tbuckley/cabot-search huggingface dataset:
Improved Consensus Network Techniques for Genome-Scale Phylogeny
Authors: B. R. Holland
Journal: Molecular Biology and Evolution (2005)

Although recent studies indicate that estimating phylogenies from alignments of concatenated genes greatly reduces the stochastic error, the potential for systematic error still remains, heightening the need for reliable methods to analyze multigene data sets. Consensus methods provide an alternative, more inclusive, approach for analyzing collections of trees arising from multiple genes. We extend a previously described consensus network method for genome-scale phylogeny (Holland, B. R., K. T. Huber, V. Moulton, and P. J. Lockhart. 2004. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol. Biol. Evol. 21:1459-1461) to incorporate additional information. This additional information could come from bootstrap analysis, Bayesian analysis, or various methods to find confidence sets of trees. The new methods can be extended to include edge weights representing genetic distance. We use three data sets to illustrate the approach: 61 genes from 14 angiosperm taxa and one gymnosperm, 106 genes from eight yeast taxa, and 46 members of a gene family from 15 vertebrate taxa.
MDR-TB and XDR-TB: drug resistance and treatment outcomes
Authors: G. B. Migliori, G. Sotgiu, M. D'Arcy Richardson, R. Centis, A. Facchini, G. Guenther, A. Spanevello, C. Lange
Journal: European Respiratory Journal (2009)

We read with interest the study by HWANG et al. [1], which continues the discussion on factors associated with poor outcomes in the treatment of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB).
Repelling class discrimination: ephrin-A5 binds to and activates EphB2 receptor signaling
Authors: Juha-Pekka Himanen, Michael J Chumley, Martin Lackmann, Chen Li, William A Barton, Phillip D Jeffrey, Christopher Vearing, Detlef Geleick, David A Feldheim, Andrew W Boyd, Mark Henkemeyer, Dimitar B Nikolov
Journal: Nature Neuroscience (2004)
Confronting the small arms pandemic
Authors: N. Arya
Journal: BMJ (2002)

Physicians throughout the world bear witness to the terrible consequences of small arms. But do we truly understand the impact and the epidemiology of the small arms pandemic, and can we devise effective strategies for prevention as we have for other major public health issues? The capacity for collecting consistent, reliable, and relevant data is limited by various cultural, economic, infrastructural, and logistic factors even in developed countries not at war. Nevertheless, we have some solid data on the size of the problem and indicators suggestive of possible solutions.

The United States, for instance, has over 28 000 deaths a year from small arms—accidents, suicides, and homicides—the highest rate in the developed world.1 In that country firearms are the leading cause of death among 15-24 year olds, slightly ahead of vehicle crashes, and the third leading cause of death in those aged under 15.2 While the US murder rate without guns is roughly equivalent to that of Canada (1.3 times), its murder rate with handguns is 15 times the Canadian rate.3 Countries with similar cultural, economic, and ethnic make up but with different gun possession rates also have widely differing firearm death rates, roughly correlating with the percentage of households with guns.4 For example, …
Case 40-1975
Authors: Richard C. Cabot, Robert E. Scully, James J. Galdabini, Betty U. McNeely, William E. Strole, Austin L. Vickery
Journal: New England Journal of Medicine (1975)

Presentation of CaseA 58-year-old woman was admitted to the hospital because of abdominal pain.Seven years previously she entered the hospital because of abdominal pain; the diagnoses of acute pancreatitis and chronic alcoholism were made. During the next six years she was readmitted on seven occasions because of acute pancreatitis. Five years before admission a cholecystectomy, gastrojejunostomy and vagotomy were performed; a biopsy of the liver disclosed Laennec's cirrhosis. Three years before entry she underwent a right total-hip replacement because of bilateral aseptic necrosis. One week before admission the patient began an alcoholic binge, consuming as much as 1 . . .
The Physiology of Blood Platelets: Recent Biochemical, Morphological and Clinical Research
Authors: Oscar D. Ratnoff
Journal: JAMA (1965)

About 30 years ago the late Dr. Leandro Tocantins summarized the state of knowledge about blood platelets in a review published in<i>Medicine</i>. Anyone reading this article now will appreciate that much of what passes as new is merely the repetition of what has long been recorded if not, alas, known. But new tools and new ideas have led to a rapid expansion of our knowledge about the platelets—their morphology, particularly as revealed by electron microscopy, their chemistry, and their peculiar multiple roles in hemostasis. All these subjects are summarized clearly and concisely in<i>The Physiology of Blood Platelets</i>, by Dr. Marcus and Dr. Zucker. This monograph, originally projected as a review for a journal, was expanded to book size to permit the inclusion of much of our current knowledge about these wondrous cell fragments. This is a happy event for anyone interested in hematology or hemostasis. This volume is
Hepatitis C virus receptor expression in normal and diseased liver tissue
Authors: Gary M. Reynolds, Helen J. Harris, Adam Jennings, Ke Hu, Joe Grove, Patricia F. Lalor, David H. Adams, Peter Balfe, Stefan G. Hübscher, Jane A. McKeating
Journal: Hepatology (2007)

The principal site of hepatitis C virus (HCV) replication is the liver. HCV pseudoparticles infect human liver derived cell lines and this suggests that liver-specific receptors contribute to defining HCV hepatotropism. At least three host cell molecules have been reported to be important for HCV entry: the tetraspanin CD81, scavenger receptor class B member I (SR-BI), and the tight junction (TJ) protein Claudin 1 (CLDN1). Hepatocytes in liver tissue coexpress CD81, SR-BI, and CLDN1, consistent with their ability to support HCV entry. CLDN1 localized at the apical-canalicular TJ region and at basolateral-sinusoidal hepatocyte surfaces in normal tissue and colocalized with CD81 at both sites. In contrast, CLDN1 appeared to colocalize with SR-BI at the basolateral-sinusoidal surface. CLDN1 expression was increased on basolateral hepatocyte membranes in HCV-infected and other chronically inflamed liver tissue compared with normal liver. In contrast, CLDN4 hepatocellular staining was comparable in normal and diseased liver tissue. Conclusion : HCV infection of Huh-7.5 hepatoma cells in vitro significantly increased CLDN1 expression levels, consistent with a direct modulation of CLDN1 by virus infection. In HCV infected livers, immunohistochemical studies revealed focal patterns of CLDN1 staining, suggesting localized areas of increased CLDN1 expression in vivo which may potentiate local viral spread within the liver. (Hepatology 2007.)
Bronchial adenoma: review of 18-year experience at the Brompton Hospital.
Authors: R M Lawson, L Ramanathan, G Hurley, K W Hinson, S C Lennox
Journal: Thorax (1976)

Continued uncertainty about the prognosis for patients with bronchial adenomata led to a review of the experience of this condition in the Brompton Hospital. Of 72 patients seen between January 1955 and December 1972, 39 were women and 33 men, mean age 45 years, range 9-73 years. The commonest presenting symptoms were haemoptysis, cough, sputum, and repeated chest infections. Positive bronchoscopic biopsy occurred in 35 of 43 cases; five of these were originally reported as carcinomata, of oat-cell type in four. Plain chest film abnormality occurred in 69 patients. Seventy-three operative procedures comprised two endoscopic removals, two wedge resections, six bronchotomies, five pneumonectomies, and 58 lobectomies (seven with sleeve resection). Recurrence in three of six bronchotomies--two with adenoid cystic carcinomata (cylindromata)--necessitated further surgery. Lobectomy and lymph node dissection is usually the operation of choice. Histology confirmed 67 carcinoids (eight with atypical histology or lymph node metastases), two adenoid cystic carcinomata, one muco-epidermoid, and two mucous gland adenomata. Prolonged follow-up is especially indicated in patients with adenoid cyst carcinoma and in those with atypical or metastatic carcinoid histology. Although such pathology is not incompatible with long survival, of 10 patients in these categories, all five late deaths were probably related to the tumour. However, of 57 patients considered to have had typical carcinoid histology and adequate removal of the tumour, there has to date been no tumour-related death, but one patient developed radiosensitive atypical carcinoid tracheal tumours nine years later. The actuarially assessed survival of 71 patients undergoing surgery for bronchial adenomata was 75% at 15 years. Specific tumour types should replace the term bronchial adenoma.
Noradrenaline concentration and turnover in different regions of the gastrointestinal tract of the rat: an approach to the evaluation of sympathetic activity in the gut
Authors: H. L. Taubin, B. Djahanguiri, L. Landsberg
Journal: Gut (1972)

The endogenous noradrenaline concentration, fractional turnover, half-life, and turnover rate of tritiated ((3)H) noradrenaline were determined in the oesophagus, non-glandular and glandular portions of the stomach, duodenum, jejunum, ileum, and colon of the rat. The highest concentration of endogenous noradrenaline was present in the duodenum and colon. The (3)H-noradrenaline fractional turnover rates and half-lives were significantly greater in the small and large intestines as compared with the oesophagus and stomach. The noradrenaline turnover rate, which is an estimate of the level of sympathetic activity, was greatest in the colon and duodenum. This method of assessing sympathetic activity in various tissues by direct measurement of the noradrenaline turnover rate may be applied to the study of the adrenergic nervous system in the physiology and pathophysiology of the gastrointestinal tract.
Frequent inactivation of the tumor suppressor Kruppel-like factor 6 (KLF6) in hepatocellular carcinoma
Authors: Sigal Kremer-Tal, Helen L. Reeves, Goutham Narla, Swan N. Thung, Myron Schwartz, Analisa Difeo, Amanda Katz, Jordi Bruix, Paulette Bioulac-Sage, John A. Martignetti, Scott L. Friedman
Journal: Hepatology (2004)

Hepatocellular carcinoma (HCC) is a leading cause of cancer death worldwide, reflecting incomplete characterization of underlying mechanisms and lack of early detection. Krüppel-like factor 6 ( KLF6 ) is a ubiquitously expressed zinc finger transcription factor that is deregulated in multiple cancers through loss of heterozygosity (LOH) and/or inactivating somatic mutation. We analyzed the potential role of the KLF6 tumor suppressor gene in 41 patients who had HCC associated with hepatitis C virus (16 patients), hepatitis B virus (12 patients, one of whom was coinfected with hepatitis C virus), and other etiologies (14 patients) by determining the presence of LOH and mutations. Overall, LOH and/or mutations were present in 20 (49%) of 41 tumors. LOH of the KLF6 gene locus was present in 39% of primary HCCs, and the mutational frequency was 15%. LOH and/or mutations were distributed across all etiologies of HCC evaluated, including patients who did not have cirrhosis. Functionally, wild-type KLF6 decreased cellular proliferation of HepG2 cells, while patient-derived mutants did not. In conclusion , we propose that KLF6 is deregulated by loss and/or mutation in HCC, and its inactivation may contribute to pathogenesis in a significant number of these tumors. (Hepatology 2004;40:1047-1052.)
The cellular impacts of diesel exhaust particles: beyond inflammation and death
Authors: N. Li, A. E. Nel
Journal: European Respiratory Journal (2006)

Epidemiological studies have demonstrated an association between exposure to ambient particulate matter (PM) and increasing respiratory mortality and morbidity 1. In western countries, exhausts from diesel and gasoline vehicles constitute a major portion of PM and have been suspected of increasing the risk of lung cancer 2. An important component of PM is the diesel exhaust particle (DEP), which is comprised of a carbon core that adsorbs a mixture of metals and organic chemicals, including carcinogens 3. The small size and large surface area of DEP allow these particles to penetrate deep into the lung and deposit toxic chemicals throughout the respiratory tract 2. Due to their location and function, epithelial cells are one of the first and major PM targets. The impact of DEP on airway epithelial cells includes inflammation, cytotoxicity and genotoxicity.

It has been established that DEP chemicals can generate reactive oxygen species (ROS) 4. The sources of ROS generation are related to the particle content of transition metals and organic chemicals 4. Excessive ROS can lead to a state of oxidative stress, which can induce a variety of cellular responses including DNA damage 4. Moreover, many polycyclic aromatic hydrocarbons (PAH) associated with DEP are genotoxic as they form a PAH-DNA adduct 5, 6. PM-induced DNA damage includes: increased frequency of mutation; single-strand breaks; and the formation of 8-oxo-7,8-dihydro-2′-deoxyguanosine and PAH-DNA adducts 2, 4.

Airway epithelial cells are at greater risk of DNA damage because of their constant exposure to PM-induced oxidative stress …
923-2 Effects of L-Carnitine on Left Ventricular Function After Acute Myocardial Infarction. Results of the CEDIM (Carnitina Ecocardiografia Digitale Infarto Miocardico) Trial
Authors: Sabino Iliceto, Vito Marangelli, Giuseppe Santoro, Luca Bani, Gaetano D’Ambrosio, Domenico Scrutinio, Paolo Bruzzi, Paul G. Hugenholtz, Paolo Rizzon
Journal: Journal of the American College of Cardiology (1995)
Left ventricular aneurysm. Preoperative hemodynamics, chamber volume, and results of aneurysmectomy.
Authors: L E Watson, D W Dickhaus, R H Martin
Journal: Circulation (1975)

Angiocardiographic characteristics of the residual contracting left ventricle (LV) have been examined in 16 patients with anterolateral ventricular aneurysms (VA). In each patient a contractile section (CS) of the LV was clearly demarcated from the remaining aneurysmal section (AS). Using a double hemispheroid model, volumes of CS and AS were separately estimated by a modified area-length method. The volume of CS plus AS agreed closely with the volume of total LV estimated by the conventional area-length method. End-diastolic volume (EDV) of total LV ranged from 79 to 312ml/72. Aneurysmal section volume ranged from 8 to 264 ml/m2. End-diastolic volume of the contractile section ranged from 52 to 159 ml/m2 (mean, 100+/-8 (se); normal, 78+/-6). Contractile section ejection fraction (EF) showed a wide range, from 15% to 79% (mean 40%+/-17% SD). Nine patients underwent resection of VA. Three of six operated patients with CS EF less than 44% died; no survivor in this group has improved by more than one functional class (New York Heart Association classification). Three operated patients had CS EF greater than 45%; all survived and are improved, two having moved from class IV to class I. These data suggest that the EF of the contracting residual LV may be an important predictor of the outcome of resection of VA.
Reply to González Lama et al. Selective Biliary Cannulation Using Pancreatic Guide-Wire Placement
Authors: S. Maeda, H. Hayashi, O. Hosokawa
Journal: Endoscopy (2004)

We are grateful to Dr. González Lama and colleagues for their interest in our article [1]. We agree that it is important to exercise caution when cannulating the bile duct using pancreatic guide-wire placement, as is also emphasized by Devière [2]. Still, we sometimes encounter difficult and demanding cases and we keep trying to improve our skills and insertion rates. Our study attempted to demonstrate the usefulness of pancreatic guide-wire placement in improving the insertion rate into the deep bile duct, and the method had no significant adverse effects or complications. Our report included some explanations, and the meaning of the figures given was clarified in it [1].
Letter: Adrenal failure in bronchial asthma.
Authors: J Dalgleish, C M Leon
Journal: BMJ (1973)

Medical technologies, e-health and personalised medicine are rapidly changing the healthcare landscape. Successful implementation depends on interactions between the technology, the actors and the context. More traditional reductionistic approaches aim to understand isolated factors and linear cause–effect relations and have difficulties in addressing inter-relatedness and interaction. Complexity theory offers a myriad of approaches that focus specifically on behaviour and mechanisms that emerge from interactions between involved actors and the environment. These approaches work from the assumption that change does not take place in isolation and that interaction and inter-relatedness are central concepts to study. However, developments are proceeding fast and along different lines. This can easily lead to confusion about differences and usefulness in clinical and healthcare research and practice. Next to this, reductionistic and complexity approaches have their own merits and much is to be gained from using both approaches complementary. To this end, we propose three lines in complexity research related to health innovation and discuss ways in which complexity approaches and reductionistic approaches can act compatibly and thereby strengthen research designs for developing, implementing and evaluating health innovations.
Role of lipoprotein lipase in the regulation of high density lipoprotein apolipoprotein metabolism. Studies in normal and lipoprotein lipase-inhibited monkeys.
Authors: I J Goldberg, W S Blaner, T M Vanni, M Moukides, R Ramakrishnan
Journal: Journal of Clinical Investigation (1990)

Mechanisms that might be responsible for the low levels of high density lipoprotein (HDL) associated with hypertriglyceridemia were studied in an animal model. Specific monoclonal antibodies were infused into female cynomolgus monkeys to inhibit lipoprotein lipase (LPL), the rate-limiting enzyme for triglyceride catabolism. LPL inhibition produced marked and sustained hypertriglyceridemia, with plasma triglyceride levels of 633-1240 mg/dl. HDL protein and cholesterol and plasma apolipoprotein (apo) AI levels decreased; HDL triglyceride (TG) levels increased. The fractional catabolic rate of homologous monkey HDL apolipoproteins injected into LPL-inhibited animals (n = 7) was more than double that of normal animals (0.094 +/- 0.010 vs. 0.037 +/- 0.001 pools of HDL protein removed per hour, average +/- SEM). The fractional catabolic rate of low density lipoprotein apolipoprotein did not differ between the two groups of animals. Using HDL apolipoproteins labeled with tyramine-cellobiose, the tissues responsible for this increased HDL apolipoprotein catabolism were explored. A greater proportion of HDL apolipoprotein degradation occurred in the kidneys of hypertriglyceridemic than normal animals; the proportions in liver were the same in normal and LPL-inhibited monkeys. Hypertriglyceridemia due to LPL deficiency is associated with low levels of circulating HDL cholesterol and apo AI. This is due, in part, to increased fractional catabolism of apo AI. Our studies suggest that variations in the rate of LPL-mediated lipolysis of TG-rich lipoproteins may lead to differences in HDL apolipoprotein fractional catabolic rate.
Inflammatory bowel disease--a radical view.
Authors: N J Simmonds, D S Rampton
Journal: Gut (1993)

Inflammatory bowel disease a radical viewAlthough the aetiology of inflammatory bowel disease remains unknown, its pathogenesis is gradually being unravelled.Increasing attention has been focused recently on the role of free radicals, in both normal metabolism and defence against disease, and also in a wide variety of conditions, for example rheumatoid arthritis, diabetes mellitus, atherosclerosis, pancreatitis, and peptic ulcer, in which oxidant stress seems to exceed homeostatic mecha- nisms.Free radical activity may contribute to the patho- genesis of both inflammation and cancer.This review examines the evidence that abnormal oxidative metabolism is of central importance to active inflammatory bowel disease.The potential pathogenicity of free radicals has been empha- sised by recent work which suggests that reactive oxygen metabolites are not just one of a number of mediators and cytokines involved in the inflammatory process in inflam- matory bowel disease but many have a pivotal role by initiating the expression of genes controlling may other aspects of the inflammatory, immune, and acute phase response, by activation of the transcription factor NF-x,.5
Covert video surveillance of children: Guidelines don't apply in Munchausen by proxy
Authors: S. Shepherd
Journal: BMJ (1993)

A survey conducted in England and Wales by the Office of Population Censuses and Surveys in 1980 showed that out of 1303 drinkers interviewed, 64 reported problems related to alcohol.Two thirds of these drinkers admitted to drinking less than 50 units a week, and only one third admitted to consumption above that.There are many similar examples from international surveys.We believe that there are no grounds for revising the guidelines on sensible drinking and that they provide an invaluable marker in assessing the clinical importance of a patient's drinking habits.
Increased D-dimer levels correlate with binding of activated protein C, but not tissue factor expression, on peripheral blood monocytes in cancer patients
Authors: M.R. Nijziel, R. van Oerle, E.C.M. van Pampus, H.C.W. de Vet, H.F.P. Hillen, K. Hamuly�k
Journal: American Journal of Hematology (2000)

Monocyte tissue factor expression is supposed to play an important role in the hypercoagulability of blood in cancer patients. The relation between coagulation parameters and the expression of monocyte membrane proteins involved in hemostasis or monocyte activation was studied in 21 patients with a disseminated malignancy and 21 age- and sex-matched healthy controls. In the cancer patient group no increase of monocyte tissue factor expression was found (8. 4% vs. 7.8%; P = 0.83), but a significant increase of monocyte-bound activated protein C (APC) (28.8% vs. 13.4%; P = 0.009) and monocyte CD16 expression (34.5% vs. 27.0%; P = 0.007) was observed. There was also a significant increase of D-dimers (2.0 vs. 0.2 microg/ml; P = 0.001), a decrease of antithrombin (83.5% vs. 102.0%; P = 0.004), but no increase of TAT complexes (1.7 vs. 1.5 microg/l; P = 0.38) or factor VII(a) (68.5% vs. 75.0%; P = 0.52). The increase of D-dimers was significantly correlated with the monocyte APC (R = 0.60; P = 0. 005), but not with monocyte tissue factor levels (R = -0.22; P = 0. 35) or TAT complexes (R = 0.12; P = 0.60). These results reflect a local rather than systemic thrombin and fibrin formation. It is suggested that the APC formed locally enters the circulation and binds to peripheral blood monocytes. APC bound on monocytes is known to inhibit monocyte cytokine production and might therefore be involved in regulatory responses of monocytes in cancer patients.
Cancer of the Ovary
Authors: Stephen A. Cannistra
Journal: New England Journal of Medicine (2004)

Patients with ovarian cancer usually present with advanced disease, and the disease is generally managed with surgical resection followed by platinum-based chemotherapy. Recent chemotherapeutic advances have led to improved survival, and a better understanding of genetic risk factors has permitted a tailored approach to preventive strategies, such as bilateral salpingo-oophorectomy in selected women. This review describes the clinical features of ovarian cancer and recent advances in postoperative management.