tbuckley/cabot-search huggingface dataset:
EGFR-mutated lunge cancer in a general Norwegian population
Authors: Lilach Kleinberg, Peter Jebsen, Marius Lund-Iversen, Åslaug Helland, Lars Fjellbirkeland
Journal: European Respiratory Journal (2014)

Background: The frequency of activating EGFR-mutations in lung cancer in Caucasians, has been said to be 15% in adenocarcinomas (AC) and very low in squamous-cell-carcinoma (SCC). From January 2011 to December 2012 the Norwegian policy was to test all NSCLC on a reflexive basis irrespective of histological subtype.  Methods: As part of a retrospective study we wanted to find the frequency of this mutation in an unbiased selection of NSCLC-patients. All tests performed at Oslo University hospital (OUH) in 2011-12 were examined. OUH does about 40% of all testing in Norway.  Results: A total of 1245 patients were tested, 55,3% men and 44,7% women. Immunohistochemistry was performed on 61% of all the specimens to help classifying the subtype of NSCLC. The histologic diagnosis was AC in 775 patients (62,3%) and SCC in 304 (24,4%). The rest had either unspecified NSCLC (8,8%), large-cell carcinoma (LCC)(2,4%) or unknown histology (2,1%). The tissue specimens came from biopsies in 68% of cases, cytology in 12% and the rest, 20%, were resections. Activating EGFR-mutations were found in 83 patients (6,7%) while no mutations were seen in 91,8%. In 19 patients, 1,5%, the tests were inconclusive. Among men 4,9% were positive and in women 8,8% were mutation positive. In AC the frequency of mutations was 10,1% (8,4% for men and 11,9% for women). Only one mutated SCC was seen, in a woman. In unspecified NSCLC, 3 patients (3,6%) had the mutation. None of the LCC tested positive.  Conclusions: In our population the frequency was lower than expected from former studies. All but four cases were AC. The frequency was higher among women than men.
An automated application for analysis of incremental exercise tests
Authors: Christopher B. Cooper, Jonathan Y. Lee, John Carney, Brett A. Dolezal, Worawan Sirichana, Maxim A. Batalin
Journal: European Respiratory Journal (2014)

Introduction   Clinical exercise tests (CXT) using symptom-limited incremental protocols can identify physiological limitations and assist with diagnosis of exercise intolerance. However, there are challenges with these tests because of lack of standardization in their performance and with data interpretation.   Methods   We developed an automated application for CXT interpretation based on novel algorithms and pattern recognition. We tested the application on 100 sequential CXT (57 men) and compared results with human interpretation by experienced physicians. Six key physiological variables were examined: maximum values for work (Wmax), oxygen uptake (VO 2 max), heart rate (fCmax), and ventilation (VEmax); and slope values for chronotropic index (CI) and ventilatory efficiency (VE). Accuracy was compared to stringent minimum clinically important differences. Agreement was assessed by Bland-Altman methods.   Results   Three studies were excluded from the analysis because of incomplete data. In three more, the heart rate signal was corrupted by interference. Accuracy and mean bias (limits of agreement) were: Wmax 96%, 1.7 (5.6, -2.2) watts, VO 2 max 80%, -0.02 (0.13, -0.18) L/min, fCmax 82%, -2.0 (8.1, -12.2) /min, VEmax 75%, 3.1 (13.7, -19.85), CI 79%, -0.7 (11.6, -10.3), VE 69%, 1.7 (16.5, -13.1). The application also provides plots for visual detection of threshold values for lactate accumulation (VO 2 θ) and ventilatory compensation (VCO 2 θ).   Conclusion   This automated application produces more consistent and reliable characterization of the human exercise response than manual reporting. Such standardization is necessary to better define the pathophysiology and to assist with diagnosis of exercise limitation.
Sequence of the ebgR gene of Escherichia coli: evidence that the EBG and LAC operons are descended from a common ancestor.
Authors: H W Stokes, B G Hall
Journal: Molecular Biology and Evolution (1985)

The sequence of ebgR, the gene that encodes the EBG repressor, was determined. There is 44% DNA sequence identity between ebgR and lacI, the gene that encodes the LAC repressor. There is also 25% identity between the amino acid sequence of lacI and the deduced amino acid sequence of ebgR. The sequence of 596 bp distal to ebgA, the structural gene for EBG beta-galactosidase, was also determined. Within that region there were two sequences, 74 and 100 bp long, that showed 46% and 50% identity, respectively, to sequences in the first 600 bp of lacY, the structural gene for the lactose permease. The organization and direction of transcription of the repressor and structural genes of the two operons are identical. Taken together with the homology between ebgA and lacZ (as demonstrated in the companion article in this issue), this provides strong evidence that the EBG and LAC operons are descended from a common ancestor. The map position of these two operons supports the notion that these operons diverged following a genome duplication event in an ancestor of Escherichia coli.
Vitamin D metabolism by alveolar immune cells in tuberculosis: correlation with calcium metabolism and clinical manifestations
Authors: JL Cadranel, M Garabedian, B Milleron, H Guillozzo, D Valeyre, F Paillard, G Akoun, AJ Hance
Journal: European Respiratory Journal (1994)

The aim of this study was to investigate the relationship between the pulmonary vitamin D metabolism in tuberculosis and the calcium metabolism abnormalities and other clinical characteristics of the disease. The metabolism of 25-hydroxyvitamin D3 (25(OH)D3) by alveolar immune cells recovered by bronchoalveolar lavage (BAL) was evaluated in parallel to the results of calcium metabolism, 25(OH) D and 1,25 dihydroxyvitamin D (1,25(OH)2D) plasma levels and other clinical parameters obtained in 14 tuberculosis patients. Whilst predominant metabolites produced by lavage cells in patients and controls were 5(E)--and 5(Z) -19-nor-10-oxo-25(OH)D3, 1,25(OH)2D3 was produced by cells from all tuberculosis patients but not by cells from controls. Calcium metabolism abnormalities were observed in only some patients, but the production of 1,25 (OH)2D3 by lavage cells was found to correlate both with 1,25(OH)2D levels (r = 0.67) and post-load urinary calcium excretion (r = 0.59). 1,25(OH)2D3 production by lavage cells was increased in patients of black origin, and those presenting with hilar adenopathy without pulmonary infiltrates, and was correlated with the number of lymphocytes recovered by lavage (r = 0.87). We conclude that 1,25(OH)2D3 production by alveolar immune cells makes a major contribution to the abnormalities in calcium metabolism seen in tuberculosis patients, and may be partly dependent on the clinical characteristics evaluated here.
A self-management programme of activity coping and education (SPACE) for COPD: 6 week results from a randomised controlled trial
Authors: Katy Wagg, Vicki Warrington, Lindsay Apps, Louise Sewell, John Bankart, Mick Steiner, Mike Morgan, Sally Singh
Journal: European Respiratory Journal (2012)

Introduction:  SPACE for COPD is a self-management programme which individuals follow independently with telephone support.   Objective:  To test the effectiveness of SPACE on health related quality of life (HRQoL) and exercise capacity compared with usual GP care at 6 weeks.   Methods:  184 patients with COPD [101male; mean (SD) age 69(9.19) yrs; FEV 1  1.45(0.56) l; BMI 27.56(5.2)] were recruited from primary care and randomised to SPACE or usual care. Blinded measurements were taken at baseline and 6 weeks and included Chronic Respiratory Questionnaire-SR [CRQ-dyspnoea (primary outcome)], Incremental Shuttle Walk Test (ISWT), Endurance Shuttle Walk Test (ESWT), and the Hospital Anxiety Depression Scale (HADS).   Results:  See Table1   Conclusion:  SPACE is effective in improving HRQoL and exercise capacity, when compared with usual care. SPACE could be used to facilitate self-management of patients with COPD in primary care.
Authors’ reply to Laurent
Authors: Salvatore Minisola, Jessica Pepe, Cristiana Cipriani
Journal: BMJ (2015)

We agree with Laurent's first two points, even though hypovitaminosis D may cause hypocalciuria, raising the doubt of familial hypocalciuria hypercalcemia. 1 2 There is much debate around the issue of vitamin D in patients with primary hyperparathyroidism 3 4 ; we believe that calcidiol should be measured because vitamin D insufficiency worsens skeletal involvement, for example.Regarding the third point, we were referring to hypocalciuria and not hypercalcaemia.The thresholds reported are those set for the distinction between primary hyperparathyroidism and familial hypocalciuria hypercalcaemia, an important step to avoid unnecessary operations.The role of magnesium is important, but because of space limitations we did not mention it.
Pregancy after bilateral dysgerminoma treated with conservative surgery and BEP chemotherapy
Authors: N. Shami, A. Shaila, A. Shaharyar, S. Asif
Journal: Journal of Clinical Oncology (2007)

16039 Background: Pregnancy after treatment of germ cell tumours of ovary is common. However patients with bilateral dysgerminoma treated with unilateral oophorectomy, wedge biopsy of opposite ovary, and conservation of uterus face difficulty in conception. This study was conducted with the objective to evaluate the fertility status of ovarian dysgerminoma patients treated with conservative surgery and BEP chemotherapy. Methods: Patients of bilateral dysgerminoma who underwent conservative surgery and chemotherapy with cisplatin 20 mg / m 2 and etoposide 100 mg / m 2 day 1 to 5 and bleomycin 30 mg on day 1, 8 and 15 of three weekly cycles were eligible. A normal AFP and beta HCG at baseline was required. Post treatment CT scans of abdomen and pelvis were obtained. Patients were regularly followed on monthly basis. Pregnancy was allowed 2 years after completion of last cycle of chemotherapy. Results: From January 1998 to December 2003, 11 patients were enrolled. Medain age was 16 years (range 13–18). All patients had complete disappearance of disease after treatment. Treatment related amenorrhea did not last beyond one year. During a median follow up of 5 years, all patients conceived and a total of 14 pregnancies were completed successfully.Three patients required use of clomiphene citrate for ovulation induction. No patient was treated with gonadotrophins. Six patients underwent lower segment caesarean section for obstetric indications and seven delivered vaginally. All babies were healthy without the signs of birth abnormalities or retardation. Conclusions: With conservative surgery and BEP chemotherapy for treatment of bilateral dysgerminoma the fertility is retained with good pregnancy outcome, when conception occurs at least two years after the last dose of chemotherapy. No significant financial relationships to disclose.
High-dose mercaptopurine followed by intermediate-dose cytarabine in relapsed acute leukemia.
Authors: S Lockhart, W Plunkett, S Jeha, I Ramirez, T Zipf, A Cork, D Pinkel
Journal: Journal of Clinical Oncology (1994)

PURPOSE This phase I/II study was designed to explore the feasibility, toxicity, and potential efficacy of administering high-dose continuous intravenous mercaptopurine (6MP) followed by intermediate-dose continuous intravenous cytarabine (Ara-C) to children with relapsed or unresponsive acute leukemia. PATIENTS AND METHODS Twenty-three children with relapsed or unresponsive acute leukemia (13 myeloid, 10 lymphoid) were entered onto the study. After initial hydration and alkalinization, 1,000 or 1,250 mg/m2 of 6MP was administered by continuous intravenous infusion over 24 hours. Following another period of hydration, 500 mg/m2 of Ara-C was administered by continuous intravenous infusion daily for 4 days. In 17 children, plasma concentrations of 6MP were measured at hours 4, 24, and 27 of the 6MP infusions. Plasma concentrations of Ara-C were measured at hours 8, 24, 48, 72, and 96 of the Ara-C infusions. Intracellular Ara-C triphosphate (Ara-CTP) concentrations were measured in peripheral-blood leukemia cells of the five patients with sufficient cells for measurement. Children who developed remission received repeated courses of this regimen every 3 to 4 weeks until relapse or completion of 12 courses. RESULTS Of 13 children with acute myeloid leukemia (AML), six developed complete remissions (CRs) lasting 7 months to nearly 4 years. Two children remain in CR with normal growth, development, and health 3 years after cessation of treatment. Of 10 children with acute lymphoid leukemia (ALL), one had a CR of 2 months' duration. Dose-limiting toxicity consisted of severe hematosuppression with fever, neutropenia, and serious infection. There were two toxic deaths. The mean steady-state plasma concentrations of 6MP were approximately 4 mumol/L and of Ara-C approximately 3 mumol/L. The median Ara-CTP concentration in peripheral-blood leukemia cells was 308 mumol/L at hour 8 of the Ara-C infusion. CONCLUSION High-dose continuous intravenous 6MP followed by intermediate-dose intravenous Ara-C produced CRs of longer than 6 months in approximately half of children with relapsed or unresponsive AML. Further study of this drug regimen is justified.
Inhibition of Chemical Carcinogen-Induced Pulmonary Neoplasia by Butylated Hydroxyanisole
Authors: Lee W. Wattenberg
Journal: JNCI Journal of the National Cancer Institute (1973)

The antioxidant, butylated hydroxyanisole (BHA), inhibited chemical carcinogen-induced pulmonary adenoma formation of the mouse under 2 experimental conditions: 1) Addition of BHA to the diet protected against pulmonary neoplasia resulting from acute exposures to 7,12-dimethylbenz[a]anthracene (DMBA), benzo[a]pyrene, urethan, or uracil mustard. 2) Addition of BHA to diets containing DMBA, 7-hydroxymethyl-12-methylbenzlalanthracene, or dibenz[a,h]anthracene likewise inhibited pulmonary tumor formation.
CFTR regulation by microRNA-145, -223 and -494 is altered in deltaF508 cystic fibrosis airway epithelium
Authors: Irene Oglesby, Sanjay Chotirmall, Noel McElvaney, Catherine Greene
Journal: European Respiratory Journal (2013)

Expression of CFTR is altered in individuals with the delF508CFTR mutation. Herein we investigated the role of miRNAs in CFTR regulation in vivo in bronchial brushings from individuals homo or heterozygous for delF508CFTR, validated our observations in vitro and assessed the impact of defective chloride ion conductance, genotype and Pseudomonas aeruginosa, Staphylococcus aureus or Aspergillus species colonization status on miRNA expression. miRNA target prediction was performed in silico, expression of miRNA and target genes was measured by qRT-PCR and western blotting. Overexpression and inhibition studies were performed with premiRs or antimiRs, respectively, and a reporter gene was used to elucidate miRNA/target interactions. CFTR function was quantified using a fluorescent membrane permeable chloride indicator. miR-145, -223 and -494 were upregulated in CF (n=14) versus non-CF (n=9) bronchial brushings and CFBE41o- versus 16HBE14o- cell lines; in delF508CFTR homozygotes vs. heterozygotes; in subjects positive for P. aeruginosa (n=9) and; in cells treated with a CFTR inhibitor or IL-1beta. Reciprocal down or upregulation of CFTR gene and/or protein expression and function was observed following miRNA manipulation and direct miRNA/target relationships demonstrated via a reporter system containing a wildtype or mutated CFTR 3’UTR. Increased expression of miR-145, -223 and -494 in vivo in bronchial epithelium of individuals carrying the delF508CFTR mutation correlates with decreased CFTR expression. Defective CFTR function, Pseudomonas colonization and inflammation may affect miRNA expression and contribute to the regulation of delF508CFTR.
Potential Impact of the financial crisis: Experience of a sleep clinic in northern Greece
Authors: Athanasia Pataka, Nicolaos Chavouzis, Katalin Fekete Passa, Asimina Paspala, Afroditi Boutou, Georgia Pitsiou, Vasilios Bagalas, Ioannis Stanopoulos, Paraskevi Argyropoulou
Journal: European Respiratory Journal (2012)

Greece has entered a long period of economic crisis with adverse effects on various aspects of daily life. From 2009, poor countries with International Monetary Fund loans displace aid from public health and report negative effects on community health. The aim of our study was to evaluate the impact of the economic crisis on the population visiting a sleep clinic of a tertiary hospital between years 2008 and 2011. Methods: Comparison of the number of patients, anthropometric data, symptoms and treatment acceptance between 2008 (-beginning of crisis) to 2011(great impact of crisis on salaries, psychology). Results: The number of patients that visited the sleep clinic was significantly reduced in 2011(n=127) compared with 2008 (n=463) and 2009 (n=465). The age, BMI and ESS did not differ between the years (mean 52.23±13.7years, 33±7.4kg/m2, and 11.4±5.4 respectively). The main symptom of the patients was daytime sleepiness and the symptoms that were worse in 2011 compared with 2008 were headache (32.4% vs. 49.6%, p<0.001) and nightmares (44% vs. 75.9%, p<0.001). In 2008, 320 (69.1%) patients required treatment for Obstructive Sleep Apnea Syndrome with CPAP and 261(81.5%) of them received CPAP. In 2011, 111 (87.4%) required treatment, but only 68% received CPAP. Conclusions: By the observation of the population visiting a Sleep Clinic, the economic crisis can be reflected in the number of patients, their symptoms and their perspective in treatment options.
Factors associated with different patterns of adherence to treatment in a smoking cessation unit
Authors: Carlos Almonacid Sanchez, Jose Gallardo Carrasco, Ignacio Sanchez Hernandez, Juan Pablo Rodriguez Gallego, Elisabeth Guzman Robles, Jorge Castelao Naval, Jesus Fernandez Frances, Saray Quiros Fernandez, Jose Luis Izquierdo Alonso, Pilar Resano Barrio, Olga Mediano
Journal: European Respiratory Journal (2011)

Objective: Identify different patterns of adherence to therapy in the treatment of patients attending a specialized smoking.

Material and methods: Retrospective cross-sectional study of a sample of smokers who come for smoking cessation. The sample was divided into 4 groups: group 1, who only attend the first visit, group 2, persons who do not attend all visits and not answering phone calls, group 3, people who do not attend all visits but answer phone calls to complete a period of 6 months of treatment, group 4, all patients attending follow-up visits.The collection period runs from January 2004 to June 2010. Data were collected at each visit following the same methodology using an electronic medical record designed for this purpose.

Results: We analyzed a total of 1545 people who attended the clinic. The results are summarized in Table 1. The quantitative variables are described as mean and standard deviation. The qualitative variables are described as total count and percentage.

![Figure][1] 



Conclusions: Age, a lower level of motivation, the coexistence of psychiatric disorders and increased consumption of cigarettesis are associated with poorer adherence to treatment.

 [1]: pending:yes
Tunneled-Cuffed Catheter Associated Infections in Hemodialysis Patients Who Are Seropositive for the Human Immunodeficiency Virus
Authors: MICHELE H. MOKRZYCKI, BERND SCHRO[Combining Diaeresis]PPEL, GERO VON GERSDORFF, HEATHER RUSH, MIROSLAW P. ZDUNEK, ROBERT FEINGOLD
Journal: Journal of the American Society of Nephrology (2000)

Abstract. Infection rates in tunneled-cuffed catheters (TCC) are reported to be higher in immunocompromised patients. The purpose of this study was to evaluate TCC-associated infection rates in patients with HIV infection (HIV+). Data were collected in 40 HIV + patients and 41 controls (C), and in 118 TCC (HIV+, 58; C, 60) for 28,146 catheter days (HIV+, 16,227; C, 11,919). There were no significant differences in the TCC bacteremia rates (HIV+, 2.23 versus C, 2.53 per 1000 TCC days, P = NS) or in the TCC exit site infection rates (HIV+, 2.20 versus C, 2.24 per 1000 TCC days, P = NS) between the groups. The number of TCC removed due to infection was also similar, (HIV+ versus C: 17 versus 15%, P = NS). In the HIV+ group, the association of hepatitis B surface antigenemia with TCC exit site infection was dependent on the history of injection drug use. Black race was a significant risk factor for higher TCC exit site infection rates, whereas prophylactic antibiotic use and high CD4 count were significantly associated with lower TCC exit site infection rates. None of the factors significantly predicted bacteremia rate in either group (HIV+ or C). In comparison to controls, HIV+ patients had a fivefold increased risk of having a Gramnegative organism ( P = 0.02) and a sevenfold increased risk of a fungal isolate ( P = 0.08), although the latter finding was not statistically significant. HIV infection is not a significant risk factor for TCC-associated infection but is associated with a higher prevalence of Gram-negative and fungal species.
Evidence of variation to drive quality improvement: The NHS atlas of variation in respiratory healthcare
Authors: Matt Kearney, Anne Moger, Bronwen Thompson, Joanna Clarke, Kevin Holton, Robert Winter, Sue Hill
Journal: European Respiratory Journal (2013)

Background   There is significant variation in the implementation of evidence based guidance in the management of chronic obstructive pulmonary disease, asthma and other lung conditions. A wide range of data is routinely published to benchmark outcomes and key processes of care. But publishing data does not automatically lead to quality improvement.   Aim   A national Atlas of Variation in Respiratory Healthcare was developed to help clinicians and commissioners recognise unjustified variation in care and outcomes.   Method   Data for 20 respiratory indicators was mapped to 151 local health areas (PCTs) in England to allow geographical comparison. For each indicator data is presented on a map of England with PCTs shaded according to performance. A bar chart ranks PCTs to highlight the scale of variation. Each map is accompanied by an improvement narrative which describes the magnitude of variation, its impact on outcomes, and the evidence-based actions PCTs can take to minimise variation and improve outcomes.   Results   There is a several-fold variation in rates of diagnosis, access to treatments, risk of admission/readmission and mortality depending on where a patient lives.   Conclusion   The NHS Atlas of Variation challenges clinicians and commissioners to question the quality of local respiratory services by identifying unjustified variation in care and outcomes. Readers are encouraged to ask questions about the structure and provision of care in their services through comparison with others. The improvement narrative proposes system-level changes to service delivery that elsewhere are associated with better outcomes. The Atlas is being used across England as a tool to drive quality improvement.
Consumption of Dairy Produce and Alcohol in a Case-Control Study of Breast Cancer2
Authors: Monique G. Lê, Lawrence H. Moulton, Catherine Hill, Andrew Kramar
Journal: JNCI Journal of the National Cancer Institute (1986)

Journal Article Consumption of Dairy Produce and Alcohol in a Case-Control Study of Breast Cancer Get access Monique G. Lê, Monique G. Lê Search for other works by this author on: Oxford Academic PubMed Google Scholar Lawrence H. Moulton, Lawrence H. Moulton Search for other works by this author on: Oxford Academic PubMed Google Scholar Catherine Hill, Catherine Hill Search for other works by this author on: Oxford Academic PubMed Google Scholar Andrew Kramar Andrew Kramar Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 77, Issue 3, September 1986, Pages 633–636, https://doi.org/10.1093/jnci/77.3.633 Published: 01 September 1986 Article history Received: 06 August 1985 Revision received: 16 April 1986 Accepted: 21 May 1986 Published: 01 September 1986