tbuckley/cabot-search huggingface dataset:
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
Authors: Simon Whelan, Nick Goldman
Journal: Molecular Biology and Evolution (2001)

Phylogenetic inference from amino acid sequence data uses mainly empirical models of amino acid replacement and is therefore dependent on those models. Two of the more widely used models, the Dayhoff and JTT models, are estimated using similar methods that can utilize large numbers of sequences from many unrelated protein families but are somewhat unsatisfactory because they rely on assumptions that may lead to systematic error and discard a large amount of the information within the sequences. The alternative method of maximum-likelihood estimation may utilize the information in the sequence data more efficiently and suffers from no systematic error, but it has previously been applicable to relatively few sequences related by a single phylogenetic tree. Here, we combine the best attributes of these two methods using an approximate maximum-likelihood method. We implemented this approach to estimate a new model of amino acid replacement from a database of globular protein sequences comprising 3,905 amino acid sequences split into 182 protein families. While the new model has an overall structure similar to those of other commonly used models, there are significant differences. The new model outperforms the Dayhoff and JTT models with respect to maximum-likelihood values for a large majority of the protein families in our database. This suggests that it provides a better overall fit to the evolutionary process in globular proteins and may lead to more accurate phylogenetic tree estimates. Potentially, this matrix, and the methods used to generate it, may also be useful in other areas of research, such as biological sequence database searching, sequence alignment, and protein structure prediction, for which an accurate description of amino acid replacement is required.
Jejunal Leiomyosarcoma Detected by Tc-99m Sulfur Colloid Gastrointestinal Bleeding Scan
Authors: SEOUNG-OH YANG, MYUNG CHUL LEE, CHANG-SOON KOH, BYUNG IHN CHOI, SEUNG HYUP KIM, CHU-WAN KIM
Journal: Clinical Nuclear Medicine (1990)

Jejunal leiomyosarcoma was initially detected in a patient by a gastrointestinal bleeding scan with Tc-99m sulfur colloid (SC). The scan showed increased blood flow and delayed persistent accumulation of radiotracer in the tumor. The Tc-99m SC gastrointestinal bleeding scan provided useful information to help determine the differential diagnosis of gastrointestinal tumor with bleeding.
Baseline serum creatinine level strongly predicts risk of precedural failure of percutaneous coronary intervention in patients with acute myocardial infarction: Results from the Japanese Multicenter AMI registry (JAMI)
Authors: Hiroshi Koganei, Hiroshi Kasanuki, Hirotaka Kimura, Yasuhiro Ishii, Yukio Tsurumi, Shinya Fujii, Masahiro Yagi, Jun-ichi Yamaguchi, Tetsuya Sumiyoshi, Kazuo Haze, Takashi Honda, Toshinobu Horie
Journal: Journal of the American College of Cardiology (2003)
Hepatic Hemangioma Diagnosis by Emission Computed Tomography
Authors: MARK A. TALLEY, DAN L. NGUYEN, JOE C. LEONARD
Journal: Clinical Nuclear Medicine (1986)

Hepatic hemangiomas in an asymptomatic patient usually require no treatment. Therefore, noninvasive diagnosis of this entity is critical to avoid an unnecessary diagnostic laparotomy and/or closed biopsy, the latter potentially leading to massive or fatal hemorrhage. Numerous authors have reported on the use of computed tomography, ultrasound, and planar nuclear imaging to establish this diagnosis (1,2,3). The findings in a case studied by all modalities, including SPECT imaging, are reported.
Profound induction of hepatic cholesteryl ester transfer protein transgene expression in apolipoprotein E and low density lipoprotein receptor gene knockout mice. A novel mechanism signals changes in plasma cholesterol levels.
Authors: L Masucci-Magoulas, A Plump, X C Jiang, A Walsh, J L Breslow, A R Tall
Journal: Journal of Clinical Investigation (1996)

The plasma cholesteryl ester transfer protein (CETP) mediates the transfer of cholesteryl esters from HDL to other lipoproteins and is a key regulated component of reverse cholesterol transport. Dietary hypercholesterolemia results in increased hepatic CETP gene transcription and higher plasma CETP levels. To investigate the mechanisms by which the liver senses hypercholesterolemia, mice containing a natural flanking region CETP transgene (NFR-CETP transgene) were bred with apo E or LDL receptor gene knockout mice (E0 or LDLr0 mice). Compared to NFR-CETP transgenic (Tg) mice with intact apo E genes, in NFR-CETP Tg/E0 mice there was an eightfold induction of plasma CETP levels and a parallel increase in hepatic CETP mRNA levels. Other sterol-responsive genes (LDL receptor and hydroxymethyl glutaryl CoA reductase) also showed evidence of altered regulation with decreased abundance of their mRNAs in the E0 background. A similar induction of plasma CETP and hepatic CETP mRNA levels resulted from breeding the NFR-CETP transgene into the LDL receptor gene knockout background. When placed on a high cholesterol diet, there was a further increase in CETP levels in both E0 and LDLr0 backgrounds. In CETP Tg, CETP Tg/E0, and CETP Tg/LDLr0 mice on different diets, plasma CETP and CETP mRNA levels were highly correlated with plasma cholesterol levels. The results indicate that hepatic CETP gene expression is driven by a mechanism which senses changes in plasma cholesterol levels independent of apo E and LDL receptors. Hepatic sterol-sensitive genes have mechanisms to sense hypercholesterolemia that do not require classical receptor-mediated lipoprotein uptake.
Combined Yeast β-Glucan and Antitumor Monoclonal Antibody Therapy Requires C5a-Mediated Neutrophil Chemotaxis via Regulation of Decay-Accelerating Factor CD55
Authors: Bing Li, Daniel J. Allendorf, Richard Hansen, Jose Marroquin, Daniel E. Cramer, Claire L. Harris, Jun Yan
Journal: Cancer Research (2007)

Abstract Administration of a combination of yeast-derived β-glucan with antitumor monoclonal antibodies (mAb) has significant therapeutic efficacy in a variety of syngeneic murine tumor models. We have now tested this strategy using human carcinomas implanted in immunocompromised severe combined immunodeficient mice. Combined immunotherapy was therapeutically effective in vivo against NCI-H23 human non–small-cell lung carcinomas, but this modality was surprisingly ineffective against SKOV-3 human ovarian carcinomas. Whereas NCI-H23 tumors responded to this combination therapy with increased intratumoral neutrophil infiltration and C5a production, these responses were lacking in treated SKOV-3 tumors. Further results suggested that SKOV-3 tumors were protected by up-regulation of the membrane complement regulatory protein CD55 (decay-accelerating factor). Blockade of CD55 in vitro led to enhanced deposition of C activation product C3b and increased cytotoxicity mediated by β-glucan–primed neutrophils. In vivo, administration of anti-CD55 mAb along with β-glucan and anti–Her-2/neu mAb caused tumor regression and greatly improved long-term survival in animals bearing the previously resistant SKOV-3 tumors. This was accompanied by increased intratumoral neutrophil accumulation and C5a production. We conclude that CD55 suppresses tumor killing by antitumor mAb plus β-glucan therapy (and, perhaps, in other circumstances). These results suggest a critical role for CD55 to regulate iC3b and C5a release and in turn to influence the recruitment of β-glucan–primed neutrophils eliciting killing activity. [Cancer Res 2007;67(15):7421–30]
A genome-wide association study in Han Chinese identifies new susceptibility loci for ankylosing spondylitis
Authors: Zhiming Lin, Jin-Xin Bei, Meixin Shen, Qiuxia Li, Zetao Liao, Yanli Zhang, Qing Lv, Qiujing Wei, Hui-Qi Low, Yun-Miao Guo, Shuangyan Cao, Mingcan Yang, Zaiying Hu, Manlong Xu, Xinwei Wang, Yanlin Wei, Li Li, Chao Li, Tianwang Li, Jianlin Huang, Yunfeng Pan, Ou Jin, Yuqiong Wu, Jing Wu, Zishi Guo, Peigen He, Shaoxian Hu, Husheng Wu, Hui Song, Feng Zhan, Shengyun Liu, Guanmin Gao, Zhangsuo Liu, Yinong Li, Changhong Xiao, Juan Li, Zhizhong Ye, Weizhen He, Dongzhou Liu, Lingxun Shen, Anbin Huang, Henglian Wu, Yi Tao, Xieping Pan, Buyun Yu, E Shyong Tai, Yi-Xin Zeng, Ee Chee Ren, Yan Shen, Jianjun Liu, Jieruo Gu
Journal: Nature Genetics (2011)
Induction of alkaline phosphatase activity in chronic myeloid leukemia cells: In vitro studies and speculative hypotheses
Authors: A. De Renzo, V. Micera, S. Vaglio, L. Luciano, C. Selleri, B. Rotoli
Journal: American Journal of Hematology (1990)

Three patients with Ph chromosome + chronic myeloid leukemia (CML) in chronic phase suffered from intercurrent pleuritis of undefined origin. At that time, leucocyte alkaline phosphatase activity (LAPA) score was low for circulating neutrophils, but high for those from pleural effusion. LAP negative circulating CML granulocytes were incubated with the pleural liquid: after 40-70 hr, almost all were intensely LAP positive. This finding suggests that the low LAPA score in resting CML neutrophils is attributable to the absence of appropriate stimuli rather than to an incapacity to synthesize the enzyme.
"The Chronic Fatigue Syndrome"
Authors: Catherine Radford
Journal: Annals of Internal Medicine (1988)

Letters and Corrections15 July 1988"The Chronic Fatigue Syndrome"Catherine Radford, MFS, MPhilCatherine Radford, MFS, MPhilSearch for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-109-2-166 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptTo the Editor: A patient diagnosed with a disease must live with its label and with lay persons' understanding of that label. Thus, as a person with what is called "chronic Epstein-Barr virus syndrome," I protest vehemently against naming this disease "chronic fatigue syndrome" as proposed by Holmes and colleagues (1).While going from one doctor to another trying to find out what was wrong with me for 4 months (and not knowing about chronic Epstein-Barr virus syndrome) I became practiced in describing my symptoms accurately. I emphasized that I did not have tiredness, lethargy, or fatigue but asthenia, in...Reference1. HolmesKaplanGantz GJN. Chronic fatigue syndrome: a working case definition. Ann Intern Med. 1988;108:387-9. LinkGoogle Scholar1. HolmesKaplanGantz GJN. Chronic fatigue syndrome: a working case definition. Ann Intern Med. 1988;108:387-9. LinkGoogle Scholar2. Bennett R. The fibrositis/fibromyalgia syndrome: Current issues and perspectives. Am J Med. 1986;81(3A):1-115. CrossrefGoogle Scholar3. Moldofsky H. Sleep and musculoskeletal pain. Am J Med. 1986;81(3A):85-9. CrossrefMedlineGoogle Scholar4. Wolfe F. Development of criteria for the diagnosis of fibrositis. Am J Med. 1986;81(3A):99-104. CrossrefMedlineGoogle Scholar1. HolmesKaplanGantz GJN. Chronic fatigue syndrome: a working case definition. Ann Intern Med. 1988;108:387-9. LinkGoogle Scholar This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAffiliations: New Haven, CT 06511 PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics Cited ByLymphocyte Markers and Natural Killer Cell Activity in Fibromyalgia Syndrome: Effects of Low-Dose, Sublingual Use of Human Interferon-alphaChronic Fatigue Syndrome: A ConundrumOld wine in new bottles: neurasthenia and ‘ME’ 15 July 1988Volume 109, Issue 2Page: 166-167KeywordsChronic fatigue syndromeEpstein-Barr virusFatigue Issue Published: 15 July 1988 PDF DownloadLoading ...
Myocardial sympathetic denervation prevents chamber-specific alteration of beta-adrenergic transmembrane signaling in rabbits with heart failure
Authors: Toshihisa Anzai, Tsutomu Yoshikawa, Akiyasu Baba, Hiroshi Nishimura, Hiroto Shiraki, Keiichi Nagami, Masahiro Suzuki, Yumiko Wainai, Satoshi Ogawa
Journal: Journal of the American College of Cardiology (1996)
BMP-2 peptide-functionalized nanopatterned substrates for enhanced osteogenic differentiation of human mesenchymal stem cells
Authors: Mun-Jung Kim, Bora Lee, Kisuk Yang, Junyong Park, Seokwoo Jeon, Soong Ho Um, Dong-Ik Kim, Sung Gap Im, Seung-Woo Cho
Journal: Biomaterials (2013)
Surgical management of pleomorphic adenoma of parotid gland in elderly patients: Role of morphological features
Authors: Germano Guerra, Domenico Testa, Stefania Montagnani, Domenico Tafuri, Francesco Antonio Salzano, Aldo Rocca, Bruno Amato, Giovanni Salzano, Giovanni Dell'Aversana Orabona, Pasquale Piombino, Gaetano Motta
Journal: International Journal of Surgery (2014)
Unusual Distribution of Multifocal Stress Fractures Involving the Upper and Lower Limbs in a Military Recruit Demonstrated by Bone Scintigraphy
Authors: Myung-Hee Sohn, Hwan-Jeong Jeong, Chang-Yeol Yim
Journal: Clinical Nuclear Medicine (2007)

A 20-year-old man performed vigorous military training despite the presence of left thigh pain, and developed 11 stress fractures involving the upper (bilateral humeri and ulnas) and lower (both femurs, right tibia, left fourth metatarsal, and right calcaneus) extremities, which were demonstrated on bone scintigraphy (Zwas grade I–IV group). He had joined the army 4 months earlier. His military training involved running on the ground for 15 minutes and carrying a trench mortar daily every morning. Sometimes he carried out a forced march carrying arms, special training in mountainous areas, and played football. The plain radiographs of all suspected fractures showed various findings from normal to periosteal thickening.
Involvement of transcriptional mechanisms in the inhibition of NOS2 expression by dexamethasone in rat mesangial cells
Authors: Marta Saura, Carlos Zaragoza, Manuela Díaz-Cazorla, Octavio Hernández-Perera, Eudora Eng, Charles J. Lowenstein, Dolores Pérez-Sala, Santiago Lamas
Journal: Kidney International (1998)
The influence of antibodies on Staphylococcus epidermidis adherence to polyvinylpyrrolidone-coated silicone elastomer in experimental biomaterial-associated infection in mice
Authors: Corine A.N. Broekhuizen, Leonie de Boer, Kim Schipper, Christopher D. Jones, Shan Quadir, Robert G. Feldman, Christina M.J.E. Vandenbroucke-Grauls, Sebastian A.J. Zaat
Journal: Biomaterials (2009)
Progressive renal failure in a remnant kidney.
Authors: L R Solomon, N P Mallick, W Lawler
Journal: BMJ (1985)

Bleedingfrom peptic ulcers and use of non-steroidal anti-inflammatory drugs (NSAIDs) in Romford area compared with local and national prescribing habits No (%) of prescriptions for NSAIDs in 1983 (thousands)t No (%) of patients with Expected values from Mean age Patients with NSAID bleeding peptic ulcers taking NSAID regional prescribing data (years) ulcer history Great Britain NE Thames region Indomethacin 9 (17) 10-8 72-1 2 3268 (17) 259 (20) Ibuprofen 2 (4)
The molecular genetics of the genodermatoses: progress to date and future directions
Authors: A.D. Irvine, W.H.I. McLean
Journal: British Journal of Dermatology (2003)

The Human Genome Mapping Project and allied rapid advances in genetic technology over the past decade have facilitated accurate association of allelic variations in several genes with specific skin phenotypes. Currently the genetic bases of the majority of the more common genodermatoses have been elucidated. In scientific terms this work has been extraordinarily successful and has yielded many new biological insights. These advances, although exciting, have yet to be translated into direct benefit for patients with these diseases. Genetic counselling has been greatly aided by gene identification, by the better understanding of genotype–phenotype correlation and by the disclosure of unexpected genetic mechanisms in some families. Knowledge of the molecular basis of these disorders has also been vital in enabling DNA-based prenatal diagnosis in several conditions and DNA-based preimplantation diagnosis has been used in a selected few. While this successful period of gene mapping is now nearing completion, progress towards the next goal, that of developing therapeutic strategies based on the knowledge of these underlying genetic mechanisms, has proven frustratingly slow. Despite the ready access to the skin compared with solid internal organs, the challenges of cutaneous gene therapy are legion and many technical issues need to be surmounted to enable gene replacement or modification of gene expression to have a useful role in these disorders. In this article we make a comprehensive review of progress to date in gene identification, genotype–phenotype correlation, prenatal diagnosis and cutaneous gene therapy, and we examine future directions for research in this field.
Preventing congenital abnormalities: Authors' reply
Authors: A. E Czeizel, B. Modell
Journal: BMJ (1993)

A substantial but prudent investment of finances is therefore essential to provide a safe service in which the clinical needs of patients are held to be primary.It is not acceptable that patients with diagnostic problems in headache, cerebrovascular disease, multiple sclerosis, spinal tumours, pain, epilepsy, space occupying lesions, and dementia-to choose limited examples- should be kept waiting for skilled professional diagnosis, investigation, sympathetic management, and treatment.Waiting times in one specialty do not correlate with waiting times in others.The slogan "reduction of waiting lists" as applied to elective surgery or outpatient appointments is simplistic and may have no relevance to actual or imminent medical needs of patients and their families.Rectification of this unbalanced approach is overdue and should be brought to the attention of management and to politicians who reorganise the health service.We are in a position to take a rational, professional lead in advising solutions to such problems, which are at the crux of proper provision for the health of the nation.
J W P Bradley
Authors: A. O. M. Bradley
Journal: BMJ (2014)

An 81-year-old woman presented with an enlarging, tender ulcer on her scalp over an 8-week period, attributing it to a prior graze with garden shears. C-reactive protein and erythrocyte sedimentation rate were elevated at 87.7 mg/L and 112 mm/hour, respectively. Incisional biopsies demonstrated ulceration and full thickness necrosis with no evidence of malignancy. Vasculitis was suggested as a likely cause of such extensive necrosis and subsequent temporal artery biopsy findings were consistent with giant cell arteritis. The patient was initially treated with high-dose oral prednisolone and achieved complete healing of the scalp necrosis within 12 months, with a gradual down-titration of steroid therapy thereafter. Scalp necrosis is a rare, potentially life-threatening complication of giant cell arteritis. This case highlights the importance of considering scalp necrosis as a manifestation of giant cell arteritis when assessing scalp ulceration. Prompt diagnosis and treatment can prevent significant morbidity and potential mortality.
ABORTION OR FETICIDE VS. HOMICIDE
Authors: William J. Robinson
Journal: JAMA (1934)

<h3>To the Editor:—</h3> I thank you for your fair review of my book "The Law Against Abortion" (The Journal, January 6, p. 71). You have let me off rather easily. Of course, I did not expect the reviewer ofThe Journalto agree with my views. There are some points, however, in the review on which I should like to be permitted to offer some comments. Your reviewer places feticide, infanticide and homicide on exactly the same level. "Why he would tolerate feticide and forbid infanticide and other forms of homicide is not apparent." he writes. May I remind your readers that when I initiated the propaganda for birth control thirty years ago, the same thing exactly was said about the prevention of conception that is now being said about abortion. Many physicians at that time and some physicians even now place prevenception on exactly the same level as murder.
Chemical Depilatories in Ancient Rome
Authors: Marianna Karamanou, Stephanie Christen-Zäch
Journal: JAMA Dermatology (2014)

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 Dermatology 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 Dermatology journal
Immune Cell Function and Recycling of Purines
Authors: Eloise R. Giblett
Journal: New England Journal of Medicine (1976)

During the course of evolution, some remarkable mechanisms have developed to ensure the cellular production of substances that are essential components of DNA and RNA. For example, two complicated series of metabolic steps, beginning with simpler compounds, are involved in the de novo synthesis of purine and pyrimidine nucleotides such as ATP by one pathway and UTP by the other. In addition, there are so-called "salvage" pathways that, under appropriate conditions, recycle the breakdown products of nucleic acids.The importance of purine salvage for metabolic homeostasis first became apparent when Lesch-Nyhan disease, an especially crippling form of gout, was found . . .
Quantification of ischaemia induced vulnerability by precordial T wave alternans analysis in dog and human
Authors: B. D Nearing, S. N Oesterle, R. L Verrier
Journal: Cardiovascular Research (1994)

Journal Article Quantification of ischaemia induced vulnerability by precordial T wave alternans analysis in dog and human Get access Bruce D Nearing, Bruce D Nearing Georgetown University School of Medicine and Hospital, 3900 Reservoir Road NW, Washington DC 20007, USA – Department of Pharmacology: B D Nearing, R L Verrier; Department of Cardiology: S N Oesterle. Correspondence to Dr Verrier. Search for other works by this author on: Oxford Academic PubMed Google Scholar Stephen N Oesterle, Stephen N Oesterle Georgetown University School of Medicine and Hospital, 3900 Reservoir Road NW, Washington DC 20007, USA – Department of Pharmacology: B D Nearing, R L Verrier; Department of Cardiology: S N Oesterle. Search for other works by this author on: Oxford Academic PubMed Google Scholar Richard L Verrier Richard L Verrier Georgetown University School of Medicine and Hospital, 3900 Reservoir Road NW, Washington DC 20007, USA – Department of Pharmacology: B D Nearing, R L Verrier; Department of Cardiology: S N Oesterle. Search for other works by this author on: Oxford Academic PubMed Google Scholar Cardiovascular Research, Volume 28, Issue 9, September 1994, Pages 1440–1449, https://doi.org/10.1093/cvr/28.9.1440 Published: 01 September 1994 Article history Received: 28 September 1993 Accepted: 02 June 1994 Published: 01 September 1994