tbuckley/cabot-search huggingface dataset:
EST-Based Identification of Genes Expressed in Skeletal Muscle of the Mandarin Fish ( Siniperca chuatsi )
Authors: Feng Ding, Wuying Chu, Peng Cui, Meng Tao, Ruixue Zhou, Falan Zhao, Songnian Hu, Jianshe Zhang
Journal: Genomics Proteomics & Bioinformatics (2011)

Abstract To enrich the genomic information of the commercially important fish species, we obtained 5,063 high-quality expressed sequence tags (ESTs) from the muscle cDNA database of the mandarin fish (Siniperca chuatsi). Clustering analysis yielded 1,625 unique sequences including 443 contigs (from 3,881 EST sequences) and 1,182 singletons. BLASTX searches showed that 959 unique sequences shared homology to proteins in the NCBI non-redundant database. A total of 740 unique sequences were functionally annotated using Gene Ontology. The 1,625 unique sequences were assigned to Kyoto Encyclopedia of Genes and Genomes reference pathways, and the results indicated that transcripts participating in nucleotide metabolism and amino acid metabolism are relatively abundant in S. chuatsi. Meanwhile, we identified 15 genes to be abundantly expressed in muscle of the mandarin fish. These genes are involved in muscle structural formation and regulation of muscle differentiation and development. The most remarkable gene in S. chuatsi is nuclease diphosphate kinase B, which is represented by 449 EST sequences accounting for 8.86% of the total EST sequences. Our work provides a transcript profile expressed in the white muscle of the mandarin fish, laying down a foundation in better understanding of fish genomics.
Abstract 1641: Concordance between mutations identified by bar-coded multiplexed sequencing of BRAF, NRAS, and KIT in formalin fixed (FFPE) tissue from melanoma patients using the Ion Torrent Personal Genome Machine (PGM) and a real-time PCR assay
Authors: George S. Watts, Marc M. Oshiro, Lee D. Cranmer
Journal: Cancer Research (2012)

Abstract The standard chemotherapy for metastatic melanoma is dacarbazine, however, progression free survival with dacarbazine is a dismal two months. Efforts to improve the treatment of melanoma have focused on specific molecular defects following the discovery that the majority of patients have a mutation in one of three members of the BRAF-MAPK signaling pathway: KIT, BRAF, and RAS. Recent clinical trials have shown promise for drugs that target the molecular defects in melanoma, including the recently approved mutant BRAF inhibitor vemurafenib. As new drugs that target specific mutations move through clinical trials, the opportunity to perform precision medicine is becoming a reality. To deliver on the promise shown by the new generation of drugs it will be necessary to detect specific mutations in patients so they can be matched with the right drug. To this end, we have used an Ion Torrent Personal Genome Machine to sequence the six most commonly mutated codons in melanoma (BRAF 600, NRAS 12 and 13, NRAS 61, KIT 576, and KIT 642) from formalin fixed paraffin embedded tissue of late stage melanoma patients. All six codons of interest were sequenced in forty-six patients and mutations identified by comparison to normal controls. The A375 cell line, containing the known mutation V600E in BRAF was used as a positive control. Samples were sequenced in a multiplexed format using bar coding of the amplicons which allowed 14 patients and two controls to be sequenced simultaneously on each chip. Results were confirmed by real time RT-PCR assay specific for the BRAF V600E mutation. We demonstrate the feasibility of using rapid low cost next-generation sequencing to provide robust detection of mutations in fixed patient samples. 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 1641. doi:1538-7445.AM2012-1641
Assessment of a genetic contribution to osteoarthritis of the hip: sibling study
Authors: P. Lanyon
Journal: BMJ (2000)

<h3>Abstract</h3> <b>Objectives:</b> To study the influence of genetics on the development of hip osteoarthritis as determined by structural change on plain radiographs. <b>Design:</b> Sibling study. <b>Setting:</b> Nottinghamshire, England. <b>Participants:</b> 392 index participants with hip osteoarthritis of sufficient severity to warrant total hip replacement, 604 siblings of the index participants, and 1718 participants who had undergone intravenous urography. <b>Main outcome measure:</b> Odds ratios for hip osteoarthritis in siblings. <b>Results:</b> The age adjusted odds ratios in siblings were 4.9 (95% confidence interval, 3.9 to 6.4) for probable hip osteoarthritis and 6.4 (4.5 to 9.1) for definite hip osteoarthritis. These values were not significantly altered by adjusting for other risk factors. <b>Conclusion:</b> Siblings have a high risk of hip osteoarthritis as shown by structural changes on plain radiographs. One explanation is that hip osteoarthritis is under strong genetic influence.
Proteomic Analysis of Waldenstrom Macroglobulinemia
Authors: Evdoxia Hatjiharissi, Hai Ngo, Alexey A. Leontovich, Xavier Leleu, Michael Timm, Mona Melhem, Diane George, Ganwei Lu, Joanna Ghobrial, Yazan Alsayed, Steven Zeismer, Miguel Cabanela, Alex Nehme, Xiaoying Jia, Anne Sophie Moreau, Steven P. Treon, Rafael Fonseca, Morie A. Gertz, Kenneth C. Anderson, Thomas E. Witzig, Irene M. Ghobrial
Journal: Cancer Research (2007)

Abstract To better understand the molecular changes that occur in Waldenstrom macroglobulinemia (WM), we employed antibody-based protein microarrays to compare patterns of protein expression between untreated WM and normal bone marrow controls. Protein expression was defined as a &amp;gt;2-fold or 1.3-fold change in at least 67% of the tumor samples. Proteins up-regulated by &amp;gt;2-fold included Ras family proteins, such as Rab-4 and p62DOK, and Rho family proteins, such as CDC42GAP and ROKα. Other proteins up-regulated by &amp;gt;1.3-fold included cyclin-dependent kinases, apoptosis regulators, and histone deacetylases (HDAC). We then compared the samples of patients with symptomatic and asymptomatic WM and showed similar protein expression signatures, indicating that the dysregulation of signaling pathways occurs early in the disease course. Three proteins were different by &amp;gt;2-fold in symptomatic versus asymptomatic, including the heat shock protein HSP90. Elevated protein expression was confirmed by immunohistochemistry and immunoblotting. Functional significance was validated by the induction of apoptosis and inhibition of proliferation using specific HDAC and HSP90 inhibitors. This study, therefore, identifies, for the first time, multiple novel proteins that are dysregulated in WM, which both enhance our understanding of disease pathogenesis and represent targets of novel therapeutics. [Cancer Res 2007;67(8):3777–8]
Assessing the cost effectiveness of using prognostic biomarkers with decision models: case study in prioritising patients waiting for coronary artery surgery
Authors: M. Henriksson, S. Palmer, R. Chen, J. Damant, N. K Fitzpatrick, K. Abrams, A. D Hingorani, U. Stenestrand, M. Janzon, G. Feder, B. Keogh, M. J Shipley, J.-C. Kaski, A. Timmis, M. Sculpher, H. Hemingway
Journal: BMJ (2010)

<b>Objective</b> To determine the effectiveness and cost effectiveness of using information from circulating biomarkers to inform the prioritisation process of patients with stable angina awaiting coronary artery bypass graft surgery. <b>Design</b> Decision analytical model comparing four prioritisation strategies without biomarkers (no formal prioritisation, two urgency scores, and a risk score) and three strategies based on a risk score using biomarkers: a routinely assessed biomarker (estimated glomerular filtration rate), a novel biomarker (C reactive protein), or both. The order in which to perform coronary artery bypass grafting in a cohort of patients was determined by each prioritisation strategy, and mean lifetime costs and quality adjusted life years (QALYs) were compared. <b>Data sources</b> Swedish Coronary Angiography and Angioplasty Registry (9935 patients with stable angina awaiting coronary artery bypass grafting and then followed up for cardiovascular events after the procedure for 3.8 years), and meta-analyses of prognostic effects (relative risks) of biomarkers. <b>Results</b> The observed risk of cardiovascular events while on the waiting list for coronary artery bypass grafting was 3 per 10 000 patients per day within the first 90 days (184 events in 9935 patients). Using a cost effectiveness threshold of £20 000-£30 000 (€22 000-€33 000; $32 000-$48 000) per additional QALY, a prioritisation strategy using a risk score with estimated glomerular filtration rate was the most cost effective strategy (cost per additional QALY was &lt;£410 compared with the Ontario urgency score). The impact on population health of implementing this strategy was 800 QALYs per 100 000 patients at an additional cost of £245 000 to the National Health Service. The prioritisation strategy using a risk score with C reactive protein was associated with lower QALYs and higher costs compared with a risk score using estimated glomerular filtration rate. <b>Conclusion</b> Evaluating the cost effectiveness of prognostic biomarkers is important even when effects at an individual level are small. Formal prioritisation of patients awaiting coronary artery bypass grafting using a routinely assessed biomarker (estimated glomerular filtration rate) along with simple, routinely collected clinical information was cost effective. Prioritisation strategies based on the prognostic information conferred by C reactive protein, which is not currently measured in this context, or a combination of C reactive protein and estimated glomerular filtration rate, is unlikely to be cost effective. The widespread practice of using only implicit or informal means of clinically ordering the waiting list may be harmful and should be replaced with formal prioritisation approaches.
Antinuclear antibodies directed against proliferating cell nuclear antigen are not specifically associated with systemic lupus erythematosus
Authors: P Vermeersch, K O. De Beeck, B R Lauwerys, K Van den Bergh, M Develter, G Marien, F A Houssiau, X Bossuyt
Journal: Annals of the Rheumatic Diseases (2009)

Proliferating cell nuclear antigen (PCNA) is an intranuclear protein that plays a role in DNA repair and replication. Anti-PCNA antibodies are considered a rare but highly specific marker for systemic lupus erythematosus (SLE).1 Anti-PCNA antibodies are reported to occur in approximately 2–6% of patients with SLE.2 3 Given the rare occurrence, however, little is known about the clinical relevance of a positive anti-PCNA test.

To examine whether anti-PCNA antibodies are specifically associated with SLE, we retrospectively identified all patients with anti-PCNA antibodies at the University Hospitals Leuven over a 10-year period (January 1998–December 2007). Patient sera submitted for antinuclear antibody testing were tested by conventional immunofluorescence using Hep2 …
Helen Jane Whiston Baker
Authors: A. Maycock
Journal: BMJ (2006)

Medical researcher who pioneered the controlled clinical trial as a gold standard and who demonstrated the efficacy of streptomycin as a treatment for tuberculosisIn a long career-he lived to 106 and worked until he was 102-Philip D'Arcy Hart showed that pneumoconiosis was an industrial disease for which sufferers should receive compensation.In a landmark controlled clinical trial with Sir Austin Bradford Hill, Hart showed that streptomycin, then newly discovered, cured tuberculosis.In 1965 he was made a CBE for this work.He did other major epidemiology, retired at 65, and spent the next 37 years making fundamental advances on the pathogenesis of tubercle bacilli.
Studies of Myocardial Actomyosin and Myosin After Shock, Acute Hemorrhage, Acute Hypoxia, and Cardiopulmonary Bypass
Authors: YOUNG W. CHO, PIERRE M. GALLETTI, LEONARD NELSON
Journal: Circulation (1963)

Decreases in cardiac efficiency have been observed in experimental endotoxic shock, acute hemorrhage, and cardiopulmonary bypass. Diminished coronary blood flow, tissue anoxia, or metabolic alteration may affect the contractile protein which, in turn, causes cardiac inefficiency. To test this hypothesis, cardiac actomyosin and myosin were extracted with Guba-Straub solution, and intrinsic viscosity, ATP (adenosinetriphosphate) activity, ATP sensitivity, the rate of ATP hydrolysis, and myosin-ATPase activity were determined. Under these experimental conditions, both myosin and actin were altered. In order to exclude the possible effect of hypoxia of the arterial blood upon the cardiac contractile system, acute hypoxia was produced in dogs and the physicochemical properties of actomyosin and myosin were studied. During acute hypoxia, the myosin-ATPase was affected, but actin appeared to remain unaltered. These changes of actomyosin and myosin may cause insufficient energy utilization by the contractile system and thereby affect the cardiac efficiency.
Where we came in
Authors: S. Cavenagh
Journal: BMJ (1995)

Afew weeks ago I acted as a locum staff grade doctor in the care of the elderly department in Tredegar General Hospital. Cottage/general practitioner/community hospitals have been an important part of my life for 20 years and I have visited a hundred or so of the 420 in Britain, including several in the Welsh valleys, but never Tredegar. Anyone alive in 1948 treats the place with a certain amount of awe, for it was here that Aneurin Bevan's convictions on how health care should be provided were formed, and for 30 years he was member of parliament for the industrial constituency of nearby Ebbw Vale. Like most of its fellows the hospital has grown and adapted to changing circumstances. Marble tablets in the hall record the prowess and long service of early medical and nursing staff, and the Aneurin Bevan Health Centre, built 12 years ago, has transformed its size and function. Here an enlarged Karsh portrait of the man himself greets you in the hall, and you are immediately aware of the efficient and dedicated staff in a hospital of which he would indeed …
Selection of spirometric measurements in a clinical trial, the Lung Health Study.
Authors: R A Wise, J Connett, K Kurnow, J Grill, L Johnson, R Kanner, P Enright
Journal: American Journal of Respiratory and Critical Care Medicine (1995)

Although current recommendations for spirometry require that the largest value of FEV1 and FVC should be taken from the largest values of different maneuvers, the validity of this approach was recently questioned. It has been suggested that selection of the maneuver with the largest peak flow or the maneuver with the largest FVC should be used for measurement of spirometric indices. The present analysis was therefore undertaken to determine which method of selection of spirometric maneuvers would give the least short-term variability in a clinical trial population. We examined the spirometry test sessions from 5,885 individuals with mild to moderate chronic airflow obstruction who were screened at two visits 24.9 +/- 17.1 d apart for entry into a multi-center clinical trial, the Lung Health Study. We compared eight potential selection methods for FEV1 and FVC. Using these different selection methods, the coefficient of variation ranged from 4.1 to 4.9% for FEV1 and from 3.5 to 5.7% for FVC. The average absolute difference between the two test sessions ranged from 110 to 123 ml for FEV1 and from 149 to 200 ml for FVC. Although all of the methods gave good results, the mean of the three highest values and the largest single value from all maneuvers provided the least short-term variability for both FEV1 and FVC. We therefore conclude that there is no reason to change the currently recommended selection methods for FEV1 and FVC.
Differences between males and females in the Hollander insulin test.
Authors: J Spencer, G P Burns, F C Cheng, A G Cox, R B Welbourn
Journal: Gut (1969)

When treating duodenal ulcer by vagotomy surgeons aim at dividing all the vagal secreto-motor fibres to the stomach.In order to assess whether this aim had been achieved, Hollander (1948) developed the insulin test which has proved a valuable clinical method of judging whether the vagi have been divided completely.The criteria by which the acid secretory response of the stomach to insulin-induced hypoglycaemia is interpreted were established on an empirical basis.Apart from Hollander's criteria, other standards have been suggested for the interpretation of the insulin test by Bachrach (1962), Stempien (1962), and Bank, Marks, and Louw (1967).None of these authors suggested that it might be necessary to employ different criteria for men and women.In this com- munication we report differences between the secretory response to insulin of male and female patients, and apply them to the interpretation of the Hollander test after vagotomy.
Lactic Dehydrogenase Electrophoresis
Authors: Albert W. Opher
Journal: JAMA (1968)

<h3>To the Editor:—</h3> A recent informative laboratory report (<b>205</b>:294, 1968) reviews the technique of agargel electrophoresis for lactic dehydrogenase isoenzymes. The authors state that the method is simple, so that it can be used in the routine laboratory, requires only about one hour for separation of the isoenzymes, and yields sharp and distinct patterns. The objection of the authors to the use of cellulose acetate is that a delicate "sandwiching" technique is needed to develop the isoenzyme pattern. This disapproval is not valid for polyacetate strips can be successfully used in a direct manner (<i>Clin Chem</i><b>12</b>:308, 1966). After electrophoresis at 200 volts for 1.5 hours, the strips are placed in a solution containing a substrate for the enzyme and a color developer which shows the zones of isoenzyme activity as dark-purple formazan bands. The overall reaction involves the oxidation of sodium lactate and the reduction of tetra-nitroblue
Comminuted Intertrochanteric Fracture
Authors: Otto E. Aufranc
Journal: JAMA (1963)

Dr. R. A.Senghas: A 74-yr-old woman fell, injuring her right hip, 2 days prior to her admission to the hospital. She had been in good general health until the time of her accident. System review was unremarkable. Physical examination revealed normal findings, with the exception of the right lower extremity. The right hip was painful and tender. The right leg was shorter than the left and was held in external rotation. Laboratory findings were normal. Radiographs on admission (Fig 1, A and B) showed a comminuted intertrochanteric fracture with displacement of the lesser trochanter medially. Dr.W.Kermond: Intertrochanteric fractures of the femur, besides presenting all the usual problems of fracture healing, have some unique features because of the particular anatomical site involved. The ability to balance the pelvis during the stance phase of gait is dependent upon the strength and function of the abduction mechanism. The abductors are
Abstract of Lecture on the Progress of Sanitary Science
Authors: W. H. Corfield
Journal: BMJ (1873)

The authors describe the case of a now 19-year-old girl who after a traumatic childhood, began to deliberately self-harm at the age of 13, often by cutting her forearms. More recently, however, swallowing inanimate objects has been her method of choice. At the time of writing, she has had over 150 accident and emergency department (A&amp;E) attendances, over 10 gastroscopies and a laparotomy. Knives, razors and six-inch sewing pins have all been removed from her gastrointestinal tract. So far, psychiatrists have been unable to stop her and her risk of accidental death rises every time she deliberately self-harms. The authors include the patient9s personal views on her illness and discuss borderline personality disorder as a condition.
Follow-up of Patients with Colorectal Adenomas
Authors: W. Matek, I. Guggenmoos-Holzmann, L. Demling
Journal: Endoscopy (1985)

With the aim of establishing suitable follow-up intervals, we examined the probability for the recurrence of relevant adenomas in the colorectum. A total of 592 adenoma patients in whom colonoscopy up to the caecum had reliably excluded relevant findings, were admitted to the study. Relevant findings were considered to be 1) colorectal carcinoma, 2) an adenoma with severe cellular atypia, 3) an adenoma of at least 5 mm in diameter, 4) a histologically unclassified polyp of at least 5 mm in diameter. We were able to show that the use of a dose-effect relationship is statistically justified for the follow-up results of the 592 patients. Thus, the probability for renewed relevant findings at any given time can be computed on the basis of the follow-up results. Renewed relevant findings were presented by 6.0% of patients with single adenomas after 4 years (confidence level 4.8-7.3%), while 5.7% of patients with multiple adenomas had relevant findings after 2 years (confidence level 4.5-7.0%). These follow-up intervals are, thanks to the adequate detection rate, economical and, at the same time, safeguard adenoma patients with a high level of reliability, against cancer of the colorectum.
In-111 DTPA Octreotide Scintigraphy and Intraoperative Gamma Probe Detection in the Diagnosis and Treatment of Residual Lymph Node Metastases of a Rectal Carcinoid Tumor
Authors: J Banzo, S Vidal-Sicat, E Prats, G Galofr??, P Razola, S Ma????, M A. Ubieto, M D. Ab??s
Journal: Clinical Nuclear Medicine (2005)

We report a case of a rectal carcinoid tumor that was treated using endoscopic resection. This case highlights the usefulness of using somatostatin receptor scintigraphy in the postresection endoscopy of the tumor and the intraoperative use of a gamma probe detector for the surgical resection of metastatic adenopathy that had not been detected using computed tomography (CT) scanning.The patient was studied using CT scanning, somatostatin receptor scintigraphy (SRS), and rectal endoscopic ultrasonography (EUS). A gamma probe detector was scheduled for use during the subsequent surgical intervention.The SRS demonstrated a pelvic metastatic lymphatic node that had not been detected on CT scanning. Additional EUS did not show regional metastatic lymph nodes. Histopathology following removal of retroperitoneal and presacral lymphatic nodes confirmed the diagnosis of metastatic carcinoid tumor. At follow up at 6 months, SRS and rectoscopy were normal.Somatostatin receptor scintigraphy is very useful in identifying the presence of lymph node metastases, even with a small rectal carcinoid tumor. This is of considerable importance when scheduling surgery and the CT and EUS are normal. The use of an intraoperative gamma-probe detector assists in the surgical excision of the metastatic lymphatic nodes, especially because they had been detected only using SRS, and when their exact location is uncertain.