tbuckley/cabot-search huggingface dataset:
Genomic Inferences of the cis-Regulatory Nucleotide Polymorphisms Underlying Gene Expression Differences between Drosophila melanogaster Mating Races
Authors: Naoki Osada, Michael H Kohn, Chung-I Wu
Journal: Molecular Biology and Evolution (2006)

Nucleotide sequence polymorphisms affecting gene expression occur in the regulatory region of genes (in cis) and elsewhere in the genome (in trans). Further study is required to weigh the relative importance of cis- and trans-acting mutations in mediating gene expression differences within and between species. Here, microarray hybridization experiments were used to isolate 363 gene expression differences between the female fly head transcriptomes of 2 Drosophila melanogaster strains. One strain (French) represented the cosmopolitan M mating race and the other strain (ZS30) represented the Z mating race derived from Zimbabwe, Africa. From chromosomal substitution strains engineered from the 2 strains, we inferred that the expression differences between M and Z alleles largely could be attributed to the genotype of the chromosomes where the differentially expressed genes were located, that is, cis-regulatory polymorphisms prominently influence gene expression differences between M and Z. The effects of trans-regulatory polymorphisms were apparent yet difficult to quantify. Results have implications for models of gene regulatory evolution as well as experimental studies trying to identify the nucleotide sequence polymorphisms underlying gene expression differences between Drosophila strains.
Double-Blind, Placebo-Controlled Trial of Oral Immunotherapy (OIT) in Peanut (PN) Allergic Children: A Follow-up
Authors: S.M. Jones, A.M. Scurlock, L. Pons, T.T. Perry, A.R. Morgan, M. Kulis, B. Vickery, P. Steele, J. Kamilaris, A.M. Hiegel, A.W. Burks
Journal: Journal of Allergy and Clinical Immunology (2010)
THE RESPONSIBILITIES OF THE CONSULTANT GRADE
Authors: U.R. Allen, B.H. Bass, T.R. Beatson, P.L. Berger, R.A. Bond, B.C. Calverley, I.S. Chatha, J.N. Cozens-Hardy, W.S. Crawford, I.D.O. Frew, D.D. Gibbs, C.I. Griffiths, E.R.S. Hooper, F.R. Hurford, F.E. Mcguinness, P.A. Manfield, D.J. Parry, I.C.F. Riach, R.S. Rihan
Journal: The Lancet (1969)
Evaluation and characterization of generalized anxiety and depression in patients with primary brain tumors
Authors: Staci D. Arnold, Leslie M. Forman, Bart D. Brigidi, Karen E. Carter, Holly A. Schweitzer, Heather E. Quinn, A. Bebe Guill, James E. Herndon, Renee H. Raynor
Journal: Neuro-Oncology (2008)

To determine clinical and sociodemographic factors that are associated with major neuropsychiatric illnesses among brain tumor patients, we administered a modified version of the Brief Patient Health Questionnaire and a demographic data form to 363 adult neuro-oncology patients. Responses were analyzed to assess for associations between demographic variables, clinical variables, and symptoms consistent with diagnoses of generalized anxiety disorder and/or depression. Multivariate logistic regression analyses showed that female gender was associated with the presence of symptoms of anxiety, depression, and combined anxiety and depression. Lower WHO tumor grade classifications, lower education level, and a history of psychiatric illness also emerged as important predictors of symptoms consistent with anxiety and/or depression. Marital status and presence of past/current medical illness trended toward being significantly associated with depression alone. Patient use of psychiatric medication was not associated with any study variables. Results of the present study suggest several hypotheses to test with neuro-oncology patients in further longitudinal analyses, which would benefit from the inclusion of a wider range of neuropsychiatric symptoms in conjunction with neurocognitive and functional impairment variables.
Exercise-induced asthma in children
Authors: KH Carlsen, J Boe
Journal: European Respiratory Journal (1993)

If from running, gymnastic exercises, or any other work, the breathing becomes difficult, it is called Asthma (<XmJlCX). Aretaeus the Cappodician; lst Century AD [1]. Exercise-induced bronchoconstriction (EIB) was long ago recognized as a manifestation of asthma [1], and exercise-induced asthma (EIA) is a common presentation of childhood asthma. BACKER and ULRIK [2] reported that 16% of 494 healthy Danish children and adolescents had a fall in forced expiratory volume in one second (FEY 1 ), of 10% or more after exercise test, and Em is reported to occur in 70-80% of asthmatic children and adults [3]. EIA represents a major impairment of the everyday life of asthmatic children, influencing their self-perception, as they appraise themselves to a major extent by their successes in physical skill and mastery. Based upon the 1988 National Health Interview Survey in USA, TA YLOR and NEWACHF.CK [4] recently reported that of 2.7 million American children with asthma, 2.6% were unable to conduct major activities, compared to 0.3% of all children without asthma. Approximately 30% of asthmatic children had some limitations in activity, compared to 4.5% of children without asthma [4]. These limitations in physical activity remain a major obstacle to the asthmatic child's social and physical functioning. When studied in a standardized way, Em may be regarded as a measure of nonspecific bronchial hyperreactivity [5]. EIB is thought to be elicited by mediator release, provoked by respiratory heat and water loss, causing a change in osmolality of the pericilliary fluid lining the respiratory tract [3]. Em is, therefore, considered an indirect measure of nonspecific bronchial responsiveness, whereas bronchial responsiveness measured by methacholine or histamine inhalation is considered a direct measure of bronchial responsiveness [6]. EIB is usually measured by the reduction in FEY 1 from preto post-exercise with a submaximal load. Running on a motor driven treadmill for 6 min. with a steady-state heart rate of 170-190 beats·min·', is a commonly used test. Running is usually more suitable than using a bicycle, as the muscles used during running are better trained as a result of daily life activity than those used during cycling. A reduction in FEV1 of 15% or more after exercise is usually taken as a sign of EIA [7, 8]. Sometimes 10%
Acute Effects of Aerosolized <i>S</i>-Nitrosoglutathione in Cystic Fibrosis
Authors: Ashley H. Snyder, Marianne E. McPherson, John F. Hunt, Michael Johnson, Jonathan S. Stamler, Benjamin Gaston
Journal: American Journal of Respiratory and Critical Care Medicine (2002)

S-Nitrosoglutathione (GSNO), a naturally occurring constituent of airway lining fluid, enhances ciliary motility, relaxes airway smooth muscle, inhibits airway epithelial amiloride-sensitive sodium transport, and prevents pathogen replication. Remarkably, airway levels of GSNO are low in patients with cystic fibrosis (CF). We hypothesized that replacement of airway GSNO would improve gas exchange in CF. In a double-blind, placebo controlled study, we administered 0.05 ml/kg of 10 mM GSNO or phosphate buffered saline by aerosol to patients with CF and followed oxygen saturation, spirometry, respiratory rate, blood pressure, heart rate, and expired nitric oxide (NO). Nine patients received GSNO and 11 placebo. GSNO inhalation was associated with a modest but sustained increase in oxygen saturation at all time points. Expired NO increased in the low ppb range with GSNO treatment, peaking at 5 minutes but remaining above baseline at 30 minutes. There were no adverse effects. We conclude that GSNO is well tolerated in patients with CF and improves oxygenation through a mechanism that may be independent of free NO. Further, GSNO breakdown increases expired NO. We suggest that therapy aimed at restoring endogenous GSNO levels in the CF airway may merit study.
Clostridium difficile associated diarrhoea in hospitalised patients: onset in the community and hospital and role of flexible sigmoidoscopy
Authors: S S Johal
Journal: Gut (2004)

<b>Objectives:</b><i>Clostridium difficile</i> associated diarrhoea (CDAD) is a hospital acquired infection in which optimal methods for diagnosis and the scale of the problem in the community remain to be determined. In hospitalised patients with CDAD, we aimed to (i) study patients in whom the onset of diarrhoea was in the community and (ii) investigate the role of bedside flexible sigmoidoscopy in diagnosis. <b>Methods:</b> Patients with CDAD (onset in hospital or community) were studied prospectively. In those with diarrhoea of unknown aetiology, flexible sigmoidoscopy was compared with stool assay for <i>C difficile</i> cytotoxin. <b>Results:</b> Of 136 patients with CDAD (which was associated with antibiotic exposure in 96%), diarrhoea started in the community in 38 (28%; majority in own home) and while an inpatient in 98 (72%). The majority with CDAD onset in the community had been hospitalised over the preceding 12 months (86.8% <i>v</i> 57.1% in the hospital onset group; p&lt;0.001). In 56 patients with pseudomembranous colitis at sigmoidoscopy, the stool <i>C difficile</i> cytotoxin test was negative in 29 (52%) but toxigenic <i>C difficile</i> was isolated from all of nine stool samples cultured. Of patients with pseudomembranous colitis, 30.4% relapsed over the subsequent 57.7(4.2) days. <b>Conclusions:</b> In a significant proportion of hospitalised patients with CDAD, diarrhoea started in the community. However, the majority of these had been hospital inpatients previously when they may have acquired <i>C difficile</i>, with the subsequent onset of diarrhoea in the community following exposure to antibiotics. Flexible sigmoidoscopy is superior to the stool <i>C difficile</i> cytotoxin test in a subgroup of patients with pseudomembranous colitis. Sigmoidoscopy should therefore be considered in all hospitalised patients with diarrhoea in whom the stool test for <i>C difficile</i> cytotoxin and enteric pathogens is negative.
Percutaneous Pacemaker and Implantable Cardioverter-Defibrillator Lead Extraction in 100 Patients With Intracardiac Vegetations Defined by Transesophageal Echocardiogram
Authors: Jon A. Grammes, Christopher M. Schulze, Mohammad Al-Bataineh, George A. Yesenosky, Christine S. Saari, Michelle J. Vrabel, Jay Horrow, Mashiul Chowdhury, John M. Fontaine, Steven P. Kutalek
Journal: Journal of the American College of Cardiology (2010)
The National Cholesterol Education Program–Adult Treatment Panel III, International Diabetes Federation, and World Health Organization Definitions of the Metabolic Syndrome as Predictors of Incident Cardiovascular Disease and Diabetes
Authors: Carlos Lorenzo, Ken Williams, Kelly J. Hunt, Steven M. Haffner
Journal: Diabetes Care (2006)

The clinical value of metabolic syndrome is uncertain. Thus, we examined cardiovascular disease (CVD) and diabetes risk prediction by the National Cholesterol Education Program (NCEP)-Adult Treatment Panel III (ATPIII), International Diabetes Federation, and World Health Organization definitions of the metabolic syndrome.We analyzed the risks associated with metabolic syndrome, the NCEP multiple risk factor categories, and 2-h glucose values in the San Antonio Heart Study (n = 2,559; age range 25-64 years; 7.4 years of follow-up).Both ATPIII metabolic syndrome plus age > or = 45 years (odds ratio 9.25 [95% CI 4.85-17.7]) and multiple (two or more) risk factors plus a 10-year coronary heart disease (CHD) risk of 10-20% (11.9 [6.00-23.6]) had similar CVD risk in men without CHD, as well as CHD risk equivalents. In women counterparts, multiple (two or more) risk factors plus a 10-year CHD risk of 10-20% was infrequent (10 of 1,254). However, either a 10-year CHD risk of 5-20% (7.72 [3.42-17.4]) or ATPIII metabolic syndrome plus age > or = 55 years (4.98 [2.08-12.0]) predicted CVD. ATPIII metabolic syndrome increased the area under the receiver operating characteristic curve of a model containing age, sex, ethnic origin, family history of diabetes, and 2-h and fasting glucose values (0.857 vs. 0.842, P = 0.013). All three metabolic syndrome definitions imparted similar CVD and diabetes risks.Metabolic syndrome is associated with a significant CVD risk, particularly in men aged > or = 45 years and women aged > or = 55 years. The metabolic syndrome predicts diabetes beyond glucose intolerance alone.
AT <sub>1</sub> Receptor Agonistic Antibodies From Preeclamptic Patients Stimulate NADPH Oxidase
Authors: Ralf Dechend, Christiane Viedt, Dominik N. Müller, Bernhard Ugele, Ralf P. Brandes, Gerd Wallukat, Joon-Keun Park, Jurgen Janke, Peter Barta, Jurgen Theuer, Anette Fiebeler, Volker Homuth, Rainer Dietz, Hermann Haller, Jörg Kreuzer, Friedrich C. Luft
Journal: Circulation (2003)

We recently identified agonistic autoantibodies directed against the angiotensin AT1 receptor (AT1-AA) in the plasma of preeclamptic women. To elucidate their role further, we studied the effects of AT1-AA on reactive oxygen species (ROS), NADPH oxidase expression, and nuclear factor-kappaB (NF-kappaB) activation.We investigated human vascular smooth muscle cells (VSMC) and trophoblasts, as well as placentas. AT1-AA were isolated from sera of preeclamptic women. Angiotensin II (Ang II) and AT1-AA increased ROS production and the NADPH oxidase components, p22, p47, and p67 phox in Western blotting. We next tested if AT1-AA lead to NF-kappaB activation in VSMC and trophoblasts. AT1-AA activated NF-kappaB. Inhibitor-kappaBalpha (I-kappaBalpha) expression was reduced in response to AT1-AA. AT1 receptor blockade with losartan, diphenylene iodonium, tiron, and antisense against p22 phox all reduced ROS production and NF-kappaB activation. VSMC from p47phox-/- mice showed markedly reduced ROS generation and NF-kappaB activation in response to Ang II and AT1-AA. The p22, p47, and p67 phox expression in placentas from preeclamptic patients was increased, compared with normal placentas. Furthermore, NF-kappaB was activated and I-kappaBalpha reduced in placentas from preeclamptic women.NADPH oxidase is potentially an important source of ROS that may upregulate NF-kappaB in preeclampsia. We suggest that AT1-AA through activation of NADPH oxidase could contribute to ROS production and inflammatory responses in preeclampsia.
Relations of serum phosphorus levels to echocardiographic left ventricular mass and incidence of heart failure in the community
Authors: Ravi Dhingra, Philimon Gona, Emelia J. Benjamin, Thomas J. Wang, Jayashri Aragam, Ralph B. D'Agostino, William B. Kannel, Ramachandran S. Vasan
Journal: European Journal of Heart Failure (2010)
Benign lymphocytic angiitis and granulomatosis.
Authors: H Tukiainen, E O Terho, K Syrjanen, S Sutinen
Journal: Thorax (1988)

A 37 year old woman underwent a lobectomy for a lesion with a tumour like appearance on the chest radiograph. This was shown microscopically to be benign lymphocytic angiitis and granulomatosis, a rare condition that responds well to cytotoxic drugs and has a good prognosis.
A Phase II Trial with Pharmacodynamic Endpoints of the Proteasome Inhibitor Bortezomib in Patients with Metastatic Colorectal Cancer
Authors: Helen Mackay, David Hedley, Pierre Major, Carol Townsley, Mary Mackenzie, Mark Vincent, Pam Degendorfer, Ming-Sound Tsao, Trudey Nicklee, Diana Birle, John Wright, Lillian Siu, Malcolm Moore, Amit Oza
Journal: Clinical Cancer Research (2005)

To evaluate the effects of the proteasome inhibitor bortezomib on tumor growth in patients with advanced colorectal cancer, and to explore the relationship between correlative studies and clinical outcome.Bortezomib (1.3 mg/m(2)) was administered i.v. on days 1, 4, 8, and 11 of a 21-day cycle. Tumor response was assessed after every two cycles. Tumor biopsies were done prior to treatment and on day 9 of the first treatment cycle. Biopsies were examined for Ser(32/36)-IkappaB, Ser(276)-nuclear factor kappaB (NFkappaB), hypoxia-inducible factor-1alpha (HIF-1alpha), carbonic anhydrase IX (CAIX), p53, and microvessel density using immunohistochemistry.Nineteen patients received 42 cycles (range 1-4) of bortezomib. No objective response was seen; three patients had stable disease at cycle 2, two patients had progressive disease after cycle 1, and 11 patients had progressive disease at cycle 2. Of the three patients with stable disease, one had progressive disease after cycle 4, and two were withdrawn due to toxicity. The median time to progression was 5.1 weeks (95% confidence interval, 5.1-11.1 weeks). There was a significant increase in the expression of HIF-1alpha relative to its transcriptional target CAIX following bortezomib, and a similar effect was also observed in a companion study using a human tumor xenograft model. Expression of p53, Ser(276)-NFkappaB, and Ser(32/36)-IkappaB was unchanged.Single agent bortezomib is inactive in metastatic colorectal cancer. Using this regimen, there was no detectable effect on NFkappaB, but a significant accumulation of HIF-1alpha was seen relative to CAIX. This suggests that proteasome inhibition alters the response to tumor hypoxia, and further investigation of this effect is indicated.
Psychiatric Comorbidity, Suicidality, and In-Home Firearm Access Among a Nationally Representative Sample of Adolescents
Authors: Joseph A. Simonetti, Jessica L. Mackelprang, Ali Rowhani-Rahbar, Douglas Zatzick, Frederick P. Rivara
Journal: JAMA Psychiatry (2014)

Suicide is the second leading cause of death among US adolescents, and in-home firearm access is an independent risk factor for suicide. Given recommendations to limit firearm access by those with mental health risk factors for suicide, we hypothesized that adolescents with such risk factors would be less likely to report in-home firearm access.To estimate the prevalence of self-reported in-home firearm access among US adolescents, to quantify the lifetime prevalence of mental illness and suicidality (ie, suicidal ideation, planning, or attempt) among adolescents living with a firearm in the home, and to compare the prevalence of in-home firearm access between adolescents with and without specific mental health risk factors for suicide.Cross-sectional analysis of data from the National Comorbidity Survey-Adolescent Supplement, a nationally representative survey of 10,123 US adolescents (age range, 13-18 years) who were interviewed between February 2001 and January 2004 (response rate 82.9%).Risk factors for suicide, including a history of any mental health disorder, suicidality, or any combination of the 2.Self-reported access to a firearm in the home.One in three respondents (2778 [29.1%]) of the weighted survey sample reported living in a home with a firearm and responded to a question about firearm access; 1089 (40.9%) of those adolescents reported easy access to and the ability to shoot that firearm. Among adolescents with a firearm in home, those with access were significantly more likely to be older (15.6 vs 15.1 years), male (70.1% vs 50.9%), of non-Hispanic white race/ethnicity (86.6% vs 78.3%), and living in high-income households (40.0% vs 31.8%), and in rural areas (28.1% vs 22.6%) (P < .05 for all). Adolescents with firearm access also had a higher lifetime prevalence of alcohol abuse (10.1% vs 3.8%, P < .001) and drug abuse (11.4% vs 6.9%, P < .01) compared with those without firearm access. In multivariable analyses, adolescents with a history of mental illness without a history of suicidality (prevalence ratio [PR], 1.13; 95% CI, 0.98-1.29) and adolescents with a history of suicidality with or without a history of mental illness (PR, 1.20; 95% CI, 0.96-1.51) were as likely to report in-home firearm access as those without such histories.Adolescents with risk factors for suicide were just as likely to report in-home firearm access as those without such risk factors. Given that firearms are the second most common means of suicide among adolescents, further attention to developing and implementing evidence-based strategies to decrease firearm access in this age group is warranted.
Reply to J. Menczer
Authors: Laurie M. Elit, Gregory Pond, Hsien-Yeang Seow
Journal: Journal of Clinical Oncology (2014)

In contrast, our study, 2 cited by the authors, that found that a delay had no impact on prognosis, included only patients with endometrial endometrioid carcinoma.Our findings are also supported by several other studies. 3-5Indeed we reported 6 a prolonged survival in a small series of untreated patients with endometrial endometrioid cancer and patients with a prolonged treatment delay.This seems to indicate that the natural progression course, even in untreated patients, may be slow in endometrial endometrioid carcinoma with favorable prognostic factors.
Concept recognition for extracting protein interaction relations from biomedical text
Authors: William A Baumgartner, Zhiyong Lu, Helen L Johnson, J Gregory Caporaso, Jesse Paquette, Anna Lindemann, Elizabeth K White, Olga Medvedeva, K Bretonnel Cohen, Lawrence Hunter
Journal: Genome biology (2008)

Abstract Background: Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present an integrated approach to concept recognition in biomedical text. Concept recognition provides key information that has been largely missing from previous biomedical information extraction efforts, namely direct links to well defined knowledge resources that explicitly cement the concept's semantics. The BioCreative II tasks discussed in this special issue have provided a unique opportunity to demonstrate the effectiveness of concept recognition in the field of biomedical language processing. Results: Through the modular construction of a protein interaction relation extraction system, we present several use cases of concept recognition in biomedical text, and relate these use cases to potential uses by the benchside biologist. Conclusion: Current information extraction technologies are approaching performance standards at which concept recognition can begin to deliver high quality data to the benchside biologist. Our system is available as part of the BioCreative Meta-Server project and on the internet http://bionlp.sourceforge.net .
Developmental and tumoral vascularization is regulated by G proteinâ€“coupled receptor kinase 2
Authors: VerÃ³nica Rivas, Rita Carmona, RamÃ³n MuÃ±oz-ChÃ¡puli, Marta Mendiola, Laura NoguÃ©s, Clara Reglero, MarÃ­a Miguel-MartÃ­n, RamÃ³n GarcÃ­a-Escudero, Gerald W. Dorn, David Hardisson, Federico Mayor, Petronila Penela
Journal: Journal of Clinical Investigation (2013)

Tumor vessel dysfunction is a pivotal event in cancer progression. Using an in vivo neovascularization model, we identified G protein–coupled receptor kinase 2 (GRK2) as a key angiogenesis regulator. An impaired angiogenic response involving immature vessels was observed in mice hemizygous for Grk2 or in animals with endothelium-specific Grk2 silencing. ECs isolated from these animals displayed intrinsic alterations in migration, TGF-β signaling, and formation of tubular networks. Remarkably, an altered pattern of vessel growth and maturation was detected in postnatal retinas from endothelium-specific Grk2 knockout animals. Mouse embryos with systemic or endothelium-selective Grk2 ablation had marked vascular malformations involving impaired recruitment of mural cells. Moreover, decreased endothelial Grk2 dosage accelerated tumor growth in mice, along with reduced pericyte vessel coverage and enhanced macrophage infiltration, and this transformed environment promoted decreased GRK2 in ECs and human breast cancer vessels. Our study suggests that GRK2 downregulation is a relevant event in the tumoral angiogenic switch.