tbuckley/cabot-search huggingface dataset:
Sensitivity and reproducibility of standardized-competitive RT-PCR for transcript quantification and its comparison with real time RT-PCR.
Authors: Vincenzo Pagliarulo, Ben George, Stephen J Beil, Susan Groshen, Peter W Laird, Jie Cai, James Willey, Richard J Cote, Ram H Datar
Journal: Molecular Cancer (2004)

Probe based detection assays form the mainstay of transcript quantification. Problems with these assays include varying hybridization efficiencies of the probes used for transcript quantification and the expense involved. We examined the ability of a standardized competitive RT-PCR (StaRT PCR) assay to quantify transcripts of 4 cell cycle associated genes (RB, E2F1, CDKN2A and PCNA) in two cell lines (T24 & LD419) and compared its efficacy with the established Taqman real time quantitative RT-PCR assay. We also assessed the sensitivity, reproducibility and consistency of StaRT PCR. StaRT PCR assay is based on the incorporation of competitive templates (CT) in precisely standardized quantities along with the native template (NT) in a PCR reaction. This enables transcript quantification by comparing the NT and CT band intensities at the end of the PCR amplification. The CT serves as an ideal internal control. The transcript numbers are expressed as copies per million transcripts of a control gene such as β-actin (ACTB). The NT and CT were amplified at remarkably similar rates throughout the StaRT PCR amplification cycles, and the coefficient of variation was least (<3.8%) when the NT/CT ratio was kept as close to 1:1 as possible. The variability between the rates of amplification in different tubes subjected to the same StaRT PCR reaction was very low and within the range of experimental noise. Further, StaRT PCR was sensitive enough to detect variations as low as 10% in endogenous actin transcript quantity (p < 0.01 by the paired student's t-test). StaRT PCR correlated well with Taqman real time RT-PCR assay in terms of transcript quantification efficacy (p < 0.01 for all 4 genes by the Spearman Rank correlation method) and the ability to discriminate between cell types and confluence patterns. StaRT PCR is thus a reliable and sensitive technique that can be applied to medium-high throughput quantitative transcript measurement. Further, it correlates well with Taqman real time PCR in terms of quantitative and discriminatory ability. This label-free, inexpensive technique may provide the ability to generate prognostically important molecular signatures unique to individual tumors and may enable identification of novel therapeutic targets.
The Shedding of the Mucosa of the Bronchial Tree in Asthma
Authors: B. Naylor
Journal: Thorax (1962)

In this paper a study is reported which indicates conclusively that excessive shedding of epithelium of the lower respiratory tract occurs dur;ng life in bronchial asthma, that it occurs especially during asthmatic attacks, and that this pheno- menon is seen almost exclusively in this disease.Other observers have reported that sputa from asthmatics often contain large, well-circumscribed, compact clusters of columnar epithelial cells; they are quite distinctive.Von Hoesslin (1921) referred to them as Epithelialzellballen, which is a good descriptive term.We have selected the eponym " Creola body," which has the merit of being euphonious and succinct. (Creola was the Christian name of the patient in whose sputum these columnar cell clusters were originally observed in our material.)They were noticed previously by Vierordt (1883), and subsequently by Farber, Wood, Pharr, and Pierson (1957), Carabelli (1958), Cohen and Prentice (1959), and Koss and Durfee (1961).The last four authors believed that they were fragments of mucosa which had become detached because it was hyperplastic, but none of the others offered reasons why they were found in the sputa of asthmatics.After studying their morphology, one has no doubt that they are fragments of shed, though not necessarily hyperplastic, mucosa, of the lower respiratory tract.If that is what they are, and if shedding of bronchial and bronchiolar mucosa occurs almost exclusively in bronchial asthma, these columnar cell clusters should be found equally exclusively in sputa of asthmatics, and more should be found during attacks of asthma than when the disease is quiescent.The sputa of asthmatics and non- asthmatics have been analysed and compared to find out if this is so. MATERIAL AND METHODA single specimen of sputum from each of 100 asthmatic and 100 non-asthmatic patients was
Effect of acetazolamide and amiloride against sodium metabisulphite-induced bronchoconstriction in mild asthma.
Authors: B J O'Connor, C T Yeo, Y M Chen-Worsdell, P J Barnes, K F Chung
Journal: Thorax (1994)

BACKGROUND--Inhaled frusemide but not bumetanide, another loop diuretic, reduces bronchial responsiveness to sodium metabisulphite (MBS). To investigate whether the effect of frusemide could be mediated through mechanisms other than Na+/K+/Cl- cotransporter inhibition, the effects of amiloride--an inhibitor of sodium channels in the airway epithelium--and of acetazolamide--a specific inhibitor of carbonic anhydrase--against MBS challenge were studied. METHODS--In two separate randomised double blind placebo controlled studies, 10 subjects with mild asthma attended on four separate occasions to inhale 7.5 mg amiloride or matched placebo, and 500 mg acetazolamide or placebo, immediately before MBS challenge. The concentration of MBS required to cause a 20% fall in baseline FEV1 (PC20) was measured. RESULTS--Amiloride and acetazolamide had no effect on baseline FEV1. Amiloride had no effect against MBS challenge, but acetazolamide increased -log PC20 from a mean (SE) of 0.75 (0.09) to 0.98 (0.06) representing a 0.77 (0.24) doubling dose increase. CONCLUSIONS--These results suggest that carbonic anhydrase activity in the airways, but not sodium flux, modulates bronchial responsiveness to MBS challenge. The action of frusemide is not likely to involve inhibition of carbonic anhydrase activity.
The genome of the stress-tolerant wild tomato species Solanum pennellii
Authors: Anthony Bolger, Federico Scossa, Marie E Bolger, Christa Lanz, Florian Maumus, Takayuki Tohge, Hadi Quesneville, Saleh Alseekh, Iben Sørensen, Gabriel Lichtenstein, Eric A Fich, Mariana Conte, Heike Keller, Korbinian Schneeberger, Rainer Schwacke, Itai Ofner, Julia Vrebalov, Yimin Xu, Sonia Osorio, Saulo Alves Aflitos, Elio Schijlen, José M Jiménez-Goméz, Malgorzata Ryngajllo, Seisuke Kimura, Ravi Kumar, Daniel Koenig, Lauren R Headland, Julin N Maloof, Neelima Sinha, Roeland C H J van Ham, René Klein Lankhorst, Linyong Mao, Alexander Vogel, Borjana Arsova, Ralph Panstruga, Zhangjun Fei, Jocelyn K C Rose, Dani Zamir, Fernando Carrari, James J Giovannoni, Detlef Weigel, Björn Usadel, Alisdair R Fernie
Journal: Nature Genetics (2014)

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.
Education and information for patients with bronchiectasis: What do patients want?
Authors: Klm Hester, P McAlinden, A DeSoyza
Journal: European Respiratory Journal (2011)

Background:  Bronchiectasis is up to three times as common as Cystic Fibrosis (CF), yet is poorly studied with variable service provision. The BTS 2010 guidelines also note lack of trials in bronchiectasis self-management. Patient information is less readily available than in other pulmonary conditions, such as CF, however with persistent symptoms and frequent exacerbations, patients could benefit from improved information and education.   Aims:  To establish patients9 needs and their views on information received about bronchiectasis.   Methods:  A formal questionnaire was conducted in adult patients with bronchiectasis attending the Freeman Hospital specialist clinic.   Results:  107 patients were surveyed with a 79% response rate. Patients reported previously having little information about bronchiectasis, particularly prognosis. 86% reported receiving new information at the specialist clinic, and 99% felt more confident about managing their condition when informed about their treatment. 86% found additional information from physiotherapists at physiotherapy training sessions beneficial. 58% had utilised a clinic helpline for advice; 100% were satisfied with the outcome. Patients wanted more information and education about bronchiectasis.   Conclusions:  Patients with bronchiectasis want more information about their condition. When better informed they feel more confident about management of their condition, with improved symptom awareness, and increased patient satisfaction. Qualitative work is underway to study patient needs further and develop improved systems and optimal formats for patient education in bronchiectasis. This has potential to improve use of resources, self management and patient outcomes.
Non-capacitative calcium entry—Extension of the possibilities for calcium entry in vascular tissue
Authors: R SCHUBERT
Journal: Cardiovascular Research (2005)

See article by Thomas et al.  [5]  (pages 56–64) in this issue. 

The functional state of blood vessels is regulated by the calcium sensitivity of the contractile elements and the intracellular calcium concentration. The latter is determined by the balance between the activity of calcium sources (influx from the extracellular space and release from intracellular stores), the activity of calcium sinks (extrusion to the extracellular space and sequestration into intracellular stores), and the capacity of calcium buffers. Contractile reactions of blood vessels are depressed considerably after removal of extracellular calcium ions, emphasizing the importance of calcium entry for vessel contractility. Classically, voltage-operated calcium influx via L-type calcium channels had been assigned a leading role in calcium entry. However, a considerable number of contractile reactions have been shown to be resistant or only partly affected by specific inhibitors of voltage-operated calcium channels. Thus, voltage-independent calcium entry must contribute to vessel contractility. Indeed, several such mechanisms have been identified in different cell types [1–3], including smooth muscle [4]: 1) receptor-operated calcium entry, activated by direct binding of an external ligand to the channel; 2) store-operated or capacitative calcium entry (CCE), activated by calcium release from intracellular stores or, more precisely, by the degree of store depletion; 3) non-store-operated or non-capacitative calcium entry (non-CCE), activated independently of store depletion. In the past, the latter was often termed receptor-operated calcium entry. However, in view of the fact that all calcium entry mechanisms can be activated … 

*Corresponding author. Tel.: +49 381 4948016; fax: +49 381 4948002. Email address: rudolf.schubert{at}medizin.uni-rostock.de
The distensibility characteristics of the capacitance vessels of the forearm in normal subjects
Authors: N. Burki, A. Guz
Journal: Cardiovascular Research (1970)

The distensibility characteristics of the forearm vascular capacitance bed have been studied in 18 resting normal subjects by a slow venous occlusion technique, and a wide range of distensibility was found. Neuromuscular blockade had no effect on distensibility, and sympathetic blockade increased distensibility.
Potential misclassification of causes of death from COPD
Authors: H. H. Jensen, N. S. Godtfredsen, P. Lange, J. Vestbo
Journal: European Respiratory Journal (2006)

Little is known about causes of death in chronic obstructive pulmonary disease (COPD) and the validity of mortality statistics in COPD. The present authors examined causes of death using data from the Copenhagen City Heart Study. Of the 12,979 subjects with sufficient data from the baseline examination during 1976-1978, 6,709 died before 2001. Of these, 242 died with COPD as cause of death. Among subjects with at least severe COPD at baseline, only 24.9% had COPD as cause of death and, in almost half of the cases where COPD was listed as cause of death, the subject had a normal forced expiratory volume in one second /forced vital capacity ratio at baseline. In COPD patients, having COPD on the death certificate was associated with chronic mucus hypersecretion (CMH) at baseline, an odds ratio (OR) of 3.6 (95% confidence interval 1.7-7.7), and being female (OR 2.7 (1.3-5.6)). In subjects without COPD, CMH and smoking were predictors of COPD as underlying cause of death, ORs 2.3 (1.5-3.7) and 2.2 (1.4-3.6), respectively. It was concluded that chronic obstructive pulmonary disease is underreported on death certificates, that biases in the use of chronic obstructive pulmonary disease as cause of death can be assessed, and that possible "over-diagnosis" of chronic obstructive pulmonary disease on death certificates in subjects unlikely to have significant disease should initiate caution when using causes of mortality in chronic obstructive pulmonary disease epidemiology.
Hemostatic abnormalities and increased vascular endothelial cell markers in patients with red cell fragmentation syndrome induced by mitomycin C
Authors: Shozaburo Nagaya, Hideo Wada, Kouzi Oka, Motoaki Tanigawa, Shigehisa Tamaki, Kouta Tsuzi, Eiki Miyanishi, Yoshihiro Wakita, Nobuyuki Minami, Katsumi Deguchi, Kozi Suzuki, Takeshi Nakano, Hiroshi Shiku
Journal: American Journal of Hematology (1995)

Abstract We examined red cell fragmentation syndrome (RCFS) induced by mitomycin C (MMC) (13 patients), by thrombotic thrombocytopenic purpura (TTP) (17 patients), and by disseminated intravascular coagulation (DIC) (15 patients). Plasma cytokine levels were increased in the TTP and DIC patients, but not in those whose RCFS was induced by MMC, suggesting that the activation of the immune system plays an important role in the pathogenesis of RCFS due to TTP and DIC but did not in RCFS due to MMC. Plasma thrombomodulin, tissue type plasminogen activator, and plasminogen activator inhibitor‐I levels were increased in all RCFS patients, suggesting that RCFS, whether MMC induced, or due to TTP or DIC, might be associated with vascular endothelial cell injury. In TTP, von Willebrand factor (vWF) antigen and high molecular weight vWF multimer levels were reduced, possibly as a result of microthrombus consumption. The hemostatic data in this study showed that the TTP patients were in a hypercoagulable state without hyperfibrinolysis, and that DIC patients were in both a hypercoagulable and a hyperfibrinolytic state, whereas hemostatic abnormalities were slight in patients with MMC induced RCFS. These findings suggest that vascular endothelial cell injuries might be associated with RCFS, and that those injuries in MMC‐induced RCFS might not be related to microthrombi or an activated immune system.
Saccharomyces boulardii upgrades cellular adaptation after proximal enterectomy in rats
Authors: J-P Buts, N De Keyser, S Marandi, D Hermans, E M Sokal, Y-H E Chae, L Lambotte, H Chanteux, P M Tulkens
Journal: Gut (1999)

<h3>BACKGROUND</h3> <i>Saccharomyces boulardii</i> is a non-pathogenic yeast which exerts trophic effects on human and rat small intestinal mucosa. <h3>AIMS</h3> To examine the effects of <i>S boulardii</i> on ileal adaptation after proximal enterectomy in rats. <h3>METHODS</h3> Wistar rats, aged eight weeks, underwent 60% proximal resection or transection and received by orogastric intubation either 1 mg/g body wt per day lyophilised <i>S boulardii</i> or the vehicle for seven days. The effects on ileal mucosal adaptation were assessed eight days after surgery. <h3>RESULTS</h3> Compared with transection, resection resulted in mucosal hyperplasia with significant decreases in the specific and total activities of sucrase, lactase, and maltase. Treatment of resected animals with <i>S boulardii</i> had no effect on mucosal hyperplasia but did upgrade disaccharidase activities to the levels of the transected group. Enzyme stimulation by <i>S boulardii</i> was associated with significant increases in diamine oxidase activity and mucosal polyamine concentrations. Likewise, sodium dependentd-glucose uptake by brush border membrane vesicles, measured as a function of time and glucose concentration in the incubation medium, was significantly (p&lt;0.05) increased by 81% and three times respectively in the resected group treated with<i>S boulardii</i>. In agreement with this, expression of the sodium/glucose cotransporter-1 in brush border membranes of resected rats treated with <i>S boulardii</i> was enhanced twofold compared with resected controls. <h3>CONCLUSION</h3> Oral administration of <i>S boulardii</i> soon after proximal enterectomy improves functional adaptation of the remnant ileum.
Microfabricated silicon nitride membranes for hepatocyte sandwich culture
Authors: Shufang Zhang, Lei Xia, Chiang Huen Kang, Guangfa Xiao, Siew Min Ong, Yi Chin Toh, Hwa Liang Leo, Danny van Noort, Shyi Herng Kan, Hui Huan Tang, Hanry Yu
Journal: Biomaterials (2008)
Patterns of resistance of Mycobacterium tuberculosis in Spanish patients infected with human immunodeficiency virus type 1 (HIV-1)
Authors: Ana Guelar, Julian Gonzalez-Martin, Jose M. Gatell, Carlos Garcia-Tejero, Jose Mallolas, Silvina Padro, Jose M. Miro, Laura Zamora, Maria T. Jimenez-de-Anta, Eladio Soriano
Journal: Clinical Microbiology and Infection (1995)
Prognostic factors for surgical resection in patients with multidrug-resistant tuberculosis
Authors: H. J. Kim, C. H. Kang, Y. T. Kim, S-W. Sung, J. H. Kim, S. M. Lee, C-G. Yoo, C-T. Lee, Y. W. Kim, S. K. Han, Y-S. Shim, J-J. Yim
Journal: European Respiratory Journal (2006)

Although surgical lung resection could improve prognosis in some patients with multidrug-resistant tuberculosis (MDR-TB), there are no reports on the optimal candidates for this surgery. The aim of the present study was to elucidate the prognostic factors for surgery in patients with MDR-TB. Patients who underwent lung resection for the treatment of MDR-TB between March 1993 and December 2004 were included in the present study. Treatment failure was defined as greater than or equal to two of the five cultures recorded in the final 12 months of treatment being positive, any one of the final three cultures being positive, or the patient having died during treatment. The variables that affected treatment outcomes were identified through univariate and multivariate logistic regression analysis. In total, 79 patients with MDR-TB were included in the present study. The treatment outcomes of 22 (27.8%) patients were classified as failure. A body mass index &lt;18.5 kg·m -2 , primary resistance, resistance to ofloxacin and the presence of a cavitary lesion beyond the range of the surgical resection were associated with treatment failure. Low body mass index, primary resistance, resistance to ofloxacin and cavitary lesions beyond the range of resection are possible poor prognostic factors for surgical lung resection in multidrug-resistant tuberculosis patients.
Change in the capability of reactive oxygen species production by neutrophils following weight reduction in female judoists
Authors: Makoto Yaegaki, Takashi Umeda, Ippei Takahashi, Masashi Matsuzaka, Norio Sugawara, Sen Shimaya, Masaru Tanabe, Arata Kojima, Noriko Mochida, Yousuke Yamamoto, Shigeyuki Nakaji
Journal: British Journal of Sports Medicine (2007)

Objective: Athletes undergoing weight reduction are recognised as being more prone to infection. Few studies exist for athletes on the weight reduction-mediated changes in neutrophil function and related activities such as reactive oxygen species (ROS) production capability, phagocytic activity (PA) and serum opsonic activity (SOA). Methods: 16 Japanese female university judoists were examined in the early morning of the first day (pre-values) and the last day (post-values) of a 20-day pre-competition training period. Of the 16 subjects, 8 needed to reduce weight (WR group) and the other 8 did not (control group). The parameters assessed were the neutrophil count, serum immunoglobulins and complements, myogenic enzymes, ROS production capability, PA and SOA. Results: Comparing the post-values with the pre-values, ROS production significantly increased in both groups (p&lt;0.01 for both). PA significantly decreased in the WR group (p&lt;0.05); it also decreased in the control group but the decrease was not significant. SOA significantly increased in the control group (p&lt;0.05), but showed no significant change in the WR group. Conclusions: The changes in the WR group were probably a direct consequence of the weight-reduction regimen coupled with the exercise regimen, suggesting that neutrophil parameters (ROS production, PA and SOA) had tended to deviate from their typical compensatory changes to maintain immune system homoeostasis.
Critical Evaluation of Oncology Clinical Practice Guidelines
Authors: Bradley N. Reames, Robert W. Krell, Sarah N. Ponto, Sandra L. Wong
Journal: Journal of Clinical Oncology (2013)

Purpose Significant concerns exist regarding the content and reliability of oncology clinical practice guidelines (CPGs). The Institute of Medicine (IOM) report “Clinical Practice Guidelines We Can Trust” established standards for developing trustworthy CPGs. By using these standards as a benchmark, we sought to evaluate recent oncology guidelines. Methods CPGs and consensus statements addressing the screening, evaluation, or management of the four leading causes of cancer-related mortality in the United States (lung, breast, prostate, and colorectal cancers) published between January 2005 and December 2010 were identified. A standardized scoring system based on the eight IOM standards was used to critically evaluate the methodology, content, and disclosure policies of CPGs. All CPGs were given two scores; points were awarded for eight standards and 20 subcriteria. Results No CPG fully met all the IOM standards. The average overall scores were 2.75 of 8 possible standards and 8.24 of 20 possible subcriteria. Less than half the CPGs were based on a systematic review. Only half the CPG panels addressed conflicts of interest. Most did not comply with standards for inclusion of patient and public involvement in the development or review process, nor did they specify their process for updating. CPGs were most consistent with IOM standards for transparency, articulation of recommendations, and use of external review. Conclusion The vast majority of oncology CPGs fail to meet the IOM standards for trustworthy guidelines. On the basis of these results, there is still much to be done to make guidelines as methodologically sound and evidence-based as possible.