tbuckley/cabot-search huggingface dataset:
Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments
Authors: T. Golubchik, M. J. Wise, S. Easteal, L. S. Jermiin
Journal: Molecular Biology and Evolution (2007)

Multiple sequence alignment (MSA) is a crucial first step in the analysis of genomic and proteomic data. Commonly occurring sequence features, such as deletions and insertions, are known to affect the accuracy of MSA programs, but the extent to which alignment accuracy is affected by the positions of insertions and deletions has not been examined independently of other sources of sequence variation. We assessed the performance of 6 popular MSA programs (ClustalW, DIALIGN-T, MAFFT, MUSCLE, PROBCONS, and T-COFFEE) and one experimental program, PRANK, on amino acid sequences that differed only by short regions of deleted residues. The analysis showed that the absence of residues often led to an incorrect placement of gaps in the alignments, even though the sequences were otherwise identical. In data sets containing sequences with partially overlapping deletions, most MSA programs preferentially aligned the gaps vertically at the expense of incorrectly aligning residues in the flanking regions. Of the programs assessed, only DIALIGN-T was able to place overlapping gaps correctly relative to one another, but this was usually context dependent and was observed only in some of the data sets. In data sets containing sequences with non-overlapping deletions, both DIALIGN-T and MAFFT (G-INS-I) were able to align gaps with near-perfect accuracy, but only MAFFT produced the correct alignment consistently. The same was true for data sets that comprised isoforms of alternatively spliced gene products: both DIALIGN-T and MAFFT produced highly accurate alignments, with MAFFT being the more consistent of the 2 programs. Other programs, notably T-COFFEE and ClustalW, were less accurate. For all data sets, alignments produced by different MSA programs differed markedly, indicating that reliance on a single MSA program may give misleading results. It is therefore advisable to use more than one MSA program when dealing with sequences that may contain deletions or insertions, particularly for high-throughput and pipeline applications where manual refinement of each alignment is not practicable.
Enhancement of Contractility With Sustained Afterload in the Intact Murine Heart
Authors: Maricela Reyes, Gregory L. Freeman, Daniel Escobedo, Shuko Lee, Mark E. Steinhelper, Marc D. Feldman
Journal: Circulation (2003)

It has been hypothesized that because of its rapid heart rate, the intact murine heart functions near maximal contractility in the basal state. If this hypothesis is correct, then the fast and slow components of myocardial length-dependent activation should be blunted compared with larger mammals.Mice (n=24) were anesthetized, and via an open chest, LV pressure-volume relationships were determined by a dual-frequency conductance catheter system. Baseline pressure-volume relationships were determined during transient occlusion of the inferior vena cava, and repeat measurements were made after 1 (n=10) and 7 (n=21) minutes of sustained aortic occlusion. Control experiments were performed in a subset of mice (n=3). For baseline to 1 minute, an increase in afterload (maximal pressure 95+/-9 to 126+/-7 mm Hg; P<0.001) and effective arterial elastance (5.9+/-3.1 to 9.2+/-3.9 mm Hg/microl; P<0.001) resulted in an increase in end-diastolic volume (31+/-8 to 35+/-9 microL; P<0.001). The result was maintenance of stroke volume (17+/-6 to 15+/-6; P=NS) owing to an increase in contractility (leftward shift in V100 [the volume of end-systolic elastance at 100 mm Hg], 24+/-9 to 16+/-5 microL; P<0.001). No additional augmentation of systolic function was found at 7 minutes.This study demonstrates that the fast phase of length-dependent activation is intact but not the slow phase, consistent with murine myocardium functioning near maximal contractility in the basal state.
TCTAP A-123 Feasibility of Transradial Coronary Intervention in Patients with Cardiac Arrest Caused by Acute Coronary Syndrome
Authors: Yukio Mizuguchi, Akihiko Takahashi, Takeshi Yamada, Norimasa Taniguchi, Shunsuke Nakajima, Tetsuya Hata
Journal: Journal of the American College of Cardiology (2014)
Improving Clinical Learning Environments for Tomorrow's Physicians
Authors: Thomas J. Nasca, Kevin B. Weiss, James P. Bagian
Journal: New England Journal of Medicine (2014)

Interview with Dr. Eileen Reynolds on the ACGME's review of clinical learning environments and its goals for residency programs. (11:33)Download On the basis of site visits that it has conducted for its Clinical Learning Environment Review program, the Accreditation Council for Graduate Medical Education reports finding a generalized lack of resident engagement in systems-based practice.
Review of Pathophysiology
Authors: Frank D. Gray
Journal: JAMA (1984)

The authors of this review of pathophysiology integrate the principles of basic medical science with the introductory principles of clinical medicine, and they manage to do this in a realistic and coherent manner. Clinical cases are described at the end of each chapter to epitomize the new principles. The text is admirably suited to the needs of a sophomore medical student taking a course in physical diagnosis or introduction to clinical medicine. However, it lacks the depth and breadth of coverage that would satisfy the advanced student, resident, or practicing physician. Although the text is generally clear and informative, some of the illustrations are less so. A few are confusing; others are excellent but lack labels sufficiently clear for second-year students. However, I do not want to be contentious about this because many of the figures are good and the text is self-explanatory without illustrations. For example, one of the
Growth in Children with Chronic Lung Disease
Authors: Pamela B. Davis, Carolyn M. Kercsmar
Journal: New England Journal of Medicine (2000)

In patients with cystic fibrosis, the inflammatory response in the airways to bacterial infection is excessive and deleterious. Thus, interrupting the inflammatory response is a goal of therapy. In a clinical trial of prednisone, given on alternate days at a dose of either 1 or 2 mg per kilogram of body weight to patients 6 to 14 years of age who had cystic fibrosis and mild-to-moderate lung disease, pulmonary function was significantly better in the group that received 1 mg of prednisone per kilogram than in the placebo group.1 However, prednisone treatment also caused diabetes, cataracts, and growth retardation at . . .
Noninvasive assessment of coronary flow reserve impairment in patients with systemic sclerosis
Authors: Roberta Montisci, Paolo Colonna, Massimo Ruscazio, LiJun Chen, Carlo Caiati, Pietro Garau, Giuseppe Passiu, Alessandra Vacca, Alessandro Mathieu, Sabino Iliceto
Journal: Journal of the American College of Cardiology (2002)
Abstract 2127: Synergistic effect of carboxyl-modified magnetic nanoparticles and docetaxel on prostate cancer cells <i>in vitro</i>.
Authors: Masatoshi Watanabe, Akiko Sato, Daiki Okamoto, Daisuke Kurioka, Hitoshi Ishiguro, Hiroji Uemura, Yoshinobu Kubota
Journal: Cancer Research (2013)

Abstract Chemotherapy is used for castration-resistant prostate cancer as one of treatment options. In this regard, docetaxel-based chemotherapy has been shown to improve the quality of life in patients with the advanced disease. However, this needs to be improved because of limitations by lack of specificity, systemic toxicity, and progression of docetaxel-resistance. Nanotechnology has served a new role in medical sciences by a variety of nanotechnology platforms, leading to therapy and diagnostics. Among these platforms, magnetic nanoparticles (Fe3O4) have potential applications in drug delivery, cancer diagnosis and therapy. We have shown that magnetic nanoparticles (MgNPs) would modify the effect of chemotherapy in cancer cells. In this study, we analyzed the combined effect of docetaxel and carboxyl-modified magnetic nanoparticles (MgNPs-COOH) on a prostate cancer cell line, DU145 and their mechanisms compared with the effect of MgNPs and docetaxel. The combination of docetaxel and MgNPs/MgNPs-COOH more effectively inhibited cancer cell growth and induced apoptosis. While only MgNPs produced reactive oxygen species (ROS) and inhibited cancer cell growth slightly, MgNPs-COOH did neither produce ROS nor inhibit cancer cell growth. In addition, these two MgNPs appear to inhibit the different cellular pathways involving apoptosis and inflammation. These results suggest that MgNPs-COOH may induce different responses compared with MgNPs, and result in favorable development of current chemotherapy for the advanced disease and leading to new tumor ablation therapies. Citation Format: Masatoshi Watanabe, Akiko Sato, Daiki Okamoto, Daisuke Kurioka, Hitoshi Ishiguro, Hiroji Uemura, Yoshinobu Kubota. Synergistic effect of carboxyl-modified magnetic nanoparticles and docetaxel on prostate cancer cells in vitro. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2127. doi:10.1158/1538-7445.AM2013-2127
The lupus anticoagulant in systemic lupus erythematosus and systemic sclerosis
Authors: N.R. Rowell, G.M. Tate
Journal: British Journal of Dermatology (1987)

The lupus anticoagulant is an acquired IgG or IgM antibody directed against specific phospholipids involved in the formation of prothrombin activators. It is identified by coagulation tests. The partial thromboplastin time and kaolin clotting time are prolonged and these abnormalities cannot be corrected by the addition of normal plasma, as in simple clotting factor deficiency. The thrombin time is normal. Five out of 36 unselected patients with systemic lupus erythematosus (SLE) showed the presence of lupus anticoagulant (14%). The duration of SLE was from 2 to 38 years. Three of the five patients gave a history of thrombosis. The only male patient suffered from myocardial infarction and venous thromboses in his twenties and is an example of a group of young males with major thrombotic episodes. One patient had a Coombs‐positive haemolytic anaemia. Thrombocytopenia is sometimes associated with the lupus anticoagulant but was not found in the present series. Anticardiolipin antibodies were not measured, but none of the patients had false‐positive serology. The lupus anticoagulant is a useful marker for those patients with SLE at risk for thrombosis. The lupus anticoagulant was not found in 24 unselected patients with systemic sclerosis and is therefore not a factor in the pathogenesis of the vascular phenomena in this disease.
Blood eosinophils from atopic donors express messenger RNA for the α, β, and γ subunits of the high-affinity IgE receptor (FcϵRI) and intracellular, but not cell surface, α subunit protein
Authors: Susan J. Smith, Sun Ying, Qui Meng, Mark H.F. Sullivan, Julia Barkans, Onn Min Kon, Bhupinder Sihra, Mark Larché, Francesca Levi-Schaffer, A.Barry Kay
Journal: Journal of Allergy and Clinical Immunology (2000)
Deaths and Obituaries.
Authors: John H. Moore
Journal: JAMA (1899)

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
Cholescintigraphy in acalculous biliary pain: If abnormal, should cholecystectomy follow?
Authors: E A Shaffer
Journal: Hepatology (1992)

A 45-minute infusion of an octapeptide of cholecystokinin (Kinevac; Squibb Diagnostics, New Brunswick, NJ) was used to measure the gallbladder ejection fraction during cholescintigraphy in 40 normal volunteers. Cholecystokinin cholescintigraphy was shown to be a reproducible test. The maximum mean gallbladder ejection fraction occurred 15 minutes after cholecystokinin infusion and was 74.5% ± 1.9% (mean ± SEM). A gallbladder ejection fraction >40% (mean – 3SD) was arbitrarily defined to be normal. The gallbladder ejection fraction test was then used to identify patients with acalculous biliary symptoms who may respond to cholecystectomy. A total of 103 patients was tested; 21 had abnormal gallbladder ejection fractions and were randomized into two groups, cholecystectomy or no operation. These patients were followed up symptomatically at 3-month intervals for 13–54 months (mean, 34 months). Of the 11 patients who underwent cholecystectomy, 10 (91%) lost their symptoms and 1 improved. Of the 10 patients in the group that did not undergo surgery, all continued to be symptomatic, 2 of whom requested cholecystectomy after 13 and 24 months, respectively. Of the 13 gallbladders obtained from surgery, 12 showed evidence of chronic cholecystitis, muscle hypertrophy, and/or narrowed cystic duct. A normal gallbladder ejection fraction was recorded in 82 patients, and further treatment was left to the discretion of their referring clinician. On follow-up, 50 patients were asymptomatic and 10 were symptomatic without specific treatment of the biliary tract; 14 underwent cholecystectomy, 8 of whom were asymptomatic. Pathological abnormalities were recorded in 6 of the removed gallbladders. It is concluded that the gallbladder ejection fraction obtained after a 45-minute infusion of cholecystokinin during cholescintigraphy is a reproducible measure of gallbladder emptying, and that cholecystectomy alleviates the biliary-type pain of patients with a reduced gallbladder ejection fraction.
Increased angiotensin-I converting enzyme gene expression in the failing human heart. Quantification by competitive RNA polymerase chain reaction.
Authors: R Studer, H Reinecke, B Müller, J Holtz, H Just, H Drexler
Journal: Journal of Clinical Investigation (1994)

Local activation of the components of the renin angiotensin system in the heart is regarded as an important modulator of cardiac phenotype and function; however, little is known about their presence, regulation, and potential activation in the human heart. To investigate the gene expression of major angiotensin-II-forming enzymes in left ventricles of normal (n = 9) and failing human hearts (n = 20), we established a competitive RNA-polymerase chain reaction (PCR) for mRNA quantification of angiotensin-I converting enzyme (ACE) and human heart chymase. For each gene, competitor RNA targets with small internal deletions were used as internal standards to quantify the original number of transcripts and to control reverse transcription and PCR. In PCR, each target and the corresponding competitor were amplified by competing for the same primer oligonucleotides. The variability of ACE RNA-PCR was 11% indicating a high reproducibility of this method. In addition, ACE mRNA levels obtained by competitive RNA-PCR correlated favorably with traditional slot blot hybridization (r = 0.69, n = 10; P < 0.05). Compared with nonfailing hearts, the number of ACE transcripts referred to 100 ng of total RNA was increased threefold in patients with chronic heart failure (4.2 +/- 2.5 vs. 12.8 +/- 6 x 10(5); P < 0.0005). In contrast, no significant difference was found in chymase gene expression between normal and failing hearts. Thus, the expression of the cardiac ACE but not of human heart chymase is upregulated in failing human heart indicating an activation of the cardiac renin-angiotensin system in patients with advanced heart failure.
Abstract 4182: Overexpression of <i>Mig-6</i> suppresses endometrial cancer development and progression in ablation of <i>Pten</i> mice
Authors: Tae Hoon Kim, Hong Im Kim, Michael J. Large, Russell R. Broaddus, John P. Lydon, Jae-Wook Jeong
Journal: Cancer Research (2012)

Abstract Endometrial cancer is the most common gynecological cancer. Estrogen-dependent endometrioid carcinoma is the most common type of endometrial cancer. In previous studies, we have identified mitogen-inducible gene 6 (Mig-6) as a downstream target of Progesterone Receptor (Pgr) action in the uterus. Ablation of Mig-6 in the murine uterus leads to the development of endometrial hyperplasia and estrogen-induced endometrial cancer. These results suggest that Mig-6 act as a tumor suppressor in endometrial cancer. To assess the effects of the overexpression Mig-6 and the PTEN/PI3K/AKT signaling pathways on uterine tumorigenesis, mice with Pten floxed (Ptenf/f) and LoxP-STOP-LoxP Mig-6 (R26Mig-6LSL) were bred to the PRCre mouse model to generate ablation of Pten and overexpression of Mig-6 in the uterus (PRcre+ R26Mig-6LSL Ptenf/f). PRcre+ R26Mig-6LSL Ptenf/f showed significantly increased survival time compared to PRcre/+ Ptenf/f mice. Double mutant mice showed significantly decreased uterine weight compared to PRcre/+Ptenf/f at 3 months of age. Gross morphology at 3 months of age showed that double mutant mice dramatically retarded the development of endometrial cancer compared to ablation of Pten alone. Histological analysis showed that endometrial adenocarcinoma with invasion into the myometrium was observed in the PRcre/+Ptenf/f mice at 3 months of age. However, double mutant mice did not develop endometrial cancer. Immunohistochemstry analysis showed significantly increased apoptosis and decreased proliferation at epithelial cells in PRcre+ R26Mig-6LSL Ptenf/f mice compared to PRcre/+ Ptenf/f mice at 3 months of age. The expression of pERK1/2 was significantly decreased in PRcre+ R26Mig-6LSL Ptenf/f mice compared to PRcre/+ Ptenf/f mice at 2 and 3 months of age. The expression of Pgr and its tartget genes was significantly increased in PRcre+ R26Mig-6LSL Ptenf/f mice compare to PRcre/+ Ptenf/f mice. However, the expression of Estrogen Receptor ≤ (Esr1) and its target genes was significantly decreased. The ability of Mig-6 to repress cancer development indicates that it exerts a tumor suppressor function in endometrial cancer. These results will contribute to the understanding of the molecular mechanism of tumorigenesis and to the development of therapeutic approaches for endometrial cancer.(Supported by NIH, R01 HD057873) Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4182. doi:1538-7445.AM2012-4182
Occupational Acroosteolysis
Authors: Rex H Wilson
Journal: JAMA (1967)

In 31 cases of acroosteolysis of the hands of workmen associated with vinyl chloride (CH CHCI) polymerization processes, the osteolysis was specific to the distal phalanges of hands and was frequently associated with Raynaud's symptoms. Affected personnel ranged in age from 26 to 47. The disorder is believed to have resulted from a combination of physical insult, chemical insult, and personal idiosyncrasy. The specific causes are unknown. The prevalence was found to be less than 3% among employees performing similar work. No cases were found in workmen using or processing the polymer or manufacturing commercial resins.
Psychological Tests and Medical Prognosis
Authors: ALBERT J. STUNKARD
Journal: Annals of Internal Medicine (1962)

Editorials1 March 1962Psychological Tests and Medical PrognosisALBERT J. STUNKARD, M.D.ALBERT J. STUNKARD, M.D.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-56-3-524 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptThe "hurricane of new scientific knowledge" discussed in the foregoing editorial has, for the most part, blown into medicine from the physical and biological sciences. It is, indeed, new knowledge, knowledge for which experience in clinical medicine has not prepared us, knowledge which has, in fact, changed the very nature of clinical medicine. Another kind of scientific knowledge, however, is also beginning to make an impact upon clinical medicine. This is a kind of knowledge which is not introduced from the outside, as it were, but is largely derived from clinical experience and consists of refinement or rather, perhaps, systematization...References1. WEINERTHALERREISERMIRSKY HMMFIA: Etiology of duodenal ulcer. I. Relation of specific psychological characteristics to rate of gastric secretion (serum pepsinogen). Psychosom. Med. 19: 1, 1957. CrossrefMedlineGoogle Scholar2. IMBODENCANTERCLUFF JBALE: Convalescence from influenza. Arch. Intern. Med. 108: 393, 1961. CrossrefMedlineGoogle Scholar3. OSTFELDPAULLEPPER AOM: An anterospective study of coronary heart disease. (Abstract) Psychosom. Med. 23: 448, 1961. Google Scholar4. HATHAWAYMCKINLEY SRJC: Minnesota Multiphasic Personality Inventory Manual, 2d ed., Psychology Corporation, New York, 1951. Google Scholar5. HOLMESJOFFEKETCHAMSHEEHY THJRJWTF: Experimental study of prognosis. J. Psychosom. Res. 5: 235, 1961. CrossrefMedlineGoogle Scholar6. BERLEPINSKYWOLFWOLFF BBRHSHG: Berle index: a clinical guide to prognosis in stress diseases. J. A. M. A. 149: 1624, 1952. CrossrefMedlineGoogle Scholar This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAffiliations: Departments of Psychiatry and Medicine University of Pennsylvania Philadelphia, Pennsylvania PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics Cited ByThe Psychiatric Consultation Patient 1 March 1962Volume 56, Issue 3Page: 524-526 Issue Published: 1 March 1962 PDF DownloadLoading ...
Persistent post-traumatic stress disorder Role of alcohol ignored
Authors: S I Cohen, D Summerfiel, F Hume, J C Hughes, L A Neal
Journal: BMJ (1994)

with uptake rates for medical prescriptions in general.4Those attending were not the "worried well" but patients referred by their general prac- titioners for help with a range of medical conditions such as obesity, hypertension, depression, and raised cholesterol concentrations.The full evaluation report is available from the leisure services department of Stockport Metropolitan Borough Council (tel 061 474 4415).There is no doubt about the validity of the findings of the Stockport scheme, and we urge general practices not to look too long before leaping into a health promotion activity that could contribute towards improved cardiovascular and mental health.