tbuckley/cabot-search huggingface dataset:
Generation of Synthetic Transcriptome Data with Defined Statistical Properties for the Development and Testing of New Analysis Methods
Authors: Guillaume Brysbaert, Sebastian Noth, Arndt Benecke
Journal: Genomics Proteomics & Bioinformatics (2007)

Abstract We have previously developed a combined signal/variance distribution model that accounts for the particular statistical properties of datasets generated on the Applied Biosystems AB1700 transcriptome system. Here we show that this model can be efficiently used to generate synthetic datasets with statistical properties virtually identical to those of the actual data by aid of the JAVA application ace.map creator 1.0 that we have developed. The fundamentally different structure of AB1700 transcriptome profiles requires re-evaluation, adaptation, or even redevelopment of many of the standard microarray analysis methods in order to avoid misinterpretation of the data on the one hand, and to draw full benefit from their increased specificity and sensitivity on the other hand. Our composite data model and the ace.map creator 1.0 application thereby not only present proof of the correctness of our parameter estimation, but also provide a tool for the generation of synthetic test data that will be useful for further development and testing of analysis methods.
Phosphoglycerate Mutase 1 Coordinates Glycolysis and Biosynthesis to Promote Tumor Growth
Authors: Taro Hitosugi, Lu Zhou, Shannon Elf, Jun Fan, Hee-Bum Kang, Jae Ho Seo, Changliang Shan, Qing Dai, Liang Zhang, Jianxin Xie, Ting-Lei Gu, Peng Jin, Masa Alečković, Gary LeRoy, Yibin Kang, Jessica A. Sudderth, Ralph J. DeBerardinis, Chi-Hao Luan, Georgia Z. Chen, Susan Muller, Dong M. Shin, Taofeek K. Owonikoko, Sagar Lonial, Martha L. Arellano, Hanna J. Khoury, Fadlo R. Khuri, Benjamin H. Lee, Keqiang Ye, Titus J. Boggon, Sumin Kang, Chuan He, Jing Chen
Journal: Cancer Cell (2012)
Book Review The Ageing Surgical Patient: Anaesthetic, Operative and Medical Management Edited by D.L. Crosby, G.A.D. Rees, and D.G. Seymour. 457 pp., illustrated. New York, John Wiley, 1992. $149.95. 0-471-92847-X
Authors: Timothy J. Eberlein
Journal: New England Journal of Medicine (1993)
Genes and ethics
Authors: T. Smith
Journal: BMJ (1995)

Recent studieshave shown that for many Americans the emer- gency room has become the main source of medical 'du care.This issue has received attention largely in the context of care for the indigent, such care being perceived as unduly expensive, impersonal, episodic, and lacking in continuity.Hurried doctors seeing unfamiliar patients under stressed conditions will always order more tests than an unhurried evaluation of a known patient would require.Dissatisfied patients with unrelieved symptoms often wander on to the next emergency room,
RELAXATION METHODS IN U. S. NAVY AIR SCHOOLS
Authors: WILLIAM NEUFELD
Journal: American Journal of Psychiatry (1951)

1. In 1943 at United States primary naval training stations many cadets (perhaps about half) showed symptoms and signs of restlessness, insomnia, fatigue, and apprehension. Questionnaires filled out by 3,181 cadets at 5 preflight schools in their ninth week of training indicated nervous complaints on the part of most of the cadets. 2. Group methods of instruction were employed with the purpose of reducing nervous irritability and excitement in cadets. In preparation, 5 officers were given a course of instruction in progressive relaxation by Dr. Edmund Jacobson. These officers subsequently instructed other officers, until a total of 100 relaxation officers became available for instruction of cadets. The cadets were taught progressive relaxation in classes numbering up to 300. 3. The course in relaxation for cadets was of 10 weeks duration, consisting of 3 periods per week of ½ hour each. This was an abbreviated course, according to Jacobson's classification, since the total was about 10% of the 150 hours of instruction required in a more thorough course. In addition, the cadets generally did not practice with daily regularity as Jacobson prescribes. Accordingly the following procedures can be regarded as tests of results secured by relaxation methods employed on groups under severe limitations, rather than tests of what could have been accomplished under more satisfactory conditions. 4. Tests at the preflight school at Iowa City on 983 cadets who had received such relaxation training indicated approximately 19% reduction of strains, sprains, fractures, and other minor injuries in the test group as compared with a control group. 5. Tests on these same groups revealed a 38% reduction of days lost from injuries. Since the control group was considerably smaller than the test group, no quantitative accuracy can be attached to these figures but they would seem to indicate that on the whole a noteworthy reduction of injuries and of days lost from injuries was probably accomplished by the relaxation training. 6. In 3 preflight schools data were secured concerning the rest in bed of 140 cadets who had received relaxation training as compared with 190 cadets without training. Marked increase of quietude, recorded in percentages as from 27 to 56, occurred in the number of full body turns, parts of body movements, and of talking or mumbling. The reports suggested a marked diminution in dreaming. Figures for the total group indicated that the cadets who had received such relaxation training went to sleep more quickly on the whole and suffered less from insomnia during the night.
Is covert attention really unnecessary?
Authors: Alexander Pollatsek, Keith Rayner
Journal: Behavioral and Brain Sciences (1999)

We are largely in agreement with the Findlay &amp; Walker model. However, they appear to dismiss the role of covert spatial attention in tasks in which people are free to move their eyes. We argue that an account of the facts about the perceptual span in reading requires a window of attention not centered around the fovea. Moreover, a computational model of reading that we (Reichle et al. 1998) developed gives a good account of eye movement control in reading and would be unable to do so without relying heavily on covert attention.
Atrioventricular nodal reentrant tachycardia: studies on upper and lower 'common pathways'.
Authors: J M Miller, M E Rosenthal, J A Vassallo, M E Josephson
Journal: Circulation (1987)

Electrophysiologic studies were performed in 28 patients with documented atrioventricular (AV) nodal reentrant supraventricular tachycardia (SVT) to investigate the presence of AV nodal tissue situated between the tachycardia circuit and both the atrium (upper common pathway, UCP) and the His bundle (lower common pathway, LCP). All patients demonstrated a 1:1 AV relationship during SVT. The study protocol consisted of atrial then ventricular pacing at the SVT cycle length. UCPs were manifested in eight of 28 (29%) patients by either antegrade AV Wenckebach (six patients) or a paced atrium-His (AH) interval exceeding the AH in SVT (two patients, differences 5 and 9 msec). LCPs were manifested in 21 of 28 (75%) patients by either retrograde Wenckebach periodicity (two patients) or a paced HA interval exceeding the HA in SVT (19 patients, mean difference 25 +/- 20 msec). By these criteria, eight patients (29%) had evidence for both UCPs and LCPs. UCPs were more likely than LCPs to be manifested by Wenckebach criteria (p less than .05). Thus the AV nodal reentrant SVT circuit appears to be intranodal and is frequently surrounded by AV nodal tissue (UCP and LCP), antegrade and retrograde conduction properties of these common pathways are discordant in some cases, and conduction properties of UCP tissue differ from those of LCP tissue. These findings may have relevance in that the UCP or LCP may limit the ability of premature extrastimuli to penetrate the circuit to initiate or terminate AV nodal SVT.
The Causal Effect of Vitamin D Binding Protein (DBP) Levels on Calcemic and Cardiometabolic Diseases: A Mendelian Randomization Study
Authors: Aaron Leong, Waheed Rehman, Zari Dastani, Celia Greenwood, Nicholas Timpson, Lisa Langsetmo, Claudie Berger, Lei Fu, Betty Y. L. Wong, Suneil Malik, Rainer Malik, David A. Hanley, David E. C. Cole, David Goltzman, J. Brent Richards
Journal: PLoS Medicine (2014)

In this study, Richards and colleagues undertook a Mendelian randomization study to determine whether vitamin D binding protein (DBP) levels have a causal effect on common calcemic and cardiometabolic diseases. They concluded that DBP has no demonstrable causal effect on any of the diseases or traits investigated here, except Vit D levels. Please see later in the article for the Editors' Summary
A Cooperative Study of Hospital Frequency and Character of Transient Ischemic Attacks
Authors: Phillip D. Swanson
Journal: JAMA (1977)

Angiographic procedures were carried out on 36% of 1,328 patients suspected of having transient ischemic attacks (TIA). Among six participating centers, this ranged from 12% to 82%. This large difference might be related to the number of patients considered good surgical candidates and differences in the use of screening noninvasive diagnostic techniques. Arch studies, using catheter techniques, were performed most often. Although 13% of the patients had transient complications, permanent neurological deficits occurred in only 0.65%. Angiographic lesions were best correlated to clinical symptoms in those patients thought to definitely have carotid artery system TIA but were commonly seen in all other groups. Thus, clinical correlation was poor. (<i>JAMA</i>237:2202-2206, 1977)
Acute Renal Tubular Necrosis
Authors: William P. McKeever
Journal: JAMA (1967)

ACUTE renal tubular necrosis is a known complication of prolonged hypotension from various causes.<sup>1</sup>Very few reports of acute tubular necrosis secondary to pulmonary embolism have appeared.<sup>2,3</sup>This report describes such a case in a young woman who had been taking an oral progestogen-estrogen agent as a contraceptive. <h3>Report of a Case</h3> A 19-year-old married white girl was admitted to the Evanston (Ill) Hospital on Feb 9, 1965. Immediately prior to admission, she had been seen on a home visit by a physician who noticed severe hypotension, administered a pressor agent, and sent her to the hospital. Her chief complaint was that three days prior to admission, she had experienced pain in her right shoulder which was aggravated by respiration. Two days prior to admission, fever developed; the pain extended to the right side of the chest and was associated with a dry cough. She had taken daily
Serial Follow-up After Optimized Ultrasound-Guided Deployment of Palmaz-Schatz Stents
Authors: Harald Mudra, Evelyn Regar, Volker Klauss, Frank Werner, Karl-Heinz Henneke, Efthia Sbarouni, Karl Theisen
Journal: Circulation (1997)

Background The effects of ultrasound-guided high-pressure stenting on late stent and reference segment dimensions are unknown. In this study, we report about angiographic and ultrasound measurements to assess the amount and distribution of neointimal ingrowth within the stent and the changes of plaque burden and dimensions within the reference segments. Methods and Results Sixty-eight consecutive patients with 72 lesions received single or multiple Palmaz-Schatz coronary stents with a standardized protocol for stent optimization under ultrasound guidance. The residual angiographic diameter stenosis was 3±12% (reference diameter, 3.16±0.61 mm). At follow-up 4.8±2.5 months later, angiography revealed a diameter stenosis of 27±21% with a restenosis rate of 15.3% (confidence interval: 7.8% to 25.6%). Lumen renarrowing within the stent was exclusively due to neointimal ingrowth; no stent compression was observed. The neointima covered 20±20% of the stent area and was more pronounced in the midportion of the stent. Volumetric assessment performed in 26 patients resulted in 13±14% or 65±28% of the stent volume occupied by neointimal ingrowth in patients without or with restenosis, respectively. Vessel remodeling had an impact on lumen dimensions only at reference sites but not within the stent. Plaque burden of 46±11% and 48±11% at the proximal and distal reference sites, respectively, did not show a relevant progression during the follow-up. Conclusions Serial ultrasound analyses did not show any evidence of stent compression or relevant vessel remodeling. Restenosis was solely due to neointimal ingrowth. Despite a considerable plaque burden within the reference segments, there was no relevant progression of the disease adjacent to the stent.
Contrasting rates of reversal of digoxin toxicity by digoxin-specific IgG and Fab fragments.
Authors: B L Lloyd, T W Smith
Journal: Circulation (1978)

Both heterologous IgG and Fab fragments of appropriate affinity and specificity have been shown capable of reversing advanced cardiac glycoside toxicity. Fab fragments are more rapidly excreted and theoretically have a smaller risk of unwanted immunologic effects, but relative rates of toxicity reversal have not been established. Rates of reversal of advanced digoxin toxicity by digoxin-specific IgG and Fab fragments were therefore compared in a dog model of advanced digoxin intoxication. Initial studies confirmed more rapid distribution of sheep Fab fragments (M.W. 50,000) than of the parent IgG molecule (M.W. 150,000) after intravenous injection. Twenty-five pentobarbital-anesthetized dogs were given 0.3 mg/kg digoxin intravenously, resulting in rapid onset of ventricular tachycardia in all animals. Eight dogs subsequently given nonspecific IgG or Fab died in asystole or ventricular fibrillation an average of 55 minutes after digoxin administration. Ten of 11 dogs given 1.33 moles of binding sites per mole of digoxin as intact IgG returned to sinus rhythm at a mean time of 85 minutes after antibody infusion. In contrast, six of six dogs given an equivalent dose of specific Fab fragments returned to sinus rhythm in a significantly shorter mean time of 36 minutes (P less than 0.01). Variability of time to arrhythmia reversion was less in Fab-treated dogs. These data demonstrate a decisive advantage of specific Fab fragments over intact IgG for potential clinical use in advanced, life-threatening digoxin intoxication.
Randomised controlled trial of vancomycin for pseudomembranous colitis and postoperative diarrhoea.
Authors: M R Keighley, D W Burdon, Y Arabi, J A Williams, H Thompson, D Youngs, M Johnson, S Bentley, R H George, G A Mogg
Journal: BMJ (1978)

The efficacy of vancomycin in pseudomembranous colitis was assessed in a prospective randomised controlled trial. Forty-four patients with postoperative diarrhoea were allocated to five days9 treatment with either 125 mg vancomycin six-hourly or a placebo. Sixteen patients had high titres of the neutralised faecal toxin characteristic of pseudomembranous colitis; nine received vancomycin and seven placebo. At the end of treatment faecal toxins were present in one patient given vancomycin compared with five of the controls. Vancomycin caused the disappearance of Clostridum difficile from the stool in all except one patient, whereas toxicogenic strains of Cl difficile persisted in all but one of the controls. Histological evidence of psuedomembranous colitis had disappeared by the end of treatment in six out of seven patients given vancomycin compared with only one out of seven patients given vancomycin compared with only one out of five patients given placebo. In patients with faecal toxins bowel habit had returned to normal in seven of the vancomycin group compared with only one of the controls, but there was no significant difference in clinical response among patients without faecaal toxins. The results suggest that vancomycin eliminates toxin-producing Cl difficile from the colon and is associated with rapid clinical and histological improvement in patients with pseudomembranous colitis.
Inhibition of p300 impairs Foxp3+ T regulatory cell function and promotes antitumor immunity
Authors: Yujie Liu, Liqing Wang, Jarrod Predina, Rongxiang Han, Ulf H Beier, Liang-Chuan S Wang, Veena Kapoor, Tricia R Bhatti, Tatiana Akimova, Sunil Singhal, Paul K Brindle, Philip A Cole, Steven M Albelda, Wayne W Hancock
Journal: Nature Medicine (2013)
Effect of somatostatin on renal function.
Authors: J P Vora, D R Owens, R Ryder, J Atiea, S Luzio, T M Hayes
Journal: BMJ (1986)

Somatostatin has profound effects on both splanchnic and portal vascular beds. The effects of intravenous somatostatin (100 micrograms/h) on urinary volume, effective renal plasma flow, and glomerular filtration rate were compared with the effects of a control infusion of physiological saline in six normal subjects. Renal plasma flow and glomerular filtration rate were measured by primed constant isotope infusions of iodine-125 iodohippurate and chromium-51 edetic acid. Urinary volume, renal plasma flow, and glomerular filtration rate were measured during 20 minute clearance periods. During the control infusion urinary volume, renal plasma flow, and glomerular filtration rate remained essentially unchanged at 254 (SEM 3) ml/20 min, 568 (5) ml/min/1.73 m2, and 110 (2) ml/min/1.73 m2 respectively. From similar basal values the infusion of somatostatin led to a rapid decrease in all three variables. After 120 minutes of infusion of somatostatin urinary volume, renal plasma flow, and glomerular filtration rate were reduced to 148 (17) ml/20 min (p less than 0.01), 422 (7) ml/min/1.73 m2 (p less than 0.001), and 93 (3) ml/min/1.73 m2 (p less than 0.05) respectively. This effect on renal function should be borne in mind whenever somatostatin is used.
Chlorzoxazone-Induced Spasmodic Torticollis
Authors: Michael A. Rosin
Journal: JAMA (1981)

<h3>To the Editor.—</h3> Chlorzoxazone is an effective adjunctive drug used to treat acute muscle spasms owing to different etiologic factors.<sup>1</sup>The most common side effects owing to chlorzoxazone are drowsiness and hepatic and gastrointestinal dysfunction. A report of a spasmodic torticollis-like syndrome that was evoked repeatedly after the ingestion of chlorzoxazone is presented, since this complication has been either not noted or well publicized. <h3>Report of a Case.—</h3> A 46-year-old woman came to a local emergency room to seek relief from muscle cramps in her neck. In the preceding eight months she had experienced seven previous episodes of a spasmodic, torticollis-like syndrome consisting of tonic deviation of the head to the right, tonic clenching of the teeth, and dysarthria. She usually took no prescription drugs, but did occasionally take overthe-counter, aspirin-containing products. In retrospect, all of these episodes occurred within two hours after the ingestion of chlorzoxazone, which had
1053. Functional Restoration of a Genetic Defect in Multipotent Germline Stem Cells by Human Artificial Chromosome Containing a Genomic Insert
Authors: Yasuhiro Kazuki, Hidetoshi Hoshiya, Yoshiteru Kai, Satoshi Abe, Masato Takiguchi, Mitsuhiko Osaki, Mito Kanatsu- Shinohara, Naoyo Kajitani, Yasuaki Shirayoshi, Masaharu Hiratuka, Astuo Ogura, Takashi Shinohara, Mitsuo Oshimura
Journal: Molecular Therapy (2006)

Although homologous recombination has been used for gene correction in ES cells, genetic defects with an unknown mutation site or a genomic large deletion could not be restored by homologous recombination. Human artificial chromosomes (HACs) may solve these problems. HACs have several advantages that require for gene therapy vectors, including an efficient transfer to stem cells, a stable episomal maintenance and the capacity for large gene inserts. Although own embryonic stem (nt ES) cells can be made by the nuclear transfer technique, there are many ethical problems. On the other hand, mGS (multipotent germline stem) cells have ES cell-like multipotency and could be generated from neonatal mouse testis. Thus, mGS cells have greater advantages than ntES cells, because individual mGS cells can be obtained without ethical problem. Here we establish a paradigm for treatment of a genetic disorder by combining mGS cells with HAC vector containing a defected gene. As a model, we used the p53 deficient mGS cells. Human p53 genome was cloned into the HAC vector using a HAC-mediated genomic insert knock in (HMGK) system. Briefly, using p53 cDNA probe, we screened RPCI-6 PAC library that had a loxP-site for cloning into the HAC, and the PAC containing p53 genome were inserted into the HAC vector in CHO cells by the Cre-loxP system. The p53-HAC was then introduced into the mouse p53-/- mGS cells using microcell-mediated chromosome transfer (MMCT). Fluorescence in situ hybridization (FISH) analyses showed that the p53-HAC was present independently in the p53-/-mGS cells. Western blot analyses in the p53-/-mGS(p53HAC) after X-ray irradiation showed that the transferred p53 trans-activated the p53-related gene, endogenous mouse p21. Further, radiosensitivity in the p53-/-mGS(p53HAC) had a significantly higher after irradiation as compared to parental p53-/-mGS cells. These data suggest that the HAC vector containing a p53 genomic insert mediates the production of functional human p53 protein and the HAC was able to rescue the p53-/-phenotypes in the p53-/-mGS cells. Next, the p53-/-mGS(p53HAC) cells were injected into nude mice to assess the capacity of differentiation. The transplanted p53-/- mGS(p53HAC) cells gave rise to typical teratomas and some differentiated cell types were detected. Thus, we demonstrated that HAC vector could be transferable to mGS cells and HAC vector containing desired genome corrected a genetic defect in mGS cells by MMCT approach. In future, a combination of mGS cells and HAC-mediated gene delivery may provide a useful treatment for genetic defects, when efficient methods for differentiation in stem cells including mGS cells are developed.
Bronchoalveolar mast cells in extrinsic asthma: a mechanism for the initiation of antigen specific bronchoconstriction.
Authors: K C Flint, K B Leung, B N Hudspith, J Brostoff, F L Pearce, N M Johnson
Journal: BMJ (1985)

Bronchoalveolar lavage performed in 10 patients with extrinsic asthma and 14 controls yielded similar recoveries of fluid and cells. Mast cells and eosinophils, however, formed a greater proportion of the cells recovered from the asthmatic subjects (p less than 0.001 for mast cells; p less than 0.01 for eosinophils), the histamine content of the lavage cells being correspondingly increased (p less than 0.01). Both the percentage of mast cells and the histamine content of lavage cells were significantly inversely correlated with the forced expiratory volume in one second (FEV1; expressed as percentage of predicted) and with the ratio of FEV1 to forced vital capacity before lavage. There was also a significant inverse correlation between the concentration of histamine required to produce a 20% fall in FEV1 and the percentage of mast cells recovered (p less than 0.05). When incubated with antihuman IgE bronchoalveolar mast cells from asthmatic subjects released a significantly increased proportion of total cellular histamine than cells from control subjects at all effective doses of anti-IgE. By contrast, dose response curves for IgE dependent histamine release from peripheral blood leucocytes were similar in asthmatics and controls. Specific antigen led to release of histamine from bronchoalveolar cells and peripheral blood leucocytes of asthmatic subjects but not controls. Lying superficially within the airways, bronchoalveolar mast cells would be readily exposed to inhaled antigen and would release mediators directly on to the airway surface. Their immunological response suggests that they are likely to be important in the pathogenesis of airflow obstruction in asthma.
REVASCULARIZING ELDERLY PATIENTS WITH ACUTE ST-SEGMENT ELEVATION MYOCARDIAL INFARCTION UNDER 90 MINUTES: IS IT ACHIEVABLE? RESULTS FROM THE AURORA ST. LUKE'S 24×7 STEMI PROGRAM
Authors: M. Fuad Jan, Naoyo Mori, Anjan Gupta, Suhail Allaqaband, Tanvir Bajwa
Journal: Journal of the American College of Cardiology (2011)