors: Xiao Li, Liyan Wan, Hong Shen, Jian Geng, Jing Nie, Guobao Wang, Nan Jia, Meng Dai, Xiaoyan Bai
Journal: Journal of Thoracic Oncology (2011)
Lateral Diverticulum of the Cervical Esophagus
Authors: Richard A. Cooper
Journal: JAMA (1979)

<h3>To the Editor.—</h3> Medical literature is replete with information on esophageal diverticula. Pulsion diverticula of the upper (Zenker's) and lower (epiphrenic) esophagus as well as traction diverticula near the carina are reported in abundance. However, a lateral pulsion diverticulum of the cervical esophagus has not, to my knowledge, previously been described. <h3>Report of a Case.—</h3> A 79-year-old woman complained of constant expectoration of foamy sputum, postprandial vomiting of bitter material, and a constant bad taste in her mouth. All complaints were of indeterminate duration. Further history and physical findings disclosed hearing loss, hemorrhoids, and osteoarthritis. Laboratory data were non-contributory. An esophagram (Figure) shows a 1.5×1.5-cm diverticulum extending from the right side of the esophagus at the level of C6-C7. A filling defect is seen within the diverticulum. The patient underwent a diverticulectomy. The surgical specimen was 2.5 cm in length, with the dilated portion measuring 1.2 cm in diameter. It
Help for Ex-Smokers?
Authors: Tracy Hampton
Journal: JAMA (2012)

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
The case for the community geriatrician
Authors: J Morris
Journal: BMJ (1994)

Geriatric medicine has developed from being a specialty that concentrated mainly on caring for chronically sick patients in long stay wards to one that deals with one third of all adult medical admissions. Inpatient services are often backed up by day hospitals bridging the gap between hospital and the community.

Many changes are underway. Between 1978-9 and 1992-3 the average length of stay in wards for older people fell from 77.5 days to 27 days. At the same time the number of people aged 85 and over who live in residential and nursing homes doubled. The introduction of social security support in 1983 for people in these homes (both voluntary and private) was responsible for the shift of many older people out of hospitals and into care homes.

The implementation …
Suitable DNA isolation method for the detection of minimal residual disease by PCR techniques
Authors: OJHM Verhagen, AJM Wijhuijs, AJ van der Sluijs-Gelling, T Szczepański, BEM van der Linden-Schrever, MJ Pongers-Willemse, ER van Wering, JJM van Dongen, CE van der Schoot
Journal: Leukemia (1999)