tbuckley/cabot-search huggingface dataset:
Impact of Distal Ureter Management on Oncologic Outcomes Following Radical Nephroureterectomy for Upper Tract Urothelial Carcinoma
Authors: Evanguelos Xylinas, Michael Rink, Eugene K. Cha, Thomas Clozel, Richard K. Lee, Harun Fajkovic, Evi Comploj, Giacomo Novara, Vitaly Margulis, Jay D. Raman, Yair Lotan, Wassim Kassouf, Hans-Martin Fritsche, Alon Weizer, Juan I. Martinez-Salamanca, Kazumasa Matsumoto, Richard Zigeuner, Armin Pycha, Douglas S. Scherr, Christian Seitz, Thomas Walton, Quoc-Dien Trinh, Pierre I. Karakiewicz, Surena Matin, Francesco Montorsi, Marc Zerbib, Shahrokh F. Shariat
Journal: European Urology (2012)
ON IODINE-SPIRIT CATGUT
Authors: J. S. Riddell
Journal: BMJ (1907)

No link in the aseptic chain requires to be more thoroughly tested than the sterility of the ligature and suture material buried in the tissues.Thousands of yards of catgut are used every year by the busy surgeon, and every inch of it is a possible source of infection.Bottle catgut as supplied by the manufacturer is expensive, and faith in it speedily wanes, so that the operator sooner or later finds it necessary to experiment in order to determine the best method by which he may prepare reliable catgut for his own use.I made a series of experiments, some of them involving complicated methods of preparation and the use of special apparatus, but many were attended by undue difficulty and by failure to secure uniformity in the finished material, and I was thus led to discard in turn Elsberg's ammoniumsulphate catgut, as used in the Eppendorf Clinic at Hamburg; cumol catgut, at one time the stand-by in Leipzig; formalin catgut, and others.It was only some two years ago that I discovered a method so simple and reliable as to mark it out as the plan of choice.The cardinal attributes of an ideal catgut were tabulated by Moschcowitz as follows :1.It should be absolutely sterile.
Accuracy and reliability of pulse oximetry at different arterial carbon dioxide pressure levels
Authors: X. Muñoz, F. Torres, G. Sampol, J. Rios, S. Martí, E. Escrich
Journal: European Respiratory Journal (2008)

The present study aimed to assess whether arterial carbon dioxide pressure (Pa,CO(2)) has an impact on agreement between oxygen saturation measured with pulse oximetry (Sp,O(2)) or arterial blood gas co-oximetry (Sa,O(2)). Sa,O(2) and Sp,O(2) determinations were obtained simultaneously from 846 patients under assessment for long-term home oxygen therapy in a specialised outpatient clinic. Both measurements were taken with patients seated and breathing room air. Agreement between Sa,O(2) and Sp,O(2) results was analysed by the Bland-Altman method and the Lin concordance coefficient. In addition, potential interactions of arterial oxygen tension (Pa,O(2)) or Pa,CO(2) on agreement were analysed by adjusted multivariate analysis. Upon comparison of Sa,O(2) and Sp,O(2) results, the Bland-Altman technique yielded a bias (95% confidence interval (CI)) of -1.24 (-6.86-4.38) and -1.32 (-7.78-5.15) when Pa,CO(2) >48 mmHg (6.39 kPa) or Pa,O(2) <54 mmHg (7.20 kPa), respectively. Estimate by Lin's coefficient (95% CI) in these cases was 0.88 (0.85-0.90) and 0.81 (0.77-0.85). Adjusted multivariate analysis, performed to assess the impact of pH, Pa,O(2), Pa,CO(2) and bicarbonate on bias, showed that Pa,O(2), Pa,CO(2) and their interaction terms were the most important predictors of the bias (standardised estimates of -0.54, -0.94, and 0.85, respectively). The effect of pH, although statistically significant, was small, and bicarbonate had no significant effect. Arterial carbon dioxide pressure status can contribute to impaired agreement between arterial oxygen saturation and arterial oxygen saturation measured with pulse oximetry, particularly in patients with hypercapnia.
Control of Alveolar Differentiation by the Lineage Transcription Factors GATA6 and HOPX Inhibits Lung Adenocarcinoma Metastasis
Authors: William K.C. Cheung, Minghui Zhao, Zongzhi Liu, Laura E. Stevens, Paul D. Cao, Justin E. Fang, Thomas F. Westbrook, Don X. Nguyen
Journal: Cancer Cell (2013)
Determinants of asthma phenotypes in supermarket bakery workers
Authors: R. Baatjies, A. L. Lopata, I. Sander, M. Raulf-Heimsoth, E. D. Bateman, T. Meijster, D. Heederik, T. G. Robins, M. F. Jeebhay
Journal: European Respiratory Journal (2009)

While baker's asthma has been well described, various asthma phenotypes in bakery workers have yet to be characterised. Our study aims to describe the asthma phenotypes in supermarket bakery workers in relation to host risk factors and self-reported exposure to flour dust. A cross-sectional study of 517 supermarket bakery workers in 31 bakeries used a questionnaire, skin prick tests, and specific immunoglobulin E to wheat, rye and fungal α-amylase and methacholine challenge testing. The prevalence of probable occupational asthma (OA, 13%) was higher than atopic (6%), nonatopic (6%) and work-aggravated asthma (WAA, 3%) phenotypes. Previous episodes of high exposure to dusts, fumes and vapours causing asthma symptoms were more strongly associated with WAA (OR 5.8, 95% CI 1.7–19.2) than OA (2.8, 1.4–5.5). Work-related ocular–nasal symptoms were significantly associated with WAA (4.3, 1.3–13.8) and OA (3.1, 1.8–5.5). Bakers with OA had an increased odds ratio of reporting adverse reactions to ingested grain products (6.4, 2.0–19.8). OA is the most common phenotype among supermarket bakery workers. Analysis of risk factors contributes to defining clinical phenotypes, which will guide ongoing medical surveillance and clinical management of bakery workers.
Where has secondary amyloid gone?
Authors: B. P C HAZENBERG
Journal: Annals of the Rheumatic Diseases (2000)

Where has secondary amyloid gone?There is a growing clinical impression that the incidence of amyloid secondary to rheumatoid disease is declining.2][3] The prevalence of amyloidosis in patients with rheumatoid arthritis who died in 1989 (about 6%) 1 was lower than in earlier studies. 4In a recent cohort of patients with early rheumatoid arthritis followed up for 8-14 years no one died from amyloidosis. 2 In a hospital for rheumatic diseases the annual number of biopsies positive for amyloid decreased from more than 60 in 1987 to fewer than 10 recently. 3The question arises whether this is a true decline of the incidence or a more concealed clinical presentation of this type of amyloidosis.
Effect of Six-Food Elimination Diet on Clinical and Histologic Outcomes in Eosinophilic Esophagitis
Authors: Amir F. Kagalwalla, Timothy A. Sentongo, Sally Ritz, Therese Hess, Suzanne P. Nelson, Karan M. Emerick, Hector Melin–Aldana, B.U.K. Li
Journal: Clinical Gastroenterology and Hepatology (2006)
High versus normal balloon pressure dilatation for coronary stent placement. 6-Month clinical and angiographic results from a randomized multicenter trial
Authors: J. Dirschinger, J. Hausleiter, H. Schühlen, W. Giehrl, H. Walter, J. Pache, A. Kastrati, S. Elezi, A. Wehinger, M. Hadamitzky, P. Boekstegers, G. Steinbeck, A. Scörnig
Journal: Journal of the American College of Cardiology (1998)
Distinct roles of apolipoprotein components within the trypanosome lytic factor complex revealed in a novel transgenic mouse model
Authors: Maria Pilar Molina-Portela, Marie Samanovic, Jayne Raper
Journal: The Journal of Experimental Medicine (2008)

Humans express a unique subset of high-density lipoproteins (HDLs) called trypanosome lytic factors (TLFs) that kill many Trypanosoma parasite species. The proteins apolipoprotein (apo) A-I, apoL-I, and haptoglobin-related protein, which are involved in TLF structure and function, were expressed through the introduction of transgenes in mice to explore their physiological roles in vivo. Transgenic expression of human apolipoprotein L-I alone conferred trypanolytic activity in vivo. Coexpression of human apolipoprotein A-I and haptoglobin-related protein (Hpr) had an effect on the integration of apolipoprotein L-I into HDL, and both proteins were required to increase the specific activity of TLF, which was measurable in vitro. Unexpectedly, truncated apolipoprotein L-I devoid of the serum resistance gene interacting domain, which was previously shown to kill human infective trypanosomes, was not trypanolytic in transgenic mice despite being coexpressed with human apolipoprotein A-I and Hpr and incorporated into HDLs. We conclude that all three human apolipoproteins act cooperatively to achieve maximal killing capacity and that truncated apolipoprotein L-I does not function in transgenic animals.
Quantitative structural changes of the rat thoracic aorta in early spontaneous hypertension. Tissue composition, and hypertrophy and hyperplasia of smooth muscle cells.
Authors: G Olivetti, M Melissari, G Marchetti, P Anversa
Journal: Circulation Research (1982)

The thoracic aorta of 21-, 28-, 35-, and 45-day-old spontaneously hypertensive (SH) and Wistar Kyoto (WK) rats was analyzed morphometrically to evaluate the cellular hypertrophy and proliferation of medial smooth muscle cells during the development of genetically determined hypertension. The absolute increase in volume of collagen and ground substance, and elastic tissue was also measured. In SH animals, cellular hypertrophy was found to be the dominant mechanism of muscle growth in the 21- to 28-day and 35- to 45-day intervals, resulting in an overall 68% enlargement of the mean cell volume from 21 to 45 days. The total number of smooth muscle cells increased only 21% (not statistically significant) and the tendency toward hyperplasia was restricted to the 28- to 35-day period. Normotensive controls showed cell proliferation mainly from 21 to 28 days and cellular hypertrophy from 35 to 45 days with an absolute 33% increase in the number of cells and a 26% larger volume of the mean smooth muscle cell at 45 days of age. from 21 to 45 days, the above changes in cell size and number provoked an overall 104% and 67% growth of the muscle mass in SH and WK rats, respectively. The initial response phase of spontaneous hypertension was also characterized by an increase of collagen and ground substance, 184%, which was slightly greater than that of the elastic component, 168%. Changes in mural concentration of fibrous proteins that were similar to but of less magnitude than those of controls, were seen. These results demonstrate that short-term spontaneous hypertension determines a simultaneous growth adaptation in every component structure of the media of the thoracic aorta leading to a disproportionate accumulation of scleroproteins that markedly exceeds that of the contractile component of the vessel wall. At a cellular level, smooth muscle cell hypertrophy is the prevailing process that underlies the tissue response of the aorta in early hypertension.
Antigen-presenting cell–derived complement modulates graft-versus-host disease
Authors: Wing-Hong Kwan, Daigo Hashimoto, Estela Paz-Artal, Katya Ostrow, Melanie Greter, Hugo Raedler, M. Edward Medof, Miriam Merad, Peter S. Heeger
Journal: Journal of Clinical Investigation (2012)

Acute graft-versus-host disease (GvHD) is a serious complication of allogeneic hematopoietic cell transplantation (allo-HCT) that results from donor allogeneic T cell attack on host tissues. Based on previous work implicating immune cell-derived C3a and C5a as regulators of T cell immunity, we examined the effects of locally produced C3a and C5a on murine T cell-mediated GvHD. We found that total body irradiation, a conditioning regimen required to permit engraftment of allo-HCT, caused upregulation and activation of alternative pathway complement components by recipient APCs. Allo-HCT with decay accelerating factor-null (Daf1(-/-)) host BM and Daf1(-/-) donor lymphocytes led to exacerbated GvHD outcome and resulted in splenic and organ-infiltrating T cell expansion. T cells deficient in C3a receptor (C3aR) and/or C5a receptor (C5aR) responded weakly in allogeneic hosts and exhibited limited ability to induce GvHD. Using a clinically relevant treatment strategy, we showed that pharmacological C5aR blockade reduced GvHD morbidity. Our data mechanistically link APC-derived complement to T cell-mediated GvHD and support complement inhibition as a therapeutic strategy for GvHD in humans.
Plasma Protein Growth Arrest–Specific 6 Levels Are Associated With Altered Glucose Tolerance, Inflammation, and Endothelial Dysfunction
Authors: Yi-Jen Hung, Chien-Hsing Lee, Nain-Feng Chu, Yi-Shing Shieh
Journal: Diabetes Care (2010)

OBJECTIVE Plasma protein growth arrest–specific 6 (Gas6) is important to the inflammatory process and is involved in the development of diabetic renal and vascular complications. We set out to determine whether plasma Gas6 levels are associated with altered glucose tolerance, insulin sensitivity, inflammation, and endothelial dysfunction. RESEARCH DESIGN AND METHODS A total of 278 adults, including 96 with normal glucose tolerance (NGT), 82 with impaired glucose tolerance (IGT), and 100 with type 2 diabetes were recruited. Plasma Gas6 concentration and biochemical, proinflammatory, and endothelial variables were determined. Insulin sensitivity was examined by homeostasis model assessment. RESULTS Plasma Gas6 concentration was significantly lower among patients with type 2 diabetes compared with subjects with NGT (P &amp;lt; 0.001). The plasma Gas6 value was inversely correlated with fasting glucose, tumor necrosis factor (TNF)-α, interleukin (IL)-6, and vascular cell adhesion molecule (VCAM)-1. In multivariate logistic regression analysis, after adjustment for established diabetes risk factors, higher plasma Gas6 concentrations were significantly associated with a decreased risk of type 2 diabetes. Moreover, the association became slightly stronger after further adjustment for TNF-α, IL-6, high-sensitive C-reactive protein, E-selectin, intercellular adhesion molecule-1, and VCAM-1. CONCLUSIONS Plasma Gas6 is associated with altered glucose tolerance, inflammation, and endothelial dysfunction. It also may represent a novel independent risk factor of type 2 diabetes and a potential surrogate marker of inflammation and endothelial dysfunction.
PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R
Authors: Bastian Pfeifer, Ulrich Wittelsbürger, Sebastian E. Ramos-Onsins, Martin J. Lercher
Journal: Molecular Biology and Evolution (2014)

Although many computer programs can perform population genetics calculations, they are typically limited in the analyses and data input formats they offer; few applications can process the large data sets produced by wholegenome resequencing projects.Furthermore, there is no coherent framework for the easy integration of new statistics into existing pipelines, hindering the development and application of new population genetics and genomics approaches.Here, we present PopGenome, a population genomics package for the R software environment (a de facto standard for statistical analyses).PopGenome can efficiently process genome-scale data as well as large sets of individual loci.It reads DNA alignments and single-nucleotide polymorphism (SNP) data sets in most common formats, including those used by the HapMap, 1000 human genomes, and 1001 Arabidopsis genomes projects.PopGenome also reads associated annotation files in GFF format, enabling users to easily define regions or classify SNPs based on their annotation; all analyses can also be applied to sliding windows.PopGenome offers a wide range of diverse population genetics analyses, including neutrality tests as well as statistics for population differentiation, linkage disequilibrium, and recombination.PopGenome is linked to Hudson's MS and Ewing's MSMS programs to assess statistical significance based on coalescent simulations.PopGenome's integration in R facilitates effortless and reproducible downstream analyses as well as the production of publication-quality graphics.Developers can easily incorporate new analyses methods into the PopGenome framework.PopGenome and R are freely available from CRAN (http://cran.r-project.org/) for all major operating systems under the GNU General Public License.
DEMONSTRATION OF A BLOCKING FACTOR IN THE PLASMA AND SPINAL FLUID OF PATIENTS WITH SUBACUTE SCLEROSING PANENCEPHALITIS
Authors: Aftab Ahmed, Douglas M. Strong, Kenneth W. Sell, Gary B. Thurman, Richard C. Knudsen, Richard Wistar, William R. Grace
Journal: The Journal of Experimental Medicine (1974)

Conflicting reports on the immune responsiveness of patients with subacute sclerosing panencephalitis (SSPE) have been reported. This report shows that the leucocytes from four SSPE patients exhibited strong sensitivity to both measles and SSPE virus preparations as measured by the macrophage migration inhibition test, mixed lymphocyte virus infected cell culture test, and the lymphotoxin assay. Earlier suggestions that a factor may be operating to suppress cellular reactivity are confirmed by the demonstration that the response of lymphocytes from SSPE patients could be blocked by the addition of SSPE spinal fluid or plasma. It was determined that the blocking factor was stable at -20 degrees C, heat labile at 56 degrees C for 30 minutes, trypsin and neuraminadase sensitive, and had a mol wt greater than 150,000 as determined by Sephadex G-200 gel chromatography. The blocking factor appeared to be specific for SSPE virus and did not block the response of lymphocytes to nonspecific mitogenic agents and other viral and bacterial agents.
Left Stellate Ganglion and Vagal Nerve Activity and Cardiac Arrhythmias in Ambulatory Dogs With Pacing-Induced Congestive Heart Failure
Authors: Masahiro Ogawa, Shengmei Zhou, Alex Y. Tan, Juan Song, Ghassan Gholmieh, Michael C. Fishbein, Huai Luo, Robert J. Siegel, Hrayr S. Karagueuzian, Lan S. Chen, Shien-Fong Lin, Peng-Sheng Chen
Journal: Journal of the American College of Cardiology (2007)
SERUM YKL-40 IS ASSOCIATED WITH LONG-TERM MORTALITY IN PATIENTS WITH STABLE COROONARY DISEASE: A PROGNOSTIC STUDY WITHIN THE CLARICOR TRIAL
Authors: Marina Harutyunyan, Per Winkel, Joergen Hilden, Julia Johansen, Jens Goetze, J&oslash;rgen Hansen, Gorm Jensen, Erik Kjoller, Christian Gluud, Hans Joern Kolmos, Jens Kastrup
Journal: Journal of the American College of Cardiology (2012)
CASE OF NASAL SARCOMA, WITH REMARKS.
Authors: Dunbar Roy
Journal: JAMA (1901)

Sarcomata within the last few years has certainly seemed to be on the increase. This may be due to the fact of a closer microscopic examination being made than formerly of all suspected tumors, especially those occurring in the nasal passages. Nor can rhinologists be too diligent in this direction. It is not my intention to go into the pathology of the sarcoma, but simply to add a few personal experiences to the report of a case. Warren, in his late book on "Surgical Pathology," states "that sarcoma of the nasal passages is not a very rare disease." Bosworth has collected 41 published cases, but I believe this number is but a small proportion of the cases which have occurred. If statistics were really obtainable, they would show a much larger percentage of these growths than is at present the case. The round-cell and alveolar forms of sarcoma seem to
A FILTERABLE VIRUS CAUSING ENTERITIS AND PNEUMONIA IN CALVES
Authors: James A. Baker
Journal: The Journal of Experimental Medicine (1943)

An infectious disease of calves has been described which is characterized by fever, diarrhea, and pneumonia, followed soon by recovery. On autopsy of animals killed at the height of the disease, there is found a catarrhal enteritis and a bronchopneumonia that is usually confined to the anterior lobes of the lungs. From this disease an agent has been secured by the serial inoculation of lung extracts that produces a pneumonia in white mice. Attempts to demonstrate by the same means a similar agent in uninoculated mice from the same stock have yielded negative results. Suspensions of the lungs of the mice with pneumonia, when inoculated intranasally or intratracheally into calves, cause a disease like the natural infection, characterized by fever, diarrhea, and pneumonia. In two experiments pen contact of normal calves with calves inoculated with the passed material resulted in the typical disease. Early in its course the causative agent is found only in the lungs and intestines, but at its height is generally distributed throughout the body. Calves that have recovered from the induced disease are resistant to subsequent infection and their blood serum will neutralize the causative agent as not previously. Sera from calves that have recovered from the natural disease also neutralize the agent. Cultures from the infected lungs of calves and mice as a rule show no growth, and material that has been passed through Berkefeld N filters produces the characteristic disease. It is therefore concluded that this disease of calves is caused by a filterable virus.
Nanoparticle-driven DNA damage mimics irradiation-related carcinogenesis pathways
Authors: R. M. Mroz, R. P. F. Schins, H. Li, L. A. Jimenez, E. M. Drost, A. Holownia, W. MacNee, K. Donaldson
Journal: European Respiratory Journal (2007)

The epidemiological association between cancer and exposure to ambient air pollution particles (particles with a 50% cut-off aerodynamic diameter of 10 microm (PM(10))) has been related to the ability of PM(10) and its constituent nanoparticles (NPs) to cause reactive oxidative species (ROS)-driven DNA damage. However, there are no data on the molecular response to these genotoxic effects. In order to assess whether PM(10), NP and ROS-driven DNA damage induce carcinogenesis pathways, A549 cells were treated with tert-butyl-hyperperoxide (Tbh), urban dust (UD), carbon black (CB), nanoparticulate CB (NPCB), benzo(a)pyrene (BaP) and NPCB coated with BaP for <or=24 h. Single- and double-strand breakage of DNA was determined by comet assay; cell cycle status was analysed using flow cytometry. Nuclear extracts or acid-extracted histones were used for Western blot analysis of p-ser15-p53 (p53 phosphorylated at ser15), p53 binding protein (53BP) 1, phospho-histone H2A.X (p-H2A.X) and phospho-BRCA1 (p-BRCA1). UD caused both single- and double-strand DNA breaks, while other tested NPs caused only single-strand DNA breaks. NPs significantly altered cell cycle kinetics. Tbh enhanced p-H2A.X after 1 and 6 h (2.1- and 2.2-fold, respectively). NP increased 53BP1 expression at 1 h (2.4-8.7-fold) and p-BRCA1 at 1-6 h. N-acetylcysteine blocked NP-driven p-ser15-p53 response. In conclusion, nanoparticles and reactive oxidative species induce DNA damage, activating p53 and proteins related to DNA repair, mimicking irradiation-related carcinogenesis pathways.