tbuckley/cabot-search huggingface dataset:
Differential expression of tenascin C splice variants in endobronchial epithelial-lining fluid in proximity of pulmonary nodules
Authors: Nicolas Kahn, Michael Meister, Ralf Eberhardt, Thomas Muley, Philipp A. Schnabel, Holger Sueltmann, Felix J.F. Herth, Ruprecht Kuner
Journal: European Respiratory Journal (2013)

Molecular biomarkers in tissues and body fluids represent a promising source to improve cancer diagnostics. Bronchoscopic Microsampling (BMS) of Endobronchial epithelial lining fluid (ELF) is a potent method to investigate potential biomarkers in lung diseases. Recent studies report Tenascin C (TNC), an important component of the extracellular matrix involved in tissue remodeling and cell signaling, to be differentially expressed in malignant pulmonary nodules.  We investigated whether specific splice variations of TNC are differentially expressed in ELF collected by the BMS method in proximity of pulmonary nodules.  ELF was collected by the BMS method from subsegmental bronchi close to the indeterminate pulmonary nodule and from the contralateral lung. Diagnosis was confirmed by transbronchial biopsy or surgery. The study includes 176 ELF samples from a total of 88 patients (65 NSCLC and 23 benign cases) with indeterminate pulmonary nodules detected by computed tomography. Quantitative real-time PCR (RT-PCR) assays were used to detect different TNC variant patterns.  All patients underwent BMS without complications. Quantitative RT-PCR was reliably applied to all ELF samples. A significant increase of TNC transcript variants close to malignant nodules was observed for most of the used qPCR assays. A better accuracy was observed for two protein-coding variants and an untranslated transcript indicating a distinct tumor-associated TNC variant pattern and a lower intraindividual variance.  Our results indicated that the analysis of individual TNC variants might improve the accuracy in detecting malignant nodules compared to the detection of whole TNC transcripts.
Chromosome Studies of a Frog Renal Adenocarcinoma Line Carried by Serial Intraocular Transplantation&lt;xref ref-type="fn" rid="FN2"&gt;2&lt;/xref&gt;
Authors: Marie A. di Berardino, Thomas J. King, Robert G. Mckinnell
Journal: JNCI Journal of the National Cancer Institute (1963)

Chromosome analyses were made on 1 primary renal adenocarcinoma of Rana pipiens and on 11 intraocular tumors, derived from the primary tumor through serial transplantation in the anterior eye chamber of adult frogs. The transplanted tumors from the second, fourth, sixth, and eighth generations were in culture from 1 to 2.7 years. Changes in chromosome number were observed in 4 transplanted tumors and constituted 3 percent of all the tumor cells examined; metaphases from normal embryonic and adult bone marrow cells were diploid. Nonspecific structural abnormalities were found in 8 of the 11 transplanted tumors; these abnormalities amounted to 14 percent of the tumor samples, whereas a 2 percent incidence of structural abnormalities was present in the normal tissues. The number and mitotic frequency of stromal cells were estimated from serial sections of some of the tumors and were found to be extremely low, which demonstrates that the chromosome studies are based mainly on epithelial cells of the tumor.
Measurements of carbon monoxide (CO) in exhaled air and calculation of alveolar-capillary membrane diffusion capacity
Authors: Evgeny Babarskov, Evgeny Stepanov, Yury Shulagin, Alexander Cherniak, Zaurbek Aisanov, Alexander Chuchalin
Journal: European Respiratory Journal (2013)

Background:  We found earlier [Babarskov E. at al. ERJ 2010; 36,suppl.54:504s] that lung diffusion capacity, DL, calculated by increasing rate of integral measured CO concenration, C M , in exhaled air at successive increasing breath holding time, corresponds membrane diffusion capacity, Dm. Measurements were performed in breathing regimes, when total dead volume (instrument+anatomic), V D , was much less than respiratory volume, ΔV, at maximal alveolar volume, V A .   Aim:  To determine the influence of V D  on C M  and to estimate the relationship beetwen DL and current alveolar volume,V.   Methods:  Mathematical modeling of CO gas exchange in lung and experimental data analysis.   Results:  Two models were considered: linear model (LM) when CO gas exchange in changing V takes place at constant DL (DL=Dm), and model of elastic membrane (MEM) when DL at breathing is changed proportionally to membrane surface area and inversely to its thickness (DL=Dm*(V/V A ) 4/3 ). Calculations were performed for two different breathing regimes at equal V A =7.0 L and Dm=60 mL/min/mmHg. Spontanios breathing, when alveolar volume is changed from V 0 =3.0 L to V 1 =4.0 L at equal mean inspiration and expiration flow rate, Q=20 L/min, and deep forced breathing at V 0 =2.0 L, V 1 =7.0 L and Q=100 L/min. Both models demonstrate strong dependence of C M  from V D  in case of spontanios breathing, but MEM more correctly aproximates experimental data, so at increasing V D  from 0 to 0.5 L, C M  is decreased by 1.7 fold.   Conclusion:  The dependence of C M  from Dm was found for different breathing regimes taking into account V D . This allows to solve inverse task - to calculate D M  using known C M  values.
Spiroergometry among smoking and non-smoking patients
Authors: Tatiana Levina, Julia Krasnova
Journal: European Respiratory Journal (2012)

Aim: To evaluate of parameters of spiroergometry at smoking and non-smoking patients.  Materials and methods. 47 patients were examined (20-were smoking (an index of smoking 15 packs/years), 27-non-smokers). The mean age of the first group was 42,6±7,4 years and second- 40,0±7,6 years, p>0,05). The next parameters of a spiroergometry were studied: Heart rates (HR), Sistolic blood pressure, Diastolic blood pressure, VO2peak, VCO2peak, VEpeak, O2-puls, EQCO2, PET CO2rest.  Results: Characteristics of parameters of spiroergometry at smoking and non-smoking patients.  Conclusions: The smoking patients had higher indicators of HR on 5 minute of rest, sistolic blood pressure of rest diastolic blood pressure upon the maximum loading and on 5 min of rest than non-smokers.
In Vivo Distribution of Recombinant lnterleukin-2-Activated Autologous Lymphocytes Administered by Intra-arterial Infusion in Patients With Renal Cell Carcinoma&lt;xref ref-type="fn" rid="FN2"&gt;2&lt;/xref&gt;
Authors: T Morita, Y Yonese, N Minato
Journal: JNCI Journal of the National Cancer Institute (1987)

Recombinant interleukin-2 (RIL 2)-activated autologous peripheral blood lymphocytes (PBL) were infused directly into the renal arteries of 3 patients with renal cell carcinoma, and the in vivo distribution of the infused cells was investigated. In vitro studies to define the optimal culture conditions indicated that maximal lymphokine-activated killer activity was observed at around 10-20 days in culture, as judged by the cytotoxicity against fresh allogenic tumor cells. Maximal expression of the interleukin-2 receptor was also obtained at around 10 days. PBL collected by leukopheresis from each patient were thus cultured for 10 days with RIL 2, labeled with 111In-oxine, and then infused directly into the renal artery of the affected kidney via a catheter. Radioactivity in the infused side of the kidneys increased immediately after the infusion but then gradually decreased. Radioactivity in the lungs also rapidly increased within the first hour but then cleared gradually, whereas that in the liver and spleen tended to increase steadily. Nevertheless, at 48 hours, the infused side of the kidneys retained levels of radioactivity comparable to those seen in the liver and spleen, while the levels seen in the lungs were already close to background levels. The radioactivity in the areas corresponding to tumors remained consistently higher than that in the normal parts of the affected kidneys. The direct comparison of the radioactivity distribution pattern with the macroscopic appearance of surgically resected kidneys indicated that the accumulation of radioactivity was indeed selectively associated with the tumor tissues in the kidneys, except for a case in which the tumor was quite necrotic and hypovascular. Histological examinations indicated intensive mononuclear cell infiltrations in and around the tumor tissues as well as in normal tissues in the kidneys. These preliminary results indicated that infusion of activated lymphocytes via major tumor-feeding arteries would be an extremely effective way to obtain the selective localization of effector cells in the tumor tissues.
Do count-based differential expression methods perform poorly when genes are expressed in only one condition?
Authors: Xiaobei Zhou, Mark D. Robinson
Journal: Genome biology (2015)

A response to ‘Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data’ by Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND and Betel D in Genome Biology, 2013, 14:R95
Randomized trial of radiotherapy to the thorax in limited small-cell carcinoma of the lung treated with multiagent chemotherapy and elective brain irradiation: a preliminary report.
Authors: C A Perez, L Einhorn, R K Oldham, F A Greco, H J Cohen, H Silberman, S Krauss, N Hornback, F Comas, G Omura
Journal: Journal of Clinical Oncology (1984)

A total of 304 patients with limited small-cell carcinoma of the lung were treated with a combination of cyclophosphamide, Adriamycin (Adria Laboratories, Columbus, Ohio), and vincristine (CAV) and elective brain irradiation (3,600 rad TD in 14 fractions). The patients were randomized to either receive or not receive thoracic irradiation (4,000 rad TD, split course). Of the 304 patients, 291 were eligible for the study. Two hundred eighteen (75%) were completely evaluable. In each group, 81% of the patients had a Karnofsky index of 80% or higher and 14% had supraclavicular or scalene lymph nodes. Patients treated with CAV and no thoracic irradiation had a complete response (CR) of 48%, in contrast to 63% for those receiving chest irradiation (P = .05). In the first group, the complete and partial response rate was 70%; in the second, 80%. The median survival for the eligible patients treated with CAV and brain radiation therapy was 49 weeks; for those treated with the same regimen plus thoracic irradiation, the median survival was 60 weeks. The actuarial two-year tumor-free survival is 19% in the first group and 28% in the second group. The median survival for the responders in the CAV plus brain irradiation group was 57 weeks and for those receiving thoracic irradiation, 78 weeks (P = .12). Thoracic failure was 52% in patients not treated with thoracic radiation therapy v 36% in those receiving it (P = .06). The distant metastases incidence was 23% in patients not treated with thoracic radiation and 35% in patients treated with thoracic radiation. Hematologic toxicity was comparable in both groups; 30% of the patients had moderate to severe granulocytopenia and 6%, low homoglobin. Two toxicity-related deaths occurred (one in each group). Moderate gastrointestinal toxicity was noted in 41% and severe in 16% of the patients receiving CAV and brain irradiation without thoracic radiotherapy v 44% and 20% in those irradiated in the thorax. Disease-free survival is enhanced in the patients receiving thoracic irradiation. More effective chemotherapy is critically needed to significantly improve overall survival. These preliminary results suggest that thoracic irradiation should be a primary component in the therapy of these patients, although this combined therapy is moderately toxic.(ABSTRACT TRUNCATED AT 400 WORDS)
Inability of computed tomography appearance of recurrent malignant astrocytoma to predict survival following reoperation.
Authors: K E Wallner, J H Galicich, M G Malkin, E Arbit, G Krol, M K Rosenblum
Journal: Journal of Clinical Oncology (1989)

Computed tomographic (CT) scans of 39 patients who underwent reoperation for recurrent malignant astrocytoma at Memorial Sloan-Kettering Cancer Center from 1980 through 1987 were reviewed and correlated with the patients' clinical course. Histologic diagnosis (anaplastic astrocytoma v glioblastoma multiforme) had a statistically significant impact on survival following reoperation (P = .038). Patients with high preoperative performance status (P = .29), total resection by postoperative CT scan (P = .15), and frontal lobe tumors (P = .17) tended to survive longer following reoperation. The size of the tumor at the time of recurrence did not correlate with survival following reoperation. Patients with a small amount of peritumoral edema at the time of recurrence tended to survive longer, but the effect was small (P = .16). Prognosis following reoperation cannot be accurately predicted on the basis of tumor appearance on CT scan.
Prevalence of chronic bronchitis in the Middle-East and North Africa: Interim results of the BREATHE study
Authors: Adel Khattab, Abdullah Sayiner, Javed Ahmed Khan, Ghali Iraqi, Salim Nafti, Ali Benkheder, Bassam Mahboub, Marie Louis Konisky, Chakib Nejjari, Nauman Rashid
Journal: European Respiratory Journal (2011)

Background: Few data are available on the epidemiology of COPD outside developed countries.

Objectives: The objective of this epidemiological study was to assess the prevalence and burden of COPD, chronic bronchitis and smoking in eleven countries (Algeria, Morocco, Tunisia, Egypt, Jordan, Lebanon, Saudi Arabia, Syria, UAE, Pakistan and Turkey).

Methods: A general population sample of 10 000 subjects ≥ 40yrs in each country was generated from random phone numbers. A structured interview was proposed to all subjects by telephone. Screening questions, including history of cough and sputum production, was used to identify subjects with chronic bronchitis. Individuals who smoked ≥ 10 pack-yrs and who had either chronic bronchitis or a previous diagnosis of COPD were considered to have possible COPD. In a subset of the study sample, assignment of COPD was confirmed by spirometry. This interim analysis assesses the prevalence of chronic bronchitis.

Results: Of 118 039 subjects contacted, 44 892 were interviewed. 978 subjects reported having symptoms of chronic bronchitis. This corresponds to a prevalence of chronic bronchitis of 2.2% [95% CI: 2.0-2.3%], ranging from 0.6% [95% CI: 0.4-1.0%] in UAE to 2.9% [95% CI: 2.1-3.7%] in Algeria. The prevalence of chronic bronchitis was higher in women (2.4%; 95% CI: 2.2-2.6%) than in men (1.8%; 95% CI: 1.6-2.0%). Prevalence increased with age: 1.6% in subjects aged 40-49 yrs, 2.2% in those aged 50 to 59 yrs and 3.0% in those aged ≥ 60 yrs.

Conclusion: The prevalence of chronic bronchitis in the Middle East and North Africa seems to be lower compared to other regions of the world.
Phylogeny of five fungus-like protoctistan Phytophthora species, inferred from the internal transcribed spacers of ribosomal DNA.
Authors: S B Lee, J W Taylor
Journal: Molecular Biology and Evolution (1992)

Ribosomal DNA variation was used to study evolutionary relationships among five fungal-like protoctistan Phytophthora species. On the basis of morphological and ecological characteristics, four of these species--P. palmivora, P. megakarya, P. capsici, and P. citrophthora--were once thought to be related. Variation within a species was extensively studied in a fifth, outgroup species--P. cinnamomi--known, on the basis of ecological, isozyme, and mitochondrial DNA studies, to be variable. Internal transcribed spacer regions (ITS I, between the 18S and 5.8S rDNAs; and ITS II, between the 5.8S and 25S rDNAs) from 27 isolates of these five species were analyzed by polymerase chain reaction amplification and direct sequencing. Intraspecific variability was undetected or low. Interspecific nucleotide difference was 0.3%-14.6%, and comparisons of variable regions permitted the evaluation of phylogenetic relationships among species. Both neighbor-joining and parsimony analysis of ITS variability support a close relationship between cacao isolates of P. capsici and P. citrophthora and a common lineage for P. palmivora and P. megakarya. Large distance values were estimated between P. cinnamomi and the other species. Inferred relationships based on ITS variability were compared with those based on other characters. The catalog of sequences provides the information necessary to design taxon-specific probes potentially useful in taxonomic, ecological, and population-level studies.
Bullous Pemphigoid Associated With Linagliptin Treatment
Authors: Roger Haber, Alice Mouna Fayad, Farid Stephan, Grace Obeid, Roland Tomb
Journal: JAMA Dermatology (2015)

and dysgeusia than the continuous regimen.Similarly, the muscle cramps and dysgeusia in the present patients resolved within 1 month after interrupting the vismodegib regimen.Although pharmacokinetic studies have shown suboptimal efficacy and similar incidence and severity of adverse effects when vismodegib, 150 mg, was used once weekly or 3 times weekly, no studies to our knowledge have investigated the efficacy of continuous daily doses with drug breaks in between. 3 We found a mean of 1.4 new surgically eligible BCCs per year per patient undergoing intermittent therapy, which is comparable to the 2.0 new surgically eligible BCCs per year per patient found by Tang et al 1 in patients undergoing a standard continuous daily regimen.Vismodegib resistance occurs in patients who undergo continuous vismodegib dosing. 4 The frequency of resistance in patients who undergo an intermittent form of treatment is largely unknown.Combination therapy with hedgehog pathway inhibitors downstream of smoothened, such as itraconazole and arsenic trioxide, provide opportunities to increase efficacy and possibly reduce the incidence of resistance. 5,6 Conclusions | Overall, our clinical experience suggests that intermittent therapy is an effective way to overcome problems with adverse effects and compliance with vismodegib treatment of BCNS.Photographic and histologic documentations of tumors and randomized clinical trials are warranted to quantify the ideal duration of the intermittent regimen and compare the addition of combination therapies to overcome potential drug resistance.
Prevalence of symptomatic gastroesophageal reflux disease in Thai patients with obstructive sleep apnea: A cross-sectional telephone survey
Authors: Thongchai Leelayuthachai, Nattapong Jaimchariyatam, Sutep Gonlachanvit
Journal: European Respiratory Journal (2012)

Background: Many studies revealed association between gastroesophageal reflux disease (GERD) and obstructive sleep apnea (OSA). Prevalence of symptomatic GERD in Thai people was 7-10%. No prior study of symptomatic GERD in Thai patients with OSA appears to have been published.

Methods: All patients underwent polysomnography within 18 months were reviewed. Telephone survey of symptoms-based GERD questions was introduced to all patients diagnosed with OSA. Unconnected patients were reviewed with chart and medication history.

Results: 413 patients were reviewed, 296 patients diagnosed with OSA. 196 patients were diagnosed with severe OSA. Baseline characteristics and sleep parameters were as follows: mean age 51.57 years (±13.96), body mass index (BMI) 28.05 kg/m2 (±7.13), neck circumference 15.37 inches (±1.74), Epworth Sleepiness Scale (ESS) 10.87 (±4.86), and respiratory disturbance index (RDI) 61.09 events/h (±41.32). Symptomatic GERD were reported in 53 (18%) patients. Prevalence of symptomatic GERD in severe OSA was 23% (46 from 196 patients), which was significantly different from that in mild-to-moderate OSA (7%, p 30 events/h) (OR 1.42, 95%CI 1.23-1.64), p<0.001). Multicollinearity revealed that these two factors was not correlated in this study.

Conclusion: Prevalence of symptomatic GERD in Thai OSA patients is higher than general Thai people. Obesity or severe OSA independently affect occurrences of symptomatic GERD in OSA patients.
Standardizing Measurement of Chronic Obstructive Pulmonary Disease Exacerbations
Authors: Nancy K. Leidy, Teresa K. Wilcox, Paul W. Jones, Laurie Roberts, John H. Powers, Sanjay Sethi
Journal: American Journal of Respiratory and Critical Care Medicine (2010)

Although exacerbations are an important problem in chronic obstructive pulmonary disease (COPD) and a target of intervention, there is no valid, standardized tool for assessing their frequency, severity, and duration.This study tested the properties of the Exacerbations of Chronic Pulmonary Disease Tool (EXACT), a new patient-reported outcome diary.A prospective, two-group, observational study was conducted in patients with COPD. The acute group (n = 222) was enrolled during a clinic visit for exacerbation with follow-up visits on Days 10, 29, and 60. The stable group (n = 188), recruited by telephone or during routine visits, was exacerbation free for at least 60 days.Acute patients completed the diary on Days 1-29 and 60-67; stable patients for 7 days. All patients provided stable-state spirometry and completed the St. George Respiratory Questionnaire-COPD (SGRQ-C). Acute patient assessments included clinician and patient global ratings of exacerbation severity and recovery. Mean age of the sample (n = 410) was 65 (± 10) years; 48% were male; stable FEV₁ was 51% predicted (± 20). Internal consistency (Pearson separation index) for the EXACT was 0.92, 1-week reproducibility (stable patients; intraclass correlation) was 0.77. EXACT scores correlated with SGRQ-C (r = 0.64; P < 0.0001) and differentiated acute and stable patients (P < 0.0001). In acute patients, scores improved over time (P < 0.0001) and differentiated between degrees of clinician-rated exacerbation severity (P < 0.05). EXACT change scores differentiated responders and nonresponders on Day 10, as judged by clinicians or patients (P < 0.0001).Results suggest the EXACT is reliable, valid, and sensitive to change with exacerbation recovery.
Antifibrosic effects of sulforaphane in human lung fibroblasts from idiopathic pulmonary fibrosis
Authors: Elise Artaud-Macari, Delphine Goven, Stéphanie Brayer, Joelle Marchal-Somme, Bruno Crestani, Anne Boutten, Marcel Bonay
Journal: European Respiratory Journal (2011)

Rationale:  Nrf2 pathway has been implicated in myofibroblastic differentiation, a key step in idiopathic pulmonary fibrosis (IPF) pathophysiology. Sulforaphane (SFN), an isothiocyanate compound found in cruciferous vegetables, is known to activate Nrf2. The aim of this study was to assess the effects of SFN on oxidative stress and fibroblast phenotype in IPF.   Methods:  The effects of SFN were assessed on human pulmonary fibroblasts from IPF and control patients in vitro. Oxidant/antioxidant balance, nuclear Nrf2 expression, fibroblast phenotype, in basal and profibrosing conditions (TGF-β or PDGF-BB stimulation) were experienced.   Results:  SFN increased antioxidant enzymes and Nrf2 nuclear expression, and decreased oxidative stress in IPF fibroblasts, in basal conditions and after TGF-β stimulation. SFN stimulation induced a myofibroblastic dedifferentiation of IPF fibroblasts with morphologic aspect of control-like fibroblasts and concomitant reduction of α-SMA and collagen I expression, proliferation, migration and contraction. Moreover, addition of SFN after TGF-β and PDGF-BB stimulation, inhibited their deleterious effects on IPF and control fibroblasts, and restored antioxidant defenses. Nrf2 siRNA transfection abolished antifibrosing effects of SFN.   Discussion:  The effects of SFN on cell differentiation have been reported in renal tubular epithelial cells in a rat model of renal fibrosis, but its effects on human pulmonary fibroblasts from IPF and control patients were unknown.   Conclusion:  These results suggest the potential therapeutic effect of SFN on pulmonary fibroblasts in IPF in vitro.