Paranasal sinus pathogens in children with cystic fibrosis: do they relate to lower respiratory tract pathogens and is eradication successful?

PubMed

Wilson, P; Lambert, C; Carr, S B; Pao, C

2014-07-01

The study aims were to assess the association of microflora between the paranasal sinus and the lower airways of children attending a regional paediatric cystic fibrosis centre and to determine the performance of an eradication treatment protocol for positive paranasal sinus samples. Paired nasal lavage and lower airway samples (cough swabs or sputum) were taken from 54 children with cystic fibrosis (median age 11 years). Positive paranasal sinus samples received eradication treatment, using oral and sinonasal nebulised antibiotics. A correlation between paranasal sinus and lower airways was detected in 33/54 paired timed samples (p<0.02). Of 4/54 children who reported sinus symptoms, only 2 had paranasal sinus positive samples. 28 positive nasal lavage samples cultured 8 Pseudomonas aeruginosa (PA), 8 Staphylococcus aureus (SA) and 12 other bacterial pathogens. Eradication using sinonasal nebulised antibiotics and oral antibiotics showed a success of 14/21 (67%) treated paranasal sinus positive samples at 1 month & 3 months after treatment. Success rate was 75% in the PA group and 71% in the SA group. Ongoing monitoring with nasal lavage will continue. There was agreement between pathogens or lack of them found in the paranasal sinus and lower airways. Paranasal infection is often asymptomatic in children with cystic fibrosis. The eradication protocol for paranasal sinus pathogens had a good success rate. Copyright © 2014 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Elemental analysis of silicon based minerals by ultrasonic slurry sampling electrothermal vaporisation ICP-MS.

PubMed

Rodríguez, Pablo Fernández; Marchante-Gayón, Juan Manuel; Sanz-Medel, Alfredo

2006-01-15

Ultrasonic slurry sampling electrothermal vaporisation inductively coupled plasma mass spectrometry (USS-ETV-ICP-MS) was applied to the elemental analysis of silicate based minerals, such as talc or quartz, without any pre-treatment except the grinding of the sample. The electrothermal vaporisation device consists of a tungsten coil connected to a home-made power supply. The voltage program, carrier gas flow rate and sonication time were optimised in order to obtain the best sensitivity for elements determined. The relationship between the amount of sample in the slurry and the signal intensity was also evaluated. Unfortunately, in all cases, quantification had to be carried out by the standard additions method owing to the strong matrix interferences. The global precision of the proposed method was always better than 12%. The limits of detection, calculated as three times the standard deviation of the blank value divided by the slope of the calibration curve, were between 0.5 ng/g for As and 3.5 ng/g for Ba. The method was validated by comparing the concentrations found for Cu, Mn, Cr, V, Li, Pb, Sn, Mg, U, Ba, Sr, Zn, Sb, Rb and Ce using the proposed methodology with those obtained by conventional nebulisation ICP-MS after acid digestion of the samples in a microwave oven. The concentration range in the solid samples was between 0.2 microg/g for Cr and 60 microg/g for Ba. All results were statistically in agreement with those found by conventional nebulisation.

Production, characterisation, and in vitro nebulisation performance of budesonide-loaded PLA nanoparticles.

PubMed

Amini, Mohammad Ali; Faramarzi, Mohammad Ali; Gilani, Kambiz; Moazeni, Esmaeil; Esmaeilzadeh-Gharehdaghi, Elina; Amani, Amir

2014-01-01

The aim of this study is to prepare a nanosuspension of budesonide for respiratory delivery using nebuliser by optimising its particle size and characterising its in vitro deposition behaviour. PLA (poly lactic acid)-budesonide nanosuspension (BNS) was prepared using high-pressure emulsification/solvent evaporation method. To optimise particle size, different parameters such as PLA concentration, sonication time, and amplitude were investigated. Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and scanning electron microscope (SEM) analyses were performed to characterise the prepared PLA-budesonide nanoparticles. The in vitro aerodynamic characteristics of the PLA-BNS using a jet nebuliser were estimated and compared with that of commercially available suspension formulation of budesonide. Budesonide-loaded PLA nanoparticles with fine particle size (an average size of 224-360 nm), narrow size distribution, and spherical and smooth surface were prepared. The optimum condition for preparation of fine particle size for aerosolisation was found to be at PLA concentration of 1.2 mg/ml and amplitude of 70 for 75 s sonication time. The in vitro aerosolisation performance of PLA-BNS compared to that of commercial budesonide indicated that it has significantly (p < 0.05) smaller mass median aerodynamic diameter (MMAD) value with an enhancement in fine particle fraction (FPF) value. Improving the in vitro deposition of budesonide, PLA-BNS could be considered as a promising alternative suspension formulation for deep lung delivery of the drug using nebuliser.

Efficacy of nebulised budesonide versus oral prednisolone in acute severe asthma.

PubMed

Arulparithi, Cuddalore Subramanian; Babu, Thirunavukkarasu Arun; Ravichandran, C; Santhanam, Indumathy; Sathyamurthi, B; Parivathini, S; Hemachitra, J

2015-04-01

To compare the efficacy of nebulised budesonide with that of oral prednisone in the treatment of acute severe asthma in children. Children aged 5-12 y with acute exacerbation of bronchial asthma were included. The study (budesonide) group received budesonide respirator solution (800 μg) at intervals of 20 min and a single dose of placebo tablets. The control (prednisolone) group received placebo solution at intervals of 20 min and a single dose of oral prednisolone (2 mg/kg). Both groups received three doses of nebulised salbutamol (0.15 mg/kg). Heart rate, respiratory rate, oxygen saturation, PEFR (Peak Expiratory Flow Rate) and fitness for discharge were assessed. Both groups showed a progressive decrease in tachycardia with treatment, but it was significantly greater in study group (p = 0.0002). There was significant decrease in tachypnea and improvement in oxygen saturation in both groups, but the difference between the groups (p = 0.334 and p = 0.814 respectively) was not significant. There was significant improvement in PEFR values in budesonide group (p = 0.024). Both groups showed significant improvement in clinical severity scores at the end of 2 h (p < 0.0001). Budesonide group had significantly higher proportion of patients fit for discharge at 2 h (based on clinical severity scores) (p = 0.0278). Nebulised budesonide significantly improves PEFR levels and fitness for discharge at 2 h when compared to oral prednisolone in children between 5 and 12 y with acute severe asthma.

SABRE: a multicentre randomised control trial of nebulised hypertonic saline in infants hospitalised with acute bronchiolitis.

PubMed

Everard, Mark L; Hind, Daniel; Ugonna, Kelechi; Freeman, Jennifer; Bradburn, Mike; Cooper, Cindy L; Cross, Elizabeth; Maguire, Chin; Cantrill, Hannah; Alexander, John; McNamara, Paul S

2014-12-01

Acute bronchiolitis is the commonest cause for hospitalisation in infancy. Supportive care remains the cornerstone of current management and no other therapy has been shown to influence the course of the disease. It has been suggested that adding nebulised hypertonic saline to usual care may shorten the duration of hospitalisation. To determine whether hypertonic saline does have beneficial effects we undertook an open, multi-centre parallel-group, pragmatic RCT in ten UK hospitals. Infants admitted to hospital with a clinical diagnosis of acute bronchiolitis and requiring oxygen therapy were randomised to receive usual care alone or nebulised 3% hypertonic saline (HS) administered 6-hourly. Randomisation was within 4 h of admission. The primary outcome was time to being assessed as 'fit' for discharge with secondary outcomes including time to discharge, incidence of adverse events together with follow up to 28 days assessing patient centred health related outcomes. A total of 317 infants were recruited to the study. 158 infants were randomised to HS (141 analysed) and 159 to standard care (149 analysed). There was no difference between the two arms in time to being declared fit for discharge (hazard ratio: 0-95, 95% CI: 0.75-1.20) nor to actual discharge (hazard ratio: 0.97, 95% CI: 0.76-1.23). There was no difference in adverse events. One infant in the HS group developed bradycardia with desaturation. This study does not support the use of nebulised HS in the treatment of acute bronchiolitis over usual care with minimal handlings. NCT01469845. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

A LC-MS method allowing the analysis of HMX and RDX present at the picogram level in natural aqueous samples without a concentration step.

PubMed

Vigneau, Olivier; Machuron-Mandard, Xavier

2009-03-15

The introduction of chloroform into the nebulising gas of a LC/MS electrospray interface (ESI), in a perfectly controlled way, leads to the formation of intense adducts ([M+Cl](-)) when a mobile phase containing HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane or octogen) and RDX (1,3,5-trintro-1,3,5-triazacyclohexane or hexogen) is eluted. This LC/MS method allows the direct analysis of aqueous samples containing HMX and RDX at the pictogram level without a concentration step. The method is used to determine HMX and RDX concentrations in ground water samples from a military site.

Steam inhalation or humidified oxygen for acute bronchiolitis in children up to three years of age.

PubMed

Umoren, Rachel; Odey, Friday; Meremikwu, Martin M

2011-01-19

Acute bronchiolitis is a common respiratory infection and a major cause of morbidity in young children. It is treated with bronchodilators (for example, salbutamol), corticosteroids or humidified air (steam inhalation or cool mist). Steam inhalation is preferred in low-income countries as it is inexpensive and easily available. It is thought to act as a secretolytic agent to lighten secretions in the respiratory tract and relieve respiratory distress. To evaluate the effect of steam inhalation or humidified oxygen to relieve respiratory distress and to evaluate adverse events in children up to three years old with acute bronchiolitis. We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2010, Issue 1) which contains the Acute Respiratory Infections Group's Specialised Register, MEDLINE (1950 to February Week 4, 2010), EMBASE.com (1974 to March 2010), CINAHL (1981 to March 2010), AMED (1985 to March 2010), Web of Science (2000 to March 2010) and LILACS (1982 to March 2010). Randomised controlled trials involving children up to three years old with bronchiolitis comparing steam inhalation (or cool mist) or humidified oxygen against bronchodilators, corticosteroids or placebo; alone or in combination. Two review authors independently assessed trial quality and extracted data. Only one study (156 children aged between seven weeks and 24 months with signs and symptoms of bronchiolitis) met the eligibility criteria for inclusion. Participants were randomised into three groups: nebulised salbutamol, nebulised saline and mist in a tent. The results showed a significant decrease in respiratory distress symptom (RDS) score in the nebulised salbutamol group but no significant decrease in the RDS score in the mist in a tent or nebulised saline groups. The study did not report on adverse effects of the interventions. Steam inhalation (or cool mist therapy) is commonly used to treat acute bronchiolitis in resource-constrained settings. One study was eligible for inclusion and found that nebulised salbutamol was an effective intervention for young children with bronchiolitis but mist in a tent did not lead to a significant decrease in RDS score. Since only one study was analysed it would be misleading to conclude that mist therapy is ineffective in children with bronchiolitis. We conclude that there is insufficient evidence to inform practice regarding using steam inhalation or mist therapy for acute bronchiolitis in children up to three years old.

Pharmacokinetics of Colistin Methansulphonate (CMS) and Colistin after CMS Nebulisation in Baboon Monkeys.

PubMed

Marchand, Sandrine; Bouchene, Salim; de Monte, Michèle; Guilleminault, Laurent; Montharu, Jérôme; Cabrera, Maria; Grégoire, Nicolas; Gobin, Patrice; Diot, Patrice; Couet, William; Vecellio, Laurent

2015-10-01

The objective of this study was to compare two different nebulizers: Eflow rapid® and Pari LC star® by scintigraphy and PK modeling to simulate epithelial lining fluid concentrations from measured plasma concentrations, after nebulization of CMS in baboons. Three baboons received CMS by IV infusion and by 2 types of aerosols generators and colistin by subcutaneous infusion. Gamma imaging was performed after nebulisation to determine colistin distribution in lungs. Blood samples were collected during 9 h and colistin and CMS plasma concentrations were measured by LC-MS/MS. A population pharmacokinetic analysis was conducted and simulations were performed to predict lung concentrations after nebulization. Higher aerosol distribution into lungs was observed by scintigraphy, when CMS was nebulized with Pari LC® star than with Eflow Rapid® nebulizer. This observation was confirmed by the fraction of CMS deposited into the lung (respectively 3.5% versus 1.3%).CMS and colistin simulated concentrations in epithelial lining fluid were higher after using the Pari LC star® than the Eflow rapid® system. A limited fraction of CMS reaches lungs after nebulization, but higher colistin plasma concentrations were measured and higher intrapulmonary colistin concentrations were simulated with the Pari LC Star® than with the Eflow Rapid® system.

A rapid and accurate method for the determination of plutonium in food using magnetic sector ICP-MS with an ultra-sonic nebuliser and ion chromatography.

PubMed

Evans, P; Elahi, S; Lee, K; Fairman, B

2003-02-01

In the event of a nuclear incident it is essential that analytical information on the distribution and level of contamination is available. An ICP-MS method is described which can provide data on plutonium contamination in food within 3 h of sample receipt without compromising detection limits or accuracy relative to traditional counting methods. The method can also provide simultaneous determinations of americium and neptunium. Samples were prepared by HNO3 closed-vessel microwave digestion, evaporated to dryness and diluted into a mobile phase comprising 1.5 M HNO3 and 0.1 mM 2,6-pyridinedicarboxylic acid. A commercially available polystyrene-divinylbenzene ion chromatography column provides on-line separation of 239Pu and 238U reducing the impact of the 238U1H interference. Oxidation of the sample using H2O2 ensures all Pu is in the Pu(+4) state. The oxidation also displaces Np away from the solvent front by changing the oxidation state from Np(+3) to Np(+4) and produces the insoluble Am(+4) ion. Simultaneous Pu, Am and Np analyses therefore require omission of the oxidation stage and some loss of Pu data quality. Analyses were performed using a magnetic sector ICP-MS (Finnigan MAT Element). The sample is introduced to the plasma via an ultrasonic nebuliser-desolvation unit (Cetac USN 6000AT+). This combination achieves an instrumental sensitivity of 238U > 2 x 10(7) cps/ppb and removes hydrogen from the sample gas, which also inhibits the formation of 238U1H. The net effect of the improved sample introduction conditions is to achieve detection levels for Pu of 0.020 pg g(-1) (4.6 x 10(-2) Bq kg(-1)) which is significantly below 1/10th of the most stringent EU (European Union) legislation, currently 0.436 pg g(-1) (1 Bq kg(-1)) set for baby food. The new method was evaluated with a range of biological samples ranging from cabbage to milk and meat. Recovery of Pu agrees with published values (100% +/- 20%).

Studies on annealed ZnO:V thin films deposited by nebulised spray pyrolysis method

NASA Astrophysics Data System (ADS)

Malini, D. Rachel

2018-04-01

Structural, optical and photoluminescence properties of annealed ZnO:V thin films deposited by nebulized spray pyrolysis technique by varying vanadium concentration are studied. Thickness of thin films varies from 1.52µm to 7.78µm. V2O5, VO2 and ZnO peaks are observed in XRD patterns deposited with high vanadium concentration and the intensity of peaks corresponding to ZnO decreases in those samples. Morphological properties were studied by analysing SEM images and annealed thin films deposited at ZnO:V = 50:50 possess dumb bell shape grains. Emission peaks corresponding to both Augur transition and deep level transition are observed in the PL spectra of the samples.

Dynamic ultrasonic nebulisation extraction coupled with headspace ionic liquid-based single-drop microextraction for the analysis of the essential oil in Forsythia suspensa.

PubMed

Yang, Jinjuan; Wei, Hongmin; Teng, Xiane; Zhang, Hanqi; Shi, Yuhua

2014-01-01

Ionic liquids have attracted much attention as an extraction solvent instead of traditional organic solvent in single-drop microextraction. However, non-volatile ionic liquids are difficult to couple with gas chromatography. Thus, the following injection system for the determination of organic compounds is described. To establish an environmentally friendly, simple, and effective extraction method for preparation and analysis of the essential oil from aromatic plants. The dynamic ultrasonic nebulisation extraction was coupled with headspace ionic liquid-based single-drop microextraction(UNE-HS/IL/SDME)for the extraction of essential oils from Forsythia suspense fruits. After 13 min of extraction for 50 mg sample, the extracts in ionic liquid were evaporated rapidly in the gas chromatography injector through a thermal desorption unit (5 s). The traditional extraction method was carried out for comparative study. The optimum conditions were: 3 μL of 1-methyl-3-octylimidazolium hexafluorophosphate was selected as the extraction solvent, the sample amount was 50 mg, the flow rate of purging gas was 200 mL/min, the extraction time was 13 min, the injection volume was 2 μL, and the thermal desorption temperature and time were 240 °C and 5 s respectively. Comparing with hydrodistillation (HD), the proposed method was environment friendly and efficient. The proposed method is environmentally friendly, time saving, with high efficiency and low consumption. It would extend the application range of the HS/SDME and would be useful especially for aromatic plants analysis. Copyright © 2013 John Wiley & Sons, Ltd.

Wheeze in childhood: is the spacer good enough?

PubMed Central

Rajkumar, Veena; Rajendra, Barathi; How, Choon How; Ang, Seng Bin

2014-01-01

Max was treated with SABA using an MDI and spacer with facemask and responded well to the initial treatment. You explained to the parents that nebulisers are neither required nor recommended in the treatment of wheezing in their child’s situation. You advised the parents on the proper technique of MDI use with spacer and facemask, as well as care of the equipment. You also gave them a clearly written action plan regarding the efficient management of the next episode of wheeze with MDI and spacer. You further explained the side effects of oral bronchodilators and nebulisers, and why you refrained from using them. Max was given a follow-up appointment to assess his progress, and his parents were advised on the situations when they should go to a doctor or the emergency department. PMID:25631964

Volumetric capnography curves as lung function test to confirm bronchoconstriction after carbachol challenge in sedated dogs.

PubMed

Scheffzek, S; Mosing, M; Hirt, R; Iff, I; Moens, Y

2012-12-01

This study investigated volumetric capnography (VC) in detecting airway responsiveness following airway challenge using carbachol in seven sedated dogs via face mask. Nebulised saline was administered, followed by increasing concentrations of nebulised carbachol until airflow limitation occurred (EP). Dead space (DS) variables and shape indices of the VC curve were calculated automatically after entering arterial carbon dioxide tension. Airway DS, airway DS to tidal volume (VT) ratio and the intercept of slope 2 of the VC curve decreased significantly at EP by 10%, 13% and 16%, respectively, minute ventilation, VT and alveolar DS increased significantly at EP by 49%, 22% and 200%, respectively. We conclude that VC and derived indices may be used to verify a reaction to airway challenge caused by carbachol in sedated dogs. Copyright © 2012 Elsevier Ltd. All rights reserved.

Treatment of acute asthma: salbutamol via jet nebuliser vs spacer and metered dose inhaler.

PubMed

Robertson, C F; Norden, M A; Fitzgerald, D A; Connor, F L; Van Asperen, P P; Cooper, P J; Francis, P W; Allen, H D

1998-04-01

To compare the efficacy of salbutamol delivered by jet nebuliser (JN) with salbutamol via a pressurised metered dose inhaler (PMDI) and a large volume spacer (Volumatic) for management of acute asthma. A total of 160 children aged from 4 to 12 years presenting to an Emergency Department with acute asthma. The study was of multicentre (n=5) randomised, double blind, parallel design. Children weighing less than 25 kg received salbutamol 2.5 mg via the JN or 600 microg (six puffs) from the PMDI. Children over 25 kg received salbutamol 5 mg via the JN or 1200 microg (12 puffs) via the PMDI. Clinical score (range 0-12) and PEF (over 7 years) were recorded at baseline and 15, 30, 45 and 60 mins post administration. The improvement from baseline at 30 min in the clinical score was 1.87 for JN and 1.43 for PMDI (P=0.09) and at 60 min was 2.15 for JN and 1.12 for PMDI (P=0.0001). The improvement in PEF at 30 min was 51 L min(-1) for JN and 27 L min(-1) for PMDI (P=0.0007) and at 60 min was 57 L min(-1) for JN and 31.5 L min(-1) for PMDI (P=0.001). Administration of salbutamol via a PMDI and a large volume spacer device provides effective relief in the management of acute asthma in children, but to a lesser extent than a jet nebuliser. This difference may represent a dose response effect.

MAGNEsium Trial In Children (MAGNETIC): a randomised, placebo-controlled trial and economic evaluation of nebulised magnesium sulphate in acute severe asthma in children.

PubMed

Powell, C V E; Kolamunnage-Dona, R; Lowe, J; Boland, A; Petrou, S; Doull, I; Hood, K; Williamson, P R

2013-10-01

There are few data on the role of nebulised magnesium sulphate (MgSO4) in the management of acute asthma in children. Those studies that have been published are underpowered, and use different methods, interventions and comparisons. Thus, no firm conclusions can be drawn. Does the use of nebulised MgSO4, when given as an adjunct to standard therapy in acute severe asthma in children, result in a clinical improvement when compared with standard treatment alone? Patients were randomised to receive three doses of MgSO4 or placebo, each combined with salbutamol and ipratropium bromide, for 1 hour. The Yung Asthma Severity Score (ASS) was measured at baseline, randomisation, and at 20, 40, 60 (T60), 120, 180 and 240 minutes after randomisation. Emergency departments and children's assessment units at 30 hospitals in the UK. Children aged 2-15 years with acute severe asthma. Patients were randomised to receive nebulised salbutamol 2.5 mg (ages 2-5 years) or 5 mg (ages ≥ 6 years) and ipratropium bromide 0.25 mg mixed with either 2.5 ml of isotonic MgSO4 (250 mmol/l, tonicity 289 mOsm; 151 mg per dose) or 2.5 ml of isotonic saline on three occasions at approximately 20-minute intervals. The primary outcome measure was the ASS after 1 hour of treatment. Secondary measures included 'stepping down' of treatment at 1 hour, number and frequency of additional salbutamol administrations, length of stay in hospital, requirement for intravenous bronchodilator treatment, and intubation and/or admission to a paediatric intensive care unit. Data on paediatric quality of life, time off school/nursery, health-care resource usage and time off work were collected 1 month after randomisation. A total of 508 children were recruited into the study; 252 received MgSO4 and 256 received placebo along with the standard treatment. There were no differences in baseline characteristics. There was a small, but statistically significant difference in ASS at T60 in those children who received nebulised MgSO4 {0.25 [95% confidence interval (CI) 0.02 to 0.48]; p = 0.034} and this difference was sustained for up to 240 minutes [0.20 (95% CI 0.01 to 0.40), p = 0.042]. The clinical significance of this gain is uncertain. Assessing treatment-covariate interactions, there is evidence of a larger effect in those children with more severe asthma exacerbations ( p = 0.034) and those with a shorter duration of symptoms ( p = 0.049). There were no significant differences in the secondary outcomes measured. Adverse events (AEs) were reported in 19% of children in the magnesium group and 20% in the placebo group. There were no clinically significant serious AEs in either group. The results of the base-case economic analyses are accompanied by considerable uncertainty, but suggest that, from an NHS and Personal Social Services perspective, the addition of magnesium to standard treatment may be cost-effective compared with standard treatment only. The results of economic evaluation show that the probability of magnesium being cost-effective is over 60% at cost-effectiveness thresholds of £1000 per unit decrement in ASS and £20,000 per quality-adjusted life-year (QALY) gained, respectively; it is noted that for some parameter variations this probability is much lower, reflecting the labile nature of the cost-effectiveness ratio in light of the small differences in benefits and costs shown in the trial and the relation between the main outcome measure (ASS) and preference based measures of quality of life used in cost-utility analysis (European Quality of Life-5 Dimensions; EQ-5D). This study supports the use of nebulised isotonic MgSO4 at the dose of 151 mg given three times in the first hour of treatment as an adjuvant to standard treatment when a child presents with an acute episode of severe asthma. No harm is done by adding magnesium to salbutamol and ipratropium bromide, and in some individuals it may be clinically helpful. The response is likely to be more marked in those children with more severe attacks and with a shorter duration of exacerbation. Although the study was not powered to demonstrate this fully, the data certainly support the hypotheses that nebulised magnesium has a greater clinical effect in children who have more severe exacerbation with shorter duration of symptoms. Current Controlled Trials ISRCTN81456894. The National Institute for Health Research Health Technology Assessment programme.

Acute bronchiolitis in a paediatric emergency department of Northern Greece. Comparisons between two decades

PubMed Central

Emporiadou, Maria; Aivazis, Victor; Mauromixalis, John; Hatzistilianou, Maria

2012-01-01

Introduction Acute bronchiolitis is the most common lower respiratory tract infection in infants and toddlers concerning small bronchi or bronchioli. This retrospective study aimed to evaluate the incidence of acute bronchiolitis and the use of β2-agonists between two different decades. Material and methods During 1990-1991 and 2001-2002, the files of the 2nd Paediatric Emergency Department of Aristotle University of Thessaloniki, AHEPA Hospital were reviewed and cases of acute bronchiolitis were recorded and analysed. Results During 1990-1991, 14 538 children were identified with respiratory infections and bronchiolitis was diagnosed in 519/14 538 children (3.56%). Only 34 out of 519 patients received nebulised salbutamol (6.6%) and 221/519 were hospitalized (42.6%). During 2001-2002, 9001 children were found to have respiratory tract infections and acute bronchiolitis was diagnosed in 641/9001 of them (7.12%). In total, 411/641 children (64.1%) received salbutamol and ipratropium, and 89/641 patients (13.88%) were hospitalized. There was a predominance of male sex in both decades (p = 0.509). There was a statistically significant difference (p < 0.001) concerning the use of nebulised salbutamol with nebulised ipratropium between the two decades. Finally, during 2001-2002, the use of bronchodilators with or without corticosteroids was more frequent and it appears to be correlated with the reduced number of admissions to hospital (p < 0.05) compared with 1990-1991. Conclusions There was an increase in the incidence of acute bronchiolitis during the last decade. The admission rate decreased probably due to the use of nebulized salbutamol and ipratropium, but further multicentre comparative trials are required to define the role of bronchodilators in the treatment of acute bronchiolitis. PMID:22852008

What happens to COPD patients before an admission with exacerbation?

PubMed

Stone, Robert; Lowe, Derek; Buckingham, Rhona; Pursey, Nancy; Potter, Jonathan; Roberts, C Michael

2012-10-01

To obtain patient-generated data relating to the management of their chronic obstructive pulmonary disease (COPD) in Primary Care before hospitalisation with exacerbation. Previous audits of COPD have shown high rates of hospital admission and readmission. There is significant interest in understanding the reasons so that useful preventative strategies may be developed. As part of the 2008 UK COPD audit, which comprised 9716 cases of COPD admission across 97% of acute units, we obtained a sample of patient-generated data to assess understanding of COPD, use of healthcare resources, access to care and self-management in Primary Care prior to hospitalisation with exacerbation. We anticipated the data would provide useful insight for directing improvement strategies. A paper-based, anonymised survey was completed by patients identified as having exacerbation by participating hospital teams. Response rate was an estimated 46%. Understanding and awareness of COPD was very variable. Patients noticed symptoms of COPD exacerbation, particularly change in sputum, for some time prior to hospitalisation but tended not to react promptly to these changes. A minority had self-care plans, many bypassed Primary Care Services and there was variable access to a named health professional or advice. Patients using home oxygen and nebulisers were at particular risk of admission. We conclude these sick patients use a lot of resources and the data suggest a need to support and educate them in the proactive management of exacerbation. There needs to be better 'exacerbation planning' so patients know how to recognise and treat flare-up but also whom to contact in the event of decline. Targetted support should be considered for the most vulnerable, particularly those using home oxygen and nebulisers, who have very high rates of hospitalisation.

ERS technical standard on bronchial challenge testing: general considerations and performance of methacholine challenge tests.

PubMed

Coates, Allan L; Wanger, Jack; Cockcroft, Donald W; Culver, Bruce H; Diamant, Zuzana; Gauvreau, Gail; Hall, Graham L; Hallstrand, Teal S; Horvath, Ildiko; de Jongh, Frans H C; Joos, Guy; Kaminsky, David A; Laube, Beth L; Leuppi, Joerg D; Sterk, Peter J

2017-05-01

This international task force report updates general considerations for bronchial challenge testing and the performance of the methacholine challenge test. There are notable changes from prior recommendations in order to accommodate newer delivery devices. Rather than basing the test result upon a methacholine concentration (provocative concentration (PC 20 ) causing a 20% fall in forced expiratory volume in 1 s (FEV 1 )), the new recommendations base the result upon the delivered dose of methacholine causing a 20% fall in FEV 1 (provocative dose (PD 20 )). This end-point allows comparable results from different devices or protocols, thus any suitable nebuliser or dosimeter may be used, so long as the delivery characteristics are known. Inhalation may be by tidal breathing using a breath-actuated or continuous nebuliser for 1 min (or more), or by a dosimeter with a suitable breath count. Tests requiring maximal inhalations to total lung capacity are not recommended because the bronchoprotective effect of a deep breath reduces the sensitivity of the test. Copyright ©ERS 2017.

Hybrid Resonant Acoustics: Exploiting a New Class of Sound Waves for Highly Efficient Microfluidic Nebulisation

NASA Astrophysics Data System (ADS)

Rezk, Amgad; Yeo, Leslie

2017-11-01

A longstanding convention in acoustomicrofluidic manipulation-a consequence of wholesale adoption from decades long application of surface acoustic waves (SAWs) in electronics and telecommunications-has been to employ pure SAWs by eliminating wave reflections and bulk resonances in single crystal piezoelectric substrates with the assumption that this provides the most efficient way to actuate or manipulate fluid flow at microscale dimensions. Despite the many advantages of SAW microfluidics, particularly for aerosolising and hence delivering next generation macromolecular-based therapeutics via inhalation, the limitation of the SAW devices, however, lies in the input power it can sustain, thus constraining the nebulisation rates that can be generated, which has, among other things, severely hampered its practical adoption in pulmonary drug administration to date. Here, we unravel the existence of a surface reflected bulk wave (SRBW)-the first new class of sound waves to have been discovered in well over five decades-and show, quite counterintuitively, that it is possible to obtain an order-of-magnitude improvement in microfluidic manipulation efficiency through this unique hybrid combination of surface and bulk waves without increasing complexity or cost.

Nanocarriers Made from Non-Ionic Surfactants or Natural Polymers for Pulmonary Drug Delivery.

PubMed

Carter, K C; Puig-Sellart, M

2016-01-01

Treatment by the pulmonary route can be used for drugs that act locally in the lungs (e.g. lung cancer) or non-invasive administration of drugs that act systemically (e.g. diabetes). The potential of using drug delivery systems (DDS) formed from non-ionic surfactants or natural products for pulmonary drug delivery are reviewed. The effectiveness of each DDS depends on it ability to not only entrap the relevant drug and alter its bio distribution, but also its ability to withstand the physical stresses during nebulization and for the nebuliser to produce aerosol particles with the size for deposition in the appropriate part of the lungs. Different methods must be used to prepare nanoparticles (NP) using non-ionic surfactants, or biocompatible polymers from natural proteins or sugars, and the aqueous solubility of the drug also influences the manufacture method. NP produced using non-ionic surfactants, proteins such as collagen, albumin or gluten, and polysaccharides such as chitosan, hyaluronate, cellulose, carrageenans, alginate or starch has successfully delivered different types of drugs given by the pulmonary route. Drug entrapment efficiency depends on the DDS constituents and the manufacture method used. Large scale manufacture of DDS from natural products is technically challenging but changing from batch manufacture to continuous manufacturing processes has addressed some of these issues, and inclusion of a spray drying step has been beneficial in some cases. DDS for lung delivery can be produced using natural products but identifying a cost effective manufacture method may be challenging and the impact of using different type of nebulisers on the physiochemical characteristics of the aerosolised formulation should be an essential part of formulation development. This would ensure that some of the development work e.g. stability studies do not have to be repeated as they will identify if a carrier to protect the DDS from the physical trauma caused by nebulisation.

Inhaled nebulised unfractionated heparin improves lung function in moderate to very severe COPD: A pilot study.

PubMed

Shute, Janis K; Calzetta, Luigino; Cardaci, Vittorio; di Toro, Stefania; Page, Clive P; Cazzola, Mario

2018-02-01

COPD is an inflammatory airway disease characterised by progressive airflow limitation and air trapping, leading to lung hyperinflation and exercise limitation. Acute worsening of symptoms, including dyspnea, cough and sputum production, occurs during exacerbations which are associated with significantly reduced health related quality of life, and increased morbidity and mortality. Chronic bronchial mucus production and productive cough are risk factors for exacerbations. Medicines targeting bronchoconstriction and airway inflammation are the current mainstays of COPD therapy. However, there is growing concern with an increased risk of pneumonia in patients with COPD receiving regular inhaled corticosteroids and there is therefore a need to find safer alternative treatments. Previous studies have indicated that inhalation of unfractionated heparin (UFH) treats local inflammation, mucus hypersecretion and lung injury, without systemic anticoagulation, and is safe. Therefore, our primary objective was to demonstrate that inhaled UFH significantly improves lung function (FEV 1 ) over 21 days of treatment in patients with COPD receiving pulmonary rehabilitation and that UFH provides a novel, safe and effective way of treating this complex disease. Forty patients with moderate to very severe COPD admitted to the IRCCS San Raffaele Pisana Hospital for 21 days pulmonary rehabilitation were randomised to receive nebulised inhaled UFH (75,000 or 150,000 IU BID) or placebo for 21 days. All patients also received nebulised salbutamol (1 mg) and beclomethasone dipropionate (400 μg) BID over the same period. Lung function was measured at day 0, 7, 14 and 21 of treatment and at a follow-up visit 7 days post-treatment. Exercise capacity (6MWT) and dyspnoea (Borg score) were measured before and after treatment. In pre-clinical studies, the ability of basic proteins found in COPD sputum to neutralise the anticoagulant activity of heparin was determined using the AMAX heparin assay kit. At both doses, UFH significantly increased FVC following 7 days of treatment and 150,000 IU BID significantly increased FEV1 (+249 ± 69 ml compared with placebo) at this time, an effect maintained to the 28 day follow-up. Clinically significant improvement in exercise capacity and dyspnoea were seen after 21 days of treatment with both doses of UFH. There were no serious adverse events or effects on systemic coagulation. Pre-clinical studies demonstrated that the basic proteins lactoferrin, platelet factor-4 (PF-4), IL-8 and polyarginine, as a model of the eosinophil cationic protein (ECP), found in COPD sputum neutralise the anticoagulant activity of heparin. Inhaled nebulised UFH is safe and provides additional clinical benefit for patients with moderate to very severe COPD through effects that are independent of its anticoagulant activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapid determination of tafenoquine in small volume human plasma samples by high-performance liquid chromatography-tandem mass spectrometry.

PubMed

Doyle, E; Fowles, S E; Summerfield, S; White, T J

2002-03-25

A method was developed for the determination of tafenoquine (I) in human plasma using high-performance liquid chromatography-tandem mass spectrometry. Prior to analysis, the protein in plasma samples was precipitated with methanol containing [2H3(15N)]tafenoquine (II) to act as an internal standard. The supernatant was injected onto a Genesis-C18 column without any further clean-up. The mass spectrometer was operated in the positive ion mode, employing a heat assisted nebulisation, electrospray interface. Ions were detected in multiple reaction monitoring mode. The assay required 50 microl of plasma and was precise and accurate within the range 2 to 500 ng/ml. The average within-run and between-run relative standard deviations were < 7% at 2 ng/ml and greater concentrations. The average accuracy of validation standards was generally within +/- 4% of the nominal concentration. There was no evidence of instability of I in human plasma following three complete freeze-thaw cycles and samples can safely be stored for at least 8 months at approximately -70 degrees C. The method was very robust and has been successfully applied to the analysis of clinical samples from patients and healthy volunteers dosed with I.

"Now We Are Going on a Journey": Meaning-Making with a Healthcare Game during Toddlers' Medical Treatment

ERIC Educational Resources Information Center

Høiseth, Marikken; Hopperstad, Marit Holm

2016-01-01

This study explores how toddlers and caregivers make meaning with an interactive healthcare game on a tablet during medical treatment. The data material consists of video recordings of six nebuliser treatments of two children. Using a social semiotic perspective and a multimodal analysis, the study identifies how children and caregivers make…

The use of a modified technique to reduce radioactive air contamination in aerosol lung ventilation imaging.

PubMed

Avison, M; Hart, G

2001-06-01

The aim of this study was to reduce airborne contamination resulting from the use of aerosols in lung ventilation scintigraphy. Lung ventilation imaging is frequently performed with 99mTc-diethylenetriaminepentaacetate aerosol (DTPA), derived from a commercial nebuliser. Airborne contamination is a significant problem with this procedure; it results in exposure of staff to radiation and can reduce gamma camera performance when the ventilation is performed in the camera room. We examined the level of airborne contamination resulting from the standard technique with one of the most popular nebuliser kits and tested a modification which significantly reduced airborne contamination. Air contamination was measured while ventilating 122 patients. The modified technique reduced air contamination by a mean value of 64% (p = 0.028) compared with the standard control technique. Additionally, differences in contamination were examined when a mask or mouthpiece was used as well as differences between operators. A simplified method of monitoring air contamination is presented using a commonly available surface contamination monitor. The index so derived was proportional to air contamination (r = 0.88). The problems and regulations associated with airborne contamination are discussed.

Use of helium-oxygen mixture in adult patients presenting with exacerbations of asthma and chronic obstructive pulmonary disease: a systematic review.

PubMed

Colebourn, C L; Barber, V; Young, J D

2007-01-01

We examined systematically all controlled and cross-over randomised trials in patients with acute exacerbations of asthma and chronic obstructive pulmonary disease comparing Heliox against air-oxygen mixtures. Fourteen studies were identified. In asthma studies, peak expiratory flow rate (PEFR) was increased by an average of 29.6% (95% CI 16.6-42.6) by Heliox-driven nebulisers, or by 13.3 l.min(-1) (95% CI 3.71-22.81) absolute. In studies of patients with chronic obstructive pulmonary disease receiving non-invasive ventilation the arterial carbon dioxide tension (P(a)co(2)) and respiratory rate were unchanged: weighted mean difference for P(a)co(2)-0.29kPa (95% CI - 0.64-0.07) favoured Heliox, and for respiratory rate 1.6 breaths.min(-1) (95% CI - 0.93, 4.14) favoured control. Heliox minimally reduced the work of breathing in intubated patients, and reduced intrinsic positive end expiratory pressure (iPEEP). The use of Heliox to drive nebulisers in patients with acute asthma slightly improves airflow measures. We were unable to determine whether this improved recovery.

[Quality of life and adherence to nebulised antibiotic therapy using a new device in non-cystic fibrosis bronchiectasis].

PubMed

Gulini, Martina; Prados, Concepción; Pérez, Amparo; Romero, David; Feliz, Darwin; Gómez Carrera, Luis; Cabanillas, Juan José; Barbero, Javier; Alvarez-Sala, Rodolfo

2012-01-01

Analysis of psychological variables, quality of life, depression and anxiety, subjective perception of compliance, level of satisfaction with the electronic device, and objective verification) in order to study the therapeutic adherence, in non-cystic fibrosis bronchiectasis (NCFB) colonized by Pseudomonas aeruginosa. A cross-sectional descriptive study was conducted on 22 NCFB stable patients colonised by Pseudomonas aeruginosa (two groups of 11 subjects: GROUP 1, Pari-LC plus nebuliser device, and GROUP 2, with the I- neb device), both containing sodium colistemethate. Different variables, were obtained, such as, self-perceived health (St George questionnaire), state of mind (HADS scale), and subjective perception of therapeutic compliance and objective verification by using the device software. There were no significant differences in questionnaire results. The therapeutic support in GROUP 2, could be proved objectively (up to 60%) using specific software, and the excellent tolerability using a specific questionnaire created for the study. These types of aerosol devices demonstrate a high level of therapeutic support, that can be measured objectively and is different from what the patients subjectively indicates. Copyright © 2011 Elsevier España, S.L. All rights reserved.

Validation of a highly sensitive ICP-MS method for the determination of platinum in biofluids: application to clinical pharmacokinetic studies with oxaliplatin.

PubMed

Morrison, J G; White, P; McDougall, S; Firth, J W; Woolfrey, S G; Graham, M A; Greenslade, D

2000-12-01

ELOXATIN (Oxaliplatin) is a novel platinum containing anti-cancer agent with a diaminocyclohexane carrier ligand which has been approved in several major European countries. Clinical studies have demonstrated that the compound exhibits marked activity against colorectal cancers in combination with 5-fluorouracil (5-FU). The aim of this work was to develop and validate a highly sensitive inductively coupled plasma mass spectrometry assay for the determination of oxaliplatin-derived platinum in plasma ultrafiltrate, plasma and whole blood and to apply this technique to clinical pharmacokinetic studies with oxaliplatin. Ultratrace detection of platinum in plasma ultrafiltrate was achieved using ultrasonic nebulisation combined with ICP-MS. This technique allows detection of platinum at the 0.001 microg Pt/ml level in only 100 microl of matrix. Assays in blood and plasma utilised a standard Meinhardt nebuliser and spray chamber, achieving detection limits of 0.1 microg Pt/ml in 100 and 200 microl of matrix, respectively. The assays were validated (accuracy and precision within +/- 15%) over the concentration ranges: 0.001-0.250 microg Pt/ml in plasma ultrafiltrate and 0.1-10 microg Pt/ml for plasma and whole blood. The effect of sample digestion. dilution, long term frozen storage and quantitation in the presence of 5-FU were also investigated and validated. The method was used to monitor platinum exposure following oxaliplatin administration (130 mg/m2) to cancer patients. Following a 2 h i.v. infusion, peak platinum levels declined in a triphasic manner in all blood compartments. Free platinum was detected in plasma ultrafiltrate at low levels (0.001 0.010 microg Pt/ml) for up to 3 weeks. In conclusion, a highly sensitive and specific assay has been developed for the determination of platinum in biofluids. This method enabled characterisation of the long term exposure to platinum in patients following oxaliplatin treatment.

Occupational asthma due to chrome and nickel electroplating

PubMed Central

Bright, P.; Burge, P. S.; O'Hickey, S. P.; Gannon, P. F.; Robertson, A. S.; Boran, A.

1997-01-01

BACKGROUND: Exposure to chromium during electroplating is a recognised though poorly characterised cause of occupational asthma. The first series of such patients referred to a specialist occupational lung disease clinic is reported. METHODS: The diagnosis of occupational asthma was made from a history of asthma with rest day improvement and confirmed by specific bronchial provocation testing with potassium dichromate and nickel chloride. RESULTS: Seven workers had been exposed to chrome and nickel fumes from electroplating for eight months to six years before asthma developed. One subject, although exposed for 11 years without symptoms, developed asthma after a single severe exposure during a ventilation failure. This was the only subject who had never smoked. The diagnosis was confirmed by specific bronchial challenges. Two workers had isolated immediate reactions, one a late asthmatic reaction, and four a dual response following exposure to nebulised potassium dichromate at 1-10 mg/ml. Two of the four subjects were also challenged with nebulised nickel chloride at 0.1-10 mg/ml. Two showed isolated late asthmatic reactions, in one at 0.1 mg/ml, where nickel was probably the primary sensitising agent. Four workers carried out two hourly measurements of peak expiratory flow over days at and away from work. All were scored as having occupational asthma using OASYS-2. Breathing zone air monitoring was carried out in 60 workers from four decorative and two hard chrome plating shops from workers with similar jobs to those sensitised. No measurement exceeded the current occupational exposure standard for chromate or nickel, the mean levels of chromate exposure for jobs similar to those of the affected workers were 9-15 micrograms/m3. CONCLUSION: Chrome used in electroplating is a potential cause of occupational asthma. Sensitivity to chrome in electroplaters may occur in situations where exposure levels are likely to be within the current exposure standards. There may be cross reactivity with nickel. Inhalation challenge with nebulised potassium dichromate solution is helpful in making the specific diagnosis where doubt exists. 


 PMID:9039236

SETTING UP OF A HOMECARE SYSTEM FOR HIGH COST NEBULISERS IN A PAEDIATRIC CYSTIC FIBROSIS CENTRE.

PubMed

Chorro-Mari, Veronica; Christiansen, Nanna

2016-09-01

Due to national changes to the commissioning process of high cost nebulisers (HCN) for Cystic Fibrosis (CF) patients, CF centres have to repatriate the prescribing of the HCN to the tertiary care centres.1 The following nebulisers will no longer be prescribed by primary care: Cayston® (Aztreonam); Colomycin®, Pomixin®, Clobreathe® (Colistimethate); Pulmozyme® (Dornase alfa); Tobi®, Tobi Podhaler ®, Bramitob® (Tobramycin).This abstract explains how the Royal London Hospital (RLH) Paediatric Pharmacy recruited over 100 paediatric (CF) patients smoothly within a period of 4 months and set up a homecare system to avoid patients and families having to travel large distances to obtain their medication. A number of homecare companies were evaluated initially. Parameters looked at were reports of customer satisfaction, delivery cost, turn-around time once the prescription was received and availability of same day delivery service.In order to capture existing patients we met with CF Specialist Nurses to establish the total number of patients on HCN, what nebulised treatment they were on and their respective doses. We prioritised patients that had known problems with GP prescribing and anybody newly starting on HCN.To communicate the change to parents, a letter was sent to all parents explaining the changeover to homecare delivery and tertiary prescribing. In addition a section in the parent bulletin was dedicated to the topic as well. Following this we contacted parents via phone and in clinic to request consent and explain the process.Up to 10 patients were contacted weekly (average of 7); the consent form and registration form were then faxed to the Homecare company for patient registration. In parallel to this prescriptions were requested for the patients that had been set up in the previous week, ensuring that prescribing was spread out over time to avoid having peak times for repeat prescriptions.In addition to the letter to parents GP surgeries were also informed in writing about the changes in commissioning and planned repatriation of HCN. This information was also included on discharge prescriptions for patients on any of the HCNs as part of the pharmacy screening process.A system for follow up prescriptions as repeat was set up between the team so we would not have unexpected urgent requests and we could avoid missed doses, urgent delivery charge or stress in the team. In order to manage the prescriptions and ease communication across the team a database was developed. From March to July 2014 (16 weeks) one hundred and four patients were successfully repatriated to tertiary care. A planned method and agreed standard operation procedure was key to effectively capture and repatriate all patients while at the same time keeping the increase on workload for the pharmacy team to a minimum. The fact of having a strong pharmacy presence as part of the multidisciplinary team attending CF clinics and ward rounds was vital in making this work. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Ice Particle Charge Transfer Studies.

DTIC Science & Technology

1987-09-30

sufficient time for the rime feathers to grow . The rimed target was then exposed to the salt droplet cloud produced by a small Unicorn nebuliser. This...limited in extent, and it was possible only to grow crystals of 100 pm diameter; whereas, in nature, crystals have time to grow several hundred microns...updraft which countered ti~e terminal fall velocity of the growing crystals. The droplet supply was main- tained and the crystals grew to about 150-200

Role of long term antibiotics in chronic respiratory diseases.

PubMed

Suresh Babu, K; Kastelik, J; Morjaria, J B

2013-06-01

Antibiotics are commonly used in the management of respiratory disorders such as cystic fibrosis (CF), non-CF bronchiectasis, asthma and COPD. In those conditions long-term antibiotics can be delivered as nebulised aerosols or administered orally. In CF, nebulised colomycin or tobramycin improve lung function, reduce number of exacerbations and improve quality of life (QoL). Oral antibiotics, such as macrolides, have acquired wide use not only as anti-microbial agents but also due to their anti-inflammatory and pro-kinetic properties. In CF, macrolides such as azithromycin have been shown to improve the lung function and reduce frequency of infective exacerbations. Similarly macrolides have been shown to have some benefits in COPD including reduction in a number of exacerbations. In asthma, macrolides have been reported to improve some subjective parameters, bronchial hyperresponsiveness and airway inflammation; however have no benefits on lung function or overall asthma control. Macrolides have also been used with beneficial effects in less common disorders such as diffuse panbronchiolitis or post-transplant bronchiolitis obliterans syndrome. In this review we describe our current knowledge the use of long-term antibiotics in conditions such as CF, non-CF bronchiectasis, asthma and COPD together with up-to-date clinical and scientific evidence to support our understanding of the use of antibiotics in those conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Antibiotic strategies for eradicating Pseudomonas aeruginosa in people with cystic fibrosis.

PubMed

Langton Hewer, Simon C; Smyth, Alan R

2017-04-25

Respiratory tract infection with Pseudomonas aeruginosa occurs in most people with cystic fibrosis. Once chronic infection is established, Pseudomonas aeruginosa is virtually impossible to eradicate and is associated with increased mortality and morbidity. Early infection may be easier to eradicate.This is an update of a Cochrane review first published in 2003, and previously updated in 2006, 2009 and 2014. To determine whether antibiotic treatment of early Pseudomonas aeruginosa infection in children and adults with cystic fibrosis eradicates the organism, delays the onset of chronic infection, and results in clinical improvement. To evaluate whether there is evidence that a particular antibiotic strategy is superior to or more cost-effective than other strategies and to compare the adverse effects of different antibiotic strategies (including respiratory infection with other micro-organisms). We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group Trials Register comprising references identified from comprehensive electronic database searches and handsearches of relevant journals and abstract books of conference proceedings.Most recent search: 10 October 2016. We included randomised controlled trials of people with cystic fibrosis, in whom Pseudomonas aeruginosa had recently been isolated from respiratory secretions. We compared combinations of inhaled, oral or intravenous antibiotics with placebo, usual treatment or other combinations of inhaled, oral or intravenous antibiotics. We excluded non-randomised trials, cross-over trials, and those utilising historical controls. Both authors independently selected trials, assessed risk of bias and extracted data. The search identified 60 trials; seven trials (744 participants) with a duration between 28 days and 27 months were eligible for inclusion. Three of the trials are over 10 years old and their results may be less applicable today given the changes in standard treatment. Some of the trials had low numbers of participants and most had relatively short follow-up periods; however, there was generally a low risk of bias from missing data. In most trials it was difficult to blind participants and clinicians to treatment given the interventions and comparators used. Two trials were supported by the manufacturers of the antibiotic used.Evidence from two trials (38 participants) at the two-month time-point showed treatment of early Pseudomonas aeruginosa infection with inhaled tobramycin results in microbiological eradication of the organism from respiratory secretions more often than placebo, odds ratio 0.15 (95% confidence interval (CI) 0.03 to 0.65) and data from one of these trials, with longer follow up, suggested that this effect may persist for up to 12 months.One randomised controlled trial (26 participants) compared oral ciprofloxacin and nebulised colistin versus usual treatment. Results after two years suggested treatment of early infection results in microbiological eradication of Pseudomonas aeruginosa more often than no anti-pseudomonal treatment, odds ratio 0.12 (95% CI 0.02 to 0.79).One trial comparing 28 days to 56 days treatment with nebulised tobramycin solution for inhalation in 88 participants showed that both treatments were effective and well-tolerated, with no notable additional improvement with longer over shorter duration of therapy. However, this trial was not powered to detect non-inferiority or equivalence .A trial of oral ciprofloxacin with inhaled colistin versus nebulised tobramycin solution for inhalation alone (223 participants) failed to show a difference between the two strategies, although it was underpowered to show this. A further trial of inhaled colistin with oral ciprofloxacin versus nebulised tobramycin solution for inhalation with oral ciprofloxacin also showed no superiority of the former, with increased isolation of Stenotrophomonas maltophilia in both groups.A recent, large trial in 306 children aged between one and 12 years compared cycled nebulised tobramycin solution for inhalation to culture-based therapy and also ciprofloxacin to placebo. The primary analysis showed no difference in time to pulmonary exacerbation or proportion of Pseudomonas aeruginosa positive cultures. An analysis performed in this review (not adjusted for age) showed fewer participants in the cycled therapy group with one or more isolates of Pseudomonas aeruginosa, odds ratio 0.51 (95% CI 0.31 to 0.28). Using GRADE, the quality of evidence for outcomes was downgraded to moderate to very low. Downgrading decisions for Pseudomonas aeruginosa eradication and lung function were based on applicability (participants mostly children) and limitations in study design, with imprecision an additional limitation for lung function, growth parameters and adverse effects. We found that nebulised antibiotics, alone or in combination with oral antibiotics, were better than no treatment for early infection with Pseudomonas aeruginosa. Eradication may be sustained for up to two years. There is insufficient evidence to determine whether antibiotic strategies for the eradication of early Pseudomonas aeruginosa decrease mortality or morbidity, improve quality of life, or are associated with adverse effects compared to placebo or standard treatment. Four trials comparing two active treatments have failed to show differences in rates of eradication of Pseudomonas aeruginosa. There have been no published randomised controlled trials that investigate the efficacy of intravenous antibiotics to eradicate Pseudomonas aeruginosa in cystic fibrosis. Overall, there is still insufficient evidence from this review to state which antibiotic strategy should be used for the eradication of early Pseudomonas aeruginosa infection in cystic fibrosis.

Effects of topical benzocaine and lignocaine on upper airway reflex sensitivity.

PubMed

Raphael, J H; Stanley, G D; Langton, J A

1996-02-01

We studied the degree and duration of effect on upper airway reflex sensitivity of oral benzocaine lozenges, nebulised lignocaine and lignocaine sprayed onto the vocal cords under direct vision, using low concentrations of ammonia as a stimulus to upper airway receptors. Ten minutes after the administration of oral benzocaine 20 mg the threshold response of the upper airway to ammonia (NH3TR) had risen significantly from baseline mean (SEM) of 680 (95) to 975 (109) ppm of ammonia with a return to baseline values after 25 min (n = 8, p < 0.05, repeated measures of ANOVA; p < 0.001, t-test). A direct spray of lignocaine 100 mg onto the vocal cords resulted in a significant elevation in NH3TR from a baseline mean (SEM) of 665 (81) to a maximum of 1600 (88) ppm of ammonia with a significant elevation in the threshold persisting for 100 min (n = 7, p < 0.001, repeated measures of ANOVA; p < 0.05, t-test). The application of 4% nebulised lignocaine 4 ml significantly increased NH3TR from a baseline mean (SEM) of 770 (56) to a maximum of 1190 (63) ppm of ammonia with a significant elevation in the threshold persisting for 30 min (n = 8, p < 0.001, repeated measures of ANOVA; p < 0.05, t-test). The maximum elevations in NH3TR with the two methods of lignocaine delivery were significantly different (p < 0.01, 2-way ANOVA).

Nebulised amphotericin B-polymethacrylic acid nanoparticle prophylaxis prevents invasive aspergillosis

PubMed Central

Shirkhani, Khojasteh; Teo, Ian; Armstrong-James, Darius; Shaunak, Sunil

2015-01-01

Aspergillus species are the major life threatening fungal pathogens in transplant patients. Germination of inhaled fungal spores initiates infection, causes severe pneumonia, and has a mortality of > 50%. This is leading to the consideration of pre-exposure prophylaxis to prevent infection. We made a very low MWt amphotericin B-polymethacrylic acid nanoparticle. It was not toxic to lung epithelial cells or monocyte-derived-macrophages in-vitro, or in an in-vivo transplant immuno-suppression mouse model of life threatening invasive aspergillosis. Three days of nebuliser based prophylaxis delivered the nanoparticle effectively to lung and prevented both fungal growth and lung inflammation. Protection from disease was associated with > 99% killing of the Aspergillus and a 90% reduction in lung TNF-α; the primary driver of tissue destructive immuno-pathology. This study provides in-vivo proof-of-principle that very small and cost-effective nanoparticles can be made simply, and delivered safely and effectively to lung by the aerosol route to prevent fungal infections. From the Clinical Editor Aspergillus is an opportunistic pathogen, which affects immunocompromised patients. One novel way to help fight against this infection is pre-exposure prophylaxis. The authors here made PMA based anionic hydrogels carrying amphotericin B, with mucoadhesive behavior. They showed that aerosol route of the drug was very effective in protecting against the disease in an in-vivo model and should provide a stepping-stone towards clinical trials in the future. PMID:25791815

Nebulised amphotericin B-polymethacrylic acid nanoparticle prophylaxis prevents invasive aspergillosis.

PubMed

Shirkhani, Khojasteh; Teo, Ian; Armstrong-James, Darius; Shaunak, Sunil

2015-07-01

Aspergillus species are the major life threatening fungal pathogens in transplant patients. Germination of inhaled fungal spores initiates infection, causes severe pneumonia, and has a mortality of >50%. This is leading to the consideration of pre-exposure prophylaxis to prevent infection. We made a very low MWt amphotericin B-polymethacrylic acid nanoparticle. It was not toxic to lung epithelial cells or monocyte-derived-macrophages in-vitro, or in an in-vivo transplant immuno-suppression mouse model of life threatening invasive aspergillosis. Three days of nebuliser based prophylaxis delivered the nanoparticle effectively to lung and prevented both fungal growth and lung inflammation. Protection from disease was associated with >99% killing of the Aspergillus and a 90% reduction in lung TNF-α; the primary driver of tissue destructive immuno-pathology. This study provides in-vivo proof-of-principle that very small and cost-effective nanoparticles can be made simply, and delivered safely and effectively to lung by the aerosol route to prevent fungal infections. Aspergillus is an opportunistic pathogen, which affects immunocompromised patients. One novel way to help fight against this infection is pre-exposure prophylaxis. The authors here made PMA based anionic hydrogels carrying amphotericin B, with mucoadhesive behavior. They showed that aerosol route of the drug was very effective in protecting against the disease in an in-vivo model and should provide a stepping-stone towards clinical trials in the future. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Magnesium sulphate in acute severe asthma in children (MAGNETIC): a randomised, placebo-controlled trial.

PubMed

Powell, Colin; Kolamunnage-Dona, Ruwanthi; Lowe, John; Boland, Angela; Petrou, Stavros; Doull, Iolo; Hood, Kerenza; Williamson, Paula

2013-06-01

Little evidence is available for the effect of nebulised magnesium sulphate (MgSO(4)) in acute asthma in children. We assessed the effect of MgSO(4) treatment in children with severe acute asthma. In this randomised placebo-controlled, multi-centre, parallel trial, we enrolled children (aged 2-16 years) with severe acute asthma who did not respond to standard inhaled treatment from 30 hospitals in the UK. Children were randomly allocated (1:1) to receive nebulised salbutamol and ipratropium bromide with either 2·5 mL of isotonic MgSO(4) (250 mmol/L; 151 mg per dose; MgSO(4) group) or 2·5 mL of isotonic saline (placebo group) on three occasions at 20-min intervals. Randomisation was done with a computer-generated randomisation sequence, with random block sizes of two to four. Both patients and researchers were masked to treatment allocation. The primary outcome measure was the Yung Asthma Severity Score (ASS) at 60 min post-randomisation. We used a statistical significance level of p<0·05 for a between-group difference, but regarded a between-group difference in ASS of 0·5 as the minimal clinically significant treatment effect. Analysis was done by intention to treat. This trial is registered with controlled-trials.com, number ISRCTN81456894. Between Jan 3, 2009, and March 20, 2011, we recruited and randomly assigned 508 children to treatment: 252 to MgSO(4) and 256 to placebo. Mean ASS at 60 min was lower in the MgSO(4) group (4·72 [SD 1·37]) than it was in the placebo group (4·95 [SD 1·40]; adjusted difference -0·25, 95% CI -0·48 to -0·02; p=0·03). This difference, however, was not clinically significant. The clinical effect was larger in children with more severe asthma exacerbation (p=0·03) and those with symptoms present for less than 6 h (p=0·049). We detected no difference in the occurrence of adverse events between groups. Overall, nebulised isotonic MgSO(4), given as an adjuvant to standard treatment, did not show a clinically significant improvement in mean ASS in children with acute severe asthma. However, the greatest clinical response was seen in children with more severe attacks (SaO(2)<92%) at presentation and those with preceding symptoms lasting less than 6 h. National Institute for Health Research Health Technology Assessment Programme. Copyright © 2013 Elsevier Ltd. All rights reserved.

Status asthmaticus in children: a one-year study.

PubMed Central

McKenzie, S A; Edmunds, A T; Godfrey, S

1979-01-01

50 children were admitted on 72 occasions during one year in status asthmaticus, defined as wheezing not relieved by two doses of bronchodilator 4 hours apart. At least one-third of children were hypercapnoeic on admission. They were managed with either oral prednisolone and nebulised salbutamol. Those with peak expiratory flow rates of greater than 25% expected for height were satisfactorily managed on the oral regimen. One child needed assisted ventilation. 73% were fit for discharge within 4 days and more than half of them needed a change in maintanance treatment. PMID:389173

Continuous inhaled iloprost in a neonate with d-transposition of the great arteries and severe pulmonary arterial hypertension.

PubMed

Dykes, John C; Torres, Marilyn; Alexander, Plato J

2016-03-01

This report describes the case of a neonate with d-transposition of the great arteries and severe pulmonary arterial hypertension stabilised in the post-operative period with continuous iloprost nebulisation. To our knowledge, this is the first documented method of treating post-operative severe pulmonary arterial hypertension with continuous inhaled iloprost in a patient with complex CHD. We found this method of delivering the drug very effective in stabilising haemodynamic swings in the setting of severe pulmonary arterial hypertension.

Effect of airway clearance techniques on the efficacy of the sputum induction procedure.

PubMed

Elkins, M R; Lane, T; Goldberg, H; Pagliuso, J; Garske, L A; Hector, E; Marchetto, L; Alison, J A; Bye, P T P

2005-11-01

Sputum induction is used in the early identification of tuberculosis (TB) and pneumocystis infections of the lung. Although manual physiotherapy techniques to clear the airways are often incorporated in the sputum induction procedure, their efficacy in this setting is unknown. This randomised, crossover trial enrolled adults referred for sputum induction for suspected TB and pneumocystis infections of the lung. All participants underwent two sputum induction procedures, inhaling 3% saline via ultrasonic nebuliser. During one randomly allocated procedure, airway clearance techniques (chest wall percussion, vibration, huffing) were incorporated. In total, 59 participants completed the trial. The airway clearance techniques had no significant effect on how the test was tolerated, the volume expectorated or the quality of the sample obtained (assessed by the presence of alveolar macrophages). The techniques did not significantly affect how often the test identified a suspected organism, nor the sensitivity or specificity of sputum induction. In conclusion, the study was unable to demonstrate any effect of airway clearance techniques on the sputum induction procedure. The results provide some justification for not including airway clearance techniques as part of the sputum induction procedure.

Microfluidic high performance liquid chromatography-chip hyphenation to inductively coupled plasma-mass spectrometry.

PubMed

Bishop, David P; Blanes, Lucas; Wilson, Alexander B; Wilbanks, Thor; Killeen, Kevin; Grimm, Rudolf; Wenzel, Ross; Major, Derek; Macka, Mirek; Clarke, David; Schmid, Robin; Cole, Nerida; Doble, Philip A

2017-05-12

The Agilent Chip Cube Interface is a microfluidic chip-based technology originally designed for nanospray molecular mass spectrometry in which the sample enrichment, nano-column, tubing, connectors and spray tip were integrated into a single biocompatible chip. Here we describe the hyphenation of the Chip Cube Interface to ICP-MS via modification of the standard HPLC chip design and a new total consumption nebuliser suitable for flow rates as low as 300nLmin -1 . The potential of the instrument to eliminate common nanoLC - ICP-MS shortcomings such as leaks, blockages and band-broadening was demonstrated via analysis of cyanocobalamin in equine plasma. The method was linear over three orders of magnitude with an r 2 of 0.9999, the peak area repeatability was 1.9% (n=7), and the detection limit was 14ngmL -1 . This novel configuration of the Chip Cube Interface coupled to ICP-MS is a suitable platform for the analysis of biomolecules associated with trace metals and speciation applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Enhanced sensitivity for Os isotope ratios by magnetic sector ICP-MS with a capacitive decoupling Pt guard electrode.

PubMed

Townsend, A T

2000-08-01

A magnetic sector ICP-MS with enhanced sensitivity was used to measure Os isotope ratios in solutions of low Os concentration (approximately 1 ng g(-1) or less). Ratios with 192Os as the basis were determined, while the geologically useful 187Os/188Os ratio was also measured. Sample introduction was via the traditional nebuliser-spray chamber method. A capacitive decoupling Pt shield torch was developed "in-house" and was found to increase Os signals by approximately 5 x under "moderate" plasma conditions (1050 W) over that found during normal operation (1250 W). Sensitivity using the guard electrode for 192Os was approximately 250-350,000 counts s(-1) per ng g(-1) Os. For a I ng g(-1) Os solution with no guard electrode, precisions of the order of 0.2-0.3% (189Os/192Os and 190Os/192Os) to approximately 1% or greater (186Os/192Os, 187Os/192Os and 187Os/188Os) were found (values as 1 sigma for n = 10). With the guard electrode in use, ratio precisions were found to improve to 0.2 to 0.8%. The total amount of Os used in the acquisition of this data was approximately 2.5 ng per measurement per replicate. At the higher concentration of 10 ng g(-1), precisions of the order of 0.15-0.3% were measured (for all ratios), irrespective of whether the shield torch was used. Ratio accuracy was confirmed by comparison with independently obtained NTIMS data. For both Os concentrations considered, the improvement in precision offered by the guard electrode (if any) was small in comparison to calculated theoretical values based on Poisson counting statistics, suggesting noise contributions from other sources (such as the sample introduction system, plasma flicker etc). At lower Os concentrations (to 100 pg g(-1)) no appreciable loss of ratio accuracy was observed, although as expected based on counting statistics, poorer precisions of the order of 0.45-3% (1 sigma, n = 5) were noted. Re was found to have a detrimental effect on the precision of Os ratios involving 187Os, indicating that separation of Re and Os samples is a necessary pre-requisite for highly accurate and precise Os isotope ratio measurements.

Radial line-scans as representative sampling strategy in dried-droplet laser ablation of liquid samples deposited on pre-cut filter paper disks

NASA Astrophysics Data System (ADS)

Nischkauer, Winfried; Vanhaecke, Frank; Bernacchi, Sébastien; Herwig, Christoph; Limbeck, Andreas

2014-11-01

Nebulising liquid samples and using the aerosol thus obtained for further analysis is the standard method in many current analytical techniques, also with inductively coupled plasma (ICP)-based devices. With such a set-up, quantification via external calibration is usually straightforward for samples with aqueous or close-to-aqueous matrix composition. However, there is a variety of more complex samples. Such samples can be found in medical, biological, technological and industrial contexts and can range from body fluids, like blood or urine, to fuel additives or fermentation broths. Specialized nebulizer systems or careful digestion and dilution are required to tackle such demanding sample matrices. One alternative approach is to convert the liquid into a dried solid and to use laser ablation for sample introduction. Up to now, this approach required the application of internal standards or matrix-adjusted calibration due to matrix effects. In this contribution, we show a way to circumvent these matrix effects while using simple external calibration for quantification. The principle of representative sampling that we propose uses radial line-scans across the dried residue. This compensates for centro-symmetric inhomogeneities typically observed in dried spots. The effectiveness of the proposed sampling strategy is exemplified via the determination of phosphorus in biochemical fermentation media. However, the universal viability of the presented measurement protocol is postulated. Detection limits using laser ablation-ICP-optical emission spectrometry were in the order of 40 μg mL- 1 with a reproducibility of 10 % relative standard deviation (n = 4, concentration = 10 times the quantification limit). The reported sensitivity is fit-for-purpose in the biochemical context described here, but could be improved using ICP-mass spectrometry, if future analytical tasks would require it. Trueness of the proposed method was investigated by cross-validation with conventional liquid measurements, and by analyzing IAEA-153 reference material (Trace Elements in Milk Powder); a good agreement with the certified value for phosphorus was obtained.

Modelling variable dropout in randomised controlled trials with longitudinal outcomes: application to the MAGNETIC study.

PubMed

Kolamunnage-Dona, Ruwanthi; Powell, Colin; Williamson, Paula Ruth

2016-04-28

Clinical trials with longitudinally measured outcomes are often plagued by missing data due to patients withdrawing or dropping out from the trial before completing the measurement schedule. The reasons for dropout are sometimes clearly known and recorded during the trial, but in many instances these reasons are unknown or unclear. Often such reasons for dropout are non-ignorable. However, the standard methods for analysing longitudinal outcome data assume that missingness is non-informative and ignore the reasons for dropout, which could result in a biased comparison between the treatment groups. In this article, as a post hoc analysis, we explore the impact of informative dropout due to competing reasons on the evaluation of treatment effect in the MAGNETIC trial, the largest randomised placebo-controlled study to date comparing the addition of nebulised magnesium sulphate to standard treatment in acute severe asthma in children. We jointly model longitudinal outcome and informative dropout process to incorporate the information regarding the reasons for dropout by treatment group. The effect of nebulised magnesium sulphate compared with standard treatment is evaluated more accurately using a joint longitudinal-competing risk model by taking account of such complexities. The corresponding estimates indicate that the rate of dropout due to good prognosis is about twice as high in the magnesium group compared with standard treatment. We emphasise the importance of identifying reasons for dropout and undertaking an appropriate statistical analysis accounting for such dropout. The joint modelling approach accounting for competing reasons for dropout is proposed as a general approach for evaluating the sensitivity of conclusions to assumptions regarding missing data in clinical trials with longitudinal outcomes. EudraCT number 2007-006227-12 . Registration date 18 Mar 2008.

Nebulised 7% hypertonic saline improves lung function and quality of life in bronchiectasis.

PubMed

Kellett, Fiona; Robert, Niven M

2011-12-01

Sputum retention is a distressing feature of non-cystic fibrosis bronchiectasis and has been shown to contribute to the vicious cycle of infection seen in this disease. In a previous study we demonstrated that nebulised 7% hypertonic saline was both safe and effective in this patient population. Patients with a clinical diagnosis of non-cystic fibrosis bronchiectasis, confirmed by HRCT, were entered into a randomised single blind cross-over study to evaluate 0.9% sodium chloride (IS) and 7% hypertonic saline (HS). Following a 4 week run in patients received a random order active HS or IS daily for 3 months. A 4 week wash-out phase was included between phases. We report lung function, quality of life, and health care utilisation responses. 32 patients mean age 56.6 years (SD 14.6), 16 male, were recruited of which 28 were randomised and completed the study. Lung function (%change from baseline) improved in HS vs. IS (FEV(1): 15.1, 1.8 p<0.01; FVC: 11.2, 0.7 p<0.01. SGRQ improved significantly from baseline (HS 6.0, IS 1.2; p<0.05). There were reductions in annualised antibiotic usage (HS 2.4, IS 5.4 courses per patient per year), annualised emergency health care utilisation visits were reduced (HS 2.1, IS 4.9 events per patient per year). There were also improvements in sputum viscosity and ease of expectoration (visual analogue scale). Regular use of 7% hypertonic saline improves lung function, quality of life and health care utilisation in non-cystic fibrosis bronchiectasis patients. Copyright © 2011 Elsevier Ltd. All rights reserved.

Treatment of atelectasis: where is the evidence?

PubMed Central

Schindler, Margrid B

2005-01-01

Lobar atelectasis is a common problem caused by a variety of mechanisms including resorption atelectasis due to airway obstruction, passive atelectasis from hypoventilation, compressive atelectsis from abdominal distension and adhesive atelectasis due to increased surface tension. However, evidence-based studies on the management of lobar atelectasis are lacking. Examination of air-bronchograms on a chest radiograph may be helpful to determine whether proximal or distal airway obstruction is involved. Chest physiotherapy, nebulised DNase and possibly fibreoptic bronchoscopy might be helpful in patients with mucous plugging of the airways. In passive and adhesive atelectasis, positive end-expiratory pressure might be a useful adjunct to treatment. PMID:16137380

Ultra low-level measurements of actinides by sector field ICP-MS.

PubMed

Pointurier, F; Baglan, N; Hémet, P

2004-01-01

In the present work, a double-focusing sector field inductively coupled plasma-mass spectrometer was optimised for ultra trace and isotopic analyses of actinide long-lived isotopes in low concentration solutions of the fgml(-1) to the ngml(-1) range. Sensitivities of about 3GHz/(microgml(-1)), with as low a background as 0.1cps, were obtained for U using a conventional concentric pneumatic nebuliser. Detection limits are below the fg range for 239Pu and 240Pu. With natural U, a precision lower than 0.5% RSD is currently obtained for 235U/238U isotopic ratio at the 200pgml(-1) level.

Electroacoustics: A New Mechanism for Driving Individually Addressable Jetting and Other Microfluidic Manipulations in Multiwell Arrays

NASA Astrophysics Data System (ADS)

Yeo, Leslie; Rezk, Amgad

2017-11-01

The low take-up of microfluidic technology at the laboratory bench despite 25 years of advances can be attributed to the reluctance of practitioners to adopt new and sophisticated technology, which requires substantial retraining, as well as the large investments that have already been made in the vast array of existing laboratory equipment. A way to circumvent this is to design microfluidic technology to retrofit existing laboratory technology such as microscope stages, microplate readers, etc. This is however not without challenge as existing microfluidic devices themselves often require large ancillary equipment to drive fluidic actuation/detection, which are not always amenable to integration into these existing laboratory formats. We have developed a low-cost and scalable modular plug-and-play microplatform that facilitates individual addressability of each well in a microarray plate for sample dispensing, mixing and preconcentration, as well as its ejection via jetting/nebulisation for subsequent analysis. As this cannot be achieved using standard acoustofluidics, we have developed a new electroacoustic mechanism that allows the transmission of high frequency sound waves into each well while uniquely confining the electric field off the piezoelectric chip.

Improved efficiency of budesonide nebulization using surface-active agents.

PubMed

Bouwman, A M; Heijstra, M P; Schaefer, N C; Duiverman, E J; Lesouëf, P N; Devadason, S G

2006-01-01

Our aim was to improve the efficiency of nebulised budesonide using surface-active agents. Cationic, anionic, and nonionic detergents were added to commercial budesonide suspension, and the particle size distribution during nebulization was measured using both cascade impaction and laser diffraction. Our results showed that the emitted dose was increased after addition of cationic (p < 0.001) and nonionic detergents (p < 0.01) compared with the commercial formulation alone. The respirable fraction was increased for all detergent formulations (p < 0.001) compared with the commercial formulation. We concluded that cationic and nonionic detergent increased the total output of budesonide from the Sidestream. All detergent formulations increased the respirable fraction of nebulized budesonide.

The use of carboxymethylcellulose gel to increase non-viral gene transfer in mouse airways

PubMed Central

Griesenbach, Uta; Meng, Cuixiang; Farley, Raymond; Wasowicz, Marguerite; Munkonge, Felix M; Chan, Mario; Stoneham, Charlotte; Sumner-Jones, Stephanie; Pringle, Ian A.; Gill, Deborah R.; Hyde, Stephen C.; Stevenson, Barbara; Holder, Emma; Ban, Hiroshi; Hasegawa, Mamoru; Cheng, Seng H; Scheule, Ronald K; Sinn, Patrick L; McCray, Paul B; Alton, Eric WFW

2014-01-01

We have assessed whether viscoelastic gels known to inhibit mucociliary clearance can increase lipid-mediated gene transfer. Methylcellulose or carboxymethylcellulose (0.25 to 1.5%) were mixed with complexes of the cationic lipid GL67A and plasmids encoding luciferase and perfused onto the nasal epithelium of mice. Survival after perfusion with 1% CMC or1% MC was 90 and 100%, respectively. In contrast 1.5% CMC was uniformly lethal likely due to the viscous solution blocking the airways. Perfusion with 0.5% CMC containing lipid/DNA complexes reproducibly increased gene expression by approximately 3-fold (n= 16, p<0.05). Given this benefit, likely related to increased duration of contact, we also assessed the effect of prolonging contact time of the liposome/DNA complexes by delivering our standard 80 μg DNA dose over either approximately 22 or 60 min of perfusion. This independently increased gene transfer by 6-fold (n=8, p<0.05) and could be further enhanced by the addition of 0.5% CMC, leading to an overall 25-fold enhancement (n=8, p<0.001) in gene expression. As a result of these interventions CFTR transgene mRNA transgene levels were increased several logs above background. Interestingly, this did not lead to correction of the ion transport defects in the nasal epithelium of cystic fibrosis mice nor for immunohistochemical quantification of CFTR expression. To assess if 0.5% CMC also increased gene transfer in the mouse lung, we used whole body nebulisation chambers. CMC was nebulised for 1 hr immediately before, or simultaneously with GL67A/pCIKLux. The former did not increase gene transfer, whereas co-administration significantly increased gene transfer by 4-fold (p<0.0001, n=18). This study suggests that contact time of non-viral gene transfer agents is a key factor for gene delivery, and suggests two methods which may be translatable for use in man. PMID:20022367

Pharmacists' perspectives on monitoring adherence to treatment in Cystic Fibrosis.

PubMed

Mooney, Karen; Ryan, Cristín; Downey, Damian G

2016-04-01

Cystic Fibrosis (CF) management requires complex treatment regimens but adherence to treatment is poor and has negative health implications. There are various methods of measuring adherence, but little is known regarding the extent of adherence measurement in CF centres throughout the UK and Ireland. To determine the adherence monitoring practices in CF centres throughout the UK and Ireland, and to establish CF pharmacists' views on these practices. UK and Ireland Cystic Fibrosis Pharmacists' Group's annual meeting (2014). A questionnaire was designed, piloted and distributed to pharmacists attending the UK and Ireland Cystic Fibrosis Pharmacists' Group's annual meeting (2014). The main outcome measures were the methods of inhaled/nebulised antibiotic supply and the methods used to measure treatment adherence in CF centres. The questionnaire also ascertained the demographic information of participating pharmacists. Closed question responses were analysed using descriptive statistics. Open questions were analysed using content analysis. Twenty-one respondents (84 % response) were included in the analysis and were mostly from English centres (66.7 %). Detailed records of patients receiving their inhaled/nebulised antibiotics were lacking. Adherence was most commonly described to be measured at 'every clinic visit' (28.6 %) and 'occasionally' (28.6 %). Patient self-reported adherence was the most commonly used method of measuring adherence in practice (90.5 %). The availability of electronic adherence monitoring in CF centres did not guarantee its use. Pharmacists attributed an equal professional responsibility for adherence monitoring in CF to Consultants, Nurses and Pharmacists. Seventy-six percent of pharmacists felt that the current adherence monitoring practices within their own unit were inadequate and associated with the absence of sufficient specialist CF pharmacist involvement. Many suggested that greater specialist pharmacist involvement could facilitate improved adherence monitoring. Current adherence knowledge is largely based on self-report. Further work is required to establish the most appropriate method of adherence monitoring in CF centres, to improve the recording of adherence and to understand the impact of increased specialist pharmacist involvement on that adherence.

Effects of obesity on lung function and airway reactivity in healthy dogs.

PubMed

Manens, J; Bolognin, M; Bernaerts, F; Diez, M; Kirschvink, N; Clercx, C

2012-07-01

The present study investigated the effects of bodyweight (BW) gain on respiratory function and airway responsiveness in healthy Beagles using barometric whole body plethysmography (BWBP). Six adult dogs were examined before and after a fattening diet. The high-energy diet induced a mean increase in BW of 41±6%. BWBP basal parameters were recorded prior to airway reactivity testing (using increasing concentrations of histamine nebulisations). An airway responsiveness index (H-Penh300) was calculated as the histamine concentration necessary to reach 300% of basal enhanced pause (Penh, bronchoconstriction index). The same dogs underwent a doxapram hydrochloride (Dxp) stimulation testing 2 weeks later. Basal measurements showed that obese dogs had tidal volume per kg (TV/BW) that was significantly decreased whilst respiratory rate (RR) increased significantly. H-Penh300 decreased significantly in obese Beagles, indicating increased bronchoreactivity. Dxp administration induced a significant increase in TV/BW, minute volume per kg (MV/BW), peak inspiratory and expiratory flows per kg (PIF/BW and PEF/BW) in both normal and obese dogs although the TV/BW increase was significantly less marked in the obese group. In conclusion, obesity induced changes in basal respiratory parameters, increased bronchoreactivity and a blunted response to Dxp-induced respiratory stimulation. This combination of basal respiratory parameters, bronchoreactivity testing and pharmacological stimulation testing using non-invasive BWBP can help characterize pulmonary function and airway responsiveness in obese dogs. Copyright © 2011 Elsevier Ltd. All rights reserved.

PDGF-BB regulates the pulmonary vascular tone: impact of prostaglandins, calcium, MAPK- and PI3K/AKT/mTOR signalling and actin polymerisation in pulmonary veins of guinea pigs.

PubMed

Rieg, Annette D; Suleiman, Said; Anker, Carolin; Verjans, Eva; Rossaint, Rolf; Uhlig, Stefan; Martin, Christian

2018-06-19

Platelet-derived growth factor (PDGF)-BB and its receptor PDGFR are highly expressed in pulmonary hypertension (PH) and mediate proliferation. Recently, we showed that PDGF-BB contracts pulmonary veins (PVs) and that this contraction is prevented by inhibition of PDGFR-β (imatinib/SU6668). Here, we studied PDGF-BB-induced contraction and downstream-signalling in isolated perfused lungs (IPL) and precision-cut lung slices (PCLS) of guinea pigs (GPs). In IPLs, PDGF-BB was perfused after or without pre-treatment with imatinib (perfused/nebulised), the effects on the pulmonary arterial pressure (P PA ), the left atrial pressure (P LA ) and the capillary pressure (P cap ) were studied and the precapillary (R pre ) and postcapillary resistance (R post ) were calculated. Perfusate samples were analysed (ELISA) to detect the PDGF-BB-induced release of prostaglandin metabolites (TXA 2 /PGI 2 ). In PCLS, the contractile effect of PDGF-BB was evaluated in pulmonary arteries (PAs) and PVs. In PVs, PDGF-BB-induced contraction was studied after inhibition of PDGFR-α/β, L-Type Ca 2+ -channels, ROCK/PKC, prostaglandin receptors, MAP2K, p38-MAPK, PI3K-α/γ, AKT/PKB, actin polymerisation, adenyl cyclase and NO. Changes of the vascular tone were measured by videomicroscopy. In PVs, intracellular cAMP was measured by ELISA. In IPLs, PDGF-BB increased P PA , P cap and R post . In contrast, PDGF-BB had no effect if lungs were pre-treated with imatinib (perfused/nebulised). In PCLS, PDGF-BB significantly contracted PVs/PAs which was blocked by the PDGFR-β antagonist SU6668. In PVs, inhibition of actin polymerisation and inhibition of L-Type Ca 2+ -channels reduced PDGF-BB-induced contraction, whereas inhibition of ROCK/PKC had no effect. Blocking of EP 1/3 - and TP-receptors or inhibition of MAP2K-, p38-MAPK-, PI3K-α/γ- and AKT/PKB-signalling prevented PDGF-BB-induced contraction, whereas inhibition of EP 4 only slightly reduced it. Accordingly, PDGF-BB increased TXA 2 in the perfusate, whereas PGI 2 was increased in all groups after 120 min and inhibition of IP-receptors did not enhance PDGF-BB-induced contraction. Moreover, PDGF-BB increased cAMP in PVs and inhibition of adenyl cyclase enhanced PDGF-BB-induced contraction, whereas inhibition of NO-formation only slightly increased it. PDGF-BB/PDGFR regulates the pulmonary vascular tone by the generation of prostaglandins, the increase of calcium, the activation of MAPK- or PI3K/AKT/mTOR signalling and actin remodelling. More insights in PDGF-BB downstream-signalling may contribute to develop new therapeutics for PH.

Saline in acute bronchiolitis RCT and economic evaluation: hypertonic saline in acute bronchiolitis - randomised controlled trial and systematic review.

PubMed

Everard, Mark L; Hind, Daniel; Ugonna, Kelechi; Freeman, Jennifer; Bradburn, Mike; Dixon, Simon; Maguire, Chin; Cantrill, Hannah; Alexander, John; Lenney, Warren; McNamara, Paul; Elphick, Heather; Chetcuti, Philip Aj; Moya, Eduardo F; Powell, Colin; Garside, Jonathan P; Chadha, Lavleen Kumar; Kurian, Matthew; Lehal, Ravinderjit S; MacFarlane, Peter I; Cooper, Cindy L; Cross, Elizabeth

2015-08-01

Acute bronchiolitis is the most common cause of hospitalisation in infancy. Supportive care and oxygen are the cornerstones of management. A Cochrane review concluded that the use of nebulised 3% hypertonic saline (HS) may significantly reduce the duration of hospitalisation. To test the hypothesis that HS reduces the time to when infants were assessed as being fit for discharge, defined as in air with saturations of > 92% for 6 hours, by 25%. Parallel-group, pragmatic randomised controlled trial, cost-utility analysis and systematic review. Ten UK hospitals. Infants with acute bronchiolitis requiring oxygen therapy were allocated within 4 hours of admission. Supportive care with oxygen as required, minimal handling and fluid administration as appropriate to the severity of the disease, 3% nebulised HS every ± 6 hours. The trial primary outcome was time until the infant met objective discharge criteria. Secondary end points included time to discharge and adverse events. The costs analysed related to length of stay (LoS), readmissions, nebulised saline and other NHS resource use. Quality-adjusted life-years (QALYs) were estimated using an existing utility decrement derived for hospitalisation in children, together with the time spent in hospital in the trial. We searched MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials and other databases from inception or from 2010 onwards, searched ClinicalTrials.gov and other registries and hand-searched Chest, Paediatrics and Journal of Paediatrics to January 2015. We included randomised/quasi-randomised trials which compared HS versus saline (± adjunct treatment) or no treatment. We used a fixed-effects model to combine mean differences for LoS and assessed statistical heterogeneity using the I (2) statistic. The trial randomised 158 infants to HS (n = 141 analysed) and 159 to standard care (n = 149 analysed). There was no difference between the two arms in the time to being declared fit for discharge [median 76.6 vs. 75.9 hours, hazard ratio (HR) 0.95, 95% confidence interval (CI) 0.75 to 1.20] or to actual discharge (median 88.5 vs. 88.7 hours, HR 0.97, 95% CI 0.76 to 1.23). There was no difference in adverse events. One infant developed bradycardia with desaturation associated with HS. Mean hospital costs were £2595 and £2727 for the control and intervention groups, respectively (p = 0.657). Incremental QALYs were 0.0000175 (p = 0.757). An incremental cost-effectiveness ratio of £7.6M per QALY gained was not appreciably altered by sensitivity analyses. The systematic review comprised 15 trials (n = 1922) including our own. HS reduced the mean LoS by -0.36 days (95% CI -0.50 to -0.22 days). High levels of heterogeneity (I (2) = 78%) indicate that the result should be treated cautiously. In this trial, HS had no clinical benefit on LoS or readiness for discharge and was not a cost-effective treatment for acute bronchiolitis. Claims that HS achieves small reductions in LoS must be treated with scepticism. Well-powered randomised controlled trials of high-flow oxygen are needed. This study is registered as NCT01469845 and CRD42014007569. This project was funded by the NIHR Health Technology Assessment (HTA) programme and will be published in full in Health Technology Assessment; Vol. 19, No. 66. See the HTA programme website for further project information.

Direct determination of the estrogenic compounds 8-prenylnaringenin, zearalenone, alpha- and beta-zearalenol in beer by liquid chromatography-mass spectrometry.

PubMed

Maragou, Niki C; Rosenberg, Erwin; Thomaidis, Nikolaos S; Koupparis, Michael A

2008-08-15

A novel LC-ESI-MS method for the simultaneous determination of four of the most significant estrogenic compounds naturally occurring in beer, 8-prenylnaringenin (8-PN), zearalenone (ZON), alpha-zearalenol (alpha-ZOL) and beta-zearalenol (beta-ZOL) which requires minimal sample preparation was developed using a chemometric approach. Experimental design was applied to assess the effects of the LC-ESI-MS parameters (mobile phase flow rate, drying gas flow, nebuliser pressure and capillary potential) on the obtained signal and to optimize the values in order to provide maximum sensitivity and detectability. The proposed method is simple, consisting only of degassing the beer and diluting with water (1:1, v/v) before injection. Comparison between the two internal standards used, zearalanone (ZAN) and 4,2'-dihydroxychalcone (4,2'-DHC), showed that ZAN performs better as internal standard not only for the mycotoxins but for 8-PN as well, giving lower % RSDs. Under inter-day conditions mean recoveries were 107% for ZON, 87.8% for alpha-ZOL, 72.8% for beta-ZOL, and 77.5% for 8-PN. The corresponding % RSDs ranged between 5.0 and 8.0. The method limits of detection were 1.3, 1.4, 1.0 and 0.8 ng mL(-1) for ZON, alpha-ZOL, beta-ZOL and 8-PN, respectively. The method was applied to 15 beer samples obtained from local supermarkets and the concentration of the phytoestrogen 8-PN in beer ranged between <0.8 and 38.6 ng mL(-1), while neither ZON nor its metabolites, alpha-ZOL and beta-ZOL, were detected.

Effect of inhaled formyl-methionyl-leucyl-phenylalanine on airway function.

PubMed Central

Berend, N; Peters, M J; Armour, C L; Black, J L; Ward, H E

1988-01-01

Formyl-methionyl-leucyl-phenylalanine (FMLP), a synthetic, acylated tripeptide analogous to bacterial chemotactic factors, has been shown to cause bronchoconstriction in guinea pig, rabbit, and human airways in vitro. To determine whether FMLP causes bronchoconstriction in man in vivo, a preliminary study was undertaken in which five non-smokers (mean age 35 years, FEV1 94% (SEM 5%) predicted) and five smokers (mean age 34 years, FEV1 93% (6%) predicted) inhaled aerosols of FMLP. None of the subjects showed airway hyperresponsiveness to histamine (the provocative concentrations of histamine causing a fall of greater than or equal to 20% in FEV1 (PC20) were over 8 mg/ml). FMLP dissolved in 50% dimethylsulphoxide and 50% saline in concentrations of 0, 0.06, 0.12, 0.25, 0.5, 1.0, 2.0, and 4.0 mg/ml was administered to the subjects by means of a French-Rosenthal dosimeter, FEV1 being recorded after inhalation of each concentration. Dose dependent falls in FEV1 occurred in five non-smokers (geometric mean 1.76, 95% confidence limits 0.87-3.53 mg/ml) and three smokers (0.23, 0.07-0.78 mg/ml), with two smokers not responding by 20% to the highest concentration of FMLP. On a separate day the FMLP dose-response curves were repeated after nebulisation of 500 micrograms of ipratropium bromide. The PC20 FMLP in the responders more than doubled. In six additional normal subjects a histamine inhalation test was performed before and four and 24 hours after inhalation of FMLP. All subjects remained unresponsive to histamine. These results show that FMLP is a potent bronchoconstrictor in some non-asthmatic individuals in vivo and this may be important in bronchoconstriction related to infection in patients with chronic obstructive lung disease. PMID:2965425

Never trust a croup…

PubMed Central

Nickinson, Andrew; Minhas, Jatinder Singh; Bhalla, Minak; Anwuzia-Iwegbu, Charles; Chapman, John

2011-01-01

A 2-year-old girl presented to the James Paget University Hospitals Trust with croup-like symptoms and was later discharged with dexamethasone syrup. The patient re-presented 6 h later following maternal concern with signs of acute respiratory distress. After a period of clinical stability, she acutely decompensated without any prior signs of a life-threatening deterioration. She was managed using nebulised epinephrine and showed signs of clinical improvement. Although improvement persisted, the child showed signs of exhaustion following the preceding events and was later intubed with an endotracheal tube and transferred to the paediatric intensive care unit at Addenbrooke’s University Hospital, Cambridge. Endotracheal aspiration later grew parainfluenza virus, rhinovirus and Staphylococcus aureus and the patient was diagnosed with the exceptionally rare life threatening complications of croup, bacterial tracheitis. The patient was discharged from intensive care 7 days later and has since made a full recovery. PMID:22689599

[Acute asthma in children--anaphylaxis].

PubMed

Carlsen, K H

1993-05-30

Acute asthma is a manifestation of chronic inflammation of airways, and may be due to inadequate control. Assessment of acute asthma is based upon respiratory rate and pattern, thoracic respiratory recessions, auscultatory rales and rhonchi, skin colour (cyanosis/pallor) and heart rate. Acute asthma in children is best treated with inhaled nebulised drugs, especially beta 2-agonists and adrenaline. Acute severe asthma should be treated with systemic steroids (by injection or orally), and it is important that this treatment is not started too late. Symptomatic treatment with intravenous theophyllamine may also be relevant. Anaphylactic shock occurs most often after injection of drugs or after bites by a wasp or a bee. Food allergy may be the cause in some patients. Speed is necessary in the treatment of anaphylactic shock, and intramuscular injection of adrenaline is the treatment of choice. Systemic steroids or antihistaminics may be used to stabilize the state of the patient.

Inhaled β-agonist therapy and respiratory muscle fatigue as under-recognised causes of lactic acidosis.

PubMed

Lau, Emily; Mazer, Jeffrey; Carino, Gerardo

2013-10-14

A 49-year-old man with chronic obstructive pulmonary disease (COPD) presented with significant tachypnoea, fevers, productive cough and increased work of breathing for the previous 4 days. Laboratory data showed elevated lactate of 3.2 mEq/L. Continuous inhaled ipratropium and albuterol nebuliser treatments were administered. Lactate levels increased to 5.5 and 3.9 mEq/L, at 6 and 12 h, respectively. No infectious source was found and the lactic acidosis cleared as the patient improved. The lactic acidosis was determined to be secondary to respiratory muscle fatigue and inhaled β-agonist therapy, two under-recognised causes of lactic acidosis in patients presenting with respiratory distress. Lactic acidosis is commonly used as a clinical marker for sepsis and shock, but in the absence of tissue hypoperfusion and severe hypoxia, alternative aetiologies for elevated levels should be sought to avoid unnecessary and potentially harmful medical interventions.

Antitussive effect of carcainium chloride in patients with chronic cough and idiopathic interstitial pneumonias: A pilot study.

PubMed

Lavorini, Federico; Spina, Domenico; Walker, Michael J; Franciosi, Lui; Page, Clive P; Fontana, Giovanni A

2016-10-01

Cough is a common presenting symptom in patients with idiopathic interstitial pneumonia (IIP); it is often disabling, and lacks effective treatment. Studies in animals suggest that carcainium chloride, a quaternary derivative of the local anesthetic lidocaine, is able to inhibit experimentally induced cough by a mechanism of action distinct from that of lidocaine. To determine the effectiveness of aerosolised carcainium chloride (VRP700) in controlling cough in patients with IIP. Eight female patients (mean age 71 years) with IIP were investigated in a double blind, randomised, placebo controlled crossover, adaptive contingency study design (EudraCT Number 2010-021350-19). The study consisted of a screening visit to assess the eligibility of patients, and two separated (48-72 h) study days. On the two study days, patients were randomised to receive either nebulized VRP700 (1.0 mg/kg) on the first study visit followed by nebulised placebo (sodium chloride 0.9%) on the second visit, or placebo on the first visit followed by VRP700 on the second visit. The primary endpoint was cough frequency over a 4-h assessment period; secondary endpoints were subjective cough-related level of discomfort as assessed by a visual analogue scale (VAS) and the subjective response to treatment as assessed by a quality of life question. Safety (ECG, spirometry, urine and blood tests) and adverse events occurring during the trial were also investigated. In all patients both VRP700 and placebo decreased cough frequency; however, mean decreases in cough frequency after treatment with VRP700 were significantly (P < 0.001) higher than with placebo. Similarly, mean reductions in VAS score were significantly (P < 0.001) higher after treatment with VRP 700 compared with placebo. All but one patient indicated that they felt better after receiving VRP700. No adverse events were reported during the study, nor were any changes in ECG variables, spirometry, urine and blood tests noted. The results of this exploratory study indicate that nebulised VRP700 improved cough and quality of life in hospitalised IIP patients with no significant side effects. A larger trial is warranted to assess these promising results. Copyright © 2016 Elsevier Ltd. All rights reserved.

Drug delivery.

PubMed

Le Souëf, Peter N

2002-09-16

What we know: In preschool children, small-volume spacers perform better than large-volume spacers. Detergent is the best antistatic agent for spacers, increasing lung delivery two- to threefold, but it must not be rinsed off. A mouthpiece should be used in children aged 2-3 years or older, as lung delivery is two- to threefold higher for oral inhalation than nasal inhalation (ie, by mask). Inhaled drug doses do not generally need to be reduced in infants and young children owing to inefficiencies of delivery in younger patients. Nebulisers are "dinosaurs" and not needed for most children with asthma. What we need to know: What is the best inhalation technique for spacers? How long should children breathe, how many breaths should they take, and at what age should they breath-hold? How should children, parents and doctors be instructed to achieve optimal levels of electrostatic charge reduction for spacers? How much should inhaled steroid dose be reduced when a spacer is used optimally? What dosing instructions should be given for beta(2)-agonists delivered by spacer?

Implementation of European standards of care for cystic fibrosis--control and treatment of infection.

PubMed

Elborn, J S; Hodson, M; Bertram, C

2009-05-01

Several guidelines on infection control and treatment of infection exist for cystic fibrosis (CF) caregivers, although the extent of implementation is variable. Adherence to European Consensus Guidelines for CF was studied by sending surveys to named healthcare professionals in 487 European CF centres/units. Qualitative data analysis was performed. A total of 177/547 (32%) surveys were returned. Infection control policies were implemented by most (77%) respondents. Separation of patients with Burkholderia cepacia was more common in adults (95%) than children (9%), and was implemented by 53% of respondents for Pseudomonas aeruginosa. Nebulised colistin plus oral ciprofloxacin was the most common (43%) therapy for P. aeruginosa infection. First infections of P. aeruginosa were usually treated with inhaled tobramycin; 41% of repondents did not intervene until lung function deteriorated. Most exacerbations were treated for less than the recommended period. European Consensus Guidelines are widely adhered to. Areas for improvement include: initiating therapy for exacerbations early, separating infected patients and optimising duration of antibiotic therapy.

Non-invasive airway health assessment: synchrotron imaging reveals effects of rehydrating treatments on mucociliary transit in-vivo.

PubMed

Donnelley, Martin; Morgan, Kaye S; Siu, Karen K W; Farrow, Nigel R; Stahr, Charlene S; Boucher, Richard C; Fouras, Andreas; Parsons, David W

2014-01-14

To determine the efficacy of potential cystic fibrosis (CF) therapies we have developed a novel mucociliary transit (MCT) measurement that uses synchrotron phase contrast X-ray imaging (PCXI) to non-invasively measure the transit rate of individual micron-sized particles deposited into the airways of live mice. The aim of this study was to image changes in MCT produced by a rehydrating treatment based on hypertonic saline (HS), a current CF clinical treatment. Live mice received HS containing a long acting epithelial sodium channel blocker (P308); isotonic saline; or no treatment, using a nebuliser integrated within a small-animal ventilator circuit. Marker particle motion was tracked for 20 minutes using PCXI. There were statistically significant increases in MCT in the isotonic and HS-P308 groups. The ability to quantify in vivo changes in MCT may have utility in pre-clinical research studies designed to bring new genetic and pharmaceutical treatments for respiratory diseases into clinical trials.

Non-invasive airway health assessment: Synchrotron imaging reveals effects of rehydrating treatments on mucociliary transit in-vivo

NASA Astrophysics Data System (ADS)

Donnelley, Martin; Morgan, Kaye S.; Siu, Karen K. W.; Farrow, Nigel R.; Stahr, Charlene S.; Boucher, Richard C.; Fouras, Andreas; Parsons, David W.

2014-01-01

To determine the efficacy of potential cystic fibrosis (CF) therapies we have developed a novel mucociliary transit (MCT) measurement that uses synchrotron phase contrast X-ray imaging (PCXI) to non-invasively measure the transit rate of individual micron-sized particles deposited into the airways of live mice. The aim of this study was to image changes in MCT produced by a rehydrating treatment based on hypertonic saline (HS), a current CF clinical treatment. Live mice received HS containing a long acting epithelial sodium channel blocker (P308); isotonic saline; or no treatment, using a nebuliser integrated within a small-animal ventilator circuit. Marker particle motion was tracked for 20 minutes using PCXI. There were statistically significant increases in MCT in the isotonic and HS-P308 groups. The ability to quantify in vivo changes in MCT may have utility in pre-clinical research studies designed to bring new genetic and pharmaceutical treatments for respiratory diseases into clinical trials.

Acinetobacter community-acquired pneumonia in a healthy child.

PubMed

Moreira Silva, G; Morais, L; Marques, L; Senra, V

2012-01-01

Acinetobacter is involved in a variety of infectious diseases primarily associated with healthcare. Recently there has been increasing evidence of the important role these pathogens play in community acquired infections. We report on the case of a previously healthy child, aged 28 months, admitted for fever, cough and pain on the left side of the chest, which on radiographic examination corresponded to a lower lobe necrotizing pneumonia. After detailed diagnostic work-up, community acquired Acinetobacter lwoffii pneumonia was diagnosed. The child had frequently shared respiratory equipment with elderly relatives with chronic obstructive pulmonary disease. As there were no other apparent risk factors, it could be assumed that the sharing of the equipment was the source of infection. The authors wish to draw attention to this possibility, that a necrotising community-acquired pneumonia due to Acinetobacter lwoffii can occur in a previously healthy child and to the dangers of inappropriate use and poor sterilisation of nebulisers. This case is a warning of the dangers that these bacteria may pose in the future in a community setting. Copyright © 2011 Sociedade Portuguesa de Pneumologia. Published by Elsevier España. All rights reserved.

Power of tests of normality for detecting contaminated normal samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thode, H.C. Jr.; Smith, L.A.; Finch, S.J.

1981-01-01

Seventeen tests of normality or goodness of fit were evaluated for power at detecting a contaminated normal sample. This study used 1000 replications each of samples of size 12, 17, 25, 33, 50, and 100 from six different contaminated normal distributions. The kurtosis test was the most powerful over all sample sizes and contaminations. The Hogg and weighted Kolmogorov-Smirnov tests were second. The Kolmogorov-Smirnov, chi-squared, Anderson-Darling, and Cramer-von-Mises tests had very low power at detecting contaminated normal random variables. Tables of the power of the tests and the power curves of certain tests are given.

Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.

PubMed

Saunders, Christopher T; Wong, Wendy S W; Swamy, Sajani; Becq, Jennifer; Murray, Lisa J; Cheetham, R Keira

2012-07-15

Whole genome and exome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity. We describe Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples. The method uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. We demonstrate that the method has superior accuracy and sensitivity on impure samples compared with approaches based on either diploid genotype likelihoods or general allele-frequency tests. The Strelka workflow source code is available at ftp://strelka@ftp.illumina.com/. csaunders@illumina.com

Indentation stiffness does not discriminate between normal and degraded articular cartilage.

PubMed

Brown, Cameron P; Crawford, Ross W; Oloyede, Adekunle

2007-08-01

Relative indentation characteristics are commonly used for distinguishing between normal healthy and degraded cartilage. The application of this parameter in surgical decision making and an appreciation of articular cartilage biomechanics has prompted us to hypothesise that it is difficult to define a reference stiffness to characterise normal articular cartilage. This hypothesis is tested for validity by carrying out biomechanical indentation of articular cartilage samples that are characterised as visually normal and degraded relative to proteoglycan depletion and collagen disruption. Compressive loading was applied at known strain rates to visually normal, artificially degraded and naturally osteoarthritic articular cartilage and observing the trends of their stress-strain and stiffness characteristics. While our results demonstrated a 25% depreciation in the stiffness of individual samples after proteoglycan depletion, they also showed that when compared to the stiffness of normal samples only 17% lie outside the range of the stress-strain behaviour of normal samples. We conclude that the extent of the variability in the properties of normal samples, and the degree of overlap (81%) of the biomechanical properties of normal and degraded matrices demonstrate that indentation data cannot form an accurate basis for distinguishing normal from abnormal articular cartilage samples with consequences for the application of this mechanical process in the clinical environment.

Oral anti-pseudomonal antibiotics for cystic fibrosis.

PubMed

Remmington, Tracey; Jahnke, Nikki; Harkensee, Christian

2016-07-14

Pseudomonas aeruginosa is the most common bacterial pathogen causing lung infections in people with cystic fibrosis and appropriate antibiotic therapy is vital. Antibiotics for pulmonary exacerbations are usually given intravenously, and for long-term treatment, via a nebuliser. Oral anti-pseudomonal antibiotics with the same efficacy and safety as intravenous or nebulised antibiotics would benefit people with cystic fibrosis due to ease of treatment and avoidance of hospitalisation. This is an update of a previous review. To determine the benefit or harm of oral anti-pseudomonal antibiotic therapy for people with cystic fibrosis, colonised with Pseudomonas aeruginosa, in the:1. treatment of a pulmonary exacerbation; and2. long-term treatment of chronic infection. We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group Trials Register comprising references identified from comprehensive electronic database searches and handsearches of relevant journals and abstract books of conference proceedings.We contacted pharmaceutical companies and checked reference lists of identified trials.Date of last search: 08 July 2016. Randomised or quasi-randomised controlled trials comparing any dose of oral anti-pseudomonal antibiotics, to other combinations of inhaled, oral or intravenous antibiotics, or to placebo or usual treatment for pulmonary exacerbations and long-term treatment. Two authors independently selected the trials, extracted data and assessed quality. We contacted trial authors to obtain missing information. We included three trials examining pulmonary exacerbations (171 participants) and two trials examining long-term therapy (85 participants). We regarded the most important outcomes as quality of life and lung function. The analysis did not identify any statistically significant difference between oral anti-pseudomonal antibiotics and other treatments for these outcome measures for either pulmonary exacerbations or long-term treatment. One of the included trials reported significantly better lung function when treating a pulmonary exacerbation with ciprofloxacin when compared with intravenous treatment; however, our analysis did not confirm this finding. We found no evidence of difference between oral anti-pseudomonal antibiotics and other treatments regarding adverse events or development of antibiotic resistance, but trials were not adequately powered to detect this. None of the studies had a low risk of bias from blinding which may have an impact particularly on subjective outcomes such as quality of life. The risk of bias for other criteria could not be clearly stated across the studies. We found no conclusive evidence that an oral anti-pseudomonal antibiotic regimen is more or less effective than an alternative treatment for either pulmonary exacerbations or long-term treatment of chronic infection with P. aeruginosa. Until results of adequately-powered future trials are available, treatment needs to be selected on a pragmatic basis, based upon any available non-randomised evidence, the clinical circumstances of the individual, the known effectiveness of drugs against local strains and upon individual preference.

Repeated nebulisation of non-viral CFTR gene therapy in patients with cystic fibrosis: a randomised, double-blind, placebo-controlled, phase 2b trial

PubMed Central

Alton, Eric W F W; Armstrong, David K; Ashby, Deborah; Bayfield, Katie J; Bilton, Diana; Bloomfield, Emily V; Boyd, A Christopher; Brand, June; Buchan, Ruaridh; Calcedo, Roberto; Carvelli, Paula; Chan, Mario; Cheng, Seng H; Collie, D David S; Cunningham, Steve; Davidson, Heather E; Davies, Gwyneth; Davies, Jane C; Davies, Lee A; Dewar, Maria H; Doherty, Ann; Donovan, Jackie; Dwyer, Natalie S; Elgmati, Hala I; Featherstone, Rosanna F; Gavino, Jemyr; Gea-Sorli, Sabrina; Geddes, Duncan M; Gibson, James S R; Gill, Deborah R; Greening, Andrew P; Griesenbach, Uta; Hansell, David M; Harman, Katharine; Higgins, Tracy E; Hodges, Samantha L; Hyde, Stephen C; Hyndman, Laura; Innes, J Alastair; Jacob, Joseph; Jones, Nancy; Keogh, Brian F; Limberis, Maria P; Lloyd-Evans, Paul; Maclean, Alan W; Manvell, Michelle C; McCormick, Dominique; McGovern, Michael; McLachlan, Gerry; Meng, Cuixiang; Montero, M Angeles; Milligan, Hazel; Moyce, Laura J; Murray, Gordon D; Nicholson, Andrew G; Osadolor, Tina; Parra-Leiton, Javier; Porteous, David J; Pringle, Ian A; Punch, Emma K; Pytel, Kamila M; Quittner, Alexandra L; Rivellini, Gina; Saunders, Clare J; Scheule, Ronald K; Sheard, Sarah; Simmonds, Nicholas J; Smith, Keith; Smith, Stephen N; Soussi, Najwa; Soussi, Samia; Spearing, Emma J; Stevenson, Barbara J; Sumner-Jones, Stephanie G; Turkkila, Minna; Ureta, Rosa P; Waller, Michael D; Wasowicz, Marguerite Y; Wilson, James M; Wolstenholme-Hogg, Paul

2015-01-01

Summary Background Lung delivery of plasmid DNA encoding the CFTR gene complexed with a cationic liposome is a potential treatment option for patients with cystic fibrosis. We aimed to assess the efficacy of non-viral CFTR gene therapy in patients with cystic fibrosis. Methods We did this randomised, double-blind, placebo-controlled, phase 2b trial in two cystic fibrosis centres with patients recruited from 18 sites in the UK. Patients (aged ≥12 years) with a forced expiratory volume in 1 s (FEV1) of 50–90% predicted and any combination of CFTR mutations, were randomly assigned, via a computer-based randomisation system, to receive 5 mL of either nebulised pGM169/GL67A gene–liposome complex or 0·9% saline (placebo) every 28 days (plus or minus 5 days) for 1 year. Randomisation was stratified by % predicted FEV1 (<70 vs ≥70%), age (<18 vs ≥18 years), inclusion in the mechanistic substudy, and dosing site (London or Edinburgh). Participants and investigators were masked to treatment allocation. The primary endpoint was the relative change in % predicted FEV1. The primary analysis was per protocol. This trial is registered with ClinicalTrials.gov, number NCT01621867. Findings Between June 12, 2012, and June 24, 2013, we randomly assigned 140 patients to receive placebo (n=62) or pGM169/GL67A (n=78), of whom 116 (83%) patients comprised the per-protocol population. We noted a significant, albeit modest, treatment effect in the pGM169/GL67A group versus placebo at 12 months' follow-up (3·7%, 95% CI 0·1–7·3; p=0·046). This outcome was associated with a stabilisation of lung function in the pGM169/GL67A group compared with a decline in the placebo group. We recorded no significant difference in treatment-attributable adverse events between groups. Interpretation Monthly application of the pGM169/GL67A gene therapy formulation was associated with a significant, albeit modest, benefit in FEV1 compared with placebo at 1 year, indicating a stabilisation of lung function in the treatment group. Further improvements in efficacy and consistency of response to the current formulation are needed before gene therapy is suitable for clinical care; however, our findings should also encourage the rapid introduction of more potent gene transfer vectors into early phase trials. Funding Medical Research Council/National Institute for Health Research Efficacy and Mechanism Evaluation Programme. PMID:26149841

Repeated nebulisation of non-viral CFTR gene therapy in patients with cystic fibrosis: a randomised, double-blind, placebo-controlled, phase 2b trial.

PubMed

Alton, Eric W F W; Armstrong, David K; Ashby, Deborah; Bayfield, Katie J; Bilton, Diana; Bloomfield, Emily V; Boyd, A Christopher; Brand, June; Buchan, Ruaridh; Calcedo, Roberto; Carvelli, Paula; Chan, Mario; Cheng, Seng H; Collie, D David S; Cunningham, Steve; Davidson, Heather E; Davies, Gwyneth; Davies, Jane C; Davies, Lee A; Dewar, Maria H; Doherty, Ann; Donovan, Jackie; Dwyer, Natalie S; Elgmati, Hala I; Featherstone, Rosanna F; Gavino, Jemyr; Gea-Sorli, Sabrina; Geddes, Duncan M; Gibson, James S R; Gill, Deborah R; Greening, Andrew P; Griesenbach, Uta; Hansell, David M; Harman, Katharine; Higgins, Tracy E; Hodges, Samantha L; Hyde, Stephen C; Hyndman, Laura; Innes, J Alastair; Jacob, Joseph; Jones, Nancy; Keogh, Brian F; Limberis, Maria P; Lloyd-Evans, Paul; Maclean, Alan W; Manvell, Michelle C; McCormick, Dominique; McGovern, Michael; McLachlan, Gerry; Meng, Cuixiang; Montero, M Angeles; Milligan, Hazel; Moyce, Laura J; Murray, Gordon D; Nicholson, Andrew G; Osadolor, Tina; Parra-Leiton, Javier; Porteous, David J; Pringle, Ian A; Punch, Emma K; Pytel, Kamila M; Quittner, Alexandra L; Rivellini, Gina; Saunders, Clare J; Scheule, Ronald K; Sheard, Sarah; Simmonds, Nicholas J; Smith, Keith; Smith, Stephen N; Soussi, Najwa; Soussi, Samia; Spearing, Emma J; Stevenson, Barbara J; Sumner-Jones, Stephanie G; Turkkila, Minna; Ureta, Rosa P; Waller, Michael D; Wasowicz, Marguerite Y; Wilson, James M; Wolstenholme-Hogg, Paul

2015-09-01

Lung delivery of plasmid DNA encoding the CFTR gene complexed with a cationic liposome is a potential treatment option for patients with cystic fibrosis. We aimed to assess the efficacy of non-viral CFTR gene therapy in patients with cystic fibrosis. We did this randomised, double-blind, placebo-controlled, phase 2b trial in two cystic fibrosis centres with patients recruited from 18 sites in the UK. Patients (aged ≥12 years) with a forced expiratory volume in 1 s (FEV1) of 50-90% predicted and any combination of CFTR mutations, were randomly assigned, via a computer-based randomisation system, to receive 5 mL of either nebulised pGM169/GL67A gene-liposome complex or 0.9% saline (placebo) every 28 days (plus or minus 5 days) for 1 year. Randomisation was stratified by % predicted FEV1 (<70 vs ≥70%), age (<18 vs ≥18 years), inclusion in the mechanistic substudy, and dosing site (London or Edinburgh). Participants and investigators were masked to treatment allocation. The primary endpoint was the relative change in % predicted FEV1. The primary analysis was per protocol. This trial is registered with ClinicalTrials.gov, number NCT01621867. Between June 12, 2012, and June 24, 2013, we randomly assigned 140 patients to receive placebo (n=62) or pGM169/GL67A (n=78), of whom 116 (83%) patients comprised the per-protocol population. We noted a significant, albeit modest, treatment effect in the pGM169/GL67A group versus placebo at 12 months' follow-up (3.7%, 95% CI 0.1-7.3; p=0.046). This outcome was associated with a stabilisation of lung function in the pGM169/GL67A group compared with a decline in the placebo group. We recorded no significant difference in treatment-attributable adverse events between groups. Monthly application of the pGM169/GL67A gene therapy formulation was associated with a significant, albeit modest, benefit in FEV1 compared with placebo at 1 year, indicating a stabilisation of lung function in the treatment group. Further improvements in efficacy and consistency of response to the current formulation are needed before gene therapy is suitable for clinical care; however, our findings should also encourage the rapid introduction of more potent gene transfer vectors into early phase trials. Medical Research Council/National Institute for Health Research Efficacy and Mechanism Evaluation Programme. Copyright © 2015 Alton et al. Open Access article distributed under the terms of CC BY. Published by Elsevier Ltd.. All rights reserved.

Best-Matched Internal Standard Normalization in Liquid Chromatography-Mass Spectrometry Metabolomics Applied to Environmental Samples.

PubMed

Boysen, Angela K; Heal, Katherine R; Carlson, Laura T; Ingalls, Anitra E

2018-01-16

The goal of metabolomics is to measure the entire range of small organic molecules in biological samples. In liquid chromatography-mass spectrometry-based metabolomics, formidable analytical challenges remain in removing the nonbiological factors that affect chromatographic peak areas. These factors include sample matrix-induced ion suppression, chromatographic quality, and analytical drift. The combination of these factors is referred to as obscuring variation. Some metabolomics samples can exhibit intense obscuring variation due to matrix-induced ion suppression, rendering large amounts of data unreliable and difficult to interpret. Existing normalization techniques have limited applicability to these sample types. Here we present a data normalization method to minimize the effects of obscuring variation. We normalize peak areas using a batch-specific normalization process, which matches measured metabolites with isotope-labeled internal standards that behave similarly during the analysis. This method, called best-matched internal standard (B-MIS) normalization, can be applied to targeted or untargeted metabolomics data sets and yields relative concentrations. We evaluate and demonstrate the utility of B-MIS normalization using marine environmental samples and laboratory grown cultures of phytoplankton. In untargeted analyses, B-MIS normalization allowed for inclusion of mass features in downstream analyses that would have been considered unreliable without normalization due to obscuring variation. B-MIS normalization for targeted or untargeted metabolomics is freely available at https://github.com/IngallsLabUW/B-MIS-normalization .

Magnetic measurements on human erythrocytes: Normal, beta thalassemia major, and sickle

NASA Astrophysics Data System (ADS)

Sakhnini, Lama

2003-05-01

In this article magnetic measurements were made on human erythrocytes at different hemoglobin states (normal and reduced hemoglobin). Different blood samples: normal, beta thalassemia major, and sickle were studied. Beta thalassemia major and sickle samples were taken from patients receiving lifelong blood transfusion treatment. All samples examined exhibited diamagnetic behavior. Beta thalassemia major and sickle samples showed higher diamagnetic susceptibilities than that for the normal, which was attributed to the increase of membrane to hemoglobin volume ratio of the abnormal cells. Magnetic measurements showed that the erythrocytes in the reduced state showed less diamagnetic response in comparison with erythrocytes in the normal state. Analysis of the paramagnetic component of magnetization curves gave an effective magnetic moment of μeff=7.6 μB per reduced hemoglobin molecule. The same procedure was applied to sickle and beta thalassemia major samples and values for μeff were found to be comparable to that of the normal erythrocytes.

Sensitivity and specificity of normality tests and consequences on reference interval accuracy at small sample size: a computer-simulation study.

PubMed

Le Boedec, Kevin

2016-12-01

According to international guidelines, parametric methods must be chosen for RI construction when the sample size is small and the distribution is Gaussian. However, normality tests may not be accurate at small sample size. The purpose of the study was to evaluate normality test performance to properly identify samples extracted from a Gaussian population at small sample sizes, and assess the consequences on RI accuracy of applying parametric methods to samples that falsely identified the parent population as Gaussian. Samples of n = 60 and n = 30 values were randomly selected 100 times from simulated Gaussian, lognormal, and asymmetric populations of 10,000 values. The sensitivity and specificity of 4 normality tests were compared. Reference intervals were calculated using 6 different statistical methods from samples that falsely identified the parent population as Gaussian, and their accuracy was compared. Shapiro-Wilk and D'Agostino-Pearson tests were the best performing normality tests. However, their specificity was poor at sample size n = 30 (specificity for P < .05: .51 and .50, respectively). The best significance levels identified when n = 30 were 0.19 for Shapiro-Wilk test and 0.18 for D'Agostino-Pearson test. Using parametric methods on samples extracted from a lognormal population but falsely identified as Gaussian led to clinically relevant inaccuracies. At small sample size, normality tests may lead to erroneous use of parametric methods to build RI. Using nonparametric methods (or alternatively Box-Cox transformation) on all samples regardless of their distribution or adjusting, the significance level of normality tests depending on sample size would limit the risk of constructing inaccurate RI. © 2016 American Society for Veterinary Clinical Pathology.

Multidimensional Normalization to Minimize Plate Effects of Suspension Bead Array Data.

PubMed

Hong, Mun-Gwan; Lee, Woojoo; Nilsson, Peter; Pawitan, Yudi; Schwenk, Jochen M

2016-10-07

Enhanced by the growing number of biobanks, biomarker studies can now be performed with reasonable statistical power by using large sets of samples. Antibody-based proteomics by means of suspension bead arrays offers one attractive approach to analyze serum, plasma, or CSF samples for such studies in microtiter plates. To expand measurements beyond single batches, with either 96 or 384 samples per plate, suitable normalization methods are required to minimize the variation between plates. Here we propose two normalization approaches utilizing MA coordinates. The multidimensional MA (multi-MA) and MA-loess both consider all samples of a microtiter plate per suspension bead array assay and thus do not require any external reference samples. We demonstrate the performance of the two MA normalization methods with data obtained from the analysis of 384 samples including both serum and plasma. Samples were randomized across 96-well sample plates, processed, and analyzed in assay plates, respectively. Using principal component analysis (PCA), we could show that plate-wise clusters found in the first two components were eliminated by multi-MA normalization as compared with other normalization methods. Furthermore, we studied the correlation profiles between random pairs of antibodies and found that both MA normalization methods substantially reduced the inflated correlation introduced by plate effects. Normalization approaches using multi-MA and MA-loess minimized batch effects arising from the analysis of several assay plates with antibody suspension bead arrays. In a simulated biomarker study, multi-MA restored associations lost due to plate effects. Our normalization approaches, which are available as R package MDimNormn, could also be useful in studies using other types of high-throughput assay data.

Does 3-Day Course of Oral Amoxycillin Benefit Children of Non-Severe Pneumonia with Wheeze: A Multicentric Randomised Controlled Trial

PubMed Central

Awasthi, Shally; Agarwal, Girdhar; Kabra, Sushil K.; Singhi, Sunit; Kulkarni, Madhuri; More, Vaishali; Niswade, Abhimanyu; Pillai, Raj Mohan; Luke, Ravi; Srivastava, Neeraj M.; Suresh, Saradha; Verghese, Valsan P.; Raghupathy, P.; Lodha, R.; Walter, Stephen D.

2008-01-01

Background WHO-defined pneumonias, treated with antibiotics, are responsible for a significant proportion of childhood morbidity and mortality in the developing countries. Since substantial proportion pneumonias have a viral etiology, where children are more likely to present with wheeze, there is a concern that currently antibiotics are being over-prescribed for it. Hence the current trial was conducted with the objective to show the therapeutic equivalence of two treatments (placebo and amoxycillin) for children presenting with non-severe pneumonia with wheeze, who have persistent fast breathing after nebulisation with salbutamol, and have normal chest radiograph. Methodology This multi-centric, randomised placebo controlled double blind clinical trial intended to investigate equivalent efficacy of placebo and amoxicillin and was conducted in ambulatory care settings in eight government hospitals in India. Participants were children aged 2–59 months of age, who received either oral amoxycillin (31–54 mg/Kg/day, in three divided doses for three days) or placebo, and standard bronchodilator therapy. Primary outcome was clinical failure on or before day- 4. Principal Findings We randomized 836 cases in placebo and 835 in amoxycillin group. Clinical failures occurred in 201 (24.0%) on placebo and 166 (19.9%) on amoxycillin (risk difference 4.2% in favour of antibiotic, 95% CI: 0.2 to 8.1). Adherence for both placebo and amoxycillin was >96% and 98.9% subjects were followed up on day- 4. Clinical failure was associated with (i) placebo treatment (adjusted OR = 1.28, 95% CI: 1.01 to1.62), (ii) excess respiratory rate of >10 breaths per minute (adjusted OR = 1.51, 95% CI: 1.19, 1.92), (iii) vomiting at enrolment (adjusted OR = 1.49, 95% CI: 1.13, 1.96), (iv) history of use of broncho-dilators (adjusted OR = 1.71, 95% CI: 1.30, 2.24) and (v) non-adherence (adjusted OR = 8.06, 95% CI: 4.36, 14.92). Conclusions Treating children with non-severe pneumonia and wheeze with a placebo is not equivalent to treatment with oral amoxycillin. Trial Registration ClinicalTrials.gov NCT00407394 PMID:18431478

Ex vivo characterization of normal and adenocarcinoma colon samples by Mueller matrix polarimetry.

PubMed

Ahmad, Iftikhar; Ahmad, Manzoor; Khan, Karim; Ashraf, Sumara; Ahmad, Shakil; Ikram, Masroor

2015-05-01

Mueller matrix polarimetry along with polar decomposition algorithm was employed for the characterization of ex vivo normal and adenocarcinoma human colon tissues by polarized light in the visible spectral range (425-725 nm). Six derived polarization metrics [total diattenuation (DT ), retardance (RT ), depolarization(ΔT ), linear diattenuation (DL), retardance (δ), and depolarization (ΔL)] were compared for normal and adenocarcinoma colon tissue samples. The results show that all six polarimetric properties for adenocarcinoma samples were significantly higher as compared to the normal samples for all wavelengths. The Wilcoxon rank sum test illustrated that total retardance is a good candidate for the discrimination of normal and adenocarcinoma colon samples. Support vector machine classification for normal and adenocarcinoma based on the four polarization properties spectra (ΔT , ΔL, RT ,and δ) yielded 100% accuracy, sensitivity, and specificity, while both DTa nd DL showed 66.6%, 33.3%, and 83.3% accuracy, sensitivity, and specificity, respectively. The combination of polarization analysis and given classification methods provides a framework to distinguish the normal and cancerous tissues.

Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Callister, Stephen J.; Barry, Richard C.; Adkins, Joshua N.

2006-02-01

Central tendency, linear regression, locally weighted regression, and quantile techniques were investigated for normalization of peptide abundance measurements obtained from high-throughput liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR MS). Arbitrary abundances of peptides were obtained from three sample sets, including a standard protein sample, two Deinococcus radiodurans samples taken from different growth phases, and two mouse striatum samples from control and methamphetamine-stressed mice (strain C57BL/6). The selected normalization techniques were evaluated in both the absence and presence of biological variability by estimating extraneous variability prior to and following normalization. Prior to normalization, replicate runs from each sample setmore » were observed to be statistically different, while following normalization replicate runs were no longer statistically different. Although all techniques reduced systematic bias, assigned ranks among the techniques revealed significant trends. For most LC-FTICR MS analyses, linear regression normalization ranked either first or second among the four techniques, suggesting that this technique was more generally suitable for reducing systematic biases.« less

Actinobacillus actinomycetemcomitans in Human Periodontal Disease: a Cross-Sectional Microbiological Investigation

PubMed Central

Slots, Jørgen; Reynolds, Homer S.; Genco, Robert J.

1980-01-01

Actinobacillus actinomycetemcomitans is a facultative gram-negative bacterium which has been associated with severe oral and nonoral infections. This study examined its occurrence in the oral cavities of 10 normal juveniles, 11 normal adults, 10 juvenile periodontitis patients, and 12 adult periodontitis patients. Four deep periodontal pockets and two normal periodontal sites were sampled in the diseased patients, and six normal periodontal sites were sampled in the healthy individuals. In all subjects samples were obtained from the cheek, tongue, and saliva. Samples from a total of 172 normal periodontal sites, 83 deep periodontal pockets, 42 cheek mucosae, 42 tongue dorsa, and 42 salivas were examined. Isolation was performed by using a medium for selective isolation of A. actinomycetemcomitans (Trypticase soy agar [BBL Microbiology Systems] supplemented with 10% serum and 75 μg of bacitracin per ml). The carrier rates were 20% for normal juveniles, 36% for normal adults, 50% for adult periodontitis patients, and 90% for juvenile periodontitis patients. A. actinomycetemcomitans was on average recovered in about fivefold-higher numbers from infected deep periodontal pockets than from infected normal subgingival areas. Samples of periodontal pockets generally contained 100-fold-more cells of A. actinomycetemcomitans than did samples of the cheek, tongue, and saliva. A. actinomycetemcomitans is commonly isolated from patients with juvenile periodontitis, often isolated from patients with adult periodontitis, and occasionally isolated from normal juveniles and adults. Its primary oral ecological niche appears to be dental plaque and periodontal pockets. PMID:6968718

Inheritance of Properties of Normal and Non-Normal Distributions after Transformation of Scores to Ranks

ERIC Educational Resources Information Center

Zimmerman, Donald W.

2011-01-01

This study investigated how population parameters representing heterogeneity of variance, skewness, kurtosis, bimodality, and outlier-proneness, drawn from normal and eleven non-normal distributions, also characterized the ranks corresponding to independent samples of scores. When the parameters of population distributions from which samples were…

Assessment of N-acetylcysteine as a therapy for phosgene-induced acute lung injury.

PubMed

Rendell, Rachel; Fairhall, Sarah; Graham, Stuart; Rutter, Steve; Auton, Philippa; Smith, Adam; Perrott, Rosi; Jugg, Bronwen

2018-06-15

The toxic industrial chemical (TIC 1 ) phosgene remains an important chemical intermediate in many industrial processes. Inhalation of phosgene can cause an acute lung injury (ALI) which, in severe cases may result in death. There are currently no effective pharmacological therapies or evidence-based treatment guidelines for managing exposed individuals. N-acetylcysteine (NAC) is a commercially available drug licensed in the UK and elsewhere for the treatment of paracetamol (acetaminophen) overdose. It has a number of mechanisms of action which may provide therapeutic benefit for the treatment of phosgene-induced ALI. It has previously been shown to provide therapeutic efficacy against the lung damaging effects of sulfur mustard vapour exposure, when given by the inhaled route, in the pig (Jugg et al., 2013). Our research objective was to determine whether inhaled NAC might also be therapeutic for other chemicals, in this case, phosgene. This study has demonstrated that multiple nebulised doses, administered from 30 min after exposure of terminally anaesthetised pigs to phosgene, is not an effective therapy when administered at the times and doses employed in this study. There remains no pharmacological treatment for phosgene-induced lung injury. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

The use of iloprost in early pregnancy in patients with pulmonary arterial hypertension.

PubMed

Elliot, C A; Stewart, P; Webster, V J; Mills, G H; Hutchinson, S P; Howarth, E S; Bu'lock, F A; Lawson, R A; Armstrong, I J; Kiely, D G

2005-07-01

In patients with pulmonary hypertension, pregnancy is associated with a high risk of maternal death. Such patients are counselled to avoid pregnancy, or if it occurs, are offered early interruption. Some patients, however, decide to continue with their pregnancy and others may present with symptoms for the first time whilst pregnant. Pulmonary vasodilator therapy provides a treatment option for these high-risk patients. The present study describes three patients with pulmonary arterial hypertension of various aetiologies who were treated with the prostacyclin analogue iloprost during pregnancy, and the post-partum period. Nebulised iloprost commenced as early as 8 weeks of gestation and patients were admitted to hospital between 24-36 weeks of gestation. All pregnancies were completed with a duration of between 25-36 weeks and all deliveries were by caesarean section under local anaesthetic. All patients delivered children free from congenital abnormalities, and there was no post-partum maternal or infant mortality. In conclusion, although pregnancy is strongly advised against in those with pulmonary hypertension, the current authors have achieved a successful outcome for mother and foetus with a multidisciplinary approach and targeted pulmonary vascular therapy.

Downregulation of external death receptor genes FAS and DR5 in colorectal cancer samples positive for human papillomavirus infection.

PubMed

Karbasi, Ashraf; Borhani, Nasim; Daliri, Karim; Kazemi, Bahram; Manoochehri, Mehdi

2015-06-01

Human papillomaviruses (HPV) have frequently been detected in colorectal cancer tumor samples, and may play a role in the pathogenesis of colorectal cancer. This study was designed to investigate the presence of DNA and RNA for the high-risk HPV genotypes 16 and 18 in samples of colorectal cancer tumors and adjacent normal tissues. We also investigated the expression of proapoptotic genes in HPV-positive colorectal tumors compared to normal tissue samples. Samples of tumoral and adjacent normal tissues were fresh-frozen, and HPV DNA was identified by nested and semiquantitative PCR. Real time PCR was used to quantitatively compare the expression of HPV-18 E6 and nine proapoptotic genes in HPV-positive tumors and samples of adjacent normal tissue. HPV-16 DNA was found in 10.5% of the tumor samples, and HPV-18 DNA was found in 23.6% of the samples. Real time PCR results showed lower expression of the E6 gene in HPV-positive tumors than in adjacent normal tissue. The expression of two proapoptotic genes, FAS and DR5, was significantly lower in tumor samples than in adjacent normal tissues. HPV infection, especially HPV-18, may play a role in colorectal cancer tumorigenesis by downregulating death receptor genes and interfering with the extrinsic pathway of apoptosis. Copyright © 2015 Elsevier GmbH. All rights reserved.

Sample normalization methods in quantitative metabolomics.

PubMed

Wu, Yiman; Li, Liang

2016-01-22

To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts. Copyright © 2015 Elsevier B.V. All rights reserved.

Morphological Differences Between Seyfert Hosts and Normal Galaxies

NASA Astrophysics Data System (ADS)

Shlosman, Isaac

Using new sub-arcsecond resolution imaging we compare large-scale stellar bar fraction in CfA sample of Seyferts and a closely matched control sample of normal galaxies. We find a difference between the samples on the 2.5σ level. We further compare the axial ratios of bars in all available samples quoted in the literature and find a deficiency of small axial ratio bars in Seyferts compared to normal galaxies.

Metabolomic analysis of urine samples by UHPLC-QTOF-MS: Impact of normalization strategies.

PubMed

Gagnebin, Yoric; Tonoli, David; Lescuyer, Pierre; Ponte, Belen; de Seigneux, Sophie; Martin, Pierre-Yves; Schappler, Julie; Boccard, Julien; Rudaz, Serge

2017-02-22

Among the various biological matrices used in metabolomics, urine is a biofluid of major interest because of its non-invasive collection and its availability in large quantities. However, significant sources of variability in urine metabolomics based on UHPLC-MS are related to the analytical drift and variation of the sample concentration, thus requiring normalization. A sequential normalization strategy was developed to remove these detrimental effects, including: (i) pre-acquisition sample normalization by individual dilution factors to narrow the concentration range and to standardize the analytical conditions, (ii) post-acquisition data normalization by quality control-based robust LOESS signal correction (QC-RLSC) to correct for potential analytical drift, and (iii) post-acquisition data normalization by MS total useful signal (MSTUS) or probabilistic quotient normalization (PQN) to prevent the impact of concentration variability. This generic strategy was performed with urine samples from healthy individuals and was further implemented in the context of a clinical study to detect alterations in urine metabolomic profiles due to kidney failure. In the case of kidney failure, the relation between creatinine/osmolality and the sample concentration is modified, and relying only on these measurements for normalization could be highly detrimental. The sequential normalization strategy was demonstrated to significantly improve patient stratification by decreasing the unwanted variability and thus enhancing data quality. Copyright © 2016 Elsevier B.V. All rights reserved.

The impact of sample non-normality on ANOVA and alternative methods.

PubMed

Lantz, Björn

2013-05-01

In this journal, Zimmerman (2004, 2011) has discussed preliminary tests that researchers often use to choose an appropriate method for comparing locations when the assumption of normality is doubtful. The conceptual problem with this approach is that such a two-stage process makes both the power and the significance of the entire procedure uncertain, as type I and type II errors are possible at both stages. A type I error at the first stage, for example, will obviously increase the probability of a type II error at the second stage. Based on the idea of Schmider et al. (2010), which proposes that simulated sets of sample data be ranked with respect to their degree of normality, this paper investigates the relationship between population non-normality and sample non-normality with respect to the performance of the ANOVA, Brown-Forsythe test, Welch test, and Kruskal-Wallis test when used with different distributions, sample sizes, and effect sizes. The overall conclusion is that the Kruskal-Wallis test is considerably less sensitive to the degree of sample normality when populations are distinctly non-normal and should therefore be the primary tool used to compare locations when it is known that populations are not at least approximately normal. © 2012 The British Psychological Society.

High-Throughput Microfludic Applications

PubMed Central

Doneanu, A.; Murphy, J.; Johnson, J.; Cohen, S.; Astarita, G.; Chakraborty, A.; Martin, LeRoy

2013-01-01

A novel platform was developed for the expansion of microfludic LC-MS beyond typical nanoscale applications into areas traditionally performed at analytical scales. The material used to fabricate the device allows for pressures of 12,000 psi. The integrated metal electrospray emitter supports flow rates from 100s of nl/min up to 8 μl/min and allows for the use of 150 μm in ID separation channels. Peak widths are on par with commercial ultra-high pressure LC instrumentation and cycle times as low as 10 min. System versatility will be demonstrated by several examples including intact proteins analysis, lipidomics and biopharmaceutical applications. All experiments were performed using a nanoflow system coupled with an oaTOF mass spectrometer fitted with an electrospray ionization source designed to accommodate the microfluidic device. The emitter is connected to a packed channel by zero dead-volume connections and incorporates the use of nebulising gas. The separation channel was 150 μm × 5 cm and packed with sub-2-μm reverse-phased particles of various chemistries. For intact protein analysis, using Ribonuclease A, Cyctochrome C, Holotransferrin and Apomyoglobin, good resolution was achieved using shorter alkyl chain resins. Additionally, light and heavy chains of reduced monoclonal antibodies could be separated. Separations were performed at 80°C, using a 3 μL/min linear gradient from 20% to 55% ACN over 5 min. Applicability for biopharmaceutical use is shown with minute amounts of Trastuzumab, demonstrating peak widths less than 6 s with 90% sequence coverage. Methionine oxidation and sites of glycosylation were also detected. The method was also employed for lipid analysis showing improved separation for the major classes, particularly inter and intra forms. The microfluidic system offered high retention time reproducibility with RSD values smaller than 0.2%. This is especially useful for lipidomic analysis, which requires the comparison of a large number of LC-MS chromatograms from multiple sample sets.

Simulation techniques for estimating error in the classification of normal patterns

NASA Technical Reports Server (NTRS)

Whitsitt, S. J.; Landgrebe, D. A.

1974-01-01

Methods of efficiently generating and classifying samples with specified multivariate normal distributions were discussed. Conservative confidence tables for sample sizes are given for selective sampling. Simulation results are compared with classified training data. Techniques for comparing error and separability measure for two normal patterns are investigated and used to display the relationship between the error and the Chernoff bound.

Systematic bias in genomic classification due to contaminating non-neoplastic tissue in breast tumor samples.

PubMed

Elloumi, Fathi; Hu, Zhiyuan; Li, Yan; Parker, Joel S; Gulley, Margaret L; Amos, Keith D; Troester, Melissa A

2011-06-30

Genomic tests are available to predict breast cancer recurrence and to guide clinical decision making. These predictors provide recurrence risk scores along with a measure of uncertainty, usually a confidence interval. The confidence interval conveys random error and not systematic bias. Standard tumor sampling methods make this problematic, as it is common to have a substantial proportion (typically 30-50%) of a tumor sample comprised of histologically benign tissue. This "normal" tissue could represent a source of non-random error or systematic bias in genomic classification. To assess the performance characteristics of genomic classification to systematic error from normal contamination, we collected 55 tumor samples and paired tumor-adjacent normal tissue. Using genomic signatures from the tumor and paired normal, we evaluated how increasing normal contamination altered recurrence risk scores for various genomic predictors. Simulations of normal tissue contamination caused misclassification of tumors in all predictors evaluated, but different breast cancer predictors showed different types of vulnerability to normal tissue bias. While two predictors had unpredictable direction of bias (either higher or lower risk of relapse resulted from normal contamination), one signature showed predictable direction of normal tissue effects. Due to this predictable direction of effect, this signature (the PAM50) was adjusted for normal tissue contamination and these corrections improved sensitivity and negative predictive value. For all three assays quality control standards and/or appropriate bias adjustment strategies can be used to improve assay reliability. Normal tissue sampled concurrently with tumor is an important source of bias in breast genomic predictors. All genomic predictors show some sensitivity to normal tissue contamination and ideal strategies for mitigating this bias vary depending upon the particular genes and computational methods used in the predictor.

Using partially labeled data for normal mixture identification with application to class definition

NASA Technical Reports Server (NTRS)

Shahshahani, Behzad M.; Landgrebe, David A.

1992-01-01

The problem of estimating the parameters of a normal mixture density when, in addition to the unlabeled samples, sets of partially labeled samples are available is addressed. The density of the multidimensional feature space is modeled with a normal mixture. It is assumed that the set of components of the mixture can be partitioned into several classes and that training samples are available from each class. Since for any training sample the class of origin is known but the exact component of origin within the corresponding class is unknown, the training samples as considered to be partially labeled. The EM iterative equations are derived for estimating the parameters of the normal mixture in the presence of partially labeled samples. These equations can be used to combine the supervised and nonsupervised learning processes.

A closer look at the effect of preliminary goodness-of-fit testing for normality for the one-sample t-test.

PubMed

Rochon, Justine; Kieser, Meinhard

2011-11-01

Student's one-sample t-test is a commonly used method when inference about the population mean is made. As advocated in textbooks and articles, the assumption of normality is often checked by a preliminary goodness-of-fit (GOF) test. In a paper recently published by Schucany and Ng it was shown that, for the uniform distribution, screening of samples by a pretest for normality leads to a more conservative conditional Type I error rate than application of the one-sample t-test without preliminary GOF test. In contrast, for the exponential distribution, the conditional level is even more elevated than the Type I error rate of the t-test without pretest. We examine the reasons behind these characteristics. In a simulation study, samples drawn from the exponential, lognormal, uniform, Student's t-distribution with 2 degrees of freedom (t(2) ) and the standard normal distribution that had passed normality screening, as well as the ingredients of the test statistics calculated from these samples, are investigated. For non-normal distributions, we found that preliminary testing for normality may change the distribution of means and standard deviations of the selected samples as well as the correlation between them (if the underlying distribution is non-symmetric), thus leading to altered distributions of the resulting test statistics. It is shown that for skewed distributions the excess in Type I error rate may be even more pronounced when testing one-sided hypotheses. ©2010 The British Psychological Society.

An explorative investigation of functional differences in plantar center of pressure of four foot types using sample entropy method.

PubMed

Mei, Zhanyong; Ivanov, Kamen; Zhao, Guoru; Li, Huihui; Wang, Lei

2017-04-01

In the study of biomechanics of different foot types, temporal or spatial parameters derived from plantar pressure are often used. However, there is no comparative study of complexity and regularity of the center of pressure (CoP) during the stance phase among pes valgus, pes cavus, hallux valgus and normal foot. We aim to analyze whether CoP sample entropy characteristics differ among these four foot types. In our experiment participated 40 subjects with normal feet, 40 with pes cavus, 19 with pes valgus and 36 with hallux valgus. A Footscan ® system was used to collect CoP data. We used sample entropy to quantify several parameters of the investigated four foot types. These are the displacement in medial-lateral (M/L) and anterior-posterior (A/P) directions, as well as the vertical ground reaction force of CoP during the stance phase. To fully examine the potential of the sample entropy method for quantification of CoP components, we provide results for two cases: calculating the sample entropy of normalized CoP components, as well as calculating it using the raw data of CoP components. We also explored what are the optimal values of parameters m (the matching length) and r (the tolerance range) when calculating the sample entropy of CoP data obtained during the stance phases. According to statistical results, some factors significantly influenced the sample entropy of CoP components. The sample entropies of non-normalized A/P values for the left foot, as well as for the right foot, were different between the normal foot and pes valgus, and between the normal foot and hallux valgus. The sample entropy of normalized M/L displacement of the right foot was different between the normal foot and pes cavus. The measured variable for A/P and M/L displacements could serve for the study of foot function.

DNA methylation profiling identifies global methylation differences and markers of adrenocortical tumors.

PubMed

Rechache, Nesrin S; Wang, Yonghong; Stevenson, Holly S; Killian, J Keith; Edelman, Daniel C; Merino, Maria; Zhang, Lisa; Nilubol, Naris; Stratakis, Constantine A; Meltzer, Paul S; Kebebew, Electron

2012-06-01

It is not known whether there are any DNA methylation alterations in adrenocortical tumors. The objective of the study was to determine the methylation profile of normal adrenal cortex and benign and malignant adrenocortical tumors. Genome-wide methylation status of CpG regions were determined in normal (n = 19), benign (n = 48), primary malignant (n = 8), and metastatic malignant (n = 12) adrenocortical tissue samples. An integrated analysis of genome-wide methylation and mRNA expression in benign vs. malignant adrenocortical tissue samples was also performed. Methylation profiling revealed the following: 1) that methylation patterns were distinctly different and could distinguish normal, benign, primary malignant, and metastatic tissue samples; 2) that malignant samples have global hypomethylation; and 3) that the methylation of CpG regions are different in benign adrenocortical tumors by functional status. Normal compared with benign samples had the least amount of methylation differences, whereas normal compared with primary and metastatic adrenocortical carcinoma samples had the greatest variability in methylation (adjusted P ≤ 0.01). Of 215 down-regulated genes (≥2-fold, adjusted P ≤ 0.05) in malignant primary adrenocortical tumor samples, 52 of these genes were also hypermethylated. Malignant adrenocortical tumors are globally hypomethylated as compared with normal and benign tumors. Methylation profile differences may accurately distinguish between primary benign and malignant adrenocortical tumors. Several differentially methylated sites are associated with genes known to be dysregulated in malignant adrenocortical tumors.

Laser-induced differential normalized fluorescence method for cancer diagnosis

DOEpatents

Vo-Dinh, Tuan; Panjehpour, Masoud; Overholt, Bergein F.

1996-01-01

An apparatus and method for cancer diagnosis are disclosed. The diagnostic method includes the steps of irradiating a tissue sample with monochromatic excitation light, producing a laser-induced fluorescence spectrum from emission radiation generated by interaction of the excitation light with the tissue sample, and dividing the intensity at each wavelength of the laser-induced fluorescence spectrum by the integrated area under the laser-induced fluorescence spectrum to produce a normalized spectrum. A mathematical difference between the normalized spectrum and an average value of a reference set of normalized spectra which correspond to normal tissues is calculated, which provides for amplifying small changes in weak signals from malignant tissues for improved analysis. The calculated differential normalized spectrum is correlated to a specific condition of a tissue sample.

Laser-induced differential normalized fluorescence method for cancer diagnosis

DOEpatents

Vo-Dinh, T.; Panjehpour, M.; Overholt, B.F.

1996-12-03

An apparatus and method for cancer diagnosis are disclosed. The diagnostic method includes the steps of irradiating a tissue sample with monochromatic excitation light, producing a laser-induced fluorescence spectrum from emission radiation generated by interaction of the excitation light with the tissue sample, and dividing the intensity at each wavelength of the laser-induced fluorescence spectrum by the integrated area under the laser-induced fluorescence spectrum to produce a normalized spectrum. A mathematical difference between the normalized spectrum and an average value of a reference set of normalized spectra which correspond to normal tissues is calculated, which provides for amplifying small changes in weak signals from malignant tissues for improved analysis. The calculated differential normalized spectrum is correlated to a specific condition of a tissue sample. 5 figs.

Predicting Sensitivity of Breast Tumors to Src-targeted Therapies Through Assessment of Cas/Src/BCAR3 Activity

DTIC Science & Technology

2017-10-01

expression is elevated in DCIS samples compared to normal mammary tissue, invasive ductal carcinoma (IDC) compared to normal mammary tissue, and DCIS... compared to IDC. (2) BCAR3 is significantly upregulated in triple negative breast cancer and normal tissue; (3) BCAR3 expression shows a modest...expression was seen to be elevated in DCIS samples compared to normal mammary tissue, invasive ductal carcinoma (IDC) compared to normal mammary tissue, and

Organised surfactant assemblies in analytical atomic spectrometry

NASA Astrophysics Data System (ADS)

Sanz-Medel, Alfredo; Fernandez de la Campa, Maria del Rosario; Gonzalez, Elisa Blanco; Fernandez-Sanchez, Maria Luisa

1999-02-01

The use of surfactant-based organised assemblies in analytical atomic spectroscopy is extensively and critically reviewed along three main lines: first, the ability of organised media to enhance detection of atomic spectroscopic methods by favourable manipulation of physical and chemical properties of the sample solution second, the extension of separation mechanisms by resorting to organised media and third a discussion of synergistic combinations of liquid chromatography separations and atomic detectors via the use of vesicular mobile phases. Changes in physical properties of sample solutions aspirated in atomic spectrometry by addition of surfactants can be advantageously used in at least four different ways: (i) to improve nebulisation efficiency; (ii) to enhance wettability of solid surfaces used for atomisation; (iii) to improve compatibility between aqueous and organic phases; and (iv) to achieve good dispersion of small particles in "slurry" techniques. Controversial results and statements published so far are critically discussed. The ability of surfactant-based organised assemblies, such as micelles and vesicles, to organise reactants at the molecular level has also been applied to enhance the characteristics of chemical generation of volalite species of metals and semi-metals (e.g., hydride or ethylide generation of As, Pb, Cd, Se, Sn, and cold vapour Hg generation) used in atomic methods. Enhancements in efficiency/transport of volatile species, increases in the reaction kinetics, stabilisation of some unstable species and changes in the selectivity of the reactions by surfactants are dealt with. Non-chromatographic cloud-point separations to design pre-concentration procedures with subsequent metal determination by atomic methods are addressed along with chromatographic separations of expanded scope by addition of surfactants to the conventional aqueous mobile phases of reversed-phase high-performance liquid chromatography. Finally, the synergistic effect of using vesicles to improve both the separation capabilities of reversed-phase HPLC and the detectability of atomic detectors by on-line vesicular hydride generation is described. In particular, the possible separation mechanisms responsible for micellar and vesicular mobile phases in reversed-phase chromatographies are analysed and compared. The possible effect of modification of stationary phases by monomers of the surfactants should also be taken into account. The application of such on-line couplings to develop new hybrid approaches to tackle modern problems of trace element speciation for As, Hg, Se, and Cd completes this revision of the present interface between analytical atomic spectroscopy and surfactant-based organised assemblies.

Sample size determination for logistic regression on a logit-normal distribution.

PubMed

Kim, Seongho; Heath, Elisabeth; Heilbrun, Lance

2017-06-01

Although the sample size for simple logistic regression can be readily determined using currently available methods, the sample size calculation for multiple logistic regression requires some additional information, such as the coefficient of determination ([Formula: see text]) of a covariate of interest with other covariates, which is often unavailable in practice. The response variable of logistic regression follows a logit-normal distribution which can be generated from a logistic transformation of a normal distribution. Using this property of logistic regression, we propose new methods of determining the sample size for simple and multiple logistic regressions using a normal transformation of outcome measures. Simulation studies and a motivating example show several advantages of the proposed methods over the existing methods: (i) no need for [Formula: see text] for multiple logistic regression, (ii) available interim or group-sequential designs, and (iii) much smaller required sample size.

The classification of secondary colorectal liver cancer in human biopsy samples using angular dispersive x-ray diffraction and multivariate analysis

NASA Astrophysics Data System (ADS)

Theodorakou, Chrysoula; Farquharson, Michael J.

2009-08-01

The motivation behind this study is to assess whether angular dispersive x-ray diffraction (ADXRD) data, processed using multivariate analysis techniques, can be used for classifying secondary colorectal liver cancer tissue and normal surrounding liver tissue in human liver biopsy samples. The ADXRD profiles from a total of 60 samples of normal liver tissue and colorectal liver metastases were measured using a synchrotron radiation source. The data were analysed for 56 samples using nonlinear peak-fitting software. Four peaks were fitted to all of the ADXRD profiles, and the amplitude, area, amplitude and area ratios for three of the four peaks were calculated and used for the statistical and multivariate analysis. The statistical analysis showed that there are significant differences between all the peak-fitting parameters and ratios between the normal and the diseased tissue groups. The technique of soft independent modelling of class analogy (SIMCA) was used to classify normal liver tissue and colorectal liver metastases resulting in 67% of the normal tissue samples and 60% of the secondary colorectal liver tissue samples being classified correctly. This study has shown that the ADXRD data of normal and secondary colorectal liver cancer are statistically different and x-ray diffraction data analysed using multivariate analysis have the potential to be used as a method of tissue classification.

Certified Normal: Alzheimer’s Disease Biomarkers and Normative Estimates of Cognitive Functioning

PubMed Central

Hassenstab, Jason; Chasse, Rachel; Grabow, Perri; Benzinger, Tammie L.S.; Fagan, Anne M.; Xiong, Chengjie; Jasielec, Mateusz; Grant, Elizabeth; Morris, John C.

2016-01-01

Normative samples drawn from older populations may unintentionally include individuals with preclinical Alzheimer’s disease (AD) pathology, resulting in reduced means, increased variability, and overestimation of age-effects on cognitive performance. 264 cognitively normal (CDR=0) older adults were classified as biomarker-negative (“Robust Normal,” n=177) or biomarker-positive (“Preclinical Alzheimer’s Disease” (PCAD), n=87) based on amyloid imaging, cerebrospinal fluid biomarkers, and hippocampal volumes. PCAD participants performed worse than Robust Normals on nearly all cognitive measures. Removing PCAD participants from the normative sample yielded higher means and less variability on episodic memory, visuospatial ability, and executive functioning measures. These results were more pronounced in participants aged 75 and older. Notably, removing PCAD participants from the sample significantly reduced age effects across all cognitive domains. Applying norms from the Robust Normal sample to a separate cohort did not improve CDR classification when using standard deviation cutoff scores. Overall, removing individuals with biomarker evidence of preclinical AD improves normative sample quality and substantially reduces age-effects on cognitive performance, but provides no substantive benefit for diagnostic classifications. PMID:27255812

DNA Methylation Patterns in Normal Tissue Correlate more Strongly with Breast Cancer Status than Copy-Number Variants.

PubMed

Gao, Yang; Widschwendter, Martin; Teschendorff, Andrew E

2018-05-04

Normal tissue at risk of neoplastic transformation is characterized by somatic mutations, copy-number variation and DNA methylation changes. It is unclear however, which type of alteration may be more informative of cancer risk. We analyzed genome-wide DNA methylation and copy-number calls from the same DNA assay in a cohort of healthy breast samples and age-matched normal samples collected adjacent to breast cancer. Using statistical methods to adjust for cell type heterogeneity, we show that DNA methylation changes can discriminate normal-adjacent from normal samples better than somatic copy-number variants. We validate this important finding in an independent dataset. These results suggest that DNA methylation alterations in the normal cell of origin may offer better cancer risk prediction and early detection markers than copy-number changes. Copyright © 2018. Published by Elsevier B.V.

Infrared trace element detection system

DOEpatents

Bien, F.; Bernstein, L.S.; Matthew, M.W.

1988-11-15

An infrared trace element detection system includes an optical cell into which the sample fluid to be examined is introduced and removed. Also introduced into the optical cell is a sample beam of infrared radiation in a first wavelength band which is significantly absorbed by the trace element and a second wavelength band which is not significantly absorbed by the trace element for passage through the optical cell through the sample fluid. The output intensities of the sample beam of radiation are selectively detected in the first and second wavelength bands. The intensities of a reference beam of the radiation are similarly detected in the first and second wavelength bands. The sensed output intensity of the sample beam in one of the first and second wavelength bands is normalized with respect to the other and similarly, the intensity of the reference beam of radiation in one of the first and second wavelength bands is normalized with respect to the other. The normalized sample beam intensity and normalized reference beam intensity are then compared to provide a signal from which the amount of trace element in the sample fluid can be determined. 11 figs.

Infrared trace element detection system

DOEpatents

Bien, Fritz; Bernstein, Lawrence S.; Matthew, Michael W.

1988-01-01

An infrared trace element detection system including an optical cell into which the sample fluid to be examined is introduced and removed. Also introduced into the optical cell is a sample beam of infrared radiation in a first wavelength band which is significantly absorbed by the trace element and a second wavelength band which is not significantly absorbed by the trace element for passage through the optical cell through the sample fluid. The output intensities of the sample beam of radiation are selectively detected in the first and second wavelength bands. The intensities of a reference beam of the radiation are similarly detected in the first and second wavelength bands. The sensed output intensity of the sample beam in one of the first and second wavelength bands is normalized with respect to the other and similarly, the intensity of the reference beam of radiation in one of the first and second wavelength bands is normalized with respect to the other. The normalized sample beam intensity and normalized reference beam intensity are then compared to provide a signal from which the amount of trace element in the sample fluid can be determined.

Real-time analysis of aromatics in combustion engine exhaust by resonance-enhanced multiphoton ionisation time-of-flight mass spectrometry (REMPI-TOF-MS): a robust tool for chassis dynamometer testing.

PubMed

Adam, T W; Clairotte, M; Streibel, T; Elsasser, M; Pommeres, A; Manfredi, U; Carriero, M; Martini, G; Sklorz, M; Krasenbrink, A; Astorga, C; Zimmermann, R

2012-07-01

Resonance-enhanced multiphoton ionisation time-of-flight mass spectrometry (REMPI-TOF-MS) is a robust method for real-time analysis of monocyclic and polycyclic aromatic hydrocarbons in complex emissions. A mobile system has been developed which enables direct analysis on site. In this paper, we utilize a multicomponent calibration scheme based on the analytes' photo-ionisation cross-sections relative to a calibrated species. This allows semi-quantification of a great number of components by only calibrating one compound of choice, here toluene. The cross-sections were determined by injecting nebulised solutions of aromatic compounds into the TOF-MS ion source with the help of a HPLC pump. Then, REMPI-TOF-MS was implemented at various chassis dynamometers and test cells and the exhaust of the following vehicles and engines investigated: a compression ignition light-duty (LD) passenger car, a compression ignition LD van, two spark ignition LD passenger cars, 2 two-stroke mopeds, and a two-stroke engine of a string gas trimmer. The quantitative time profiles of benzene are shown. The results indicate that two-stroke engines are a significant source for toxic and cancerogenic compounds. Air pollution and health effects caused by gardening equipment might still be underestimated.

Electrostatics of Pharmaceutical Aerosols for Pulmonary Delivery.

PubMed

Lip Kwok, Philip Chi

2015-01-01

This paper provides a review on key research findings in the rapidly developing area of pharmaceutical aerosol electrostatics. Solids and liquids can become charged without electric fields, the former by contact or friction and the latter by flowing or spraying. Therefore, charged particles and droplets carrying net charges are produced from pharmaceutical inhalers (e.g. dry powder inhalers, metered dose inhalers, and nebulisers) due to the mechanical processes involved in aerosolisation. The charging depends on many physicochemical factors, such as formulation composition, solid state properties, inhaler material and design, and relative humidity. In silico, in vitro, and limited in vivo studies have shown that electrostatic charges may potentially influence particle deposition in the airways. However, the evidence is not yet conclusive. Furthermore, there are currently no regulatory requirements on the characterisation and control of the electrostatic properties of inhaled formulations. Besides the need for further investigations on the relationship between physicochemical factors and charging characteristics of the aerosols, controlled and detailed in vivo studies are also required to confirm whether charges can affect particle deposition in the airways. Since pharmaceutical aerosol electrostatics is a relatively new research area, much remains to be explored. Thus there is certainly potential for development. New findings in the future may contribute to the advancement of pharmaceutical aerosol formulations and respiratory drug delivery.

Typical aqueous rare earth element behavior in co-produced Brines, Wyoming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nye, Charles; Quillinan, Scott; McLing, Travis

Normalization of Rare Earth Elements (REEs) is important to remove the distracting effects of the Oddo–Harkins rule and provide a meaningful baseline. Normalizations for rocks are well developed and include chondritic meteorites, UCC, PM, PAAS, and NASC. However normalizations for aqueous REEs are limited to oceanic regions such as the North Pacific Deep Water or North Atlantic Surface Water. This leaves water in contact with continental lithologies without a suitable normalization. We present a preliminary continental aqueous REE normalization derived from 38 deep basin hydrocarbon brines in Wyoming. The REEs in these waters are seven orders of magnitude more dilutemore » than NASC but with significant europium enrichment. Gromet 1984 reports NASC Eu/Eu* is 0.2179, whereas in the normalization offered here, Eu/Eu* is 3.868. These waters also are free from the distracting reduction-oxidation cerium behavior found in ocean normalizations. Because these samples exhibit both the uniform behavior of NASC and the absolute concentration of seawater, a normalization based upon them offers a unique combination of the advantages of both. We used single-peak gaussian analysis to quantify the mean values for each REE and estimate the distribution variability. Additional sample collection during the last year revealed that the Powder River Basin (PRB) is atypical relative to the other sampled basins of Wyoming. Those other basins are the Wind River Basin (WRB) Green River Basin (GRB) and Wamsutter Area (WA). A pre-normalization gadolinium anomaly (Gd/Gd*) of between 4 and 23 with a mean of 11.5, defines the PRB samples. Other basins in this study range from 1 to 7 with a mean of 2.8. Finally, we present a preliminary model for ligand-based behavior of REEs in these samples. This model identifies bicarbonate, bromide, and chloride as forming significant complexes with REEs contributing to REE solubility. The ligand model explains observed REEs in the sampled Cretaceous and Paleocene clastic reservoirs. However, the presence of more REEs than predicted in six samples suggests that there is an additional, unconsidered ligand contributing to REE dissolution. Further work will identify this ligand, which appears to be confined to calcium-cemented and dolostone systems.« less

Quantitative Profiling of Colorectal Cancer-Associated Bacteria Reveals Associations between Fusobacterium spp., Enterotoxigenic Bacteroides fragilis (ETBF) and Clinicopathological Features of Colorectal Cancer

PubMed Central

Viljoen, Katie S.; Dakshinamurthy, Amirtha; Goldberg, Paul; Blackburn, Jonathan M.

2015-01-01

Various studies have presented clinical or in vitro evidence linking bacteria to colorectal cancer, but these bacteria have not previously been concurrently quantified by qPCR in a single cohort. We quantify these bacteria (Fusobacterium spp., Streptococcus gallolyticus, Enterococcus faecalis, Enterotoxigenic Bacteroides fragilis (ETBF), Enteropathogenic Escherichia coli (EPEC), and afaC- or pks-positive E. coli) in paired tumour and normal tissue samples from 55 colorectal cancer patients. We further investigate the relationship between a) the presence and b) the level of colonisation of each bacterial species with site and stage of disease, age, gender, ethnicity and MSI-status. With the exception of S. gallolyticus, we detected all bacteria profiled here in both tumour and normal samples at varying frequencies. ETBF (FDR = 0.001 and 0.002 for normal and tumour samples) and afaC-positive E. coli (FDR = 0.03, normal samples) were significantly enriched in the colon compared to the rectum. ETBF (FDR = 0.04 and 0.002 for normal and tumour samples, respectively) and Fusobacterium spp. (FDR = 0.03 tumour samples) levels were significantly higher in late stage (III/IV) colorectal cancers. Fusobacterium was by far the most common bacteria detected, occurring in 82% and 81% of paired tumour and normal samples. Fusobacterium was also the only bacterium that was significantly higher in tumour compared to normal samples (p = 6e-5). We also identified significant associations between high-level colonisation by Fusobacterium and MSI-H (FDR = 0.05), age (FDR = 0.03) or pks-positive E. coli (FDR = 0.01). Furthermore, we exclusively identified atypical EPEC in our cohort, which has not been previously reported in association with colorectal cancer. By quantifying colorectal cancer-associated bacteria across a single cohort, we uncovered inter- and intra-individual patterns of colonization not previously recognized, as well as important associations with clinicopathological features, especially in the case of Fusobacterium and ETBF. PMID:25751261

The Effect on Non-Normal Distributions on the Integrated Moving Average Model of Time-Series Analysis.

ERIC Educational Resources Information Center

Doerann-George, Judith

The Integrated Moving Average (IMA) model of time series, and the analysis of intervention effects based on it, assume random shocks which are normally distributed. To determine the robustness of the analysis to violations of this assumption, empirical sampling methods were employed. Samples were generated from three populations; normal,…

Telomere length in normal and neoplastic canine tissues.

PubMed

Cadile, Casey D; Kitchell, Barbara E; Newman, Rebecca G; Biller, Barbara J; Hetler, Elizabeth R

2007-12-01

To determine the mean telomere restriction fragment (TRF) length in normal and neoplastic canine tissues. 57 solid-tissue tumor specimens collected from client-owned dogs, 40 samples of normal tissue collected from 12 clinically normal dogs, and blood samples collected from 4 healthy blood donor dogs. Tumor specimens were collected from client-owned dogs during diagnostic or therapeutic procedures at the University of Illinois Veterinary Medical Teaching Hospital, whereas 40 normal tissue samples were collected from 12 control dogs. Telomere restriction fragment length was determined by use of an assay kit. A histologic diagnosis was provided for each tumor by personnel at the Veterinary Diagnostic Laboratory at the University of Illinois. Mean of the mean TRF length for 44 normal samples was 19.0 kilobases (kb; range, 15.4 to 21.4 kb), and the mean of the mean TRF length for 57 malignant tumors was 19.0 kb (range, 12.9 to 23.5 kb). Although the mean of the mean TRF length for tumors and normal tissues was identical, tumor samples had more variability in TRF length. Telomerase, which represents the main mechanism by which cancer cells achieve immortality, is an attractive therapeutic target. The ability to measure telomere length is crucial to monitoring the efficacy of telomerase inhibition. In contrast to many other mammalian species, the length of canine telomeres and the rate of telomeric DNA loss are similar to those reported in humans, making dogs a compelling choice for use in the study of human anti-telomerase strategies.

Is this the right normalization? A diagnostic tool for ChIP-seq normalization.

PubMed

Angelini, Claudia; Heller, Ruth; Volkinshtein, Rita; Yekutieli, Daniel

2015-05-09

Chip-seq experiments are becoming a standard approach for genome-wide profiling protein-DNA interactions, such as detecting transcription factor binding sites, histone modification marks and RNA Polymerase II occupancy. However, when comparing a ChIP sample versus a control sample, such as Input DNA, normalization procedures have to be applied in order to remove experimental source of biases. Despite the substantial impact that the choice of the normalization method can have on the results of a ChIP-seq data analysis, their assessment is not fully explored in the literature. In particular, there are no diagnostic tools that show whether the applied normalization is indeed appropriate for the data being analyzed. In this work we propose a novel diagnostic tool to examine the appropriateness of the estimated normalization procedure. By plotting the empirical densities of log relative risks in bins of equal read count, along with the estimated normalization constant, after logarithmic transformation, the researcher is able to assess the appropriateness of the estimated normalization constant. We use the diagnostic plot to evaluate the appropriateness of the estimates obtained by CisGenome, NCIS and CCAT on several real data examples. Moreover, we show the impact that the choice of the normalization constant can have on standard tools for peak calling such as MACS or SICER. Finally, we propose a novel procedure for controlling the FDR using sample swapping. This procedure makes use of the estimated normalization constant in order to gain power over the naive choice of constant (used in MACS and SICER), which is the ratio of the total number of reads in the ChIP and Input samples. Linear normalization approaches aim to estimate a scale factor, r, to adjust for different sequencing depths when comparing ChIP versus Input samples. The estimated scaling factor can easily be incorporated in many peak caller algorithms to improve the accuracy of the peak identification. The diagnostic plot proposed in this paper can be used to assess how adequate ChIP/Input normalization constants are, and thus it allows the user to choose the most adequate estimate for the analysis.

CAN'T MISS--conquer any number task by making important statistics simple. Part 2. Probability, populations, samples, and normal distributions.

PubMed

Hansen, John P

2003-01-01

Healthcare quality improvement professionals need to understand and use inferential statistics to interpret sample data from their organizations. In quality improvement and healthcare research studies all the data from a population often are not available, so investigators take samples and make inferences about the population by using inferential statistics. This three-part series will give readers an understanding of the concepts of inferential statistics as well as the specific tools for calculating confidence intervals for samples of data. This article, Part 2, describes probability, populations, and samples. The uses of descriptive and inferential statistics are outlined. The article also discusses the properties and probability of normal distributions, including the standard normal distribution.

Certified normal: Alzheimer's disease biomarkers and normative estimates of cognitive functioning.

PubMed

Hassenstab, Jason; Chasse, Rachel; Grabow, Perri; Benzinger, Tammie L S; Fagan, Anne M; Xiong, Chengjie; Jasielec, Mateusz; Grant, Elizabeth; Morris, John C

2016-07-01

Normative samples drawn from older populations may unintentionally include individuals with preclinical Alzheimer's disease (AD) pathology, resulting in reduced means, increased variability, and overestimation of age effects on cognitive performance. A total of 264 cognitively normal (Clinical Dementia Rating = 0) older adults were classified as biomarker negative ("Robust Normal," n = 177) or biomarker positive ("Preclinical Alzheimer's Disease" [PCAD], n = 87) based on amyloid imaging, cerebrospinal fluid biomarkers, and hippocampal volumes. PCAD participants performed worse than robust normals on nearly all cognitive measures. Removing PCAD participants from the normative sample yielded higher means and less variability on episodic memory, visuospatial ability, and executive functioning measures. These results were more pronounced in participants aged 75 years and older. Notably, removing PCAD participants from the sample significantly reduced age effects across all cognitive domains. Applying norms from the robust normal sample to a separate cohort did not improve Clinical Dementia Rating classification when using standard deviation cutoff scores. Overall, removing individuals with biomarker evidence of preclinical AD improves normative sample quality and substantially reduces age effects on cognitive performance but provides no substantive benefit for diagnostic classifications. Copyright © 2016 Elsevier Inc. All rights reserved.

Structural Equation Analysis of the Wechsler Adult Intelligence Scale-Revised in a Normal Elderly Sample.

ERIC Educational Resources Information Center

Burton, D. Bradley; And Others

1994-01-01

A maximum-likelihood confirmatory factor analysis was performed by applying LISREL VII to the Wechsler Adult Intelligence Scale-Revised results of a normal elderly sample of 225 adults. Results indicate that a three-factor model fits best across all sample combinations. A mild gender effect is discussed. (SLD)

Urine melanin test

MedlinePlus

Thormahlen's test; Melanin - urine ... A clean-catch urine sample is needed. ... this substance that it shows up in the urine. ... Normally, melanin is not present in urine. Normal value ranges may ... measurements or test different samples. Talk to your health ...

Overcoming confounded controls in the analysis of gene expression data from microarray experiments.

PubMed

Bhattacharya, Soumyaroop; Long, Dang; Lyons-Weiler, James

2003-01-01

A potential limitation of data from microarray experiments exists when improper control samples are used. In cancer research, comparisons of tumour expression profiles to those from normal samples is challenging due to tissue heterogeneity (mixed cell populations). A specific example exists in a published colon cancer dataset, in which tissue heterogeneity was reported among the normal samples. In this paper, we show how to overcome or avoid the problem of using normal samples that do not derive from the same tissue of origin as the tumour. We advocate an exploratory unsupervised bootstrap analysis that can reveal unexpected and undesired, but strongly supported, clusters of samples that reflect tissue differences instead of tumour versus normal differences. All of the algorithms used in the analysis, including the maximum difference subset algorithm, unsupervised bootstrap analysis, pooled variance t-test for finding differentially expressed genes and the jackknife to reduce false positives, are incorporated into our online Gene Expression Data Analyzer ( http:// bioinformatics.upmc.edu/GE2/GEDA.html ).

Study of gastric cancer samples using terahertz techniques

NASA Astrophysics Data System (ADS)

Wahaia, Faustino; Kasalynas, Irmantas; Seliuta, Dalius; Molis, Gediminas; Urbanowicz, Andrzej; Carvalho Silva, Catia D.; Carneiro, Fatima; Valusis, Gintaras; Granja, Pedro L.

2014-08-01

In the present work, samples of healthy and adenocarcinoma-affected human gastric tissue were analyzed using transmission time-domain THz spectroscopy (THz-TDS) and spectroscopic THz imaging at 201 and 590 GHz. The work shows that it is possible to distinguish between normal and cancerous regions in dried and paraffin-embedded samples. Plots of absorption coefficient α and refractive index n of normal and cancer affected tissues, as well as 2-D transmission THz images are presented and the conditions for discrimination between normal and affected tissues are discussed.

A bias in the "mass-normalized" DTT response - An effect of non-linear concentration-response curves for copper and manganese

NASA Astrophysics Data System (ADS)

Charrier, Jessica G.; McFall, Alexander S.; Vu, Kennedy K.-T.; Baroi, James; Olea, Catalina; Hasson, Alam; Anastasio, Cort

2016-11-01

The dithiothreitol (DTT) assay is widely used to measure the oxidative potential of particulate matter. Results are typically presented in mass-normalized units (e.g., pmols DTT lost per minute per microgram PM) to allow for comparison among samples. Use of this unit assumes that the mass-normalized DTT response is constant and independent of the mass concentration of PM added to the DTT assay. However, based on previous work that identified non-linear DTT responses for copper and manganese, this basic assumption (that the mass-normalized DTT response is independent of the concentration of PM added to the assay) should not be true for samples where Cu and Mn contribute significantly to the DTT signal. To test this we measured the DTT response at multiple PM concentrations for eight ambient particulate samples collected at two locations in California. The results confirm that for samples with significant contributions from Cu and Mn, the mass-normalized DTT response can strongly depend on the concentration of PM added to the assay, varying by up to an order of magnitude for PM concentrations between 2 and 34 μg mL-1. This mass dependence confounds useful interpretation of DTT assay data in samples with significant contributions from Cu and Mn, requiring additional quality control steps to check for this bias. To minimize this problem, we discuss two methods to correct the mass-normalized DTT result and we apply those methods to our samples. We find that it is possible to correct the mass-normalized DTT result, although the correction methods have some drawbacks and add uncertainty to DTT analyses. More broadly, other DTT-active species might also have non-linear concentration-responses in the assay and cause a bias. In addition, the same problem of Cu- and Mn-mediated bias in mass-normalized DTT results might affect other measures of acellular redox activity in PM and needs to be addressed.

The influence of normal and high ultimate muscle pH on the microbiology and colour stability of previously frozen black wildebeest (Connochaetes gnou) meat.

PubMed

Shange, Nompumelelo; Makasi, Thandeka N; Gouws, Pieter A; Hoffman, Louwrens C

2018-01-01

Changes in pH, colour and microbiological counts were investigated in previously frozen Biceps femoris (BF) muscles from black wildebeest. Samples were stored under vacuum at refrigerated conditions (4.2±0.8°C) for 12days. Seven BF muscles had a high pH (DFD) (pH≥6) and five had a normal pH (pH<6). Overtime the pH of DFD did not significantly change whilst that of normal pH meat decreased. Browning under anaerobic storage conditions was seen, more for normal meat than DFD meat. Initial total viable counts, lactic acid bacteria and coliform counts from samples with normal pH, were significantly higher than counts from the DFD samples. However, overtime DFD meat showed a faster increase for all microorganisms tested compared to normal pH meat. Overall, this study revealed that DFD meat can have a shorter shelf-life than normal pH meat stored at 4.2±0.8°C. Copyright © 2017 Elsevier Ltd. All rights reserved.

High resolution DNA melting analysis: an application for prenatal control of alpha-thalassemia.

PubMed

Sirichotiyakul, Supatra; Wanapirak, Chanane; Saetung, Rattika; Sanguansermsri, Torpong

2010-04-01

To report the use of real-time gap-PCR using SYTO9 with high-resolution melting analysis (HRMA) in prenatal diagnosis of alpha-thalassemia 1. Real-time gap-PCR using SYTO9 with HRMA was performed in 33 DNA samples from chorionic villi sampling (8 normal, 16 heterozygous, and 9 homozygous) to determine the alpha-thalassemia 1 gene [normal and Southeast Asia (-SEA) allele]. The dissociation curve analysis in normal and - SEA allele gave a peak of T(m) at 91.80 +/- 0.14 degrees C and 88.67 +/- 0.08 degrees C, respectively. Normal genotype and homozygous alpha-thalassemia 1 showed a single peak of T(m) that corresponded to their alleles. The heterozygotes gave both peaks with higher normal peak and smaller - SEA peak. Thirty one samples showed consistent results with the conventional gap-PCR. Two samples with ambiguous results were confirmed to be maternal DNA contamination on real-time quantitative PCR and microsatellite assay. HRMA from both samples showed similar pattern to that of heterozygotes. However, they showed much smaller normal peak compared with the - SEA peak, which is in contrast to those of heterozygotes and can readily be distinguished. HRMA with SYTO9 is feasible for prenatal diagnosis of alpha-thalassemia. It had potential advantage of prompt detection maternal DNA contamination. Copyright (c) 2010 John Wiley & Sons, Ltd.

Internal Kinematics of AGN Hosts

NASA Astrophysics Data System (ADS)

Masegosa, Josefa; Márquez, Isabel; Durret, Florence; DEGAS Consortium

In order to understand the fueling mechanism to power AGNs, a large effort has been done by the DEGAS (Dynamics and nuclear Engine of GAlaxies of Spiral type) consortium to collect the necessary observational material. We defined an AGN sample which is not contaminated by interacting galaxies and a control sample made of normal spirals with the same properties than the AGN sample, i.e. luminosity and redshift distribution, morphology and percentage of bars. In total we have analyzed a sample of 17 active galaxies and 16 normal spirals. All the galaxies are isolated with the following criteria: not having a companion within 0.4 Mpc and cz < 500 km/s. We want to stress this aspect of our sample, since claimed differences between active and normal galaxies (Knapen et al. 2000) disappear when the samples are decontaminated of interacting systems.

Effects of normalization on quantitative traits in association test

PubMed Central

2009-01-01

Background Quantitative trait loci analysis assumes that the trait is normally distributed. In reality, this is often not observed and one strategy is to transform the trait. However, it is not clear how much normality is required and which transformation works best in association studies. Results We performed simulations on four types of common quantitative traits to evaluate the effects of normalization using the logarithm, Box-Cox, and rank-based transformations. The impact of sample size and genetic effects on normalization is also investigated. Our results show that rank-based transformation gives generally the best and consistent performance in identifying the causal polymorphism and ranking it highly in association tests, with a slight increase in false positive rate. Conclusion For small sample size or genetic effects, the improvement in sensitivity for rank transformation outweighs the slight increase in false positive rate. However, for large sample size and genetic effects, normalization may not be necessary since the increase in sensitivity is relatively modest. PMID:20003414

Instrumental texture characteristics of broiler pectoralis major with the wooden breast condition.

PubMed

Chatterjee, D; Zhuang, H; Bowker, B C; Rincon, A M; Sanchez-Brambila, G

2016-10-01

The objective was to characterize texture properties of raw and cooked broiler fillets (Pectoralis major) with the wooden breast condition (WBC) using the instrumental texture techniques of Meullenet-Owens Razor Shear (MORS) and Texture Profile Analysis (TPA). Deboned (3 h postmortem) broiler fillets were collected from a commercial plant and categorized as normal, moderate, or severe WBC based on the incidence and severity of diffuse hardened areas throughout fillets and the degree of palpable hardness. The fillets were then either stored at 4°C overnight or in a -20°C freezer. The MORS and TPA of the raw samples were determined at 24 h postmortem for fresh samples and after thawing overnight for frozen samples. The same measurements were also taken after the samples were cooked to 78°C. Regardless of freshness (fresh vs. frozen-thawed), cooking (raw vs. cooked), and degree of WBC, both MORS force and energy of the WBC samples were higher than that of the normal samples (P < 0.05). For TPA adhesiveness and resilience, there were no differences between normal and WBC samples (P > 0.05). However, average TPA hardness and chewiness measurements of the fillets with WBC were higher than the normal fillets (P < 0.05). Regardless of texture measurement, there were no interactions between freshness and the wooden condition or no differences between moderate and severe WBC fillets (P > 0.05). These results demonstrate that there are significant differences in instrumental texture properties between normal fillets and those exhibiting the WBC. The WBC fillets required more force to cut through, harder, and chewier than normal breast muscles. These results suggest that cooked WBC meat would likely be tougher than cooked normal meat. Published by Oxford University Press on behalf of Poultry Science Association 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients.

PubMed

Rapin, Nicolas; Bagger, Frederik Otzen; Jendholm, Johan; Mora-Jensen, Helena; Krogh, Anders; Kohlmann, Alexander; Thiede, Christian; Borregaard, Niels; Bullinger, Lars; Winther, Ole; Theilgaard-Mönch, Kim; Porse, Bo T

2014-02-06

Gene expression profiling has been used extensively to characterize cancer, identify novel subtypes, and improve patient stratification. However, it has largely failed to identify transcriptional programs that differ between cancer and corresponding normal cells and has not been efficient in identifying expression changes fundamental to disease etiology. Here we present a method that facilitates the comparison of any cancer sample to its nearest normal cellular counterpart, using acute myeloid leukemia (AML) as a model. We first generated a gene expression-based landscape of the normal hematopoietic hierarchy, using expression profiles from normal stem/progenitor cells, and next mapped the AML patient samples to this landscape. This allowed us to identify the closest normal counterpart of individual AML samples and determine gene expression changes between cancer and normal. We find the cancer vs normal method (CvN method) to be superior to conventional methods in stratifying AML patients with aberrant karyotype and in identifying common aberrant transcriptional programs with potential importance for AML etiology. Moreover, the CvN method uncovered a novel poor-outcome subtype of normal-karyotype AML, which allowed for the generation of a highly prognostic survival signature. Collectively, our CvN method holds great potential as a tool for the analysis of gene expression profiles of cancer patients.

Strength of Wet and Dry Montmorillonite

NASA Astrophysics Data System (ADS)

Morrow, C. A.; Lockner, D. A.; Moore, D. E.

2015-12-01

Montmorillonite, an expandable smectite clay, is a common mineral in fault zones to a depth of around 3 km. Its low strength relative to other common fault gouge minerals is important in many models of fault rheology. However, the coefficient of friction is not well constrained in the literature due to the difficulty of establishing fully drained or fully dried states in the laboratory. For instance, in some reported studies, samples were either partially saturated or possibly over pressured, leading to wide variability in reported shear strength. In this study, the coefficient of friction, μ, of both saturated and oven-dried (at 150°C) Na-montmorillonite was measured at normal stresses up to 680 MPa at room temperature and shortening rates from 1.0 to 0.01 μm/s. Care was taken to shear saturated samples slowly enough to avoid pore fluid overpressure in the clay layers. Coefficients of friction are reported after 8 mm of axial displacement in a triaxial apparatus on saw-cut samples containing a layer of montmorillonite gouge, with either granite or sandstone driving blocks. For saturated samples, μ increased from around 0.1 at low pressure to 0.25 at the highest test pressures. In contrast, values for oven-dried samples decreased asymptotically from approximately 0.78 at 10 MPa normal stress to around 0.45 at 400-680 MPa. While wet and dry strengths approached each other with increasing effective normal stress, wet strength remained only about half of the dry strength at 600 MPa effective normal stress. The increased coefficient of friction can be correlated with a reduction in the number of loosely bound lubricating surface water layers on the clay platelets due to applied normal stress under saturated conditions. The steady-state rate dependence of friction, a-b, was positive and dependent on normal stress. For saturated samples, a-b increased linearly with applied normal stress from ~0 to 0.004, while for dry samples a-b decreased with increasing normal stress from 0.008 to 0.002. All values were either neutral or rate strengthening, indicating a tendency for stable sliding.

Differential diagnosis of urothelial carcinoma in situ from non-neoplastic urothelia: Analysis of CK20, CD44, P53 and Ki67

PubMed Central

Asgari, Mojgan; Nabi Maybodi, Mahtab; Abolhasani, Maryam

2016-01-01

Background: Flat urothelial lesions comprise a spectrum of morphologic changes ranging from reactive atypia to carcinoma in situ (CIS). Urothelial dysplasia and CIS are associated with the recurrence and progression of urothelial carcinoma. Distinguishing CIS and dysplasia from reactive atypia based on histolopathogical features alone is often difficult. Using different immunohistochemical markers such as Cytokeratin 20 (CK20), CD44, p53, and Ki-67 is recommended for differential diagnosis. The aim of this study was to evaluate the immunohistochemical pattern of these antibodies to differentiate different flat urothelial lesions. Methods: In this cross- sectional study, three groups of bladder biopsy specimens were evaluated: 20 samples with reactive urothelial lesions, 20 histologically diagnosed as CIS, and 20 morphologically normal samples. Immunohistochemical staining of CK20, p53, CD44 and Ki-67 markers was performed on paraffin-embedded blocks. The groups were compared using chi square test, and the diagnostic value of the markers were evaluated with sensitivity, specificity, positive and negative predictive values. Results: CK20 was full thickness positive in 15 (75%) CIS samples and negative in all samples of the normal and reactive groups (p<0.001); CD44 was positive in 2 (10%) cases of the CIS group and in 17 (85%) of the reactive group; this marker was negative in all the normal samples (p<0.001). P53 was positive in 12 (60%) samples of the CIS group and negative in all samples of the normal and reactive groups (p<0.001). Ki67 was positive in 13 (65%) samples of the CIS group and 1 (5%) sample of the reactive group. This marker was negative in all samples of the normal group (p<0.001). Conclusion: The results of this study revealed that CK20, CD44, P53 and Ki67 are useful in distinguishing CIS from reactive and normal samples. However, they should be used in a panel including at least three markers. Correlation with the morphologic features is necessary. PMID:27579290

[A semimicroquality evaluation method on Panax notoginseng and its application in analysis of continuous cropping obstacles research samples].

PubMed

Cao, Yi; Wang, Chao-Qun; Xu, Feng; Jia, Xiu-Hong; Liu, Guang-Xue; Yang, Sheng-Chao; Long, Guang-Qiang; Chen, Zhong-Jian; Wei, Fu-Zhou; Yang, Shao-Zhou; Fukuda, Kozo; Wang, Xuan; Cai, Shao-Qing

2016-10-01

Panax notoginseng is a commonly used traditional Chinese medicine with blood activating effect while has continuous cropping obstacle problem in planting process. In present study, a semimicroextraction method with water-saturated n-butanol on 0.1 g notoginseng sample was established with good repeatability (RSD<2.5%) and 9.6%-20.6% higher extraction efficiency of seven saponins than the conventional method. A total of 16 characteristic peaks were identified by LC-MS-IT-TOF, including eight 20(S)-protopanaxatriol (PPT) type saponins and eight 20(S)-protopanaxadiol (PPD) type saponins. The established method was utilized to evaluate the quality of notoginseng samples cultivated by manual intervened methods to overcome continuous cropping obstacles.As a result, HPLC fingerprint similarity, content of Fa and ratio of notoginsenoside K and notoginsenoside Fa (N-K/Fa) were found out to be as valuatable markers of the quality of samples in continuous cropping obstacle research, of which N-K/Fa could also be applied to the analysis of notoginseng samples with different growth years.Notoginseng samples with continuous cropping obstacle had HPLC fingerprint similarity lower than 0.87, in consistent with normal sample, and had significant lower content of notoginsenoside Fa and significant higher N-K/Fa (2.35-4.74) than normal group (0.45-1.33). All samples in the first group with manual intervention showed high similarity with normal group (>0.87), similar content of common peaks and N-K/Fa (0.42-2.06). The content of notoginsenoside K in the second group with manual intervention was higher than normal group. All samples except two displayed similarity higher than 0.87 and possessed content of 16 saponins close to normal group. The result showed that notoginseng samples with continuous cropping obstacle had lower quality than normal sample. And manual intervened methods could improve their quality in different levels.The method established in this study was simple, fast and accurate, and the markers may provide new guides for quality control in continuous cropping obstacle research of notoginseng. Copyright© by the Chinese Pharmaceutical Association.

77 FR 38585 - Fisheries of the Caribbean, Gulf of Mexico, and South Atlantic; Reef Fish Fishery of the Gulf of...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-28

... to temporarily possess goliath grouper for non-lethal sampling during the course of their normal fishing activities. This non-lethal sampling would include measuring, tagging, and removing a portion of... temporarily possess goliath grouper for non-lethal sampling during the course of their normal fishing...

Digital-computer normal shock position and restart control of a Mach 2.5 axisymmetric mixed-compression inlet

NASA Technical Reports Server (NTRS)

Neiner, G. H.; Cole, G. L.; Arpasi, D. J.

1972-01-01

Digital computer control of a mixed-compression inlet is discussed. The inlet was terminated with a choked orifice at the compressor face station to dynamically simulate a turbojet engine. Inlet diffuser exit airflow disturbances were used. A digital version of a previously tested analog control system was used for both normal shock and restart control. Digital computer algorithms were derived using z-transform and finite difference methods. Using a sample rate of 1000 samples per second, the digital normal shock and restart controls essentially duplicated the inlet analog computer control results. At a sample rate of 100 samples per second, the control system performed adequately but was less stable.

The Properties of the Massive Star-forming Galaxies with an Outside-in Assembly Mode

NASA Astrophysics Data System (ADS)

Wang, Enci; Kong, Xu; Wang, Huiyuan; Wang, Lixin; Lin, Lin; Gao, Yulong; Liu, Qing

2017-08-01

Previous findings show that massive ({M}* > {10}10 {M}⊙ ) star-forming (SF) galaxies usually have an “inside-out” stellar mass assembly mode. In this paper, we have for the first time selected a sample of 77 massive SF galaxies with an “outside-in” assembly mode (called the “targeted sample”) from the Mapping Nearby Galaxies at the Apache Point Observatory (MaNGA) survey. For comparison, two control samples are constructed from the MaNGA sample matched in stellar mass: a sample of 154 normal SF galaxies and a sample of 62 quiescent galaxies. In contrast to normal SF galaxies, the targeted galaxies appear to be smoother and more bulge-dominated and have a smaller size and higher concentration, star formation rate, and gas-phase metallicity as a whole. However, they have a larger size and lower concentration than quiescent galaxies. Unlike the normal SF sample, the targeted sample exhibits a slightly positive gradient of the 4000 Å break and a pronounced negative gradient of Hα equivalent width. Furthermore, the median surface mass density profile is between those of the normal SF and quiescent samples, indicating that the gas accretion of quiescent galaxies is not likely to be the main approach for the outside-in assembly mode. Our results suggest that the targeted galaxies are likely in the transitional phase from normal SF galaxies to quiescent galaxies, with rapid ongoing central stellar mass assembly (or bulge growth). We discuss several possible formation mechanisms for the outside-in mass assembly mode.

Development of the technique of terahertz pulse spectroscopy for diagnostic malignant tumors during gastrointestinal surgeries

NASA Astrophysics Data System (ADS)

Goryachuk, A. A.; Khodzitsky, M. K.; Borovkova, M. A.; Khamid, A. K.; Dutkinskii, P. S.; Shishlo, D. A.

2016-08-01

Samples of fresh excised tissues obtained from patients who had undergone gastric cancer have been investigated. Samples were consisted of cancer zone, normal zone and zone mixed of normal and cancer tissues. Their optical properties and spectral features were investigated by terahertz time-domain spectroscopy (TDS) in reflection mode. It was found that waveforms of reflected signals from normal and cancer tissues were well distinguished so it can be concluded that it is easy to discriminate gastric cancer tissue from normal by using THz TDS.

Normalization to specific gravity prior to analysis improves information recovery from high resolution mass spectrometry metabolomic profiles of human urine.

PubMed

Edmands, William M B; Ferrari, Pietro; Scalbert, Augustin

2014-11-04

Extraction of meaningful biological information from urinary metabolomic profiles obtained by liquid-chromatography coupled to mass spectrometry (MS) necessitates the control of unwanted sources of variability associated with large differences in urine sample concentrations. Different methods of normalization either before analysis (preacquisition normalization) through dilution of urine samples to the lowest specific gravity measured by refractometry, or after analysis (postacquisition normalization) to urine volume, specific gravity and median fold change are compared for their capacity to recover lead metabolites for a potential future use as dietary biomarkers. Twenty-four urine samples of 19 subjects from the European Prospective Investigation into Cancer and nutrition (EPIC) cohort were selected based on their high and low/nonconsumption of six polyphenol-rich foods as assessed with a 24 h dietary recall. MS features selected on the basis of minimum discriminant selection criteria were related to each dietary item by means of orthogonal partial least-squares discriminant analysis models. Normalization methods ranked in the following decreasing order when comparing the number of total discriminant MS features recovered to that obtained in the absence of normalization: preacquisition normalization to specific gravity (4.2-fold), postacquisition normalization to specific gravity (2.3-fold), postacquisition median fold change normalization (1.8-fold increase), postacquisition normalization to urinary volume (0.79-fold). A preventative preacquisition normalization based on urine specific gravity was found to be superior to all curative postacquisition normalization methods tested for discovery of MS features discriminant of dietary intake in these urinary metabolomic datasets.

[Cross-sectional study on high-normal blood pressure and chronic kidney disease in occupational physical examination population in Changsha].

PubMed

Cao, Xia; Xie, Xiumei; Xu, Guo; Yuan, Hong; Chen, Zhiheng

2014-06-01

To investigate the relationship between high-normal blood pressure and chronic kidney disease (CKD) in occupational physical examination population in Changsha. With a convenient sampling method, a cross-sectional survey of representative sample of 11 274 white collar workers was conducted in Changsha between March 2011 and May 2011 in a large comprehensive hospital. All subjects were assigned into 4 groups: a normal blood pressure group, a high-normal blood pressure group, an undiagnosed hypertension group, and a diagnosed hypertension group. Anthropometry, blood pressure, blood sample and urine sample were measured with standard instruments and methodology for all the subjects. Multiple logistic regression analysis was used to identify risk factors for CKD. The prevalence of CKD in the normal blood pressure, high-normal blood pressure, undiagnosed hypertension, and diagnosed hypertension were 3.31%, 6.60%, 11.78%, and 17.35%, respectively. The prevalence of CKD in males was significantly higher than that in females (P<0.01). For males with high-normal blood pressure, the CKD risk was significantly greater (OR, 1.30; 95% CI:1.03 - 1.63) than those with optimal blood pressure. The logistic regression analysis showed that there was an additive effect of hyperuricemia on CKD risk in men with high-normal blood pressure compared with men with optimal blood pressure (OR, 2.25; 95% CI, 1.59 - 3.19; P<0.05). The prevalence of CKD in people with the high-normal blood pressure is 6.60% in occupational physical examination population in Changsha. CKD is a high risk for men with highnormal blood pressure and hyperuricemia is an independent risk factor.

Pattern of somatostatin receptors expression in normal and bladder cancer tissue samples.

PubMed

Karavitakis, Markos; Msaouel, Pavlos; Michalopoulos, Vassilis; Koutsilieris, Michael

2014-06-01

Known risks factors for bladder cancer progression and recurrence are limited regarding their prognostic ability. Therefore identification of molecular determinants of disease progression could provide with more specific prognostic information and could be translated into new approaches for biomarker development. In the present study we evaluated, the expression patterns of somatostatin receptors 1-5 (SSTRs) in normal and tumor bladder tissues. The expression of SSTR1-5 was characterized in 45 normal and bladder cancer tissue samples using reverse transcriptase-polymerase chain reaction (RT-PCR). SSTR1 was expressed in 24 samples, SSTR2 in 15, SSTR3 in 23, SSTR4 in 16 and SSTR5 in all but one sample. Bladder cancer tissue samples expressed lower levels of SSTR3. Co-expression of SSTRs was associated with superficial disease. Our results demonstrate, for the first time, that there is expression of SSTR in normal and bladder cancer urothelium. Further studies are required to evaluate the prognostic and therapeutic significance of these findings. Copyright© 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Creatinine as a normalization factor to estimate the representativeness of urine sample - Intra-subject and inter-subject variability studies.

PubMed

Sawant, Pramilla D; Kumar, Suja Arun; Wankhede, Sonal; Rao, D D

2018-06-01

In-vitro bioassay monitoring generally involves analysis of overnight urine samples (~12 h) collected from radiation workers to estimate the excretion rate of radionuclides from the body. The unknown duration of sample collection (10-16 h) adds to the overall uncertainty in computation of internal dose. In order to minimize this, IAEA recommends measurement of specific gravity or creatinine excretion rate in urine. Creatinine is excreted at a steady rate with normally functioning kidneys therefore, can be used as a normalization factor to infer the duration of collection and/or dilution of the sample, if any. The present study reports the chemical procedure standardized and its application for the estimation of creatinine as well as creatinine co-efficient in normal healthy individuals. Observations indicate higher inter-subject variability and lower constancy in daily excretion of creatinine for the same subject. Thus creatinine excretion rate may not be a useful indicator for extrapolating to 24 h sample collection. Copyright © 2018 Elsevier Ltd. All rights reserved.

Smooth quantile normalization.

PubMed

Hicks, Stephanie C; Okrah, Kwame; Paulson, Joseph N; Quackenbush, John; Irizarry, Rafael A; Bravo, Héctor Corrada

2018-04-01

Between-sample normalization is a critical step in genomic data analysis to remove systematic bias and unwanted technical variation in high-throughput data. Global normalization methods are based on the assumption that observed variability in global properties is due to technical reasons and are unrelated to the biology of interest. For example, some methods correct for differences in sequencing read counts by scaling features to have similar median values across samples, but these fail to reduce other forms of unwanted technical variation. Methods such as quantile normalization transform the statistical distributions across samples to be the same and assume global differences in the distribution are induced by only technical variation. However, it remains unclear how to proceed with normalization if these assumptions are violated, for example, if there are global differences in the statistical distributions between biological conditions or groups, and external information, such as negative or control features, is not available. Here, we introduce a generalization of quantile normalization, referred to as smooth quantile normalization (qsmooth), which is based on the assumption that the statistical distribution of each sample should be the same (or have the same distributional shape) within biological groups or conditions, but allowing that they may differ between groups. We illustrate the advantages of our method on several high-throughput datasets with global differences in distributions corresponding to different biological conditions. We also perform a Monte Carlo simulation study to illustrate the bias-variance tradeoff and root mean squared error of qsmooth compared to other global normalization methods. A software implementation is available from https://github.com/stephaniehicks/qsmooth.

Positron Spectroscopy Investigation of Normal Brain Section and Brain Section with Glioma Derived from a Rat Glioma Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, SH.; Ballmann, C.; Quarles, C. A.

2009-03-10

The application of positron annihilation lifetime spectroscopy (PALS) and Doppler broadening spectroscopy (DBS) to the study of animal or human tissue has only recently been reported [G. Liu, et al. phys. stat. sol. (C) 4, Nos. 10, 3912-3915 (2007)]. We have initiated a study of normal brain section and brain section with glioma derived from a rat glioma model. For the rat glioma model, 200,000 C6 cells were implanted in the basal ganglion of adult Sprague Dawley rats. The rats were sacrificed at 21 days after implantation. The brains were harvested, sliced into 2 mm thick coronal sections, and fixedmore » in 4% formalin. PALS lifetime runs were made with the samples soaked in formalin, and there was not significant evaporation of formalin during the runs. The lifetime spectra were analyzed into two lifetime components. While early results suggested a small decrease in ortho-Positronium (o-Ps) pickoff lifetime between the normal brain section and brain section with glioma, further runs with additional samples have showed no statistically significant difference between the normal and tumor tissue for this type of tumor. The o-Ps lifetime in formalin alone was lower than either the normal tissue or glioma sample. So annihilation in the formalin absorbed in the samples would lower the o-Ps lifetime and this may have masked any difference due to the glioma itself. DBS was also used to investigate the difference in positronium formation between tumor and normal tissue. Tissue samples are heterogeneous and this needs to be carefully considered if PALS and DBS are to become useful tools in distinguishing tissue samples.« less

DNA methylation markers for diagnosis and prognosis of common cancers

PubMed Central

Hao, Xiaoke; Luo, Huiyan; Krawczyk, Michal; Wei, Wei; Wang, Wenqiu; Wang, Juan; Flagg, Ken; Hou, Jiayi; Zhang, Heng; Yi, Shaohua; Jafari, Maryam; Lin, Danni; Chung, Christopher; Caughey, Bennett A.; Li, Gen; Dhar, Debanjan; Shi, William; Zheng, Lianghong; Hou, Rui; Zhu, Jie; Zhao, Liang; Fu, Xin; Zhang, Edward; Zhang, Charlotte; Zhu, Jian-Kang; Karin, Michael; Xu, Rui-Hua; Zhang, Kang

2017-01-01

The ability to identify a specific cancer using minimally invasive biopsy holds great promise for improving the diagnosis, treatment selection, and prediction of prognosis in cancer. Using whole-genome methylation data from The Cancer Genome Atlas (TCGA) and machine learning methods, we evaluated the utility of DNA methylation for differentiating tumor tissue and normal tissue for four common cancers (breast, colon, liver, and lung). We identified cancer markers in a training cohort of 1,619 tumor samples and 173 matched adjacent normal tissue samples. We replicated our findings in a separate TCGA cohort of 791 tumor samples and 93 matched adjacent normal tissue samples, as well as an independent Chinese cohort of 394 tumor samples and 324 matched adjacent normal tissue samples. The DNA methylation analysis could predict cancer versus normal tissue with more than 95% accuracy in these three cohorts, demonstrating accuracy comparable to typical diagnostic methods. This analysis also correctly identified 29 of 30 colorectal cancer metastases to the liver and 32 of 34 colorectal cancer metastases to the lung. We also found that methylation patterns can predict prognosis and survival. We correlated differential methylation of CpG sites predictive of cancer with expression of associated genes known to be important in cancer biology, showing decreased expression with increased methylation, as expected. We verified gene expression profiles in a mouse model of hepatocellular carcinoma. Taken together, these findings demonstrate the utility of methylation biomarkers for the molecular characterization of cancer, with implications for diagnosis and prognosis. PMID:28652331

A Monte Carlo Study of Levene's Test of Homogeneity of Variance: Empirical Frequencies of Type I Error in Normal Distributions.

ERIC Educational Resources Information Center

Neel, John H.; Stallings, William M.

An influential statistics test recommends a Levene text for homogeneity of variance. A recent note suggests that Levene's test is upwardly biased for small samples. Another report shows inflated Alpha estimates and low power. Neither study utilized more than two sample sizes. This Monte Carlo study involved sampling from a normal population for…

Impact of dietary fiber fermentation from cereal grains on metabolite production by the fecal microbiota from normal weight and obese individuals.

PubMed

Yang, Junyi; Keshavarzian, Ali; Rose, Devin J

2013-09-01

Gut bacteria may influence obesity through the metabolites produced by dietary fiber fermentation (mainly, short-chain fatty acids [SCFA]). Five cereal grain samples (wheat, rye, maize [corn], rice, and oats) were subjected to in vitro digestion and fermentation using fecal samples from 10 obese and nine normal weight people. No significant differences in total SCFA production between the normal weight and obese groups were observed [279 (12) vs. 280 (12), mean (standard error), respectively; P=.935]. However, the obese microbiota resulted in elevated propionate production compared with that of normal weight [24.8(2.2) vs. 17.8(1.9), respectively; P=.008]. Rye appeared to be particularly beneficial among grain samples due to the lowest propionate production and highest butyrate production during fermentation. These data suggest that the dietary fibers from cereal grains affect bacterial metabolism differently in obese and normal weight classes and that certain grains may be particularly beneficial for promoting gut health in obese states.

Relative expression of rRNA transcripts and 45S rDNA promoter methylation status are dysregulated in tumors in comparison with matched-normal tissues in breast cancer.

PubMed

Karahan, Gurbet; Sayar, Nilufer; Gozum, Gokcen; Bozkurt, Betul; Konu, Ozlen; Yulug, Isik G

2015-06-01

Ribosomal RNA (rRNA) expression, one of the most important factors regulating ribosome production, is primarily controlled by a CG-rich 45 S rDNA promoter. However, the DNA methylation state of the 45 S rDNA promoter, as well as its effect on rRNA gene expression in types of human cancers is controversial. In the present study we analyzed the methylation status of the rDNA promoter (-380 to +53 bp) as well as associated rRNA expression levels in breast cancer cell lines and breast tumor-normal tissue pairs. We found that the aforementioned regulatory region was extensively methylated (74-96%) in all cell lines and in 68% (13/19 tumor-normal pairs) of the tumors. Expression levels of rRNA transcripts 18 S, 28 S, 5.8 S and 45 S external transcribed spacer (45 S ETS) greatly varied in the breast cancer cell lines regardless of their methylation status. Analyses of rRNA transcript expression levels in the breast tumor and normal matched tissues showed no significant difference when normalized with TBP. On the other hand, using the geometric mean of the rRNA expression values (GM-rRNA) as reference enabled us to identify significant changes in the relative expression of rRNAs in the tissue samples. We propose GM-rRNA normalization as a novel strategy to analyze expression differences between rRNA transcripts. Accordingly, the 18S rRNA/GM-rRNA ratio was significantly higher whereas the 5.8S rRNA/GM-rRNA ratio was significantly lower in breast tumor samples than this ratio in the matched normal samples. Moreover, the 18S rRNA/GM-rRNA ratio was negatively correlated with the 45 S rDNA promoter methylation level in the normal breast tissue samples, yet not in the breast tumors. Significant correlations observed between the expression levels of rRNA transcripts in the normal samples were lost in the tumor samples. We showed that the expression of rRNA transcripts may not be based solely on promoter methylation. Carcinogenesis may cause dysregulation of the correlation between spliced rRNA expression levels, possibly due to changes in rRNA processing, which requires further investigation.

Comparison of Sample Size by Bootstrap and by Formulas Based on Normal Distribution Assumption.

PubMed

Wang, Zuozhen

2018-01-01

Bootstrapping technique is distribution-independent, which provides an indirect way to estimate the sample size for a clinical trial based on a relatively smaller sample. In this paper, sample size estimation to compare two parallel-design arms for continuous data by bootstrap procedure are presented for various test types (inequality, non-inferiority, superiority, and equivalence), respectively. Meanwhile, sample size calculation by mathematical formulas (normal distribution assumption) for the identical data are also carried out. Consequently, power difference between the two calculation methods is acceptably small for all the test types. It shows that the bootstrap procedure is a credible technique for sample size estimation. After that, we compared the powers determined using the two methods based on data that violate the normal distribution assumption. To accommodate the feature of the data, the nonparametric statistical method of Wilcoxon test was applied to compare the two groups in the data during the process of bootstrap power estimation. As a result, the power estimated by normal distribution-based formula is far larger than that by bootstrap for each specific sample size per group. Hence, for this type of data, it is preferable that the bootstrap method be applied for sample size calculation at the beginning, and that the same statistical method as used in the subsequent statistical analysis is employed for each bootstrap sample during the course of bootstrap sample size estimation, provided there is historical true data available that can be well representative of the population to which the proposed trial is planning to extrapolate.

Positive "alveolar" responses to antigen inhalation provocation tests: their validity and recognition.

PubMed Central

Hendrick, D J; Marshall, R; Faux, J A; Krall, J M

1980-01-01

The validity of inhalation tests in the investigation of extrinsic allergic alveolitis was assessed from the results of 144 antigen and control tests in 31 subjects. A definitive pattern of positive late responses was observed. Reactions to nebulised bird serum and droppings in subjects with bird fancier's lung were identical to reactions after "natural" exposures in aviaries or lofts, and to reactions after "occupational" challenges in subjects with farmer's lung and mushroom worker's lung. In general, positive tests were easily recognised subjectively from symptoms and signs appropriate to an influenza-like illness and undue respiratory effort on exercise. They were associated with significant changes in six readily available objective monitoring measurements--exercise minute ventilation (greater than or equal to +15%), body temperature (> 37.2 degrees C), circulating neutrophils (greater than or equal to +2500/mm3), exercise respiratory frequency (greater than or equal to +25%), circulating lymphocytes (greater than ore equal to -500/mm3 with lymphopenia), and forced vital capacity (greater than or equal to -15%). These confirmatory monitoring tests had specificities of approximately 95% and sensitivities of 85-48%. Measurement of diffusing capacity, lung volume subdivisions, or resting minute ventilation/respiratory frequency proved to be too insensitive to be useful, as did auscultation and chest radiography. We conclude that responses that do provoke significant changes in these less sensitive tests are unnecessarily distressing and, presumable, unnecessarily hazardous. PMID:7434297

Delivery of ENaC siRNA to epithelial cells mediated by a targeted nanocomplex: a therapeutic strategy for cystic fibrosis.

PubMed

Manunta, Maria D I; Tagalakis, Aristides D; Attwood, Martin; Aldossary, Ahmad M; Barnes, Josephine L; Munye, Mustafa M; Weng, Alexander; McAnulty, Robin J; Hart, Stephen L

2017-04-06

The inhibition of ENaC may have therapeutic potential in CF airways by reducing sodium hyperabsorption, restoring lung epithelial surface fluid levels, airway hydration and mucociliary function. The challenge has been to deliver siRNA to the lung with sufficient efficacy for a sustained therapeutic effect. We have developed a self-assembling nanocomplex formulation for siRNA delivery to the airways that consists of a liposome (DOTMA/DOPE; L), an epithelial targeting peptide (P) and siRNA (R). LPR formulations were assessed for their ability to silence expression of the transcript of the gene encoding the α-subunit of the sodium channel ENaC in cell lines and primary epithelial cells, in submerged cultures or grown in air-liquid interface conditions. LPRs, containing 50 nM or 100 nM siRNA, showed high levels of silencing, particularly in primary airway epithelial cells. When nebulised these nanocomplexes still retained their biophysical properties and transfection efficiencies. The silencing ability was determined at protein level by confocal microscopy and western blotting. In vivo data demonstrated that these nanoparticles had the ability to silence expression of the α-ENaC subunit gene. In conclusion, these findings show that LPRs can modulate the activity of ENaC and this approach might be promising as co-adjuvant therapy for cystic fibrosis.

Lewis x is highly expressed in normal tissues: a comparative immunohistochemical study and literature revision.

PubMed

Croce, María V; Isla-Larrain, Marina; Rabassa, Martín E; Demichelis, Sandra; Colussi, Andrea G; Crespo, Marina; Lacunza, Ezequiel; Segal-Eiras, Amada

2007-01-01

An immunohistochemical analysis was employed to determine the expression of carbohydrate antigens associated to mucins in normal epithelia. Tissue samples were obtained as biopsies from normal breast (18), colon (35) and oral cavity mucosa (8). The following carbohydrate epitopes were studied: sialyl-Lewis x, Lewis x, Lewis y, Tn hapten, sialyl-Tn and Thomsen-Friedenreich antigen. Mucins were also studied employing antibodies against MUC1, MUC2, MUC4, MUC5AC, MUC6 and also normal colonic glycolipid. Statistical analysis was performed and Kendall correlations were obtained. Lewis x showed an apical pattern mainly at plasma membrane, although cytoplasmic staining was also found in most samples. TF, Tn and sTn haptens were detected in few specimens, while sLewis x was found in oral mucosa and breast tissue. Also, normal breast expressed MUC1 at a high percentage, whereas MUC4 was observed in a small number of samples. Colon specimens mainly expressed MUC2 and MUC1, while most oral mucosa samples expressed MUC4 and MUC1. A positive correlation between MUC1VNTR and TF epitope (r=0.396) was found in breast samples, while in colon specimens MUC2 and colonic glycolipid versus Lewis x were statistically significantly correlated (r=0.28 and r=0.29, respectively). As a conclusion, a defined carbohydrate epitope expression is not exclusive of normal tissue or a determined localization, and it is possible to assume that different glycoproteins and glycolipids may be carriers of carbohydrate antigens depending on the tissue localization considered.

Analysis of the variability of human normal urine by 2D-GE reveals a "public" and a "private" proteome.

PubMed

Molina, Laurence; Salvetat, Nicolas; Ameur, Randa Ben; Peres, Sabine; Sommerer, Nicolas; Jarraya, Fayçal; Ayadi, Hammadi; Molina, Franck; Granier, Claude

2011-12-10

The characterization of the normal urinary proteome is steadily progressing and represents a major interest in the assessment of clinical urinary biomarkers. To estimate quantitatively the variability of the normal urinary proteome, urines of 20 healthy people were collected. We first evaluated the impact of the sample conservation temperature on urine proteome integrity. Keeping the urine sample at RT or at +4°C until storage at -80°C seems the best way for long-term storage of samples for 2D-GE analysis. The quantitative variability of the normal urinary proteome was estimated on the 20 urines mapped by 2D-GE. The occurrence of the 910 identified spots was analysed throughout the gels and represented in a virtual 2D gel. Sixteen percent of the spots were found to occur in all samples and 23% occurred in at least 90% of urines. About 13% of the protein spots were present only in 10% or less of the samples, thus representing the most variable part of the normal urinary proteome. Twenty proteins corresponding to a fraction of the fully conserved spots were identified by mass spectrometry. In conclusion, a "public" urinary proteome, common to healthy individuals, seems to coexist with a "private" urinary proteome, which is more specific to each individual. Copyright © 2011 Elsevier B.V. All rights reserved.

Metal dispersion and transportational activities using food crops as biomonitors.

PubMed

Ward, N I; Savage, J M

1994-05-23

The multielement (Al, Ca, Cd, Ce, Cr, Cu, Fe, Mg, Mn, Ni, Pb, Si, and Zn) levels of various common vegetables (bean, broccoli, cabbage, cauliflower, lettuce, marrow, onion, parsnip, spinach, sprouts, sweet corn, and tomato); fruits (grape and strawberry); herbs (garlic, lemon balm, marjoram, mint, rosemary and tarragon); local pasture species and surface soils collected from a commercial garden centre located within a distance of 30 m of the London Orbital Motorway (M25) is presented. Comparative values are given from a background area, namely a domestic garden located in the North Yorkshire Dales National Park area. Analysis was undertaken by inductively coupled plasma optical emission spectrometry (ICP-OES) and inductively coupled plasma-source mass spectrometry (ICP-MS) with quality control assessment using four international biological reference materials; BCR:CRM 62 Olive Leaves, NIST 1575 Pine Needles, NIST 1573 Tomato Leaves, and NIST 1572 Citrus Leaves. Inter-analytical method comparison is given using two methods of ICP-MS; namely conventional pneumatic nebulisation of sample solution, and direct solids analysis by laser ablation; and neutron activation analysis methods (NAA). For the elements listed there is a good precision obtained by ICP-MS and NAA. In particular levels of < +/- 1-10% (rsd) are obtained. Comparison of data with certified values and other analytical methods are generally of very good agreement. Lead levels in background areas ranged from 0.0008 to 0.340 microgram/g (fresh weight) for plant material; with the lead magnitude greater for grasses > herbs > vegetables > cereals > fruits. Measured values are in good agreement with reported literature values. The lowest Pb values are for marrow, lettuce, tomato and sweet corn samples (approximately 0.001-0.021 microgram/g). 'Green' leaf material levels were approximately 0.02-0.10 microgram/g (i.e. sprouts and cabbage). Root vegetables contain higher levels, approximately 0.02-0.125 microgram/g (especially carrot), reflecting possible metal uptake from soil. The highest vegetable Pb values are for leek and onion (approximately 0.35 microgram/g). Background values are also provided for nineteen elements (Al, As, B, Ba, Br, Cd, Co, Cr, Cu, Fe, Li, Mn, Mo, Ni, Rb, Se, Sr, V, and Zn). Exposure to motor vehicle activities at a site some 30 m from the M25 shows only significant increases in Pb for unwashed plant material and surface soils. Typically Pb levels of 40-80% can be removed by washing plant surfaces resulting in metal levels similar to background areas.(ABSTRACT TRUNCATED AT 400 WORDS)

Predicting the required number of training samples. [for remotely sensed image data based on covariance matrix estimate quality criterion of normal distribution

NASA Technical Reports Server (NTRS)

Kalayeh, H. M.; Landgrebe, D. A.

1983-01-01

A criterion which measures the quality of the estimate of the covariance matrix of a multivariate normal distribution is developed. Based on this criterion, the necessary number of training samples is predicted. Experimental results which are used as a guide for determining the number of training samples are included. Previously announced in STAR as N82-28109

Identification and Characterization of Post-Translational Modifications on EAF1 and EAF2 in Prostate Cancer

DTIC Science & Technology

2013-04-01

1nM R1881). All samples were normalized to renilla . B) Activity of PSA- luciferase in the presence of FOXA1 when EAF2 is over-expressed. All...samples performed in the presence of 1nM R1881. All samples were normalized to renilla . *=pɘ.05 All experiments were performed in C4-2 cells. FOXA1

A large-scale study of the ultrawideband microwave dielectric properties of normal, benign and malignant breast tissues obtained from cancer surgeries

NASA Astrophysics Data System (ADS)

Lazebnik, Mariya; Popovic, Dijana; McCartney, Leah; Watkins, Cynthia B.; Lindstrom, Mary J.; Harter, Josephine; Sewall, Sarah; Ogilvie, Travis; Magliocco, Anthony; Breslin, Tara M.; Temple, Walley; Mew, Daphne; Booske, John H.; Okoniewski, Michal; Hagness, Susan C.

2007-10-01

The development of microwave breast cancer detection and treatment techniques has been driven by reports of substantial contrast in the dielectric properties of malignant and normal breast tissues. However, definitive knowledge of the dielectric properties of normal and diseased breast tissues at microwave frequencies has been limited by gaps and discrepancies across previously published studies. To address these issues, we conducted a large-scale study to experimentally determine the ultrawideband microwave dielectric properties of a variety of normal, malignant and benign breast tissues, measured from 0.5 to 20 GHz using a precision open-ended coaxial probe. Previously, we reported the dielectric properties of normal breast tissue samples obtained from reduction surgeries. Here, we report the dielectric properties of normal (adipose, glandular and fibroconnective), malignant (invasive and non-invasive ductal and lobular carcinomas) and benign (fibroadenomas and cysts) breast tissue samples obtained from cancer surgeries. We fit a one-pole Cole-Cole model to the complex permittivity data set of each characterized sample. Our analyses show that the contrast in the microwave-frequency dielectric properties between malignant and normal adipose-dominated tissues in the breast is considerable, as large as 10:1, while the contrast in the microwave-frequency dielectric properties between malignant and normal glandular/fibroconnective tissues in the breast is no more than about 10%.

Fetal scalp pH testing

MedlinePlus

... such as HIV/AIDS or hepatitis C. Normal Results Normal fetal blood sample results are: Normal pH: ... meaning of your specific test results. What Abnormal Results Mean A fetal scalp blood pH level of ...

Is Coefficient Alpha Robust to Non-Normal Data?

PubMed Central

Sheng, Yanyan; Sheng, Zhaohui

2011-01-01

Coefficient alpha has been a widely used measure by which internal consistency reliability is assessed. In addition to essential tau-equivalence and uncorrelated errors, normality has been noted as another important assumption for alpha. Earlier work on evaluating this assumption considered either exclusively non-normal error score distributions, or limited conditions. In view of this and the availability of advanced methods for generating univariate non-normal data, Monte Carlo simulations were conducted to show that non-normal distributions for true or error scores do create problems for using alpha to estimate the internal consistency reliability. The sample coefficient alpha is affected by leptokurtic true score distributions, or skewed and/or kurtotic error score distributions. Increased sample sizes, not test lengths, help improve the accuracy, bias, or precision of using it with non-normal data. PMID:22363306

Point-of-Care Quantitative Measure of Glucose-6-Phosphate Dehydrogenase Enzyme Deficiency.

PubMed

Bhutani, Vinod K; Kaplan, Michael; Glader, Bertil; Cotten, Michael; Kleinert, Jairus; Pamula, Vamsee

2015-11-01

Widespread newborn screening on a point-of-care basis could prevent bilirubin neurotoxicity in newborns with glucose-6-phosphate dehydrogenase (G6PD) deficiency. We evaluated a quantitative G6PD assay on a digital microfluidic platform by comparing its performance with standard clinical methods. G6PD activity was measured quantitatively by using digital microfluidic fluorescence and the gold standard fluorescence biochemical test on a convenience sample of 98 discarded blood samples. Twenty-four samples were designated as G6PD deficient. Mean ± SD G6PD activity for normal samples using the digital microfluidic method and the standard method, respectively, was 9.7 ± 2.8 and 11.1 ± 3.0 U/g hemoglobin (Hb), respectively; for G6PD-deficient samples, it was 0.8 ± 0.7 and 1.4 ± 0.9 U/g Hb. Bland-Altman analysis determined a mean difference of -0.96 ± 1.8 U/g Hb between the digital microfluidic fluorescence results and the standard biochemical test results. The lower and upper limits for the digital microfluidic platform were 4.5 to 19.5 U/g Hb for normal samples and 0.2 to 3.7 U/g Hb for G6PD-deficient samples. The lower and upper limits for the Stanford method were 5.5 to 20.7 U/g Hb for normal samples and 0.1 to 2.8 U/g Hb for G6PD-deficient samples. The measured activity discriminated between G6PD-deficient samples and normal samples with no overlap. Pending further validation, a digital microfluidics platform could be an accurate point-of-care screening tool for rapid newborn G6PD screening. Copyright © 2015 by the American Academy of Pediatrics.

Evaluation of the repeatability of a crude adult indirect Ostertagia ostertagi ELISA and methods of expressing test results.

PubMed

Sanchez, J; Dohoo, I R; Markham, F; Leslie, K; Conboy, G

2002-10-16

An indirect enzyme-linked immunosorbent assay (ELISA) for the detection of antibodies against Ostertagia ostertagi using a crude adult worm antigen was evaluated using serum and milk samples from adult cows, as well as from bulk tank milk. Within and between plate repeatabilities were determined. In addition, the effects of factors such as antigen batch, freezing, preserving of the samples and somatic cell counts (SCCs) of the samples were evaluated. Raw optical densities (ODs) and normalized values were compared using the concordance correlation coefficient (CCC), the coefficient of variation (CV), Bland-Altman plots (BA). Based on raw OD values, there was a high repeatability within a plate (CCC approximately 0.96 and CV<10%). Repeatability between plates was evaluated following normalization of OD values by four methods. Computing normalized values as (OD-Nt)/(Pst-Nt), gave the most repeatable results, with the CCC being approximately 0.95 and the CV approximately 11%. When the OD values were higher than 1.2 and 0.3 for the positive and the negative controls, respectively, none of the normalization methods evaluated provided highly repeatable results and it was necessary to repeat the test. Two batches of the crude antigen preparation were evaluated for repeatability, and no difference was found (CCC=0.96). The use of preservative (bronopol) did not affect test results, nor did freezing the samples for up to 8 months. A significant positive relationship between ELISA OD for milk samples and SCC score was found. Therefore, the use of composite milk samples, which have less variable SCC than samples taken from each quarter, would be more suitable when the udder health status is unknown. The analytical methods used to evaluate repeatability provided a practical way to select among normalization procedures.

Normalized inverse characterization of sound absorbing rigid porous media.

PubMed

Zieliński, Tomasz G

2015-06-01

This paper presents a methodology for the inverse characterization of sound absorbing rigid porous media, based on standard measurements of the surface acoustic impedance of a porous sample. The model parameters need to be normalized to have a robust identification procedure which fits the model-predicted impedance curves with the measured ones. Such a normalization provides a substitute set of dimensionless (normalized) parameters unambiguously related to the original model parameters. Moreover, two scaling frequencies are introduced, however, they are not additional parameters and for different, yet reasonable, assumptions of their values, the identification procedure should eventually lead to the same solution. The proposed identification technique uses measured and computed impedance curves for a porous sample not only in the standard configuration, that is, set to the rigid termination piston in an impedance tube, but also with air gaps of known thicknesses between the sample and the piston. Therefore, all necessary analytical formulas for sound propagation in double-layered media are provided. The methodology is illustrated by one numerical test and by two examples based on the experimental measurements of the acoustic impedance and absorption of porous ceramic samples of different thicknesses and a sample of polyurethane foam.

True non-contact atomic force microscopy imaging of heterogeneous biological samples in liquids: topography and material contrast.

PubMed

Almonte, Lisa; Colchero, Jaime

2017-02-23

The present work analyses how the tip-sample interaction signals critically determine the operation of an Atomic Force Microscope (AFM) set-up immersed in liquid. On heterogeneous samples, the conservative tip-sample interaction may vary significantly from point to point - in particular from attractive to repulsive - rendering correct feedback very challenging. Lipid membranes prepared on a mica substrate are analyzed as reference samples which are locally heterogeneous (material contrast). The AFM set-up is operated dynamically at low oscillation amplitude and all available experimental data signals - the normal force, as well as the amplitude and frequency - are recorded simultaneously. From the analysis of how the dissipation (oscillation amplitude) and the conservative interaction (normal force and resonance frequency) vary with the tip-sample distance we conclude that dissipation is the only appropriate feedback source for stable and correct topographic imaging. The normal force and phase then carry information about the sample composition ("chemical contrast"). Dynamic AFM allows imaging in a non-contact regime where essentially no forces are applied, rendering dynamic AFM a truly non-invasive technique.

Sample entropy analysis of cervical neoplasia gene-expression signatures

PubMed Central

Botting, Shaleen K; Trzeciakowski, Jerome P; Benoit, Michelle F; Salama, Salama A; Diaz-Arrastia, Concepcion R

2009-01-01

Background We introduce Approximate Entropy as a mathematical method of analysis for microarray data. Approximate entropy is applied here as a method to classify the complex gene expression patterns resultant of a clinical sample set. Since Entropy is a measure of disorder in a system, we believe that by choosing genes which display minimum entropy in normal controls and maximum entropy in the cancerous sample set we will be able to distinguish those genes which display the greatest variability in the cancerous set. Here we describe a method of utilizing Approximate Sample Entropy (ApSE) analysis to identify genes of interest with the highest probability of producing an accurate, predictive, classification model from our data set. Results In the development of a diagnostic gene-expression profile for cervical intraepithelial neoplasia (CIN) and squamous cell carcinoma of the cervix, we identified 208 genes which are unchanging in all normal tissue samples, yet exhibit a random pattern indicative of the genetic instability and heterogeneity of malignant cells. This may be measured in terms of the ApSE when compared to normal tissue. We have validated 10 of these genes on 10 Normal and 20 cancer and CIN3 samples. We report that the predictive value of the sample entropy calculation for these 10 genes of interest is promising (75% sensitivity, 80% specificity for prediction of cervical cancer over CIN3). Conclusion The success of the Approximate Sample Entropy approach in discerning alterations in complexity from biological system with such relatively small sample set, and extracting biologically relevant genes of interest hold great promise. PMID:19232110

An enzyme-linked immunosorbent assay for the evaluation of thrombocytopenia induced by heparin.

PubMed

Howe, S E; Lynch, D M

1985-05-01

Five patients with heparin-associated thrombocytopenia (HAT) were evaluated by platelet aggregation and quantitation of immunoglobulin binding to intact target platelets in both the presence and absence of heparin. These patients developed thrombocytopenia (12,000 to 70,000 platelets/microliter) 7 to 15 days and embolic and hemorrhagic complications 9 to 15 days after the initiation of heparin therapy. Platelet aggregation after the addition of heparin was demonstrated in two of four HAT serum samples, whereas normal serum samples showed no significant platelet aggregation. The five HAT serum samples showed normal to elevated baseline serum platelet-bindable immunoglobulin (SPBIg) with a range of 4.3 to 11.4 fg/platelet (normal less than or equal to 1.0 to 6.5 fg/platelet). When HAT sera were incubated with target platelets and heparin (5 U/ml), the SPBIg increased to 8.5 to 37.5 fg/platelet, a mean increase of 148% in the presence of heparin. Normal and control serum samples (from 10 normal laboratory volunteers, nine patients without thrombocytopenia receiving heparin, nine patients with autoimmune thrombocytopenic purpura, and nine patients with nonimmune thrombocytopenia not receiving heparin) showed only a slight increase in SPBIg of 0 to 2.8 fg/platelet above baseline, a mean increase of 15% after heparin incubation with the serum samples. The measurement of SPBIg of washed platelets incubated with test serum samples in the presence and absence of heparin is potentially a specific and sensitive in vitro test for the diagnosis of HAT and may prove more sensitive than platelet aggregation studies with heparin.

Characterization of DNA isolated from normal and cancerous ovarian tissues by ultraviolet resonance Raman spectroscopy

NASA Astrophysics Data System (ADS)

Zhao, Xiaojie; Vinson, Michael A.; Malins, Donald C.; Spiro, Thomas G.

2000-05-01

We report significant differences in UV resonance Raman (UVRR) spectra of DNA samples from normal and cancerous tissues. The four bases of DNA, adenosine, thymine, guanosine and cytidine, can be enhanced in UVRR spectra, and their intensities are very sensitive to base stacking and DNA H-bonding. 14 DNA samples from patients at different stages of ovarian cancer, 5 from normal, 2 from primary, 3 from metastasis primary and 4 from distant metastasis tumor tissues, were characterized by 257, 238, 229, 220 and 210 nm-excited UVRR spectra. Raman spectral difference between normal and tumor DNA could be readily detected.

A comparative study on the mechanical energy of the normal, ACL, osteoarthritis, and Parkinson subjects.

PubMed

Bahreinizad, Hossein; Salimi Bani, Milad; Hasani, Mojtaba; Karimi, Mohammad Taghi; Sharifmoradi, Keyvan; Karimi, Alireza

2017-08-09

The influence of various musculoskeletal disorders has been evaluated using different kinetic and kinematic parameters. But the efficiency of walking can be evaluated by measuring the effort of the subject, or by other words the energy that is required to walk. The aim of this study was to identify mechanical energy differences between the normal and pathological groups. Four groups of 15 healthy subjects, 13 Parkinson subjects, 4 osteoarthritis subjects, and 4 ACL reconstructed subjects have participated in this study. The motions of foot, shank and thigh were recorded using a three dimensional motion analysis system. The kinetic, potential and total mechanical energy of each segment was calculated using 3D markers positions and anthropometric measurements. Maximum value and sample entropy of energies was compared between the normal and abnormal subjects. Maximum value of potential energy of OA subjects was lower than the normal subjects. Furthermore, sample entropy of mechanical energy for Parkinson subjects was low in comparison to the normal subjects while sample entropy of mechanical energy for the ACL subjects was higher than that of the normal subjects. Findings of this study suggested that the subjects with different abilities show different mechanical energy during walking.

Influence of substrate temperature on structural, morphological, optical and electrical properties of Bi-doped MnInS4 thin films prepared by nebuliser spray pyrolysis technique

NASA Astrophysics Data System (ADS)

Kennedy, A.; Senthil Kumar, V.; Pradeev Raj, K.

2017-11-01

Bismuth (Bi)-doped manganese indium sulphide (MnInS4) thin films were deposited on heated glass substrates using an aqueous solution of MnCl2, InCl3, (NH2)2CS and BiCl3 by the common nebuliser spray pyrolysis technique. The thin films were grown at various substrate temperatures ranging from 250 to 400 °C with a constant spray time (5 min). The present work aims to study the effect of substrate temperature on the structural, optical, photoluminescence and electrical properties of the grown thin films using various techniques like X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), energy dispersive spectrum (EDS), UV-Vis absorption spectroscopy, photoluminescence spectra (PL) and four probe methods. The XRD pattern reveals that the Bi-doped MnInS4 thin films were polycrystalline in nature with a cubic spinel structure whose particle size varies between 8.2 and 23.5 nm. From the FE-SEM micrographs, due to the change in the substrate temperature, shapes such as spherical, needle-shaped and T-shaped grains were observed throughout the surface of the films. The energy dispersive analysis spectrum (EDS) shows the presence of Mn, In, S and Bi in the film grown at 250 °C. It is interesting to note that the structural homogeneity and crystallinity of the film is improved due to the decrease in the absorption coefficient (α) and extinction coefficient (K) with an increase in substrate temperature. Also, with an increase in the substrate temperature, the calculated band gap energy was found to decrease from 1.87 to 1.59 eV. From the PL spectra, several intense peaks corresponding to blue, green, yellow, orange and red band emissions were observed in the wavelength region of 350-650 nm. Moreover as the intensity of the peak increases with increase in the substrate temperature, the crystallinity of the material of the film greatly improves concomitant with minimum strain and defect states. From the electrical studies, the electrical conductivity increases with increase in substrate temperature and a maximum electrical conductivity of 3.73 × 10-3 Ω-1m-1 were obtained for the film prepared at 400 °C. The thickness of the films was also measured and the values ranged between 743 nm (250 °C) to 629 nm (400 °C). The high absorption coefficient (1.85 × 104 cm-1) and high transmittance of the films make them an efficient window layer for solar cell applications. Incorporation of Bismuth (Bi) into MnInS4 matrix leads to improve the optical transmittance (85%) and electrical conductivity (3.11 × 10-3 Ω-1 m-1) of the film grown at 400 °C. Other important parameters like dislocation density (δ), strain (ε), the number of crystallites per unit area (N) and lattice distortion (LD), which are commonly used to describe the structural analysis were also presented. Bi-doped MnInS4 thin films were grown by a variety of deposition methods. Among them, spray pyrolysis is an eco-friendly method because of its low cost, mass production capacity, large area coatings and minimum wastage of the source materials.

Optimizing fish sampling for fish - mercury bioaccumulation factors

USGS Publications Warehouse

Scudder Eikenberry, Barbara C.; Riva-Murray, Karen; Knightes, Christopher D.; Journey, Celeste A.; Chasar, Lia C.; Brigham, Mark E.; Bradley, Paul M.

2015-01-01

Fish Bioaccumulation Factors (BAFs; ratios of mercury (Hg) in fish (Hgfish) and water (Hgwater)) are used to develop Total Maximum Daily Load and water quality criteria for Hg-impaired waters. Both applications require representative Hgfish estimates and, thus, are sensitive to sampling and data-treatment methods. Data collected by fixed protocol from 11 streams in 5 states distributed across the US were used to assess the effects of Hgfish normalization/standardization methods and fish sample numbers on BAF estimates. Fish length, followed by weight, was most correlated to adult top-predator Hgfish. Site-specific BAFs based on length-normalized and standardized Hgfish estimates demonstrated up to 50% less variability than those based on non-normalized Hgfish. Permutation analysis indicated that length-normalized and standardized Hgfish estimates based on at least 8 trout or 5 bass resulted in mean Hgfish coefficients of variation less than 20%. These results are intended to support regulatory mercury monitoring and load-reduction program improvements.

Determination of Zn/Cu ratio and oligoelements in serum samples by total reflection X-ray fluorescence spectrometry for cancer diagnosis

NASA Astrophysics Data System (ADS)

Marcó P., L. M.; Jiménez, E.; Hernández C., E. A.; Rojas, A.; Greaves, E. D.

2001-11-01

The method of quantification using the Compton peak as an internal standard, developed in a previous work, was applied to the routine determination of Fe, Cu, Zn and Se in serum samples from normal individuals and cancer patients by total reflection X-ray fluorescence spectrometry. Samples were classified according to age and sex of the donor, in order to determine reference values for normal individuals. Results indicate that the Zn/Cu ratio and the Cu concentration could prove to be useful tools for cancer diagnosis. Significant differences in these parameters between the normal and cancer group were found for all age ranges. The multielemental character of the technique, coupled with the small amounts of sample required and the short analysis time make it a valuable tool in clinical analysis.

Technical note: An improved approach to determining background aerosol concentrations with PILS sampling on aircraft

NASA Astrophysics Data System (ADS)

Fukami, Christine S.; Sullivan, Amy P.; Ryan Fulgham, S.; Murschell, Trey; Borch, Thomas; Smith, James N.; Farmer, Delphine K.

2016-07-01

Particle-into-Liquid Samplers (PILS) have become a standard aerosol collection technique, and are widely used in both ground and aircraft measurements in conjunction with off-line ion chromatography (IC) measurements. Accurate and precise background samples are essential to account for gas-phase components not efficiently removed and any interference in the instrument lines, collection vials or off-line analysis procedures. For aircraft sampling with PILS, backgrounds are typically taken with in-line filters to remove particles prior to sample collection once or twice per flight with more numerous backgrounds taken on the ground. Here, we use data collected during the Front Range Air Pollution and Photochemistry Éxperiment (FRAPPÉ) to demonstrate that not only are multiple background filter samples are essential to attain a representative background, but that the chemical background signals do not follow the Gaussian statistics typically assumed. Instead, the background signals for all chemical components analyzed from 137 background samples (taken from ∼78 total sampling hours over 18 flights) follow a log-normal distribution, meaning that the typical approaches of averaging background samples and/or assuming a Gaussian distribution cause an over-estimation of background samples - and thus an underestimation of sample concentrations. Our approach of deriving backgrounds from the peak of the log-normal distribution results in detection limits of 0.25, 0.32, 3.9, 0.17, 0.75 and 0.57 μg m-3 for sub-micron aerosol nitrate (NO3-), nitrite (NO2-), ammonium (NH4+), sulfate (SO42-), potassium (K+) and calcium (Ca2+), respectively. The difference in backgrounds calculated from assuming a Gaussian distribution versus a log-normal distribution were most extreme for NH4+, resulting in a background that was 1.58× that determined from fitting a log-normal distribution.

Classification of normal and malignant human gastric mucosa tissue with confocal Raman microspectroscopy and wavelet analysis

NASA Astrophysics Data System (ADS)

Hu, Yaogai; Shen, Aiguo; Jiang, Tao; Ai, Yong; Hu, Jiming

2008-02-01

Thirty-two samples from the human gastric mucosa tissue, including 13 normal and 19 malignant tissue samples were measured by confocal Raman microspectroscopy. The low signal-to-background ratio spectra from human gastric mucosa tissues were obtained by this technique without any sample preparation. Raman spectral interferences include a broad featureless sloping background due to fluorescence and noise. They mask most Raman spectral feature and lead to problems with precision and quantitation of the original spectral information. A preprocessed algorithm based on wavelet analysis was used to reduce noise and eliminate background/baseline of Raman spectra. Comparing preprocessed spectra of malignant gastric mucosa tissues with those of counterpart normal ones, there were obvious spectral changes, including intensity increase at ˜1156 cm -1 and intensity decrease at ˜1587 cm -1. The quantitative criterion based upon the intensity ratio of the ˜1156 and ˜1587 cm -1 was extracted for classification of the normal and malignant gastric mucosa tissue samples. This could result in a new diagnostic method, which would assist the early diagnosis of gastric cancer.

Scanning transmission ion microscopy mass measurements for quantitative trace element analysis within biological samples and validation using atomic force microscopy thickness measurements

NASA Astrophysics Data System (ADS)

Devès, Guillaume; Cohen-Bouhacina, Touria; Ortega, Richard

2004-10-01

We used the nuclear microprobe techniques, micro-PIXE (particle-induced X-ray emission), micro-RBS (Rutherford backscattering spectrometry) and scanning transmission ion microscopy (STIM) in order to perform the characterization of trace element content and spatial distribution within biological samples (dehydrated cultured cells, tissues). The normalization of PIXE results was usually expressed in terms of sample dry mass as determined by micro-RBS recorded simultaneously to micro-PIXE. However, the main limit of RBS mass measurement is the sample mass loss occurring during irradiation and which could be up to 30% of the initial sample mass. We present here a new methodology for PIXE normalization and quantitative analysis of trace element within biological samples based on dry mass measurement performed by mean of STIM. The validation of STIM cell mass measurements was obtained in comparison with AFM sample thickness measurements. Results indicated the reliability of STIM mass measurement performed on biological samples and suggested that STIM should be performed for PIXE normalization. Further information deriving from direct confrontation of AFM and STIM analysis could as well be obtained, like in situ measurements of cell specific gravity within cells compartment (nucleolus and cytoplasm).

Normalization for Relative Quantification of mRNA and microRNA in Soybean Exposed to Various Abiotic Stresses

PubMed Central

Zhou, Yonggang; Chen, Huan; Dong, Yuanyuan; Wang, Nan; Li, Xiaowei; Jameel, Aysha; Yang, He; Zhang, Min; Chen, Kai; Wang, Fawei; Li, Haiyan

2016-01-01

Plant microRNAs are small non-coding, endogenic RNA molecule (containing 20–24 nucleotides) produced from miRNA precursors (pri-miRNA and pre-miRNA). Evidence suggests that up and down regulation of the miRNA targets the mRNA genes involved in resistance against biotic and abiotic stresses. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a powerful technique to analyze variations in mRNA levels. Normalizing the data using reference genes is essential for the analysis of reliable RT-qPCR data. In this study, two groups of candidate reference mRNAs and miRNAs in soybean leaves and roots treated with various abiotic stresses (PEG-simulated drought, salinity, alkalinity, salinity+alkalinity, and abscisic acid) were analyzed by RT-qPCR. We analyzed the most appropriate reference mRNA/miRNAs using the geNorm, NormFinder, and BestKeeper algorithms. According to the results, Act and EF1b were the most suitable reference mRNAs in leaf and root samples, for mRNA and miRNA precursor data normalization. The most suitable reference miRNAs found in leaf and root samples were 166a and 167a for mature miRNA data normalization. Hence the best combinations of reference mRNAs for mRNA and miRNA precursor data normalization were EF1a + Act or EF1b + Act in leaf samples, and EF1a + EF1b or 60s + EF1b in root samples. For mature miRNA data normalization, the most suitable combinations of reference miRNAs were 166a + 167d in leaf samples, and 171a + 156a or 167a + 171a in root samples. We identified potential reference mRNA/miRNAs for accurate RT-qPCR data normalization for mature miRNA, miRNA precursors, and their targeted mRNAs. Our results promote miRNA-based studies on soybean plants exposed to abiotic stress conditions. PMID:27176476

Normalization of RNA-seq data using factor analysis of control genes or samples

PubMed Central

Risso, Davide; Ngai, John; Speed, Terence P.; Dudoit, Sandrine

2015-01-01

Normalization of RNA-seq data has proven essential to ensure accurate inference of expression levels. Here we show that usual normalization approaches mostly account for sequencing depth and fail to correct for library preparation and other more-complex unwanted effects. We evaluate the performance of the External RNA Control Consortium (ERCC) spike-in controls and investigate the possibility of using them directly for normalization. We show that the spike-ins are not reliable enough to be used in standard global-scaling or regression-based normalization procedures. We propose a normalization strategy, remove unwanted variation (RUV), that adjusts for nuisance technical effects by performing factor analysis on suitable sets of control genes (e.g., ERCC spike-ins) or samples (e.g., replicate libraries). Our approach leads to more-accurate estimates of expression fold-changes and tests of differential expression compared to state-of-the-art normalization methods. In particular, RUV promises to be valuable for large collaborative projects involving multiple labs, technicians, and/or platforms. PMID:25150836

Experiments with central-limit properties of spatial samples from locally covariant random fields

USGS Publications Warehouse

Barringer, T.H.; Smith, T.E.

1992-01-01

When spatial samples are statistically dependent, the classical estimator of sample-mean standard deviation is well known to be inconsistent. For locally dependent samples, however, consistent estimators of sample-mean standard deviation can be constructed. The present paper investigates the sampling properties of one such estimator, designated as the tau estimator of sample-mean standard deviation. In particular, the asymptotic normality properties of standardized sample means based on tau estimators are studied in terms of computer experiments with simulated sample-mean distributions. The effects of both sample size and dependency levels among samples are examined for various value of tau (denoting the size of the spatial kernel for the estimator). The results suggest that even for small degrees of spatial dependency, the tau estimator exhibits significantly stronger normality properties than does the classical estimator of standardized sample means. ?? 1992.

Fluorescence spectroscopy using excitation and emission matrix for quantification of tissue native fluorophores and cancer diagnosis

NASA Astrophysics Data System (ADS)

Wu, Binlin; Gayen, S. K.; Xu, M.

2014-03-01

Native fluorescence spectrum of normal and cancerous human prostate tissues is studied to distinguish between normal and cancerous tissues, and cancerous tissues at different cancer grade. The tissue samples were obtained from Cooperative Human Tissue Network (CHTN) and National Disease Research Interchange(NDRI). An excitation and emission matrix (EEM) was generated for each tissue sample by acquiring native fluorescence spectrum of the sample using multiple excitation wavelengths. The non-negative matrix factorization algorithm was used to generate fluorescence EEMs that correspond to the fluorophores in biological tissues, including tryptophan, collagen, elastin, nicotinamide adenine dinucleotide (NADH), flavin adenine dinucleotide (FAD) and the background paraffin. We hypothesize that, as a consequence of metabolic changes associated with the development of cancer, the concentrations of NADH and FAD are different in normal and cancerous tissues, and also different for different cancer grades. We used the ratio of the abundances of FAD and NADH to distinguish between normal and cancerous tissues, and the tissue cancer grade. The FAD-to-NADH ratio was found to be the highest for normal tissue and decreased as the cancer grade increased.

Optimal Scaling of Digital Transcriptomes

PubMed Central

Glusman, Gustavo; Caballero, Juan; Robinson, Max; Kutlu, Burak; Hood, Leroy

2013-01-01

Deep sequencing of transcriptomes has become an indispensable tool for biology, enabling expression levels for thousands of genes to be compared across multiple samples. Since transcript counts scale with sequencing depth, counts from different samples must be normalized to a common scale prior to comparison. We analyzed fifteen existing and novel algorithms for normalizing transcript counts, and evaluated the effectiveness of the resulting normalizations. For this purpose we defined two novel and mutually independent metrics: (1) the number of “uniform” genes (genes whose normalized expression levels have a sufficiently low coefficient of variation), and (2) low Spearman correlation between normalized expression profiles of gene pairs. We also define four novel algorithms, one of which explicitly maximizes the number of uniform genes, and compared the performance of all fifteen algorithms. The two most commonly used methods (scaling to a fixed total value, or equalizing the expression of certain ‘housekeeping’ genes) yielded particularly poor results, surpassed even by normalization based on randomly selected gene sets. Conversely, seven of the algorithms approached what appears to be optimal normalization. Three of these algorithms rely on the identification of “ubiquitous” genes: genes expressed in all the samples studied, but never at very high or very low levels. We demonstrate that these include a “core” of genes expressed in many tissues in a mutually consistent pattern, which is suitable for use as an internal normalization guide. The new methods yield robustly normalized expression values, which is a prerequisite for the identification of differentially expressed and tissue-specific genes as potential biomarkers. PMID:24223126

MicroRNA Expression in Formalin-fixed Paraffin-embedded Cancer Tissue: Identifying Reference MicroRNAs and Variability.

PubMed

Boisen, Mogens Karsbøl; Dehlendorff, Christian; Linnemann, Dorte; Schultz, Nicolai Aagaard; Jensen, Benny Vittrup; Høgdall, Estrid Vilma Solyom; Johansen, Julia Sidenius

2015-12-29

Archival formalin-fixed paraffin-embedded (FFPE) cancer tissue samples are a readily available resource for microRNA (miRNA) biomarker identification. No established standard for reference miRNAs in FFPE tissue exists. We sought to identify stable reference miRNAs for normalization of miRNA expression in FFPE tissue samples from patients with colorectal (CRC) and pancreatic (PC) cancer and to quantify the variability associated with sample age and fixation. High-throughput miRNA profiling results from 203 CRC and 256 PC FFPE samples as well as from 37 paired frozen/FFPE samples from nine other CRC tumors (methodological samples) were used. Candidate reference miRNAs were identified by their correlation with global mean expression. The stability of reference genes was analyzed according to published methods. The association between sample age and global mean miRNA expression was tested using linear regression. Variability was described using correlation coefficients and linear mixed effects models. Normalization effects were determined by changes in standard deviation and by hierarchical clustering. We created lists of 20 miRNAs with the best correlation to global mean expression in each cancer type. Nine of these miRNAs were present in both lists, and miR-103a-3p was the most stable reference miRNA for both CRC and PC FFPE tissue. The optimal number of reference miRNAs was 4 in CRC and 10 in PC. Sample age had a significant effect on global miRNA expression in PC (50% reduction over 20 years) but not in CRC. Formalin fixation for 2-6 days decreased miRNA expression 30-65%. Normalization using global mean expression reduced variability for technical and biological replicates while normalization using the expression of the identified reference miRNAs reduced variability only for biological replicates. Normalization only had a minor impact on clustering results. We identified suitable reference miRNAs for future miRNA expression experiments using CRC- and PC FFPE tissue samples. Formalin fixation decreased miRNA expression considerably, while the effect of increasing sample age was estimated to be negligible in a clinical setting.

Vitrification of neat semen alters sperm parameters and DNA integrity.

PubMed

Khalili, Mohammad Ali; Adib, Maryam; Halvaei, Iman; Nabi, Ali

2014-05-06

Our aim was to evaluate the effect of neat semen vitrification on human sperm vital parameters and DNA integrity in men with normal and abnormal sperm parameters. Semen samples were 17 normozoospermic samples and 17 specimens with abnormal sperm parameters. Semen analysis was performed according to World Health Organization (WHO) criteria. Then, the smear was provided from each sample and fixed for terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining. Vitrification of neat semen was done by plunging cryoloops directly into liquid nitrogen and preserved for 7 days. The samples were warmed and re-evaluated for sperm parameters as well as DNA integrity. Besides, the correlation between sperm parameters and DNA fragmentation was assessed pre- and post vitrification. Cryopreserved spermatozoa showed significant decrease in sperm motility, viability and normal morphology after thawing in both normal and abnormal semen. Also, the rate of sperm DNA fragmentation was significantly higher after vitrification compared to fresh samples in normal (24.76 ± 5.03 and 16.41 ± 4.53, P = .002) and abnormal (34.29 ± 10.02 and 23.5 ± 8.31, P < .0001), respectively. There was negative correlation between sperm motility and sperm DNA integrity in both groups after vitrification. Vitrification of neat ejaculates has negative impact on sperm parameters as well as DNA integrity, particularly among abnormal semen subjects. It is, therefore, recommend to process semen samples and vitrify the sperm pellets.

Considerations for potency equivalent calculations in the Ah receptor-based CALUX bioassay: Normalization of superinduction results for improved sample potency estimation

PubMed Central

Baston, David S.; Denison, Michael S.

2011-01-01

The chemically activated luciferase expression (CALUX) system is a mechanistically based recombinant luciferase reporter gene cell bioassay used in combination with chemical extraction and clean-up methods for the detection and relative quantitation of 2,3,7,8-tetrachlorodibenzo-p-dioxin and related dioxin-like halogenated aromatic hydrocarbons in a wide variety of sample matrices. While sample extracts containing complex mixtures of chemicals can produce a variety of distinct concentration-dependent luciferase induction responses in CALUX cells, these effects are produced through a common mechanism of action (i.e. the Ah receptor (AhR)) allowing normalization of results and sample potency determination. Here we describe the diversity in CALUX response to PCDD/Fs from sediment and soil extracts and not only report the occurrence of superinduction of the CALUX bioassay, but we describe a mechanistically based approach for normalization of superinduction data that results in a more accurate estimation of the relative potency of such sample extracts. PMID:21238730

High throughput image cytometry for detection of suspicious lesions in the oral cavity

NASA Astrophysics Data System (ADS)

MacAulay, Calum; Poh, Catherine F.; Guillaud, Martial; Michele Williams, Pamela; Laronde, Denise M.; Zhang, Lewei; Rosin, Miriam P.

2012-08-01

The successful management of oral cancer depends upon early detection, which relies heavily on the clinician's ability to discriminate sometimes subtle alterations of the infrequent premalignant lesions from the more common reactive and inflammatory conditions in the oral mucosa. Even among experienced oral specialists this can be challenging, particularly when using new wide field-of-view direct fluorescence visualization devices clinically introduced for the recognition of at-risk tissue. The objective of this study is to examine if quantitative cytometric analysis of oral brushing samples could facilitate the assessment of the risk of visually ambiguous lesions. About 369 cytological samples were collected and analyzed: (1) 148 samples from pathology-proven sites of SCC, carcinoma in situ or severe dysplasia; (2) 77 samples from sites with inflammation, infection, or trauma, and (3) 144 samples from normal sites. These were randomly separated into training and test sets. The best algorithm correctly recognized 92.5% of the normal samples, 89.4% of the abnormal samples, 86.2% of the confounders in the training set as well as 100% of the normal samples, and 94.4% of the abnormal samples in the test set. These data suggest that quantitative cytology could reduce by more than 85% the number of visually suspect lesions requiring further assessment by biopsy.

Evaluation of Interleukin-17 and Interleukin-23 in Pterygium: Immunohistochemistry Study.

PubMed

Tiong, Kiew Ing; Mohd Zahidin, Aida Zairani; Sumugam, S Kala A/P; Uchang, Joseph; Mohd Isa, Hazlita Dato'

2017-01-01

To compare the interleukin-17 (IL-17) and interleukin-23 (IL-23) positive cell counts between pterygium and normal conjunctiva. A case-control study. This study received ethical approval (NMRR Research ID 23957) and informed consent was obtained from all participants. It involved 20 participants with 20 samples of pterygium and 20 samples of normal conjunctiva that were obtained from the same eye of each participant. All the participants underwent history taking, slit lamp examination, and pterygium excision surgery. Both samples underwent immunohistochemistry procedure. Pretreatment procedure was conducted using heat-induced epitope retrieval with PT link, subsequently followed by EnVision FLEX staining procedure and incubation with anti‒IL-17 antibody and anti‒IL-23 antibody. Slides were examined in high-power fields (400x) for both samples in 3 different fields. Total positive stained cell counts in all 3 fields with IL-17 and IL-23 between pterygium and normal conjunctiva were analyzed by using Wilcoxon signed rank test. IL-17 positive cell counts for normal conjunctiva showed mean 196.10 ± 80.487 but for pterygium was 331.10 ± 108.416. As for IL-23, the mean for positive cell counts for normal conjunctiva was 62.10 ± 33.462 and IL-23 positive cell counts for pterygium showed mean 102.95 ± 41.378. Both IL-17 and IL-23 were significantly increased in pterygium compared with normal conjunctiva (P < 0.001). Both IL-17 and IL-23 were found to be significantly higher in the pterygium group than in the normal conjunctiva group with P < 0.001 by Wilcoxon signed rank test. Copyright 2017 Asia-Pacific Academy of Ophthalmology.

A systematic evaluation of normalization methods in quantitative label-free proteomics.

PubMed

Välikangas, Tommi; Suomi, Tomi; Elo, Laura L

2018-01-01

To date, mass spectrometry (MS) data remain inherently biased as a result of reasons ranging from sample handling to differences caused by the instrumentation. Normalization is the process that aims to account for the bias and make samples more comparable. The selection of a proper normalization method is a pivotal task for the reliability of the downstream analysis and results. Many normalization methods commonly used in proteomics have been adapted from the DNA microarray techniques. Previous studies comparing normalization methods in proteomics have focused mainly on intragroup variation. In this study, several popular and widely used normalization methods representing different strategies in normalization are evaluated using three spike-in and one experimental mouse label-free proteomic data sets. The normalization methods are evaluated in terms of their ability to reduce variation between technical replicates, their effect on differential expression analysis and their effect on the estimation of logarithmic fold changes. Additionally, we examined whether normalizing the whole data globally or in segments for the differential expression analysis has an effect on the performance of the normalization methods. We found that variance stabilization normalization (Vsn) reduced variation the most between technical replicates in all examined data sets. Vsn also performed consistently well in the differential expression analysis. Linear regression normalization and local regression normalization performed also systematically well. Finally, we discuss the choice of a normalization method and some qualities of a suitable normalization method in the light of the results of our evaluation. © The Author 2016. Published by Oxford University Press.

Biomonitoring of 33 Elements in Blood and Urine Samples from Coastal Populations in Sanmen County of Zhejiang Province.

PubMed

Zhang, Su-jing; Luo, Ru-xin; Ma, Dong; Zhuo, Xian-yi

2016-04-01

To determine the normal reference values of 33 elements, Ag, Al, As, Au, B, Ba, Be, Ca, Cd, Co, Cr, Cs, Cu, Fe, Ga, Hg, Li, Mg, Mn, Mo, Ni, Pb, Rb, Sb, Se, Sr, Th, Ti, Tl, U, V, Zn and Zr, in the blood and urine samples from the general population in Sanmen County of Zhejiang province, a typical coastal area of eastern China. The 33 elements in 272 blood and 300 urine samples were determined by inductively coupled plasma-mass spectrometry (ICP-MS). The normality test of data was conducted using SPSS 17.0 Statistics. The data was compared with other reports. The normal reference values of the 33 elements in the blood and urine samples from the general population in Sanmen County were obtained, which of some elements were found to be similar with other reports, such as Co, Cu, Mn and Sr, while As, Cd, Hg and Pb were generally found to be higher than those previously reported. There was a wide variation between the reports from different countries in blood Ba. The normal reference values of the 33 elements in the blood and urine samples from the general population in Sanmen County are established, and successfully applied to two poisoning cases.

Normally Expected Aberrations in the 8-hour Dynamic EKG

NASA Technical Reports Server (NTRS)

Fleck, R. L.; Arnoldi, L. B.; Townsend, J. C.; Tonesk, X.

1970-01-01

The establishment of norms for interpreting long term dynamic electrocardiograms is attempted by correlating a completely disease symptom and cardiac risk factor free sample with a non-pure sample in the direction of normality on various variables. Out of a population of 362 subjects exposed to dynamic electrocardiogram testing, a discrimination between normals and abnormals in terms of traditional risk factors was observed. The two groups differed significantly on the following variables: cholesterol, smoking, systolic blood pressure, white blood count, fasting blood sugar, uric acid, resting EKG, year of birth, and coronary insufficiency.

Improvement of High-throughput Genotype Analysis After Implementation of a Dual-curve Sybr Green I-based Quantification and Normalization Procedure

USDA-ARS?s Scientific Manuscript database

The ability to rapidly screen a large number of individuals is the key to any successful plant breeding program. One of the primary bottlenecks in high throughput screening is the preparation of DNA samples, particularly the quantification and normalization of samples for downstream processing. A ...

Tissue spray ionization mass spectrometry for rapid recognition of human lung squamous cell carcinoma

NASA Astrophysics Data System (ADS)

Wei, Yiping; Chen, Liru; Zhou, Wei; Chingin, Konstantin; Ouyang, Yongzhong; Zhu, Tenggao; Wen, Hua; Ding, Jianhua; Xu, Jianjun; Chen, Huanwen

2015-05-01

Tissue spray ionization mass spectrometry (TSI-MS) directly on small tissue samples has been shown to provide highly specific molecular information. In this study, we apply this method to the analysis of 38 pairs of human lung squamous cell carcinoma tissue (cancer) and adjacent normal lung tissue (normal). The main components of pulmonary surfactants, dipalmitoyl phosphatidylcholine (DPPC, m/z 757.47), phosphatidylcholine (POPC, m/z 782.52), oleoyl phosphatidylcholine (DOPC, m/z 808.49), and arachidonic acid stearoyl phosphatidylcholine (SAPC, m/z 832.43), were identified using high-resolution tandem mass spectrometry. Monte Carlo sampling partial least squares linear discriminant analysis (PLS-LDA) was used to distinguish full-mass-range mass spectra of cancer samples from the mass spectra of normal tissues. With 5 principal components and 30 - 40 Monte Carlo samplings, the accuracy of cancer identification in matched tissue samples reached 94.42%. Classification of a tissue sample required less than 1 min, which is much faster than the analysis of frozen sections. The rapid, in situ diagnosis with minimal sample consumption provided by TSI-MS is advantageous for surgeons. TSI-MS allows them to make more informed decisions during surgery.

Cy5 total protein normalization in Western blot analysis.

PubMed

Hagner-McWhirter, Åsa; Laurin, Ylva; Larsson, Anita; Bjerneld, Erik J; Rönn, Ola

2015-10-01

Western blotting is a widely used method for analyzing specific target proteins in complex protein samples. Housekeeping proteins are often used for normalization to correct for uneven sample loads, but these require careful validation since expression levels may vary with cell type and treatment. We present a new, more reliable method for normalization using Cy5-prelabeled total protein as a loading control. We used a prelabeling protocol based on Cy5 N-hydroxysuccinimide ester labeling that produces a linear signal response. We obtained a low coefficient of variation (CV) of 7% between the ratio of extracellular signal-regulated kinase (ERK1/2) target to Cy5 total protein control signals over the whole loading range from 2.5 to 20.0μg of Chinese hamster ovary cell lysate protein. Corresponding experiments using actin or tubulin as controls for normalization resulted in CVs of 13 and 18%, respectively. Glyceraldehyde-3-phosphate dehydrogenase did not produce a proportional signal and was not suitable for normalization in these cells. A comparison of ERK1/2 signals from labeled and unlabeled samples showed that Cy5 prelabeling did not affect antibody binding. By using total protein normalization we analyzed PP2A and Smad2/3 levels with high confidence. Copyright © 2015 Elsevier Inc. All rights reserved.

Subtle imitation behaviour in convenience samples of normal, demented, and currently depressed elderly subjects.

PubMed

von Gunten, Armin; Duc, René

2007-06-01

The clinical significance of imitation behaviour (IB) is unclear. The aim of this study was to investigate the prevalence of subtle naïve and obstinate IB in convenience samples of normal elderly, demented, and depressed subjects. Subtle IB was assessed using a protocol constructed ad hoc in 146 patients, consecutively referred to a memory clinic having received an ICD-10 diagnosis of either dementia or depression, and in 241 healthy subjects. The prevalence of IB in the three groups was determined and the association with possible demographic, cognitive, and non-cognitive variables analysed. Subtle naïve IB was frequent in the elderly with dementia, intermediate in the depressed, and rare in the normal elderly except that the latter frequently stretched out their arms. Obstinate IB never occurred in the normal elderly. IB was predicted by none of the variables used. The groups included were convenience samples with the depressed being a small group precluding further distinction of depressive subtypes. Although naïve IB is a frequent clinical feature in the demented, it also accompanies depressive disorders in the elderly. It can be observed as context-specific IB in the normal elderly. Obstinate IB does not occur in the normal elderly. Copyright 2006 John Wiley & Sons, Ltd.

Differential Expression of c-fos Proto-Oncogene in Normal Oral Mucosa versus Squamous Cell Carcinoma

PubMed Central

Krishna, Akhilesh; Bhatt, Madan Lal Brahma; Singh, Vineeta; Singh, Shraddha; Gangwar, Pravin Kumar; Singh, Uma Shankar; Kumar, Vijay; Mehrotra, Divya

2018-01-01

Background: The c-Fos nuclear protein dimerizes with Jun family proteins to form the transcription factor AP-1 complex which participates in signal transduction and regulation of normal cellular processes. In tumorigenesis, c-Fos promotes invasive growth through down-regulation of tumor suppressor genes but its role in oral carcinogenesis is not clear. Objectives: This study concerned c-fos gene expression in normal and malignant tissues of the oral cavity, with attention to associations between expression status and clinico-pathological profiles of OSCC patients. Method: A total of 65 histopathologically confirmed OSCC tissue samples were included in case group along with an equal number of age and sex-matched normal tissue samples of oral cavity for the control group. c-Fos protein and m-RNA expressions were analyzed using immunohistochemistry and qRT-PCR, respectively. Results: A significant low expression of c-Fos protein was observed in OSCC cases than normal control subjects (p= <0.001). The mean percent positivity of c-Fos protein in cases vs. controls was 24.91± 2.7 vs. 49.68± 2.2 (p= <0.001). Most OSCC tissue samples showed weak or moderate c-Fos expression whereas 53.8% of normal tissue sections presented with strong immunostaining. Moreover, the relative m-RNA expression for the c-fos gene was significantly decreased in case group (0.93± 0.48) as compared to the control group (1.22± 0.87). Majority of c-Fos positive cases were diagnosed with well developed tumor. The mean percent positivity of c-Fos protein was significantly lower in higher grade tumor as compared with normal oral mucosa (p= < 0.001). Conclusion: The present study suggested that the c-fos gene is downregulated in oral carcinomas. The disparity of c-Fos protein levels in different pathological grades of tumor and normal oral tissue samples may indicate that loss of c-Fos expression is related with the progression of OSCC. PMID:29582647

Application of Monte Carlo cross-validation to identify pathway cross-talk in neonatal sepsis.

PubMed

Zhang, Yuxia; Liu, Cui; Wang, Jingna; Li, Xingxia

2018-03-01

To explore genetic pathway cross-talk in neonates with sepsis, an integrated approach was used in this paper. To explore the potential relationships between differently expressed genes between normal uninfected neonates and neonates with sepsis and pathways, genetic profiling and biologic signaling pathway were first integrated. For different pathways, the score was obtained based upon the genetic expression by quantitatively analyzing the pathway cross-talk. The paired pathways with high cross-talk were identified by random forest classification. The purpose of the work was to find the best pairs of pathways able to discriminate sepsis samples versus normal samples. The results found 10 pairs of pathways, which were probably able to discriminate neonates with sepsis versus normal uninfected neonates. Among them, the best two paired pathways were identified according to analysis of extensive literature. Impact statement To find the best pairs of pathways able to discriminate sepsis samples versus normal samples, an RF classifier, the DS obtained by DEGs of paired pathways significantly associated, and Monte Carlo cross-validation were applied in this paper. Ten pairs of pathways were probably able to discriminate neonates with sepsis versus normal uninfected neonates. Among them, the best two paired pathways ((7) IL-6 Signaling and Phospholipase C Signaling (PLC); (8) Glucocorticoid Receptor (GR) Signaling and Dendritic Cell Maturation) were identified according to analysis of extensive literature.

Use of the Keele injector for sample introduction for gas chromatographic analysis of vinclozolin in lettuces.

PubMed

Shim, J H; Lee, Y S; Kim, M R; Lee, C J; Kim, I S

2003-10-10

We examined a Keele injector for sample introduction for gas chromatographic analysis of vinclozolin treated in lettuces. Samples in milligram quantity were introduced into a glass tube in a Keele injector at a gas chromatograph injection port. The glass tube was then crushed to allow the sample to carry onto a capillary column in a normal manner. The standard calibration curve for quantitative detection of vinclozolin was obtained by determining vinclozolin spiked in samples at variable concentrations. The calibration curve showed a linear response to vinclozolin ranging from 0.05 to 1.0 microg/g, giving a slope value of 174.8, the y-intercept value of -2.8146 and the mean r2-value of 0.9994. Limit of quantification for vinclozolin was 0.05 microg/g by this method, comparable to 0.01 microg/g by a normal injector. When samples treated previously with vinclozolin were determined by the Keele injector, vinclozolin was found to be about 30% lower as compared to a normal method, suggesting about 70% recovery of the spiked vinclozolin by the Keele injector. From these results, the Keele injector was suggested to be potential for sample introduction in gas chromatographic analysis of vinclozolin in lettuce samples.

Sexual self-esteem in mothers of normal and mentally-retarded children.

PubMed

Tavakolizadeh, Jahanshir; Amiri, Mostafa; Nejad, Fahimeh Rastgoo

2017-06-01

Sexual self-esteem is negatively influenced by the stressful experiences in lifetime. This study compared the sexual self-esteem and its components in mothers with normal and mentally-retarded children in Qaen city, in 2014. A total of 120 mothers were selected and assigned into two groups of 60 samples based on convenient sampling method and randomized multiple stage sampling. Both groups completed sexual self-esteem questionnaire. The data were analyzed employing t-test through SPSS software version15. The results showed that the rate of sexual self-esteem in mothers of mentally-retarded children decreased significantly compared with that of mothers with normal children (p<0.05). Moreover, the mean scores of all components of sexual self-esteem including skill and experience, attractiveness, control, moral judgment, and adaptiveness in mothers of mentally-retarded children were significantly less than those of mothers with normal children (p <0.05). Therefore, it is recommended that self-esteem, especially the sexual one, be taught to mothers of mentally-retarded children by specialists.

Normalized stiffness ratios for mechanical characterization of isotropic acoustic foams.

PubMed

Sahraoui, Sohbi; Brouard, Bruno; Benyahia, Lazhar; Parmentier, Damien; Geslain, Alan

2013-12-01

This paper presents a method for the mechanical characterization of isotropic foams at low frequency. The objective of this study is to determine the Young's modulus, the Poisson's ratio, and the loss factor of commercially available foam plates. The method is applied on porous samples having square and circular sections. The main idea of this work is to perform quasi-static compression tests of a single foam sample followed by two juxtaposed samples having the same dimensions. The load and displacement measurements lead to a direct extraction of the elastic constants by means of normalized stiffness and normalized stiffness ratio which depend on Poisson's ratio and shape factor. The normalized stiffness is calculated by the finite element method for different Poisson ratios. The no-slip boundary conditions imposed by the loading rigid plates create interfaces with a complex strain distribution. Beforehand, compression tests were performed by means of a standard tensile machine in order to determine the appropriate pre-compression rate for quasi-static tests.

The Power of Exclusion using Automated Osteometric Sorting: Pair-Matching.

PubMed

Lynch, Jeffrey James; Byrd, John; LeGarde, Carrie B

2018-03-01

This study compares the original pair-matching osteometric sorting model (J Forensic Sci 2003;48:717) against two new models providing validation and performance testing across three samples. The samples include the Forensic Data Bank, USS Oklahoma, and the osteometric sorting reference used within the Defense POW/MIA Accounting Agency. A computer science solution to generating dynamic statistical models across a commingled assemblage is presented. The issue of normality is investigated showing the relative robustness against non-normality and a data transformation to control for normality. A case study is provided showing the relative exclusion power of all three models from an active commingled case within the Defense POW/MIA Accounting Agency. In total, 14,357,220 osteometric t-tests were conducted. The results indicate that osteometric sorting performs as expected despite reference samples deviating from normality. The two new models outperform the original, and one of those is recommended to supersede the original for future osteometric sorting work. © 2017 American Academy of Forensic Sciences.

Normal Approximations to the Distributions of the Wilcoxon Statistics: Accurate to What "N"? Graphical Insights

ERIC Educational Resources Information Center

Bellera, Carine A.; Julien, Marilyse; Hanley, James A.

2010-01-01

The Wilcoxon statistics are usually taught as nonparametric alternatives for the 1- and 2-sample Student-"t" statistics in situations where the data appear to arise from non-normal distributions, or where sample sizes are so small that we cannot check whether they do. In the past, critical values, based on exact tail areas, were…

Sensory Motor Inhibition as a Prerequisite for Theory-of-Mind: A Comparison of Clinical and Normal Preschoolers Differing in Sensory Motor Abilities

ERIC Educational Resources Information Center

Chasiotis, Athanasios; Kiessling, Florian; Winter, Vera; Hofer, Jan

2006-01-01

After distinguishing between neocortical abilities for executive control and subcortical sensory motor skills for proprioceptive and vestibular integration, we compare a sample of 116 normal preschoolers with a sample of 31 preschoolers receiving occupational therapeutical treatment. This is done in an experimental design controlled for age (mean:…

Laboratory-based ROTEM(®) analysis: implementing pneumatic tube transport and real-time graphic transmission.

PubMed

Colucci, G; Giabbani, E; Barizzi, G; Urwyler, N; Alberio, L

2011-08-01

ROTEM(®) is considered a helpful point-of-care device to monitor blood coagulation. Centrally performed analysis is desirable but rapid transport of blood samples and real-time transmission of graphic results are an important prerequisite. The effect of sample transport through a pneumatic tube system on ROTEM(®) results is unknown. The aims of the present work were (i) to determine the influence of blood sample transport through a pneumatic tube system on ROTEM(®) parameters compared to manual transportation, and (ii) to verify whether graphic results can be transmitted on line via virtual network computing using local area network to the physician in charge of the patient. Single centre study with 30 normal volunteers. Two whole blood samples were transferred to the central haematology laboratory by either normal transport or pneumatic delivery. EXTEM, INTEM, FIBTEM and APTEM were analysed in parallel with two ROTEM(®) devices and compared. Connection between central laboratory, emergency and operating rooms was established using local area network. All collected ROTEM(®) parameters were within normal limits. No statistically significant differences between normal transport and pneumatic delivery were observed. Real-time transmission of the original ROTEM(®) curves using local area network is feasible and easy to establish. At our institution, transport of blood samples by pneumatic delivery does not influence ROTEM(®) parameters. Blood samples can be analysed centrally, and results transmitted live via virtual network computing to emergency or operating rooms. Prior to analyse blood samples centrally, the type of sample transport should be tested to exclude in vitro blood activation by local pneumatic transport system. © 2011 Blackwell Publishing Ltd.

COX-2 expression in canine anal sac adenocarcinomas and in non-neoplastic canine anal sacs.

PubMed

Knudsen, C S; Williams, A; Brearley, M J; Demetriou, J L

2013-09-01

Anal sac adenocarcinoma (ASAC) is a clinically significant canine neoplasm characterized by early lymphatic invasion. Up-regulation of cyclooxygenase isoform 2 (COX-2) has been confirmed in several animal and human neoplastic tissues. The aim of the current study was primarily to evaluate COX-2 expression in canine ASAC and compare it to COX-2 expression in non-neoplastic canine anal sac tissue using immunohistochemistry with scoring for percentage positivity and intensity. Twenty-five ASAC samples and 22 normal anal sacs were available for evaluation. All canine ASAC samples and the normal anal sac tissues stained positively for COX-2. However, while normal anal sac tissue showed strong staining of the ductal epithelial cells, ASAC samples showed staining of the neoplastic glandular epithelial cells, with varying percentage positivity and intensity between ASAC samples. COX-2 immunoreactivity of ASAC samples was of low intensity in 52% and high in 12% of the cases; the remaining samples were of intermediate intensity. Seventy-six per cent of the ASAC had over 50% of the neoplastic glandular cells staining positive. These results confirm that COX-2 is expressed in the neoplastic glandular epithelial cells in canine ASAC and suggest a potential role for COX-2 inhibitors in the management of ASAC. Furthermore, the results indicate that COX-2 is expressed in ductal epithelial cells of the normal anal sac. Copyright © 2013 Elsevier Ltd. All rights reserved.

Array-based comparative genomic hybridization-guided identification of reference genes for normalization of real-time quantitative polymerase chain reaction assay data for lymphomas, histiocytic sarcomas, and osteosarcomas of dogs.

PubMed

Tsai, Pei-Chien; Breen, Matthew

2012-09-01

To identify suitable reference genes for normalization of real-time quantitative PCR (RT-qPCR) assay data for common tumors of dogs. Malignant lymph node (n = 8), appendicular osteosarcoma (9), and histiocytic sarcoma (12) samples and control samples of various nonneoplastic canine tissues. Array-based comparative genomic hybridization (aCGH) data were used to guide selection of 9 candidate reference genes. Expression stability of candidate reference genes and 4 commonly used reference genes was determined for tumor samples with RT-qPCR assays and 3 software programs. LOC611555 was the candidate reference gene with the highest expression stability among the 3 tumor types. Of the commonly used reference genes, expression stability of HPRT was high in histiocytic sarcoma samples, and expression stability of Ubi and RPL32 was high in osteosarcoma samples. Some of the candidate reference genes had higher expression stability than did the commonly used reference genes. Data for constitutively expressed genes with high expression stability are required for normalization of RT-qPCR assay results. Without such data, accurate quantification of gene expression in tumor tissue samples is difficult. Results of the present study indicated LOC611555 may be a useful RT-qPCR assay reference gene for multiple tissue types. Some commonly used reference genes may be suitable for normalization of gene expression data for tumors of dogs, such as lymphomas, osteosarcomas, or histiocytic sarcomas.

Evaluation of Bias-Variance Trade-Off for Commonly Used Post-Summarizing Normalization Procedures in Large-Scale Gene Expression Studies

PubMed Central

Qiu, Xing; Hu, Rui; Wu, Zhixin

2014-01-01

Normalization procedures are widely used in high-throughput genomic data analyses to remove various technological noise and variations. They are known to have profound impact to the subsequent gene differential expression analysis. Although there has been some research in evaluating different normalization procedures, few attempts have been made to systematically evaluate the gene detection performances of normalization procedures from the bias-variance trade-off point of view, especially with strong gene differentiation effects and large sample size. In this paper, we conduct a thorough study to evaluate the effects of normalization procedures combined with several commonly used statistical tests and MTPs under different configurations of effect size and sample size. We conduct theoretical evaluation based on a random effect model, as well as simulation and biological data analyses to verify the results. Based on our findings, we provide some practical guidance for selecting a suitable normalization procedure under different scenarios. PMID:24941114

An investigation into the enzyme histochemistry of adenocarcinomas of human large intestine and of the transitional epithelium immediately adjacent to them

PubMed Central

Marsden, J. R.; Dawson, I. M. P.

1974-01-01

Histochemical enzymatic studies were performed on 30 freshly resected large bowel carcinomas, 30 samples of normal colonic epithelium, and six samples of the histologically normal epithelium (so-called transitional epithelium) immediately adjacent to a carcinoma. Five enzymes were studied: nicotine adenine dinucleotide tetrazolium reductase (NADH-TR), glucose-6-phosphate dehydrogenase, succinate dehydrogenase, monoamine oxidase, and acid phosphatase. Quantitative and qualitative differences in enzyme activity were observed between normal, transitional, and carcinomatous mucosa as follows: monoamine oxidase activity was moderate in normal mucosa, high in transitional mucosa, and low in carcinoma. Succinate dehydrogenase activity was high in transitional mucosa and low or moderate in normal and carcinomatous mucosa. Glucose-6-phosphate dehydrogenase activity showed a gradation from low in normal mucosa to high in carcinoma while acid phosphatase showed the reverse of this pattern. The tetrazolium reductase activity was low or moderate in normal and transitional mucosa and high in carcinoma. These differences in enzyme activity and their possible clinical and metabolic significance are discussed. ImagesFig 2Fig 3 PMID:4154840

Optimal consistency in microRNA expression analysis using reference-gene-based normalization.

PubMed

Wang, Xi; Gardiner, Erin J; Cairns, Murray J

2015-05-01

Normalization of high-throughput molecular expression profiles secures differential expression analysis between samples of different phenotypes or biological conditions, and facilitates comparison between experimental batches. While the same general principles apply to microRNA (miRNA) normalization, there is mounting evidence that global shifts in their expression patterns occur in specific circumstances, which pose a challenge for normalizing miRNA expression data. As an alternative to global normalization, which has the propensity to flatten large trends, normalization against constitutively expressed reference genes presents an advantage through their relative independence. Here we investigated the performance of reference-gene-based (RGB) normalization for differential miRNA expression analysis of microarray expression data, and compared the results with other normalization methods, including: quantile, variance stabilization, robust spline, simple scaling, rank invariant, and Loess regression. The comparative analyses were executed using miRNA expression in tissue samples derived from subjects with schizophrenia and non-psychiatric controls. We proposed a consistency criterion for evaluating methods by examining the overlapping of differentially expressed miRNAs detected using different partitions of the whole data. Based on this criterion, we found that RGB normalization generally outperformed global normalization methods. Thus we recommend the application of RGB normalization for miRNA expression data sets, and believe that this will yield a more consistent and useful readout of differentially expressed miRNAs, particularly in biological conditions characterized by large shifts in miRNA expression.

Terahertz spectroscopy for the study of paraffin-embedded gastric cancer samples

NASA Astrophysics Data System (ADS)

Wahaia, Faustino; Kasalynas, Irmantas; Seliuta, Dalius; Molis, Gediminas; Urbanowicz, Andrzej; Carvalho Silva, Catia D.; Carneiro, Fatima; Valusis, Gintaras; Granja, Pedro L.

2015-01-01

Terahertz (THz) spectroscopy constitute promising technique for biomedical applications as a complementary and powerful tool for diseases screening specially for early cancer diagnostic. The THz radiation is not harmful to biological tissues. As increased blood supply in cancer-affected tissues and consequent local increase in tissue water content makes THz technology a potentially attractive. In the present work, samples of healthy and adenocarcinoma-affected gastric tissue were analyzed using transmission time-domain THz spectroscopy (THz-TDS). The work shows the capability of the technique to distinguish between normal and cancerous regions in dried and paraffin-embedded samples. Plots of absorption coefficient α and refractive index n of normal and cancer affected tissues, are presented and the conditions for discrimination between normal and affected tissues are discussed.

MicroRNA array normalization: an evaluation using a randomized dataset as the benchmark.

PubMed

Qin, Li-Xuan; Zhou, Qin

2014-01-01

MicroRNA arrays possess a number of unique data features that challenge the assumption key to many normalization methods. We assessed the performance of existing normalization methods using two microRNA array datasets derived from the same set of tumor samples: one dataset was generated using a blocked randomization design when assigning arrays to samples and hence was free of confounding array effects; the second dataset was generated without blocking or randomization and exhibited array effects. The randomized dataset was assessed for differential expression between two tumor groups and treated as the benchmark. The non-randomized dataset was assessed for differential expression after normalization and compared against the benchmark. Normalization improved the true positive rate significantly in the non-randomized data but still possessed a false discovery rate as high as 50%. Adding a batch adjustment step before normalization further reduced the number of false positive markers while maintaining a similar number of true positive markers, which resulted in a false discovery rate of 32% to 48%, depending on the specific normalization method. We concluded the paper with some insights on possible causes of false discoveries to shed light on how to improve normalization for microRNA arrays.

MicroRNA Array Normalization: An Evaluation Using a Randomized Dataset as the Benchmark

PubMed Central

Qin, Li-Xuan; Zhou, Qin

2014-01-01

MicroRNA arrays possess a number of unique data features that challenge the assumption key to many normalization methods. We assessed the performance of existing normalization methods using two microRNA array datasets derived from the same set of tumor samples: one dataset was generated using a blocked randomization design when assigning arrays to samples and hence was free of confounding array effects; the second dataset was generated without blocking or randomization and exhibited array effects. The randomized dataset was assessed for differential expression between two tumor groups and treated as the benchmark. The non-randomized dataset was assessed for differential expression after normalization and compared against the benchmark. Normalization improved the true positive rate significantly in the non-randomized data but still possessed a false discovery rate as high as 50%. Adding a batch adjustment step before normalization further reduced the number of false positive markers while maintaining a similar number of true positive markers, which resulted in a false discovery rate of 32% to 48%, depending on the specific normalization method. We concluded the paper with some insights on possible causes of false discoveries to shed light on how to improve normalization for microRNA arrays. PMID:24905456

Vector wind and vector wind shear models 0 to 27 km altitude for Cape Kennedy, Florida, and Vandenberg AFB, California

NASA Technical Reports Server (NTRS)

Smith, O. E.

1976-01-01

The techniques are presented to derive several statistical wind models. The techniques are from the properties of the multivariate normal probability function. Assuming that the winds can be considered as bivariate normally distributed, then (1) the wind components and conditional wind components are univariate normally distributed, (2) the wind speed is Rayleigh distributed, (3) the conditional distribution of wind speed given a wind direction is Rayleigh distributed, and (4) the frequency of wind direction can be derived. All of these distributions are derived from the 5-sample parameter of wind for the bivariate normal distribution. By further assuming that the winds at two altitudes are quadravariate normally distributed, then the vector wind shear is bivariate normally distributed and the modulus of the vector wind shear is Rayleigh distributed. The conditional probability of wind component shears given a wind component is normally distributed. Examples of these and other properties of the multivariate normal probability distribution function as applied to Cape Kennedy, Florida, and Vandenberg AFB, California, wind data samples are given. A technique to develop a synthetic vector wind profile model of interest to aerospace vehicle applications is presented.

[Intraocular and serum antibody titers to Leptospira in 150 horses with equine recurrent uveitis (ERU) subjected to vitrectomy].

PubMed

Wollanke, B; Gerhards, H; Brem, S; Kopp, H; Meyer, P

1998-04-01

Between February 1993 and July 1997, 150 horses suffering from recurrent uveitis were subjected to parsplana vitrectomy. In these horses, antibody titers to Leptospira serovars were determined in serum samples and in samples from diluted vitreous collected during vitrectomy. Although the vitreous samples were diluted with 250 ml of balanced salt solution, in 86 of the 150 vitreous samples (= 57%) the antibody titers were higher than in the serum samples. Additionally, serum samples from 77 horses suffering from ERU, but which were not subjected to vitrectomy, and serum samples from 97 horses with clinically normal eyes were analyzed for antibodies to Leptospira serovars. Among the 227 horses with ERU (150 treated surgically, 77 treated conservatively) 50 horses (50 of 227 = 22%) had serum antibody titers to Leptospira serovars of > or = 1:800. Among the 97 horses with clinically normal eyes, 24 horses (24 of 97 = 25%) had serum antibody titers to Leptospira serovars of > or = 1:800. In undiluted vitreous samples from 20 horses with clinically normal eyes, no antibody titers to Leptospira serovars could be detected. Among the 150 horses with ERU, 90 animals (90 of 150 = 60%) had antibody titers of > or = 1:100 in the diluted vitreous samples, the difference being highly significant (p < 0.001). The findings are discussed in relation to the etiology of recurrent uveitis in horses.

Intrinsic fluorescence based in-vivo detection of cervical precancer with hand held prototype device

NASA Astrophysics Data System (ADS)

Meena, Bharat Lal; Raikwar, Akanksha; Pandey, Kiran; Agarwal, Asha; Pantola, Chayanika; Pradhan, Asima

2018-02-01

A prototype device (hand held probe) designed and fabricated in the lab has been tested for cervical precancer detection using intrinsic fluorescence. The intrinsic fluorescence gets strongly modulated by the interplay of scattering and absorption. This masks valuable biochemical information which is present in the intrinsic fluorescence. These distortion effects can be minimized by normalizing the polarized fluorescence spectra by the polarized elastic scattering spectra. The measurements have been made with a in-house fabricated device using a 405 nm diode laser and white light source respectively. 166 sites of different grades of cervical pre-cancer biopsy samples (CIN I and CIN II) (CIN: cervical intraepithelial neoplastic) have been discriminated from 29 sites of normal biopsy samples using principal component analysis (PCA) based linear discriminant analysis (LDA). The sensitivity and specificity for discrimination of normal samples from CIN I are found to be 99% and 96% respectively. Further the normal samples can be discriminated from CIN II samples with 96% sensitivity and 96% specificity. Based on these promising ex-vivo results an in-vivo study on patients has been initiated in the hospital. The hand held device built in-house shows promise as a useful tool for in vivo cervical precancer detection by polarized fluorescence. Preliminary in-vivo results on 10 patients indicate the efficacy of the hand held device for screening cervical precancers using intrinsic fluorescence.

The behaviour of cross-helicity and residual energy at different heliolatitudes - Ulysses data

NASA Astrophysics Data System (ADS)

Popescu, Emil; Popescu, Nedelia Antonia

In this paper we analyze the variations of the normalized cross-helicity (?C ) and normalized residual energy (σR), that characterize the Alfvenic fluctuations in the solar wind. For this purpose we consider data from SWOOPS and VHM instruments on board of Ulysses mission, for solar wind plasma parameters and magnetic field data, for the year 2001. In order to analyze the behaviour of the normalized cross-helicity, σC, and normalized residual energy, σR, at different heliolatitudes, as well as the relation between σR and σC, we determine their distributions for three periods of time: DOY 240 - DOY 348 (for a data sample at high heliolatitudes, between 69°N - 82.2°N), DOY 154 - DOY 181.5 (for a data sample at middle heliolatitudes, between 15°N - 35°N), and DOY 88 - DOY 118 (for a data sample at middle heliolatitudes, between 15°S - 35°S). The results on the residual energy σR versus cross-helicity σC distribution reveal a middle heliolatitude data sample that presents a more dispersed distribution than the high heliolatitude data sample. A different behaviour of the σC distributions was observed for the periods covering the middle heliolatitudes for the southern and northern hemispheres. This is because during the third period of time, transient events as ICMEs with strong magnetic field strength and high velocity are encountered.

Glucose transporter-1 (GLUT-1) immunoreactivity in benign, premalignant and malignant lesions of the gallbladder.

PubMed

Legan, Mateja; Tevžič, Spela; Tolar, Ana; Luzar, Boštjan; Marolt, Vera Ferlan

2011-03-01

GLUT-1 is a transmembrane glucose transport protein that allows the facilitated transport of glucose into cells, normally expressed in tissues which depend mainly on glucose metabolism. Enhanced expression of GLUT-1 can also be found in a large spectrum of carcinomas. This study aimed to investigate GLUT-1 expression in gallbladder tissue: from normal tissue samples, hyperplasias, low-grade and high-grade dysplasias to gallbladder carcinomas. In all, 115 archived samples of gallbladder tissue from 68 patients, presented after cholecystectomy, were immunohistochemically stained for GLUT-1. According to the intensity of GLUT-1 immunoreactivity, samples were divided into negative (stained 0-10% of cells stained), positive with weak to moderate (10-50%) and positive with strong (>50%) GLUT-1 expression. The GLUT-1 immunoreactivity of the samples showed a characteristic increase from premalignant lesions to carcinomas. Normal gallbladder tissue samples did not express GLUT-1 (100%). Weak expression was shown only focally in hyperplasias, but to a greater extent with low-grade dysplasias (20%), high-grade dysplasias (40%) and carcinomas (51.8%). Normal gallbladder tissue is GLUT-1 negative. GLUT-1 expression in carcinoma tissue is significantly higher than in dysplastic lesions. Strong GLUT-1 expression indicates 100% specificity for detecting gallbladder carcinomas. Therefore, GLUT-1 is a candidate as a diagnostic as well as a tissue prognostic marker in gallbladder carcinoma patients.

Spray Dried Chitosan Microparticles for Intravesical Delivery of Celecoxib: Preparation and Characterization.

PubMed

Lopedota, Angela; Cutrignelli, Annalisa; Laquintana, Valentino; Denora, Nunzio; Iacobazzi, Rosa Maria; Perrone, Mara; Fanizza, Elisabetta; Mastrodonato, Maria; Mentino, Donatella; Lopalco, Antonio; Depalo, Nicoletta; Franco, Massimo

2016-09-01

Chitosan microparticles containing celecoxib (CB), were developed as chemoprevention of bladder cancer. Furthermore two inclusion complexes of CB with methyl-β-cyclodextrin (C1 and C2) were prepared to improve the solubility of the drug. C1 and C2 were obtained by freeze-drying and characterized in the solid state and in solution. Microparticles loaded with CB or C1 or C2 were prepared by spray drying and fully characterized. The yield and encapsulation efficiencies of microparticles depended by both the viscosity and the presence of the inclusion complex in the feed medium nebulised. Generally, the microparticles exhibited a spherical shape with mean diameter of approximately 2 μm which was compatible with local intravesical administration using a catheter. The CB release studies from the microparticles allowed us to identify both immediate release systems (microparticles including the complexes) and prolonged release systems (microparticles including CB alone). The latter exhibited good adhesion to the bladder mucosa, as highlighted by a mucoadhesion study. Histological studies revealed a desquamation of the superficial cells when the bladder mucosa was treated with microparticles loaded with CB, while the morphology of the urothelium did not change when it was treated with microparticles loaded with the inclusion complex. A new CB intravesical formulation than can easily be administered with a catheter and is able to release the drug at the target site for several hours was realized. This new delivery system could be a good alternative to classic oral CB administration.

Repellent and mosquitocidal effects of leaf extracts of Clausena anisata against the Aedes aegypti mosquito (Diptera: Culicidae).

PubMed

Mukandiwa, Lillian; Eloff, Jacobus Nicolaas; Naidoo, Vinny

2016-06-01

Mosquitoes are rapidly developing resistance to insecticides that millions of people relied on to protect themselves from the diseases they carry, thereby creating a need to develop new insecticides. Clausena anisata is used traditionally as an insect repellent by various communities in Africa and Asia. For this study, the repellency and adulticidal activities of leaf extracts and compounds isolated from this plant species were evaluated against the yellow fever mosquito, Aedes aegypti. In the topical application assays, using total bites as an indicator, repellency was dose dependent, with the acetone crude extract (15 %) having 93 % repellence and the hexane fraction (7.5 %) 67 % repellence after 3 h. Fractionation resulted in a loss of total repellence. As mosquito-net treating agents, the acetone and hexane extracts of C. anisata, both at 15 %, had average repellences of 46.89 ± 2.95 and 50.13 ± 2.02 %, respectively, 3 h after exposure. The C. anisata acetone extract and its hexane fraction caused mosquito knockdown and eventually death when nebulised into the testing chamber, with an EC50 of 78.9 mg/ml (7.89 %) and 71.6 mg/ml (7.16 %) in the first 15 min after spraying. C. anisata leaf extracts have potential to be included in protection products against mosquitoes due to the repellent and cidal compounds contained therein.

Subcutaneous adrenaline versus terbutaline in the treatment of acute severe asthma.

PubMed Central

Spiteri, M A; Millar, A B; Pavia, D; Clarke, S W

1988-01-01

Subcutaneous adrenaline and terbutaline have been compared in a double blind study of 20 patients with acute severe asthma presenting to an accident and emergency department. Ten patients received adrenaline 0.5 mg (0.5 ml) and 10 terbutaline 0.5 mg (0.5 ml) subcutaneously. Further treatment with nebulised salbutamol (5 mg), hydrocortisone (200 mg), and aminophylline (0.9 mg/kg/hour) was started 15 minutes later. All patients reported a reduction in chest tightness within three minutes of receiving both adrenaline and terbutaline and reported no adverse effects. Mean baseline values of peak expiratory flow (PEF) and forced expiratory volume in one second (FEV1) did not differ significantly between the adrenaline group (130 1 min-1 and 0.83 l) and the terbutaline group (111 1 min-1 and 0.63 l). After administration of adrenaline PEF had increased by 21% and FEV1 by 40% five minutes after the injection, and by 35% and 64% at 15 minutes. Terbutaline caused a 23% increase in PEF and a 37% increase in FEV1 at five minutes, and a 40% and 58% increase at 15 minutes. There was no significant difference in PEF, FEV1, heart rate, blood pressure, or pulsus paradoxus between the two groups at any time. Continuous electrocardiographic recording showed no abnormalities in either group. Thus in this study subcutaneous adrenaline (0.5 mg) and terbutaline (0.5 mg) produced effective rapid bronchodilatation without serious side effects. PMID:3281307

Management of hyperkalaemia.

PubMed

Maxwell, A P; Linden, K; O'Donnell, S; Hamilton, P K; McVeigh, G E

2013-01-01

Hyperkalaemia, an elevated extracellular fluid potassium concentration, is a common electrolyte disorder and is present in 1-10% of hospitalised patients. Elevated serum potassium concentrations are usually asymptomatic but may be associated with electrocardiogram (ECG) changes. Hyperkalaemia occasionally leads to life-threatening cardiac arrhythmias. Prompt recognition of this disorder, patient risk management and administration of appropriate treatment can prevent serious cardiac complications of hyperkalaemia. Further assessment of the underlying basis for hyperkalaemia usually reveals a problem with renal potassium excretion (rather than transcellular shift of potassium or excess potassium intake). Reduced potassium excretion is typically associated with decreased potassium secretion in the aldosterone-sensitive distal nephron of the kidney. Common causes for hyperkalaemia include kidney failure, limited delivery of sodium and water to the distal nephron and drugs that inhibit the renin-angiotensin-aldosterone system. Treatment of life-threatening hyperkalaemia (particularly those patients with ECG changes) involves administration of intravenous calcium salts to stabilise the resting cardiac membrane potential. The potassium concentration can be lowered by administration of intravenous insulin combined with an infusion of glucose to stimulate intracellular uptake of potassium. Nebulised β-2 adrenoceptor agonists can augment the effects of intravenous insulin and glucose pending more definitive management of the recurrent hyperkalaemia risk. Additional management steps include stopping further potassium intake and careful review of prescribed drugs that may be adversely affecting potassium homeostasis. Changes to prescribing systems and an agreed institutional protocol for management of hyperkalaemia can improve patient safety for this frequently encountered electrolyte disorder.

Vapours, gargles, darts and bougies: Victorian ENT treatments.

PubMed

Montgomery, J; Robertson, A

2012-11-01

Sir Morell Mackenzie (1837-1892), the pre-eminent early laryngologist in the UK, is nowadays perhaps better remembered for his role in the management of the Crown Prince of Germany in 1887, than for his major contribution to the development of laryngology as a specialty. In this article we focus upon his text The Pharmacopoeia of the Hospital for Diseases of the Throat (fourth edition), and attempt a comparison of Victorian ENT treatments with today's management of ENT diseases. Some of these Victorian treatments bear a resemblance to modern day practices. Others have not withstood the test of time, in particular: silver nitrate sticks for syphilitic ulcers of the larynx (not epistaxis); nebulised sulphuric acid, which was used as a stimulant; nasal bougies, including scotch pine and lead acetate; chloroform vapour for the treatment of hay fever; 'London paste', a non-surgical treatment for the reduction of the tonsils, (which was perhaps the Victorian equivalent of coblation); and zinc chloride darts, which were plunged into intractable goitres. Some of these remedies bear no resemblance to today's evidence-based practices, while other treatments (such as silver nitrate) are still in common use. In Victorian times, however, Mackenzie's books were widely read throughout Europe and were the standard references for a specialty in its infancy. The Pharmacopoeia was published in 1872, and major advances in medicine have been made since then. We have no way of knowing which treatments in today's British National Formulary will still be in use in 140 years.

Validation of the ERS standard citric acid cough challenge in healthy adult volunteers

PubMed Central

2010-01-01

Protocols measuring cough sensitivity can vary in terms of nebuliser, tussive agent, single and dose response. A definitive method for measuring cough sensitivity needs to be established. The ERS guidelines recommend the KoKo DigiDoser (KD) delivery system. Study aim, was to compare the reproducibility of this citric acid (CA) cough challenge and previously established Mefar dosimeter (MD) protocol. 39 (female 26) volunteers mean age (40.4 yrs) were randomised to either KD or MD. Intra-day and inter-day reproducibility was compared. We calculated the concentration of citric acid evoking 2 coughs (C2). The geometric mean C2 (95%CI) was similar for both KD and MD, of 263 (200,339) mM and 209 (151,288) mM respectively. The mean KD C2 was not significantly different. (F = 0.807, p = 0.93) from baseline over 1, 2, and 4 hrs however, the MD demonstrated significant variability (F = 7.85, P < 0.001) Measuring mean log C2 at baseline and at 2 weeks, the KD demonstrated a stronger intraclass correlation of log C2 at baseline with 2 week log C2, ICC = 0.70 than was shown with the Mefar, ICC = 0.41 Administering CA from KD offers a reproducible cough challenge in healthy volunteers. The results correlate well with the MD challenge but offer greater intra-day and inter-day reproducibility. Trial Registration Current controlled trials ISRCTN98385033 PMID:20698995

Considerations for potency equivalent calculations in the Ah receptor-based CALUX bioassay: normalization of superinduction results for improved sample potency estimation.

PubMed

Baston, David S; Denison, Michael S

2011-02-15

The chemically activated luciferase expression (CALUX) system is a mechanistically based recombinant luciferase reporter gene cell bioassay used in combination with chemical extraction and clean-up methods for the detection and relative quantitation of 2,3,7,8-tetrachlorodibenzo-p-dioxin and related dioxin-like halogenated aromatic hydrocarbons in a wide variety of sample matrices. While sample extracts containing complex mixtures of chemicals can produce a variety of distinct concentration-dependent luciferase induction responses in CALUX cells, these effects are produced through a common mechanism of action (i.e. the Ah receptor (AhR)) allowing normalization of results and sample potency determination. Here we describe the diversity in CALUX response to PCDD/Fs from sediment and soil extracts and not only report the occurrence of superinduction of the CALUX bioassay, but we describe a mechanistically based approach for normalization of superinduction data that results in a more accurate estimation of the relative potency of such sample extracts. Copyright © 2010 Elsevier B.V. All rights reserved.

A feasibility study in adapting Shamos Bickel and Hodges Lehman estimator into T-Method for normalization

NASA Astrophysics Data System (ADS)

Harudin, N.; Jamaludin, K. R.; Muhtazaruddin, M. Nabil; Ramlie, F.; Muhamad, Wan Zuki Azman Wan

2018-03-01

T-Method is one of the techniques governed under Mahalanobis Taguchi System that developed specifically for multivariate data predictions. Prediction using T-Method is always possible even with very limited sample size. The user of T-Method required to clearly understanding the population data trend since this method is not considering the effect of outliers within it. Outliers may cause apparent non-normality and the entire classical methods breakdown. There exist robust parameter estimate that provide satisfactory results when the data contain outliers, as well as when the data are free of them. The robust parameter estimates of location and scale measure called Shamos Bickel (SB) and Hodges Lehman (HL) which are used as a comparable method to calculate the mean and standard deviation of classical statistic is part of it. Embedding these into T-Method normalize stage feasibly help in enhancing the accuracy of the T-Method as well as analysing the robustness of T-method itself. However, the result of higher sample size case study shows that T-method is having lowest average error percentages (3.09%) on data with extreme outliers. HL and SB is having lowest error percentages (4.67%) for data without extreme outliers with minimum error differences compared to T-Method. The error percentages prediction trend is vice versa for lower sample size case study. The result shows that with minimum sample size, which outliers always be at low risk, T-Method is much better on that, while higher sample size with extreme outliers, T-Method as well show better prediction compared to others. For the case studies conducted in this research, it shows that normalization of T-Method is showing satisfactory results and it is not feasible to adapt HL and SB or normal mean and standard deviation into it since it’s only provide minimum effect of percentages errors. Normalization using T-method is still considered having lower risk towards outlier’s effect.

The Relations between Children's Reading Comprehension, Working Memory, Language Skills and Components of Reading Decoding in a Normal Sample

ERIC Educational Resources Information Center

Goff, Deborah A.; Pratt, Chris; Ong, Ben

2005-01-01

The primary aim of the current study was to identify the strongest independent predictors of reading comprehension using word reading, language and memory variables in a normal sample of 180 children in grades 3-5, with a range of word reading skills. It was hypothesized that orthographic processing, receptive vocabulary and verbal working memory…

The Effect of Multicollinearity and the Violation of the Assumption of Normality on the Testing of Hypotheses in Regression Analysis.

ERIC Educational Resources Information Center

Vasu, Ellen S.; Elmore, Patricia B.

The effects of the violation of the assumption of normality coupled with the condition of multicollinearity upon the outcome of testing the hypothesis Beta equals zero in the two-predictor regression equation is investigated. A monte carlo approach was utilized in which three differenct distributions were sampled for two sample sizes over…

Investigation of phosphoserine and cytidine 5'-phosphate by heteronuclear two-dimensional spectroscopy: samples with strong proton coupling

NASA Astrophysics Data System (ADS)

Bolton, Philip H.

Heteronuclear two-dimensional magnetic resonance is a novel method for investigating the conformations of cellular phosphates. The two-dimensional proton spectra are detected indirectly via the phosphorus-31 nucleus and thus allow determination of proton chemical shifts and coupling constants in situations in which the normal proton spectrum is obscured. Previous investigations of cellular phosphates with relatively simple spin systems have shown that the two-dimensional proton spectrum can be readily related to the normal proton spectrum by subspectral analysis. The normal proton spectrum can be decomposed into two subspectra, one for each polarization of the phosphorus-31 nucleus. The two-dimensional spectrum arises from the difference between the subspectra, and the normal proton spectrum is the sum. This allows simulation of the two-dimensional spectra and hence determination of the proton chemical shifts and coupling constants. Many cellular phosphates of interest, such as 5'-nucleotides and phosphoserine, contain three protons coupled to the phosphorus which are strongly coupled to one another. These samples are amenable to the two-dimensional method and the straightforward subspectral analysis is preserved when a 90° pulse is applied to the protons in the magnetization transfer step. The two-dimensional proton spectra of the samples investigated here have higher resolution than the normal proton spectra, revealing spectral features not readily apparent in the normal proton spectra.

Assessment of 1H NMR-based metabolomics analysis for normalization of urinary metals against creatinine.

PubMed

Cassiède, Marc; Nair, Sindhu; Dueck, Meghan; Mino, James; McKay, Ryan; Mercier, Pascal; Quémerais, Bernadette; Lacy, Paige

2017-01-01

Proton nuclear magnetic resonance ( 1 H NMR, or NMR) spectroscopy and inductively coupled plasma-mass spectrometry (ICP-MS) are commonly used for metabolomics and metal analysis in urine samples. However, creatinine quantification by NMR for the purpose of normalization of urinary metals has not been validated. We assessed the validity of using NMR analysis for creatinine quantification in human urine samples in order to allow normalization of urinary metal concentrations. NMR and ICP-MS techniques were used to measure metabolite and metal concentrations in urine samples from 10 healthy subjects. For metabolite analysis, two magnetic field strengths (600 and 700MHz) were utilized. In addition, creatinine concentrations were determined by using the Jaffe method. Creatinine levels were strongly correlated (R 2 =0.99) between NMR and Jaffe methods. The NMR spectra were deconvoluted with a target database containing 151 metabolites that are present in urine. A total of 50 metabolites showed good correlation (R 2 =0.7-1.0) at 600 and 700MHz. Metal concentrations determined after NMR-measured creatinine normalization were comparable to previous reports. NMR analysis provided robust urinary creatinine quantification, and was sufficient for normalization of urinary metal concentrations. We found that NMR-measured creatinine-normalized urinary metal concentrations in our control subjects were similar to general population levels in Canada and the United Kingdom. Copyright © 2016 Elsevier B.V. All rights reserved.

Statistical analysis tables for truncated or censored samples

NASA Technical Reports Server (NTRS)

Cohen, A. C.; Cooley, C. G.

1971-01-01

Compilation describes characteristics of truncated and censored samples, and presents six illustrations of practical use of tables in computing mean and variance estimates for normal distribution using selected samples.

The association between content of the elements S, Cl, K, Fe, Cu, Zn and Br in normal and cirrhotic liver tissue from Danes and Greenlandic Inuit examined by dual hierarchical clustering analysis.

PubMed

Laursen, Jens; Milman, Nils; Pind, Niels; Pedersen, Henrik; Mulvad, Gert

2014-01-01

Meta-analysis of previous studies evaluating associations between content of elements sulphur (S), chlorine (Cl), potassium (K), iron (Fe), copper (Cu), zinc (Zn) and bromine (Br) in normal and cirrhotic autopsy liver tissue samples. Normal liver samples from 45 Greenlandic Inuit, median age 60 years and from 71 Danes, median age 61 years. Cirrhotic liver samples from 27 Danes, median age 71 years. Element content was measured using X-ray fluorescence spectrometry. Dual hierarchical clustering analysis, creating a dual dendrogram, one clustering element contents according to calculated similarities, one clustering elements according to correlation coefficients between the element contents, both using Euclidian distance and Ward Procedure. One dendrogram separated subjects in 7 clusters showing no differences in ethnicity, gender or age. The analysis discriminated between elements in normal and cirrhotic livers. The other dendrogram clustered elements in four clusters: sulphur and chlorine; copper and bromine; potassium and zinc; iron. There were significant correlations between the elements in normal liver samples: S was associated with Cl, K, Br and Zn; Cl with S and Br; K with S, Br and Zn; Cu with Br. Zn with S and K. Br with S, Cl, K and Cu. Fe did not show significant associations with any other element. In contrast to simple statistical methods, which analyses content of elements separately one by one, dual hierarchical clustering analysis incorporates all elements at the same time and can be used to examine the linkage and interplay between multiple elements in tissue samples. Copyright © 2013 Elsevier GmbH. All rights reserved.

EEG based topography analysis in string recognition task

NASA Astrophysics Data System (ADS)

Ma, Xiaofei; Huang, Xiaolin; Shen, Yuxiaotong; Qin, Zike; Ge, Yun; Chen, Ying; Ning, Xinbao

2017-03-01

Vision perception and recognition is a complex process, during which different parts of brain are involved depending on the specific modality of the vision target, e.g. face, character, or word. In this study, brain activities in string recognition task compared with idle control state are analyzed through topographies based on multiple measurements, i.e. sample entropy, symbolic sample entropy and normalized rhythm power, extracted from simultaneously collected scalp EEG. Our analyses show that, for most subjects, both symbolic sample entropy and normalized gamma power in string recognition task are significantly higher than those in idle state, especially at locations of P4, O2, T6 and C4. It implies that these regions are highly involved in string recognition task. Since symbolic sample entropy measures complexity, from the perspective of new information generation, and normalized rhythm power reveals the power distributions in frequency domain, complementary information about the underlying dynamics can be provided through the two types of indices.

Electron localization mechanism in the normal state of high- T c superconductors

NASA Astrophysics Data System (ADS)

Yamani, Z.; Akhavan, M.

The ceramic compounds Gd 1- xPr xCu 3O 7- y (GdPr-123) with 0.0 ≤ x≤1.0, were synthesized by standard solid state reaction technique. XRD analysis shows a predominantly single phase perovskite structure with the orthorhombic Pmmm symmetry. The samples have been examined for superconductivity by measuring electrical resistivity within the temperature range 10-300 K. These measurements show a suppression of superconductivity with increasing x. It is observed that the critical Pr concentration ( x cr) required to suppress superconductivity is about 0.45, the samples with x < 0.45 become superconducting and are metallic in their normal state, the samples with x ≥ 0.45 do not become superconducting and show a semiconducting behavior above 10 K. To interpret the normal state properties of the samples, the quantum percolation theory based on localized states is applied. A cross-over between variable-range hopping (VRH) and Coulomb gap (CG) mechanisms is observed as a result of decreasing the Pr content.

DEVELOPMENT OF MOTIVATION SCALE - CLINICAL VALIDATION WITH ALCOHOL DEPENDENTS

PubMed Central

Neeliyara, Teresa; Nagalakshmi, S.V.

1994-01-01

This study focusses on the development of a comprehensive multi-dimensional scale for assessing motivation for change in the alcohol dependent population. After establishing face validity, the items evolved were administered to a normal sample of 600 male subjects in whom psychiatric illness was ruled out. The data thus obtained was subjected to factor analysis. Six factors were obtained which accounted for 55.2% of variance. These together formed a 80 item five point scale and norms were established on a sample of 600 normal subjects. Further clinical validation was established on 30 alcohol dependent subjects and 30 normals. The status of motivation was found to be inadequate in alcohol dependent individuals as compared to the normals. Split-half reliability was carried out and the tool was found to be highly reliable. PMID:21743674

[Identification and management of intra-operative suspicious tissues in 20 transsphenoidal surgery cases].

PubMed

Liu, Jun-Feng; Ke, Chang-Shu; Chen, Xi; Xu, Yu; Zhang, Hua-Qiu; Chen, Juan; Gan, Chao; Li, Chao-Xi; Lei, Ting

2013-05-01

To determine appropriate protocols for the identification and management of intra operative suspicious tissues during transsphenoidal surgery. Clinical data and pathological reports of 20 patients with intra-operative suspicious tissues during transsphenoidal surgeries were analyzed retrospectively. The methods for discriminating between adenoma and normal pituitary tissues were reviewed. The postoperative pathological reports revealed that adenoma and normal pituitary tissues coexisted in 9 samples, while 5 samples were identified as normal pituitary tissues, 2 as adenoma tissues, and 4 as other tissues. Adenomas were distinguished from normal pituitary tissues on the basis of intra-operative appearance, texture, blood supply and possible existence of boundary. If decisions are difficult to made during surgeries from the appearance of the suspicious tissues, pathological examinations are advised as a guidance for the next steps.

Interpreting the concordance statistic of a logistic regression model: relation to the variance and odds ratio of a continuous explanatory variable.

PubMed

Austin, Peter C; Steyerberg, Ewout W

2012-06-20

When outcomes are binary, the c-statistic (equivalent to the area under the Receiver Operating Characteristic curve) is a standard measure of the predictive accuracy of a logistic regression model. An analytical expression was derived under the assumption that a continuous explanatory variable follows a normal distribution in those with and without the condition. We then conducted an extensive set of Monte Carlo simulations to examine whether the expressions derived under the assumption of binormality allowed for accurate prediction of the empirical c-statistic when the explanatory variable followed a normal distribution in the combined sample of those with and without the condition. We also examine the accuracy of the predicted c-statistic when the explanatory variable followed a gamma, log-normal or uniform distribution in combined sample of those with and without the condition. Under the assumption of binormality with equality of variances, the c-statistic follows a standard normal cumulative distribution function with dependence on the product of the standard deviation of the normal components (reflecting more heterogeneity) and the log-odds ratio (reflecting larger effects). Under the assumption of binormality with unequal variances, the c-statistic follows a standard normal cumulative distribution function with dependence on the standardized difference of the explanatory variable in those with and without the condition. In our Monte Carlo simulations, we found that these expressions allowed for reasonably accurate prediction of the empirical c-statistic when the distribution of the explanatory variable was normal, gamma, log-normal, and uniform in the entire sample of those with and without the condition. The discriminative ability of a continuous explanatory variable cannot be judged by its odds ratio alone, but always needs to be considered in relation to the heterogeneity of the population.

Clinical flow cytometric screening of SAP and XIAP expression accurately identifies patients with SH2D1A and XIAP/BIRC4 mutations.

PubMed

Gifford, Carrie E; Weingartner, Elizabeth; Villanueva, Joyce; Johnson, Judith; Zhang, Kejian; Filipovich, Alexandra H; Bleesing, Jack J; Marsh, Rebecca A

2014-07-01

X-linked lymphoproliferative disease is caused by mutations in two genes, SH2D1A and XIAP/BIRC4. Flow cytometric methods have been developed to detect the gene products, SAP and XIAP. However, there is no literature describing the accuracy of flow cytometric screening performed in a clinical lab setting. We reviewed the clinical flow cytometric testing results for 656 SAP and 586 XIAP samples tested during a 3-year period. Genetic testing was clinically performed as directed by the managing physician in 137 SAP (21%) and 115 XIAP (20%) samples. We included these samples for analyses of flow cytometric test accuracy. SH2D1A mutations were detected in 15/137 samples. SAP expression was low in 13/15 (sensitivity 87%, CI 61-97%). Of the 122 samples with normal sequencing, SAP was normal in 109 (specificity 89%, CI 82-94%). The positive predictive values (PPVs) and the negative predictive values (NPVs) were 50% and 98%, respectively. XIAP/BIRC4 mutations were detected in 19/115 samples. XIAP expression was low in 18/19 (sensitivity 95%, CI 73-100%). Of the 96 samples with normal sequencing, 59 had normal XIAP expression (specificity 61%, CI 51-71%). The PPVs and NPVs were 33% and 98%, respectively. Receiver-operating characteristic analysis was able to improve the specificity to 75%. Clinical flow cytometric screening tests for SAP and XIAP deficiencies offer good sensitivity and specificity for detecting genetic mutations, and are characterized by high NPVs. We recommend these tests for patients suspected of having X-linked lymphoproliferative disease type 1 (XLP1) or XLP2. © 2014 Clinical Cytometry Society.

Cytogenetic study is not essential in patients with aplastic anemia

PubMed Central

Dutta, Atreyee; De, Rajib; Dolai, Tuphan K; Mitra, Pradip K; Halder, Ajanta

2017-01-01

Depending on contemporary treatment approach of aggressive immunosuppression, Aplastic Anemia (AA) is caused by immunological destruction of otherwise normal hematopoietic stem cells. The aim was to summarize the cytogenetic abnormalities in AA patients and the frequency of Fanconi Anemia (FA) in morphologically normal AA patients in eastern India. Ethical clearances were obtained from both institutions involved in this study. Out of 72800 patients attending the outpatient department, 520 pancytopenia patients were screened for AA after Bone marrow (BM) aspiration and biopsy. Samples were collected from 117 cases in 3 phases. 51 peripheral venous blood (PVB) samples in the first phase, 19 BM & PVB paired samples in the second phase and 47 BM samples in third phase were collected followed by leukocyte and/or BM stem cell culture. Next GTG banding and karyotyping were performed. PVB was collected from 63 (< 50 years) AA patients and stress cytogenetics was done to diagnose FA. In the first phase of the study, out of 51 PVB samples, 1 (1.96%) showed a unique chromosomal abnormality, i.e. 45,XY,rob(14:21)(p10:q10)[20]. In the second phase of study, among 19 BM & PVB paired samples, 1 (5.26%) showed abnormal karyotype i.e. 45,X,-Y[3]/46,XY[47]. In the third phase of the study, 47 BM samples showed normal karyotype. Only 6 (9.52%) cases were found positive for stress cytogenetics. A negligible percentage showing cytogenetic abnormality in such a considerable number of AA cases indicates that routine cytogenetic analysis of AA patient is not essential. A significant percentage was positive for stress cytogenetics; suggestive for FA, even the patients were morphologically normal. PMID:29181263

Relationships between coping style and PAI profiles in a community sample.

PubMed

Deisinger, J A; Cassisi, J E; Whitaker, S L

1996-05-01

Relationships between coping style and psychological functioning were examined in a heterogeneous community sample (N = 168). Psychological functioning was categorized with the Personality Assessment Inventory (PAI; Morey, 1991). Subjects were assigned to PAI configural profile clusters, using T-scores from PAI clinical scales. Three PAI clusters were prominent in this sample: normal, anxious, and eccentric. Multivariate analysis of covariance revealed that these clusters differed significantly in coping style, as measured by the dispositional format of the COPE Inventory (Carver, Scheier, & Weintraub, 1989). Normals coped through avoidance significantly less than anxious or eccentric subjects. Also, normals engaged in seeking social support and venting more than eccentric but less than anxious subjects. Gender differences also were noted, with women more likely to cope by seeking social support and men more likely to cope through hedonistic escapism.

Does Cognitive Function Increase over Time in the Healthy Elderly?

PubMed Central

de Rotrou, Jocelyne; Wu, Ya-Huei; Mabire, Jean-Bernard; Moulin, Florence; de Jong, Laura W.; Rigaud, Anne-Sophie; Hanon, Olivier; Vidal, Jean-Sébastien

2013-01-01

Background In dementia screening, most studies have focused on early cognitive impairment by comparing patients suffering from mild dementia or mild cognitive impairment with normal subjects. Few studies have focused on modifications over time of the cognitive function in the healthy elderly. The objective of the present study was to analyze the cognitive function changes of two different samples, born > 15 years apart. Method A first sample of 204 cognitively normal participants was recruited in the memory clinic of Broca hospital between 1991 and 1997. A second sample of 177 cognitively normal participants was recruited in 2008–2009 in the same institution. Both samples were from the same districts of Paris and were assessed with the same neuropsychological test battery. Mean cognitive test scores were compared between 1991 and 2008 samples, between < 80 years old and ≥ 80 years old in 1991 and 2008 samples, and finally between subjects < 80 year old of 1991 sample and subjects ≥ 80 years old of the 2008 sample. Means were compared with T-tests stratified on gender, age-groups and educational level. Results Cognitive scores were significantly higher in the 2008 sample. Participants < 80 years old outperformed those ≥ 80 in both samples. However, participants < 80 years old in 1991 sample and subjects ≥ 80 in the 2008 sample, born on average in 1923, performed mostly identically. Conclusion This study showed a significant increase of cognitive scores over time. Further, contemporary octogenarians in the later sample performed like septuagenarians in the former sample. These findings might be consistent with the increase in life expectancy and life span in good health. The study highlights the necessity to take into account factors which may contaminate and artificially inflate the age-related differences in favor of younger to the older adults. PMID:24244332

Investigation of c-KIT and Ki67 expression in normal, preneoplastic and neoplastic canine prostate.

PubMed

Fonseca-Alves, Carlos Eduardo; Kobayashi, Priscilla Emiko; Palmieri, Chiara; Laufer-Amorim, Renée

2017-12-06

c-KIT expression has been related to bone metastasis in human prostate cancer, but whether c-KIT expression can be similarly classified in canine prostatic tissue is unknown. This study assessed c-KIT and Ki67 expression in canine prostate cancer (PC). c-KIT gene and protein expression and Ki67 expression were evaluated in forty-four canine prostatic tissues by immunohistochemistry, RT-qPCR and western blot. Additionally, we have investigated c-KIT protein expression by immunoblotting in two primary canine prostate cancer cell lines. Eleven normal prostates, 12 proliferative inflammatory atrophy (PIA) prostates, 18 PC, 3 metastatic lesions and two prostate cancer cell cultures (PC1 and PC2) were analysed. The prostatic tissue exhibited varying degrees of membranous, cytoplasmic or membranous/cytoplasmic c-KIT staining. Four normal prostates, 4 PIA and 5 prostatic carcinomas showed positive c-KIT expression. No c-KIT immunoexpression was observed in metastases. Canine prostate cancer and PIA samples contained a higher number of Ki67-positive cells compared to normal samples. The median relative quantification (RQ) for c-KIT expression in normal, PIA and prostate cancer and metastatic samples were 0.6 (0.1-2.5), 0.7 (0.09-2.1), 0.7 (0.09-5.1) and 0.1 (0.07-0.6), respectively. A positive correlation between the number of Ki67-positive cells and c-KIT transcript levels was observed in prostate cancer samples. In the cell line, PC1 was negative for c-KIT protein expression, while PC2 was weakly positive. The present study identified a strong correlation between c-KIT expression and proliferative index, suggesting that c-KIT may influence cell proliferation. Therefore, c-KIT heterogeneous protein expression among the samples (five positive and thirteen negative prostate cancer samples) indicates a personalized approach for canine prostate cancer.

Expression of heat shock protein 70 in transport-stressed broiler pectoralis major muscle and its relationship with meat quality.

PubMed

Xing, T; Wang, M F; Han, M Y; Zhu, X S; Xu, X L; Zhou, G H

2017-09-01

Omics research has indicated that heat shock protein 70 (HSP70) is a potential biomarker of meat quality. However, the specific changes and the potential role of HSP70 in postmortem meat quality development need to be further defined. In this study, Arbor Acres broiler chickens (n=126) were randomly categorized into three treatment groups of unstressed control (C), 0.5-h transport (T) and subsequent water shower spray following transport (T/W). Each treatment consisted of six replicates with seven birds each. The birds were transported according to a designed protocol. The pectoralis major (PM) muscles of the transport-stressed broilers were categorized as normal and pale, soft and exudative (PSE)-like muscle samples according to L* and pH24 h values to test the expression and location of HSP70. Results revealed that the activities of plasma creatine kinase and lactate dehydrogenase increased significantly (P<0.05) in normal and PSE-like muscle samples after transportation. The mRNA expression of HSP70 in normal muscle samples increased significantly (P<0.05) compared with that in the controls after stress. The protein expression of HSP70 increased significantly in normal muscle samples and decreased significantly (P<0.05) in PSE-like muscles. Immuno-fluorescence showed that HSP70 was present in the cytoplasm and on surface membranes of PM muscle cells in the normal samples following stress. Meanwhile, HSP70 was present on the surface membranes and extracellular matrix but was barely visible in the cytoplasm of the PSE-like samples. Principal component analysis showed high correlations between HSP70 and meat quality and stress indicators. In conclusion, this research suggests that the variation in HSP70 expression may provide a novel insight into the pathways underlying meat quality development.

A comprehensive quality control workflow for paired tumor-normal NGS experiments.

PubMed

Schroeder, Christopher M; Hilke, Franz J; Löffler, Markus W; Bitzer, Michael; Lenz, Florian; Sturm, Marc

2017-06-01

Quality control (QC) is an important part of all NGS data analysis stages. Many available tools calculate QC metrics from different analysis steps of single sample experiments (raw reads, mapped reads and variant lists). Multi-sample experiments, as sequencing of tumor-normal pairs, require additional QC metrics to ensure validity of results. These multi-sample QC metrics still lack standardization. We therefore suggest a new workflow for QC of DNA sequencing of tumor-normal pairs. With this workflow well-known single-sample QC metrics and additional metrics specific for tumor-normal pairs can be calculated. The segmentation into different tools offers a high flexibility and allows reuse for other purposes. All tools produce qcML, a generic XML format for QC of -omics experiments. qcML uses quality metrics defined in an ontology, which was adapted for NGS. All QC tools are implemented in C ++ and run both under Linux and Windows. Plotting requires python 2.7 and matplotlib. The software is available under the 'GNU General Public License version 2' as part of the ngs-bits project: https://github.com/imgag/ngs-bits. christopher.schroeder@med.uni-tuebingen.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Bladder cancer diagnosis during cystoscopy using Raman spectroscopy

NASA Astrophysics Data System (ADS)

Grimbergen, M. C. M.; van Swol, C. F. P.; Draga, R. O. P.; van Diest, P.; Verdaasdonk, R. M.; Stone, N.; Bosch, J. H. L. R.

2009-02-01

Raman spectroscopy is an optical technique that can be used to obtain specific molecular information of biological tissues. It has been used successfully to differentiate normal and pre-malignant tissue in many organs. The goal of this study is to determine the possibility to distinguish normal tissue from bladder cancer using this system. The endoscopic Raman system consists of a 6 Fr endoscopic probe connected to a 785nm diode laser and a spectral recording system. A total of 107 tissue samples were obtained from 54 patients with known bladder cancer during transurethral tumor resection. Immediately after surgical removal the samples were placed under the Raman probe and spectra were collected and stored for further analysis. The collected spectra were analyzed using multivariate statistical methods. In total 2949 Raman spectra were recorded ex vivo from cold cup biopsy samples with 2 seconds integration time. A multivariate algorithm allowed differentiation of normal and malignant tissue with a sensitivity and specificity of 78,5% and 78,9% respectively. The results show the possibility of discerning normal from malignant bladder tissue by means of Raman spectroscopy using a small fiber based system. Despite the low number of samples the results indicate that it might be possible to use this technique to grade identified bladder wall lesions during endoscopy.

Confidence intervals for correlations when data are not normal.

PubMed

Bishara, Anthony J; Hittner, James B

2017-02-01

With nonnormal data, the typical confidence interval of the correlation (Fisher z') may be inaccurate. The literature has been unclear as to which of several alternative methods should be used instead, and how extreme a violation of normality is needed to justify an alternative. Through Monte Carlo simulation, 11 confidence interval methods were compared, including Fisher z', two Spearman rank-order methods, the Box-Cox transformation, rank-based inverse normal (RIN) transformation, and various bootstrap methods. Nonnormality often distorted the Fisher z' confidence interval-for example, leading to a 95 % confidence interval that had actual coverage as low as 68 %. Increasing the sample size sometimes worsened this problem. Inaccurate Fisher z' intervals could be predicted by a sample kurtosis of at least 2, an absolute sample skewness of at least 1, or significant violations of normality hypothesis tests. Only the Spearman rank-order and RIN transformation methods were universally robust to nonnormality. Among the bootstrap methods, an observed imposed bootstrap came closest to accurate coverage, though it often resulted in an overly long interval. The results suggest that sample nonnormality can justify avoidance of the Fisher z' interval in favor of a more robust alternative. R code for the relevant methods is provided in supplementary materials.

Evaluation of genetic variability among "Early Mature" Juglans regia using microsatellite markers and morphological traits.

PubMed

Ebrahimi, Aziz; Zarei, Abdolkarim; Zamani Fardadonbeh, Mojtaba; Lawson, Shaneka

2017-01-01

Limiting the juvenile phase and reducing tree size are the two main challenges for breeders to improve most fruit crops. Early maturation and dwarf cultivars have been reported for many fruit species. "Early mature" and low vigor walnut genotypes were found among seedlings of Persian walnut. Nine microsatellite markers were used to evaluate genetic diversity among "Early Mature" Persian walnut accessions and provide a comparison with "normal growth" accessions. Six maturation related characteristics were also measured in "Early Mature" samples. Phenotypic traits and diversity indices showed relatively high levels of genetic diversity in "Early Mature" seedlings and indicated high differentiation between individuals. Seedling height, the most diverse phenotypic trait, has an important role in the clustering of "Early Mature" accessions. The "Early Mature" type had higher number of alleles, number of effective allele, and Shannon index compared to the "Normal Growth" group. The two types of studied walnuts had different alleles, with more than half of produced alleles specific to a specific group. "Early Mature" and "Normal Growth" walnuts had 27 and 17 private alleles, respectively. Grouping with different methods separated "Early Mature" and "Normal Growth" samples entirely. The presence of moderate to high genetic diversity in "Early Mature" walnuts and high genetic differentiation with "Normal Growth" walnuts, indicated that "Early Mature" walnuts were more diverse and distinct from "Normal Growth" samples. Moreover, our results showed SSR markers were useful for differentiating between "Early Mature" and "Normal Growth" walnuts. A number of identified loci have potential in breeding programs for identification of "Early Mature" walnuts at the germination phase.

24-hour urine protein

MedlinePlus

... one urine sample (protein-to-creatinine ratio). Normal Results The normal value is less than 100 milligrams ... meaning of your specific test results. What Abnormal Results Mean Abnormal results may be due to: A ...

EFFECT ON PERFUSION VALUES OF SAMPLING INTERVAL OF CT PERFUSION ACQUISITIONS IN NEUROENDOCRINE LIVER METASTASES AND NORMAL LIVER

PubMed Central

Ng, Chaan S.; Hobbs, Brian P.; Wei, Wei; Anderson, Ella F.; Herron, Delise H.; Yao, James C.; Chandler, Adam G.

2014-01-01

Objective To assess the effects of sampling interval (SI) of CT perfusion acquisitions on CT perfusion values in normal liver and liver metastases from neuroendocrine tumors. Methods CT perfusion in 16 patients with neuroendocrine liver metastases were analyzed by distributed parameter modeling to yield tissue blood flow, blood volume, mean transit time, permeability, and hepatic arterial fraction, for tumor and normal liver. CT perfusion values for the reference sampling interval of 0.5s (SI0.5) were compared with those of SI datasets of 1s, 2s, 3s and 4s, using mixed-effects model analyses. Results Increases in SI beyond 1s were associated with significant and increasing departures of CT perfusion parameters from reference values at SI0.5 (p≤0.0009). CT perfusion values deviated from reference with increasing uncertainty with increasing SIs. Findings for normal liver were concordant. Conclusion Increasing SIs beyond 1s yield significantly different CT perfusion parameter values compared to reference values at SI0.5. PMID:25626401

Expression of BMI-1 and Mel-18 in breast tissue - a diagnostic marker in patients with breast cancer

PubMed Central

2010-01-01

Background Polycomb Group (PcG) proteins are epigenetic silencers involved in maintaining cellular identity, and their deregulation can result in cancer. Expression of Mel-18 and Bmi-1 has been studied in tumor tissue, but not in adjacent non-cancerous breast epithelium. Our study compares the expression of the two genes in normal breast epithelium of cancer patients and relates it to the level of expression in the corresponding tumors as well as in breast epithelium of healthy women. Methods A total of 79 tumors, of which 71 malignant tumors of the breast, 6 fibroadenomas, and 2 DCIS were studied and compared to the reduction mammoplastic specimens of 11 healthy women. In addition there was available adjacent cancer free tissue for 23 of the malignant tumors. The tissue samples were stored in RNAlater, RNA was isolated to create expression microarray profile. These two genes were then studied more closely first on mRNA transcription level by microarrays (Agilent 44 K) and quantitative RT-PCR (TaqMan) and then on protein expression level using immunohistochemistry. Results Bmi-1 mRNA is significantly up-regulated in adjacent normal breast tissue in breast cancer patients compared to normal breast tissue from noncancerous patients. Conversely, mRNA transcription level of Mel-18 is lower in normal breast from patients operated for breast cancer compared to breast tissue from mammoplasty. When protein expression of these two genes was evaluated, we observed that most of the epithelial cells were positive for Bmi-1 in both groups of tissue samples, although the expression intensity was stronger in normal tissue from cancer patients compared to mammoplasty tissue samples. Protein expression of Mel-18 showed inversely stronger intensity in tissue samples from mammoplasty compared to normal breast tissue from patients operated for breast cancer. Conclusion Bmi-1 mRNA level is consistently increased and Mel-18 mRNA level is consistently decreased in adjacent normal breast tissue of cancer patients as compared to normal breast tissue in women having had reduction mammoplasties. Bmi-1/Mel-18 ratio can be potentially used as a tool for stratifying women at risk of developing malignancy. PMID:21162745

Compton profiles of some composite materials normalized by a new method

NASA Astrophysics Data System (ADS)

Sankarshan, B. M.; Umesh, T. K.

2018-03-01

Recently, we have shown that as a novel approach, in the case of samples which can be treated as pure incoherent scatterers, the effective atomic number Zeff itself could be conveniently used to normalize their un-normalized Compton profiles. In the present investigation, we have attempted to examine the efficacy of this approach. For this purpose, we have first determined the single differential Compton scattering cross sections (SDCS) of the elements C and Al as well as of some H, C, N and O based polymer samples such as bakelite, epoxy, nylon and teflon which are pure incoherent scatterers. The measurements were made at 120° in a goniometer assembly that employs a high resolution high purity germanium detector. The SDCS values were used to obtain the Zeff and the un-normalized Compton profiles. These Compton profiles were separately normalized with their Zeff values (for Compton scattering) as well as with the normalization constant obtained by integrating their Hartree-Fock Biggs et al Compton profiles based on the mixture rule. These two sets of values agreed well within the range of experimental errors, implying that Zeff can be conveniently used to normalize the experimental Compton profiles of pure incoherent scatterers.

Development of a novel precision instrument for high-resolution simultaneous normal and shear force measurements between small planar samples

NASA Astrophysics Data System (ADS)

Lundstrom, Troy; Clark, William; Jalili, Nader

2017-05-01

In the design and development of end effector pads for silicon wafer handling robots, it is imperative that the static friction/adhesion force properties of the pads with respect to a variety of planar surfaces be characterized. In this work, the overall design, calibration, and data acquisition procedure of an instrument developed for performing these measurements on small (<10 mm × 10 mm) planar samples is presented. This device was used to perform adhesion/maximum shear force measurements on polydimethylsiloxane, a silicon wafer, and custom carbon nanotubes forest surfaces. The device was successfully able to measure an effective, mean profile adhesion force of 715 μN between a silicon wafer and a polydimethylsiloxane (2.768 × 10-6 m2) sample. In addition, a nonlinear maximum shear over normal force relationship was also measured between custom carbon nanotubes forest and the silicon wafer surfaces. The maximum shear over a normal force coefficient was found to decrease with increasing initial normal force. Currently, there are numerous devices for measuring normal/shear forces at the nano/micro- and macroscales; however, this device allows for the consistent measurement of these same types of forces on components with surface dimensions ranging from 0.1 mm to 10 mm.

Photoacoustic spectroscopy based investigatory approach to discriminate breast cancer from normal: a pilot study

NASA Astrophysics Data System (ADS)

Priya, Mallika; Rao, Bola Sadashiva Satish; Chandra, Subhash; Ray, Satadru; Mathew, Stanley; Datta, Anirbit; Nayak, Subramanya G.; Mahato, Krishna Kishore

2016-02-01

In spite of many efforts for early detection of breast cancer, there is still lack of technology for immediate implementation. In the present study, the potential photoacoustic spectroscopy was evaluated in discriminating breast cancer from normal, involving blood serum samples seeking early detection. Three photoacoustic spectra in time domain were recorded from each of 20 normal and 20 malignant samples at 281nm pulsed laser excitations and a total of 120 spectra were generated. The time domain spectra were then Fast Fourier Transformed into frequency domain and 116.5625 - 206.875 kHz region was selected for further analysis using a combinational approach of wavelet, PCA and logistic regression. Initially, wavelet analysis was performed on the FFT data and seven features (mean, median, area under the curve, variance, standard deviation, skewness and kurtosis) from each were extracted. PCA was then performed on the feature matrix (7x120) for discriminating malignant samples from the normal by plotting a decision boundary using logistic regression analysis. The unsupervised mode of classification used in the present study yielded specificity and sensitivity values of 100% in each respectively with a ROC - AUC value of 1. The results obtained have clearly demonstrated the capability of photoacoustic spectroscopy in discriminating cancer from the normal, suggesting its possible clinical implications.

A large-scale study of the ultrawideband microwave dielectric properties of normal breast tissue obtained from reduction surgeries.

PubMed

Lazebnik, Mariya; McCartney, Leah; Popovic, Dijana; Watkins, Cynthia B; Lindstrom, Mary J; Harter, Josephine; Sewall, Sarah; Magliocco, Anthony; Booske, John H; Okoniewski, Michal; Hagness, Susan C

2007-05-21

The efficacy of emerging microwave breast cancer detection and treatment techniques will depend, in part, on the dielectric properties of normal breast tissue. However, knowledge of these properties at microwave frequencies has been limited due to gaps and discrepancies in previously reported small-scale studies. To address these issues, we experimentally characterized the wideband microwave-frequency dielectric properties of a large number of normal breast tissue samples obtained from breast reduction surgeries at the University of Wisconsin and University of Calgary hospitals. The dielectric spectroscopy measurements were conducted from 0.5 to 20 GHz using a precision open-ended coaxial probe. The tissue composition within the probe's sensing region was quantified in terms of percentages of adipose, fibroconnective and glandular tissues. We fit a one-pole Cole-Cole model to the complex permittivity data set obtained for each sample and determined median Cole-Cole parameters for three groups of normal breast tissues, categorized by adipose tissue content (0-30%, 31-84% and 85-100%). Our analysis of the dielectric properties data for 354 tissue samples reveals that there is a large variation in the dielectric properties of normal breast tissue due to substantial tissue heterogeneity. We observed no statistically significant difference between the within-patient and between-patient variability in the dielectric properties.

Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis.

PubMed

Li, Bo; Tang, Jing; Yang, Qingxia; Cui, Xuejiao; Li, Shuang; Chen, Sijie; Cao, Quanxing; Xue, Weiwei; Chen, Na; Zhu, Feng

2016-12-13

In untargeted metabolomics analysis, several factors (e.g., unwanted experimental &biological variations and technical errors) may hamper the identification of differential metabolic features, which requires the data-driven normalization approaches before feature selection. So far, ≥16 normalization methods have been widely applied for processing the LC/MS based metabolomics data. However, the performance and the sample size dependence of those methods have not yet been exhaustively compared and no online tool for comparatively and comprehensively evaluating the performance of all 16 normalization methods has been provided. In this study, a comprehensive comparison on these methods was conducted. As a result, 16 methods were categorized into three groups based on their normalization performances across various sample sizes. The VSN, the Log Transformation and the PQN were identified as methods of the best normalization performance, while the Contrast consistently underperformed across all sub-datasets of different benchmark data. Moreover, an interactive web tool comprehensively evaluating the performance of 16 methods specifically for normalizing LC/MS based metabolomics data was constructed and hosted at http://server.idrb.cqu.edu.cn/MetaPre/. In summary, this study could serve as a useful guidance to the selection of suitable normalization methods in analyzing the LC/MS based metabolomics data.

Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis

PubMed Central

Li, Bo; Tang, Jing; Yang, Qingxia; Cui, Xuejiao; Li, Shuang; Chen, Sijie; Cao, Quanxing; Xue, Weiwei; Chen, Na; Zhu, Feng

2016-01-01

In untargeted metabolomics analysis, several factors (e.g., unwanted experimental & biological variations and technical errors) may hamper the identification of differential metabolic features, which requires the data-driven normalization approaches before feature selection. So far, ≥16 normalization methods have been widely applied for processing the LC/MS based metabolomics data. However, the performance and the sample size dependence of those methods have not yet been exhaustively compared and no online tool for comparatively and comprehensively evaluating the performance of all 16 normalization methods has been provided. In this study, a comprehensive comparison on these methods was conducted. As a result, 16 methods were categorized into three groups based on their normalization performances across various sample sizes. The VSN, the Log Transformation and the PQN were identified as methods of the best normalization performance, while the Contrast consistently underperformed across all sub-datasets of different benchmark data. Moreover, an interactive web tool comprehensively evaluating the performance of 16 methods specifically for normalizing LC/MS based metabolomics data was constructed and hosted at http://server.idrb.cqu.edu.cn/MetaPre/. In summary, this study could serve as a useful guidance to the selection of suitable normalization methods in analyzing the LC/MS based metabolomics data. PMID:27958387

Biomarkers for lymphoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zangar, Richard C.; Varnum, Susan M.

A biomarker, method, test kit, and diagnostic system for detecting the presence of lymphoma in a person are disclosed. The lymphoma may be Hodgkin's lymphoma or non-Hodgkin's lymphoma. The person may be a high-risk subject. In one embodiment, a plasma sample from a person is obtained. The level of at least one protein listed in Table S3 in the plasma sample is measured. The level of at least one protein in the plasma sample is compared with the level in a normal or healthy subject. The lymphoma is diagnosed based upon the level of the at least one protein inmore » the plasma sample in comparison to the normal or healthy level.« less

Exact Interval Estimation, Power Calculation, and Sample Size Determination in Normal Correlation Analysis

ERIC Educational Resources Information Center

Shieh, Gwowen

2006-01-01

This paper considers the problem of analysis of correlation coefficients from a multivariate normal population. A unified theorem is derived for the regression model with normally distributed explanatory variables and the general results are employed to provide useful expressions for the distributions of simple, multiple, and partial-multiple…

The Effect of the Multivariate Box-Cox Transformation on the Power of MANOVA.

ERIC Educational Resources Information Center

Kirisci, Levent; Hsu, Tse-Chi

Most of the multivariate statistical techniques rely on the assumption of multivariate normality. The effects of non-normality on multivariate tests are assumed to be negligible when variance-covariance matrices and sample sizes are equal. Therefore, in practice, investigators do not usually attempt to remove non-normality. In this simulation…

Gang Youth, Substance Use Patterns, and Drug Normalization

ERIC Educational Resources Information Center

Sanders, Bill

2012-01-01

Gang membership is an indicator of chronic illicit substance use and such patterns of use may have a normalized character. Using epidemiological and qualitative data collected between 2006 and 2007, this manuscript examines the drug normalization thesis among a small sample (n=60) of gang youth aged 16-25 years from Los Angeles. Overall, while…

Lactate dehydrogenase test

MedlinePlus

Normal value range is 105 to 333 international units per liter (IU/L). Normal value ranges may vary slightly among different laboratories. Some labs use different measurements or test different samples. Talk to your provider about ...

Metabolomic Profiling of Extracellular Vesicles and Alternative Normalization Methods Reveal Enriched Metabolites and Strategies to Study Prostate Cancer-Related Changes

PubMed Central

Puhka, Maija; Takatalo, Maarit; Nordberg, Maria-Elisa; Valkonen, Sami; Nandania, Jatin; Aatonen, Maria; Yliperttula, Marjo; Laitinen, Saara; Velagapudi, Vidya; Mirtti, Tuomas; Kallioniemi, Olli; Rannikko, Antti; Siljander, Pia R-M; af Hällström, Taija Maria

2017-01-01

Body fluids are a rich source of extracellular vesicles (EVs), which carry cargo derived from the secreting cells. So far, biomarkers for pathological conditions have been mainly searched from their protein, (mi)RNA, DNA and lipid cargo. Here, we explored the small molecule metabolites from urinary and platelet EVs relative to their matched source samples. As a proof-of-concept study of intra-EV metabolites, we compared alternative normalization methods to profile urinary EVs from prostate cancer patients before and after prostatectomy and from healthy controls. Methods: We employed targeted ultra-performance liquid chromatography-tandem mass spectrometry to profile over 100 metabolites in the isolated EVs, original urine samples and platelets. We determined the enrichment of the metabolites in the EVs and analyzed their subcellular origin, pathways and relevant enzymes or transporters through data base searches. EV- and urine-derived factors and ratios between metabolites were tested for normalization of the metabolomics data. Results: Approximately 1 x 1010 EVs were sufficient for detection of metabolite profiles from EVs. The profiles of the urinary and platelet EVs overlapped with each other and with those of the source materials, but they also contained unique metabolites. The EVs enriched a selection of cytosolic metabolites including members from the nucleotide and spermidine pathways, which linked to a number of EV-resident enzymes or transporters. Analysis of the urinary EVs from the patients indicated that the levels of glucuronate, D-ribose 5-phosphate and isobutyryl-L-carnitine were 2-26-fold lower in all pre-prostatectomy samples compared to the healthy control and post-prostatectomy samples (p < 0.05). These changes were only detected from EVs by normalization to EV-derived factors or with metabolite ratios, and not from the original urine samples. Conclusions: Our results suggest that metabolite analysis of EVs from different samples is feasible using a high-throughput platform and relatively small amount of sample material. With the knowledge about the specific enrichment of metabolites and normalization methods, EV metabolomics could be used to gain novel biomarker data not revealed by the analysis of the original EV source materials. PMID:29109780

Performance of statistical models to predict mental health and substance abuse cost.

PubMed

Montez-Rath, Maria; Christiansen, Cindy L; Ettner, Susan L; Loveland, Susan; Rosen, Amy K

2006-10-26

Providers use risk-adjustment systems to help manage healthcare costs. Typically, ordinary least squares (OLS) models on either untransformed or log-transformed cost are used. We examine the predictive ability of several statistical models, demonstrate how model choice depends on the goal for the predictive model, and examine whether building models on samples of the data affects model choice. Our sample consisted of 525,620 Veterans Health Administration patients with mental health (MH) or substance abuse (SA) diagnoses who incurred costs during fiscal year 1999. We tested two models on a transformation of cost: a Log Normal model and a Square-root Normal model, and three generalized linear models on untransformed cost, defined by distributional assumption and link function: Normal with identity link (OLS); Gamma with log link; and Gamma with square-root link. Risk-adjusters included age, sex, and 12 MH/SA categories. To determine the best model among the entire dataset, predictive ability was evaluated using root mean square error (RMSE), mean absolute prediction error (MAPE), and predictive ratios of predicted to observed cost (PR) among deciles of predicted cost, by comparing point estimates and 95% bias-corrected bootstrap confidence intervals. To study the effect of analyzing a random sample of the population on model choice, we re-computed these statistics using random samples beginning with 5,000 patients and ending with the entire sample. The Square-root Normal model had the lowest estimates of the RMSE and MAPE, with bootstrap confidence intervals that were always lower than those for the other models. The Gamma with square-root link was best as measured by the PRs. The choice of best model could vary if smaller samples were used and the Gamma with square-root link model had convergence problems with small samples. Models with square-root transformation or link fit the data best. This function (whether used as transformation or as a link) seems to help deal with the high comorbidity of this population by introducing a form of interaction. The Gamma distribution helps with the long tail of the distribution. However, the Normal distribution is suitable if the correct transformation of the outcome is used.

[Salivary microbiome in people with obesity: a pilot study].

PubMed

Wu, Y J; Chi, X P; Chen, F; Deng, X L

2018-02-18

To investigate the characterization of the salivary microbiome in people with obesity and the differences in microbial composition, gene function and metabolic pathways of salivary microbiome between people with obesity and normal weight controls. The study was carried out in people with obesity and age- and sex-matched normal weight controls. None of these selected participants had the systemic disease, oral mucosal disease or periodontal disease. Unstimulated saliva samples were collected and oral examination was conducted. DNAs from saliva samples were extracted and sequenced in an Illumina NextSeq 500 platform. Community composition, linear discriminant analysis of taxonomic differences,gene prediction, gene set construction and annotation of gene function were performed. The classified bacterial reads of the samples were 2 630 428 for each sample. A total of 11 phyla, 19 classes, 26 orders, 41 families, 62 genera and 164 species were detected ultimately. All samples had the same predominant phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria). There were statistical differences between the groups at the class, order, family, genus and species levels. At the class level, Negativicutes and Erysipelotrichia were more abundant in the obesity group, while Flavobacteriia and Bateroidetes dominated in normal weight group (P<0.05). At the species level, 16 showed significant differences in relative abundance among the groups, in which Prevotella melaninogenica,Prevotella salivae,Solobacterium moorei and Atopobium parvulum ware more abundant in the obesity group, whereas Streptococcus sanguinis dominated in normal weight group (P<0.05). The people with obesity had a higher number of salivary microbial genes (P<0.05). We produced statistics on gene prediction and found salivary microbiome of obesity group had a higher number of genes (P < 0.05). Genes associated with the pathways of metabolism and environmental information processing and human diseases were significantly enriched in the saliva samples of people with obesity (P < 0.01). Significant differences were seen in composition, gene function and metabolic pathways of salivary microbiome between people with obesity and normal weight people. We hope to go on further study with larger sample size in the near future.

The effects of sample preparation on measured concentrations of eight elements in edible tissues of fish from streams contaminated by lead mining

USGS Publications Warehouse

Schmitt, Christopher J.; Finger, Susan E.

1987-01-01

The influence of sample preparation on measured concentrations of eight elements in the edible tissues of two black basses (Centrarchidae), two catfishes (Ictaluridae), and the black redhorse,Moxostoma duquesnei (Catostomidae) from two rivers in southeastern Missouri contaminated by mining and related activities was investigated. Concentrations of Pb, Cd, Cu, Zn, Fe, Mn, Ba, and Ca were measured in two skinless, boneless samples of axial muscle from individual fish prepared in a clean room. One sample (normally-processed) was removed from each fish with a knife in a manner typically used by investigators to process fish for elemental analysis and presumedly representative of methods employed by anglers when preparing fish for home consumption. A second sample (clean-processed) was then prepared from each normally-processed sample by cutting away all surface material with acid-cleaned instruments under ultraclean conditions. The samples were analyzed as a single group by atomic absorption spectrophotometry. Of the elements studied, only Pb regularly exceeded current guidelines for elemental contaminants in foods. Concentrations were high in black redhorse from contaminated sites, regardless of preparation method; for the other fishes, whether or not Pb guidelines were exceeded depended on preparation technique. Except for Mn and Ca, concentrations of all elements measured were significantly lower in cleanthan in normally-processed tissue samples. Absolute differences in measured concentrations between clean- and normally-processed samples were most evident for Pb and Ba in bass and catfish and for Cd and Zn in redhorse. Regardless of preparation method, concentrations of Pb, Ca, Mn, and Ba in individual fish were closely correlated; samples that were high or low in one of these four elements were correspondingly high or low in the other three. In contrast, correlations between Zn, Fe, and Cd occurred only in normallyprocessed samples, suggesting that these correlations resulted from high concentrations on the surfaces of some samples. Concentrations of Pb and Ba in edible tissues of fish from contaminated sites were highly correlated with Ca content, which was probably determined largely by the amount of tissue other than muscle in the sample because fish muscle contains relatively little Ca. Accordingly, variation within a group of similar samples can be reduced by normalizing Pb and Ba concentrations to a standard Ca concentration. When sample size (N) is large, this can be accomplished statistically by analysis of covariance; whenN is small, molar ratios of [Pb]/[Ca] and [Ba]/[Ca] can be computed. Without such adjustments, unrealistically large Ns are required to yield statistically reliable estimates of Pb concentrations in edible tissues. Investigators should acknowledge that reported concentrations of certain elements are only estimates, and that regardless of the care exercised during the collection, preparation, and analysis of samples, results should be interpreted with the awareness that contamination from external sources may have occurred.

Factor analysis of Wechsler Adult Intelligence Scale-Revised in developmentally disabled persons.

PubMed

Di Nuovo, Santo F; Buono, Serafino

2006-12-01

The results of previous studies on the factorial structure of Wechsler Intelligence Scales are somewhat inconsistent across normal and pathological samples. To study specific clinical groups, such as developmentally disabled persons, it is useful to examine the factor structure in appropriate samples. A factor analysis was carried out using the principal component method and the Varimax orthogonal rotation on the Wechsler Adult Intelligence Scale (WAIS-R) in a sample of 203 developmentally disabled persons, with a mean age of 25 years 4 months. Developmental disability ranged from mild to moderate. Partially contrasting with previous studies on normal samples, results found a two-factor solution. Wechsler's traditional Verbal and Performance scales seems to be more appropriate for this sample than the alternative three-factor solution.

The performance of multimodal hyperspectral spectroscopy in the detection of precancerous cervical lesions

NASA Astrophysics Data System (ADS)

Trahmono; Lusiana, N.; Indarti, J.

2017-08-01

The aim of this study was to compare the performance of multimodal hyperspectral spectroscopy (MHS), which combines fluorescence and reflectance spectroscopy, with that of conventional laboratory-based screening tests, such as the Papanicolaou (Pap) smear test and human papilloma virus (HPV) DNA test, for detecting precancerous lesions of the cervix. The study utilized a cross-sectional design, and the kappa test was used in the analytical assessment. MHS scans were obtained from a sample of 70 consecutive patients, followed by sample collection for Pap and HPV DNA analysis and colposcopy referral, if indicated. Of the 70 patients evaluated, the results of cervical spectroscopy were normal in 38 (54.3%) patients, and they were abnormal in 32 (45.7%) patients. Based on the cytology results, 45 (64.3%) samples were normal, and 25 (35.7%) samples were abnormal. According to the results of the HPV DNA test, 47 (67.14%) samples were normal, and 17 (24.28%) samples were abnormal. Based on the results of the kappa test, the agreement between MHS and cytology was 0.793 (p < 0.001). The agreement between MHS and the HPV DNA test was 0.195 (p = 0.086), and the agreement between MHS and colposcopy was 0.479 (p < 0.001).

Microbiological profile and potential hazards associated with imported and local brands of tomato paste in Nigeria.

PubMed

Efiuvwevwere, B J; Atirike, O I

1998-03-01

Cans of three tomato paste brands (two of which are imported and one produced locally) showing defective or normal appearance were purchased from various retail outlets and analysed for microbial composition and pH values. Substantially higher total viable counts were observed in samples from defective cans but the lowest population was found in the local brand. Ratio of mesophilic to thermophilic micro-organisms increased in samples obtained from cans showing visible defects. Anaerobic spore counts were higher than the aerobic population in both normal and defective cans, but the counts varied with the brands. Four dominant bacterial genera (Bacillus, Clostridium, Lactobacillus and Leuconostoc) were isolated from the samples with the greater proportion being spore-formers. Percentage occurrence of Clostridium thermosaccharolyticum was appreciably higher in samples from defective cans while a preponderance of Lactobacillus occurred in samples from normal cans. Of the moulds isolated, Absidia and Aspergillus fumigatus showed a higher percentage in defective cans. pH values higher than the critical safe level of 4.6 were found in cans with visible defects and greater microbial diversity with higher microbial load was more often associated with these samples. Imported brands showed more undesirable microbial quality and pH values, making them potentially hazardous.

A Cancer-Indicative microRNA Pattern in Normal Prostate Tissue

PubMed Central

Hellwinkel, Olaf J. C.; Sellier, Christina; Sylvester, Yu-Mi Jessica; Brase, Jan C.; Isbarn, Hendrik; Erbersdobler, Andreas; Steuber, Thomas; Sültmann, Holger; Schlomm, Thorsten; Wagner, Christina

2013-01-01

We analyzed the levels of selected micro-RNAs in normal prostate tissue to assess their potential to indicate tumor foci elsewhere in the prostate. Histologically normal prostate tissue samples from 31 prostate cancer patients and two cancer negative control groups with either unsuspicious or elevated prostate specific antigen (PSA) levels (14 and 17 individuals, respectively) were analyzed. Based on the expression analysis of 157 microRNAs in a pool of prostate tissue samples and information from data bases/literature, we selected eight microRNAs for quantification by real-time polymerase chain reactions (RT-PCRs). Selected miRNAs were analyzed in histologically tumor-free biopsy samples from patients and healthy controls. We identified seven microRNAs (miR-124a, miR-146a & b, miR-185, miR-16 and let-7a & b), which displayed significant differential expression in normal prostate tissue from men with prostate cancer compared to both cancer negative control groups. Four microRNAs (miR-185, miR-16 and let-7a and let-7b) remained to significantly discriminate normal tissues from prostate cancer patients from those of the cancer negative control group with elevated PSA levels. The transcript levels of these microRNAs were highly indicative for the presence of cancer in the prostates, independently of the PSA level. Our results suggest a microRNA-pattern in histologically normal prostate tissue, indicating prostate cancer elsewhere in the organ. PMID:23459235

Sample-independent approach to normalize two-dimensional data for orthogonality evaluation using whole separation space scaling.

PubMed

Jáčová, Jaroslava; Gardlo, Alžběta; Friedecký, David; Adam, Tomáš; Dimandja, Jean-Marie D

2017-08-18

Orthogonality is a key parameter that is used to evaluate the separation power of chromatography-based two-dimensional systems. It is necessary to scale the separation data before the assessment of the orthogonality. Current scaling approaches are sample-dependent, and the extent of the retention space that is converted into a normalized retention space is set according to the retention times of the first and last analytes contained in a unique sample to elute. The presence or absence of a highly retained analyte in a sample can thus significantly influence the amount of information (in terms of the total amount of separation space) contained in the normalized retention space considered for the calculation of the orthogonality. We propose a Whole Separation Space Scaling (WOSEL) approach that accounts for the whole separation space delineated by the analytical method, and not the sample. This approach enables an orthogonality-based evaluation of the efficiency of the analytical system that is independent of the sample selected. The WOSEL method was compared to two currently used orthogonality approaches through the evaluation of in silico-generated chromatograms and real separations of human biofluids and petroleum samples. WOSEL exhibits sample-to-sample stability values of 3.8% on real samples, compared to 7.0% and 10.1% for the two other methods, respectively. Using real analyses, we also demonstrate that some previously developed approaches can provide misleading conclusions on the overall orthogonality of a two-dimensional chromatographic system. Copyright © 2017 Elsevier B.V. All rights reserved.

Obesity and risk taking. A male phenomenon.

PubMed

Koritzky, Gilly; Yechiam, Eldad; Bukay, Irit; Milman, Uzi

2012-10-01

There is a growing tendency to regard overeating as an addiction, with obesity as its primary symptom. We propose that similar to other addictions, obesity is associated with excessive risk-taking in men, though not in women. To examine this suggestion we conducted two studies, one involving a sample of overweight and normal-weight students, and the other involving obese adults drawn from a dataset of health care clients, and a control sample of normal-weight adults. In both of these studies, we found that overweight and obese men took more risk in a laboratory task than normal-weight men, while overweight and obese women did not differ from normal-weight women in this respect. At the same time, obese women (but not overweight women) displayed higher impulsivity levels than normal-weight women. These findings shed light on the cognitive characteristics of obesity in men, and accent the importance of taking gender into account when developing research paradigms and treatment methods for obesity. Copyright © 2012 Elsevier Ltd. All rights reserved.

IDLN-MSP: Idiolocal normalization of real-time methylation-specific PCR for genetic imbalanced DNA specimens.

PubMed

Santourlidis, Simeon; Ghanjati, Foued; Beermann, Agnes; Hermanns, Thomas; Poyet, Cédric

2016-02-01

Sensitive, accurate, and reliable measurements of tumor cell-specific DNA methylation changes are of fundamental importance in cancer diagnosis, prognosis, and monitoring. Real-time methylation-specific PCR (MSP) using intercalating dyes is an established method of choice for this purpose. Here we present a simple but crucial adaptation of this widely applied method that overcomes a major obstacle: genetic abnormalities in the DNA samples, such as aneuploidy or copy number variations, that could result in inaccurate results due to improper normalization if the copy numbers of the target and reference sequences are not the same. In our idiolocal normalization (IDLN) method, the locus for the normalizing, methylation-independent reference amplification is chosen close to the locus of the methylation-dependent target amplification. This ensures that the copy numbers of both the target and reference sequences will be identical in most cases if they are close enough to each other, resulting in accurate normalization and reliable comparative measurements of DNA methylation in clinical samples when using real-time MSP.

Application of Atomic Dielectric Resonance Spectroscopy for the screening of blood samples from patients with clinical variant and sporadic CJD

PubMed Central

Fagge, Timothy J; Barclay, G Robin; Stove, G Colin; Stove, Gordon; Robinson, Michael J; Head, Mark W; Ironside, James W; Turner, Marc L

2007-01-01

Background Sub-clinical variant Creutzfeldt-Jakob disease (vCJD) infection and reports of vCJD transmission through blood transfusion emphasise the need for blood screening assays to ensure the safety of blood and transplanted tissues. Most assays aim to detect abnormal prion protein (PrPSc), although achieving required sensitivity is a challenge. Methods We have used innovative Atomic Dielectric Resonance Spectroscopy (ADRS), which determines dielectric properties of materials which are established by reflectivity and penetration of radio/micro waves, to analyse blood samples from patients and controls to identify characteristic ADR signatures unique to blood from vCJD and to sCJD patients. Initial sets of blood samples from vCJD, sCJD, non-CJD neurological diseases and normal healthy adults (blood donors) were screened as training samples to determine group-specific ADR characteristics, and provided a basis for classification of blinded sets of samples. Results Blood sample groups from vCJD, sCJD, non-CJD neurological diseases and normal healthy adults (blood donors) screened by ADRS were classified with 100% specificity and sensitivity, discriminating these by a co-variance expert analysis system. Conclusion ADRS appears capable of recognising and discriminating serum samples from vCJD, sCJD, non-CJD neurological diseases, and normal healthy adults, and might be developed to provide a system for primary screening or confirmatory assay complementary to other screening systems. PMID:17760958

Parental Perceptions of the Outcome and Meaning of Normalization

PubMed Central

Knafl, Kathleen A.; Darney, Blair G.; Gallo, Agatha M.; Angst, Denise B.

2010-01-01

The purpose of this secondary analysis was to identify the meaning of normalization for parents of a child with a chronic genetic condition. The sample was comprised of 28 families (48 parents), selected to reflect two groups: Normalization Present (NP) and Normalization Absent (NA). Constant comparison analysis was used to identify themes characterizing parents' perceptions of the meaning of normalization. The meanings parents attributed to normalization reflected their evaluation of condition management, parenting role, and condition impact, with parents in the NP and NA groups demonstrating distinct patterns of meaning. These meaning patterns are discussed as an outcome of normalization. Providers can play a pivotal role in helping families achieve normalization by providing guidance on how to balance condition management with normal family life. PMID:20108258

LIMS for Lasers 2015 for achieving long-term accuracy and precision of δ2H, δ17O, and δ18O of waters using laser absorption spectrometry

USGS Publications Warehouse

Coplen, Tyler B.; Wassenaar, Leonard I

2015-01-01

Although laser absorption spectrometry (LAS) instrumentation is easy to use, its incorporation into laboratory operations is not easy, owing to extensive offline manipulation of comma-separated-values files for outlier detection, between-sample memory correction, nonlinearity (δ-variation with water amount) correction, drift correction, normalization to VSMOW-SLAP scales, and difficulty in performing long-term QA/QC audits. METHODS: A Microsoft Access relational-database application, LIMS (Laboratory Information Management System) for Lasers 2015, was developed. It automates LAS data corrections and manages clients, projects, samples, instrument-sample lists, and triple-isotope (δ(17) O, δ(18) O, and δ(2) H values) instrumental data for liquid-water samples. It enables users to (1) graphically evaluate sample injections for variable water yields and high isotope-delta variance; (2) correct for between-sample carryover, instrumental drift, and δ nonlinearity; and (3) normalize final results to VSMOW-SLAP scales. RESULTS: Cost-free LIMS for Lasers 2015 enables users to obtain improved δ(17) O, δ(18) O, and δ(2) H values with liquid-water LAS instruments, even those with under-performing syringes. For example, LAS δ(2) HVSMOW measurements of USGS50 Lake Kyoga (Uganda) water using an under-performing syringe having ±10 % variation in water concentration gave +31.7 ± 1.6 ‰ (2-σ standard deviation), compared with the reference value of +32.8 ± 0.4 ‰, after correction for variation in δ value with water concentration, between-sample memory, and normalization to the VSMOW-SLAP scale. CONCLUSIONS: LIMS for Lasers 2015 enables users to create systematic, well-founded instrument templates, import δ(2) H, δ(17) O, and δ(18) O results, evaluate performance with automatic graphical plots, correct for δ nonlinearity due to variable water concentration, correct for between-sample memory, adjust for drift, perform VSMOW-SLAP normalization, and perform long-term QA/QC audits easily.

Complex conductivity of volcanic rocks and the geophysical mapping of alteration in volcanoes

NASA Astrophysics Data System (ADS)

Ghorbani, A.; Revil, A.; Coperey, A.; Soueid Ahmed, A.; Roque, S.; Heap, M. J.; Grandis, H.; Viveiros, F.

2018-05-01

Induced polarization measurements can be used to image alteration at the scale of volcanic edifices to a depth of few kilometers. Such a goal cannot be achieved with electrical conductivity alone, because too many textural and environmental parameters influence the electrical conductivity of volcanic rocks. We investigate the spectral induced polarization measurements (complex conductivity) in the frequency band 10 mHz-45 kHz of 85 core samples from five volcanoes: Merapi and Papandayan in Indonesia (32 samples), Furnas in Portugal (5 samples), Yellowstone in the USA (26 samples), and Whakaari (White Island) in New Zealand (22 samples). This collection of samples covers not only different rock compositions (basaltic andesite, andesite, trachyte and rhyolite), but also various degrees of alteration. The specific surface area is found to be correlated to the cation exchange capacity (CEC) of the samples measured by the cobalthexamine method, both serving as rough proxies of the hydrothermal alteration experienced by these materials. The in-phase (real) conductivity of the samples is the sum of a bulk contribution associated with conduction in the pore network and a surface conductivity that increases with alteration. The quadrature conductivity and the normalized chargeability are two parameters related to the polarization of the electrical double layer coating the minerals of the volcanic rocks. Both parameters increase with the degree of alteration. The surface conductivity, the quadrature conductivity, and the normalized chargeability (defined as the difference between the in-phase conductivity at high and low frequencies) are linearly correlated to the CEC normalized by the bulk tortuosity of the pore space. The effects of temperature and pyrite-content are also investigated and can be understood in terms of a physics-based model. Finally, we performed a numerical study of the use of induced polarization to image the normalized chargeability of a volcanic edifice. Induced polarization tomography can be used to map alteration of volcanic edifices with applications to geohazard mapping.

A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation

PubMed Central

Brim, Hassan; Yooseph, Shibu; Lee, Edward; Sherif, Zaki A.; Abbas, Muneer; Laiyemo, Adeyinka O.; Varma, Sudhir; Torralba, Manolito; Dowd, Scot E.; Nelson, Karen E.; Pathmasiri, Wimal; Sumner, Susan; de Vos, Willem; Liang, Qiaoyi; Yu, Jun; Zoetendal, Erwin; Ashktorab, Hassan

2017-01-01

Increasing evidence suggests a role of the gut microbiota in colorectal carcinogenesis (CRC). To detect bacterial markers of colorectal cancer in African Americans a metabolomic analysis was performed on fecal water extracts. DNA from stool samples of adenoma and healthy subjects and from colon cancer and matched normal tissues was analyzed to determine the microbiota composition (using 16S rDNA) and genomic content (metagenomics). Metagenomic functions with discriminative power between healthy and neoplastic specimens were established. Quantitative Polymerase Chain Reaction (q-PCR) using primers and probes specific to Streptococcus sp. VT_162 were used to validate this bacterium association with neoplastic transformation in stool samples from two independent cohorts of African Americans and Chinese patients with colorectal lesions. The metabolomic analysis of adenomas revealed low amino acids content. The microbiota in both cancer vs. normal tissues and adenoma vs. normal stool samples were different at the 16S rRNA gene level. Cross-mapping of metagenomic data led to 9 markers with significant discriminative power between normal and diseased specimens. These markers identified with Streptococcus sp. VT_162. Q-PCR data showed a statistically significant presence of this bacterium in advanced adenoma and cancer samples in an independent cohort of CRC patients. We defined metagenomic functions from Streptococcus sp. VT_162 with discriminative power among cancers vs. matched normal and adenomas vs. healthy subjects’ stools. Streptococcus sp. VT_162 specific 16S rDNA was validated in an independent cohort. These findings might facilitate non-invasive screening for colorectal cancer. PMID:29120399

PERFLUORINATED COMPOUNDS IN ARCHIVED HOUSE-DUST SAMPLES

EPA Science Inventory

Archived house-dust samples were analyzed for 13 perfluorinated compounds (PFCs). Results show that PFCs are found in house-dust samples, and the data are log-normally distributed. PFOS/PFOA were present in 94.6% and 96.4% of the samples respectively. Concentrations ranged fro...

Delta 14CO2 Record from Vermunt, Austria, February 1959 - June 1983

DOE Data Explorer

Levin, Ingeborg [Institut fur Umweltphysik, University of Heidelberg, Germany; Kromer, Bernd [Institut fur Umweltphysik, University of Heidelberg, Germany; Schoch-Fischer, H. [Institut fur Umweltphysik, University of Heidelberg, Germany; Bruns, M. [Institut fur Umweltphysik, University of Heidelberg, Germany; Munnich, M. [Institut fur Umweltphysik, University of Heidelberg, Germany; Berdau, D. [Institut fur Umweltphysik, University of Heidelberg, Germany; Vogel, J. C. [Institut fur Umweltphysik, University of Heidelberg, Germany; Munnich, K. O. [Institut fur Umweltphysik, University of Heidelberg, Germany

1994-01-01

The sampling at Vermunt was discontinued in 1983. During sampling from 1959 to 1983, the sampling methods were modified twice (Levin et al. 1985). From 1959 through November 1965, three dishes with 1.5 L of 0.5 normal sodium hydroxide (NaOH) carbonate-free solution were exposed to the atmosphere for ~3 days, and the atmospheric CO2 absorbed during that time was recovered by acid evolution. From November 1965 through May 1975, samples were collected by pumping fresh air continuously for 10 days through a box containing 1.5 L of a 0.5 normal NaOH solution. The method has been described by Münnich and Vogel (1959). From May 1975 to the time sampling stopped, a technique described by Levin et al. (1980) was used. Air was pumped through a rotating glass tube filled with a packed bed of Raschig rings (hard glass) to enlarge the surface of the absorbing NaOH solution (200 ml of 4 normal NaOH). The CO2 absorption was quantitative and samples represent mean values of 10 days to 2 weeks. In the laboratory, the samples were extracted from the NaOH solution in a vacuum system by adding hydrochloric or sulfuric acid. The CO2 gas samples were purified over charcoal and counted in a proportional counter (Schoch et al. 1980). Delta 14C values are given relative to the NIST oxalic acid activity corrected for decay (Stuiver and Polach 1970).

The value of Bayes' theorem for interpreting abnormal test scores in cognitively healthy and clinical samples.

PubMed

Gavett, Brandon E

2015-03-01

The base rates of abnormal test scores in cognitively normal samples have been a focus of recent research. The goal of the current study is to illustrate how Bayes' theorem uses these base rates--along with the same base rates in cognitively impaired samples and prevalence rates of cognitive impairment--to yield probability values that are more useful for making judgments about the absence or presence of cognitive impairment. Correlation matrices, means, and standard deviations were obtained from the Wechsler Memory Scale--4th Edition (WMS-IV) Technical and Interpretive Manual and used in Monte Carlo simulations to estimate the base rates of abnormal test scores in the standardization and special groups (mixed clinical) samples. Bayes' theorem was applied to these estimates to identify probabilities of normal cognition based on the number of abnormal test scores observed. Abnormal scores were common in the standardization sample (65.4% scoring below a scaled score of 7 on at least one subtest) and more common in the mixed clinical sample (85.6% scoring below a scaled score of 7 on at least one subtest). Probabilities varied according to the number of abnormal test scores, base rates of normal cognition, and cutoff scores. The results suggest that interpretation of base rates obtained from cognitively healthy samples must also account for data from cognitively impaired samples. Bayes' theorem can help neuropsychologists answer questions about the probability that an individual examinee is cognitively healthy based on the number of abnormal test scores observed.

A STUDY OF COGNITIVE DEVELOPMENT AND PERFORMANCE IN CHILDREN WITH NORMAL AND DEFECTIVE HEARING.

ERIC Educational Resources Information Center

TEMPLIN, MILDRED C.

A COMPARATIVE, LONGITUDINAL STUDY WAS CONDUCTED TO EXAMINE SPECIFIC PERFORMANCE CHARACTERISTICS OF DEAF AND NORMAL CHILDREN ON SELECTED COGNITIVE TASKS. THE SAMPLE, DISTRIBUTED INTO 3 AGE CATEGORIES, CONSISTED OF 72 NORMAL AND 60 DEAF CHILDREN. MEASURES WERE SELECTED TO ASSESS THE PERFORMANCE OF SUBJECTS (1) IN DIFFERENT AREAS OF COGNITION, (2) BY…

Multiple Regression with Varying Levels of Correlation among Predictors: Monte Carlo Sampling from Normal and Non-Normal Populations.

ERIC Educational Resources Information Center

Vasu, Ellen Storey

1978-01-01

The effects of the violation of the assumption of normality in the conditional distributions of the dependent variable, coupled with the condition of multicollinearity upon the outcome of testing the hypothesis that the regression coefficient equals zero, are investigated via a Monte Carlo study. (Author/JKS)

Getting DNA copy numbers without control samples

PubMed Central

2012-01-01

Background The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias. We propose NSA (Normality Search Algorithm), a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Results Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM), Ovarian, Prostate and Lung Cancer experiments) have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs). These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. Conclusions NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the data. The method is available in the open-source R package NSA, which is an add-on to the aroma.cn framework. http://www.aroma-project.org/addons. PMID:22898240

Getting DNA copy numbers without control samples.

PubMed

Ortiz-Estevez, Maria; Aramburu, Ander; Rubio, Angel

2012-08-16

The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias.We propose NSA (Normality Search Algorithm), a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM), Ovarian, Prostate and Lung Cancer experiments) have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs). These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the data. The method is available in the open-source R package NSA, which is an add-on to the aroma.cn framework. http://www.aroma-project.org/addons.

Robust gene network analysis reveals alteration of the STAT5a network as a hallmark of prostate cancer.

PubMed

Reddy, Anupama; Huang, C Chris; Liu, Huiqing; Delisi, Charles; Nevalainen, Marja T; Szalma, Sandor; Bhanot, Gyan

2010-01-01

We develop a general method to identify gene networks from pair-wise correlations between genes in a microarray data set and apply it to a public prostate cancer gene expression data from 69 primary prostate tumors. We define the degree of a node as the number of genes significantly associated with the node and identify hub genes as those with the highest degree. The correlation network was pruned using transcription factor binding information in VisANT (http://visant.bu.edu/) as a biological filter. The reliability of hub genes was determined using a strict permutation test. Separate networks for normal prostate samples, and prostate cancer samples from African Americans (AA) and European Americans (EA) were generated and compared. We found that the same hubs control disease progression in AA and EA networks. Combining AA and EA samples, we generated networks for low low (<7) and high (≥7) Gleason grade tumors. A comparison of their major hubs with those of the network for normal samples identified two types of changes associated with disease: (i) Some hub genes increased their degree in the tumor network compared to their degree in the normal network, suggesting that these genes are associated with gain of regulatory control in cancer (e.g. possible turning on of oncogenes). (ii) Some hubs reduced their degree in the tumor network compared to their degree in the normal network, suggesting that these genes are associated with loss of regulatory control in cancer (e.g. possible loss of tumor suppressor genes). A striking result was that for both AA and EA tumor samples, STAT5a, CEBPB and EGR1 are major hubs that gain neighbors compared to the normal prostate network. Conversely, HIF-lα is a major hub that loses connections in the prostate cancer network compared to the normal prostate network. We also find that the degree of these hubs changes progressively from normal to low grade to high grade disease, suggesting that these hubs are master regulators of prostate cancer and marks disease progression. STAT5a was identified as a central hub, with ~120 neighbors in the prostate cancer network and only 81 neighbors in the normal prostate network. Of the 120 neighbors of STAT5a, 57 are known cancer related genes, known to be involved in functional pathways associated with tumorigenesis. Our method is general and can easily be extended to identify and study networks associated with any two phenotypes.

Culture-Independent Evaluation of the Appendix and Rectum Microbiomes in Children with and without Appendicitis

PubMed Central

Davenport, Katherine P.; Fraser, Claire M.; Sandler, Anthony D.; Zeichner, Steven L.

2014-01-01

Purpose The function of the appendix is largely unknown, but its microbiota likely contributes to function. Alterations in microbiota may contribute to appendicitis, but conventional culture studies have not yielded conclusive information. We conducted a pilot, culture-independent 16S rRNA-based microbiota study of paired appendix and rectal samples. Methods We collected appendix and rectal swabs from 21 children undergoing appendectomy, six with normal appendices and fifteen with appendicitis (nine perforated). After DNA extraction, we amplified and sequenced 16S rRNA genes and analyzed sequences using CLoVR. We identified organisms differing in relative abundance using ANOVA (p<0.05) by location (appendix vs. rectum), disease (appendicitis vs. normal), and disease severity (perforated vs. non-perforated). Results We identified 290 taxa in the study's samples. Three taxa were significantly increased in normal appendices vs. normal rectal samples: Fusibacter (p = 0.009), Selenomonas (p = 0.026), and Peptostreptococcus (p = 0.049). Five taxa were increased in abundance in normal vs. diseased appendices: Paenibacillaceae (p = 0.005), Acidobacteriaceae GP4 (p = 0.019), Pseudonocardinae (p = 0.019), Bergeyella (p = 0.019) and Rhizobium (p = 0.045). Twelve taxa were increased in the appendices of appendicitis patients vs. normal appendix: Peptostreptococcus (p = 0.0003), Bilophila (p = 0.0004), Bulleidia (p = 0.012), Fusobacterium (p = 0.018), Parvimonas (p = 0.003), Mogibacterium (p = 0.012), Aminobacterium (p = 0.019), Proteus (p = 0.028), Actinomycineae (p = 0.028), Anaerovorax (p = 0.041), Anaerofilum (p = 0.045), Porphyromonas (p = 0.010). Five taxa were increased in appendices in patients with perforated vs. nonperforated appendicitis: Bulleidia (p = 0.004), Fusibacter (p = 0.005), Prevotella (p = 0.021), Porphyromonas (p = 0.030), Dialister (p = 0.035). Three taxa were increased in rectum samples of patients with appendicitis compared to the normal patients: Bulleidia (p = 0.034), Dialister (p = 0.003), and Porphyromonas (p = 0.026). Conclusion Specific taxa are more abundant in normal appendices compared to the rectum, suggesting that a distinctive appendix microbiota exists. Taxa with altered abundance in diseased and severely diseased (perforated) samples may contribute to appendicitis pathogenesis, and may provide microbial signatures in the rectum useful for guiding both treatment and diagnosis of appendicitis. PMID:24759879

Albumin - blood (serum)

MedlinePlus

The normal range is 3.4 to 5.4 g/dL (34 to 54 g/L). Normal value ranges may vary slightly among different laboratories. Some labs use different measurements or test different samples. Talk to your provider about ...

[Arf6, RalA and BIRC5 protein expression in non small cell lung cancer].

PubMed

Knizhnik, A V; Kovaleva, O B; Laktionov, K K; Mochal'nikova, V V; Komel'kov, A V; Chevkina, E M; Zborovskaia, I B

2011-01-01

Evaluation of tumor markers expression pattern which determines individual progression parameters is one of the major topics in molecular oncopathology research. This work presents research on expression analysis of several Ras-Ral associated signal transduction pathway proteins (Arf6, RalA and BIRC5) in accordance with clinical criteria in non small cell lung cancer patients. Using Western-blot analysis and RT-PCR Arf6, RalA and BIRC5 expression has been analyzed in parallel in 53 non small cell lung cancer samples of different origin. Arf6 protein expression was elevated in 55% non small cell lung cancer tumor samples in comparison with normal tissue. In the group of squamous cell lung cancer Arf6 expression elevation was observed more often. RalA protein expression was decreased in comparison to normal tissue samples in 64% of non small cell lung cancer regardless to morphological structure. Correlation between RalA protein expression decrease and absence of regional metastases was revealed for squamous cell lung cancer. BIRC5 protein expression in tumor samples versus corresponding normal tissue was 1.3 times more often elevated in the squamous cell lung cancer group (in 76% tumor samples). At the same time elevation of BIRC5 expression was fixed only in 63% of adenocarcinoma tumor samples. A statistically significant decrease (p = 0.0158) of RalA protein expression and increase (p = 0.0498) of Arf6 protein expression in comparison with normal tissue was found for T1-2N0M0 and T1-2N1-2M0 groups of squamous cell lung cancer correspondingly.

Mutagenicity and in vivo toxicity of combined particulate and semivolatile organic fractions of gasoline and diesel engine emissions.

PubMed

Seagrave, JeanClare; McDonald, Jacob D; Gigliotti, Andrew P; Nikula, Kristen J; Seilkop, Steven K; Gurevich, Michael; Mauderly, Joe L

2002-12-01

Exposure to engine emissions is associated with adverse health effects. However, little is known about the relative effects of emissions produced by different operating conditions, fuels, or technologies. Rapid screening techniques are needed to compare the biological effects of emissions with different characteristics. Here, we examined a set of engine emission samples using conventional bioassays. The samples included combined particulate material and semivolatile organic compound fractions of emissions collected from normal- and high-emitter gasoline and diesel vehicles collected at 72 degrees F, and from normal-emitter groups collected at 30 degrees F. The relative potency of the samples was determined by statistical analysis of the dose-response curves. All samples induced bacterial mutagenicity, with a 10-fold range of potency among the samples. Responses to intratracheal instillation in rats indicated generally parallel rankings of the samples by multiple endpoints reflecting cytotoxic, inflammatory, and lung parenchymal changes, allowing selection of a more limited set of parameters for future studies. The parameters selected to assess oxidative stress and macrophage function yielded little useful information. Responses to instillation indicated little difference in potency per unit of combined particulate material and semivolatile organic compound mass between normal-emitter gasoline and diesel vehicles, or between emissions collected at different temperatures. However, equivalent masses of emissions from high-emitter vehicles of both types were more potent than those from normal-emitters. While preliminary in terms of assessing contributions of different emissions to health hazards, the results indicate that a subset of this panel of assays will be useful in providing rapid, cost-effective feedback on the biological impact of modified technology.

Colon Cancer Associated Transcript-1 (CCAT1) Expression in Adenocarcinoma of the Stomach.

PubMed

Mizrahi, Ido; Mazeh, Haggi; Grinbaum, Ronit; Beglaibter, Nahum; Wilschanski, Michael; Pavlov, Vera; Adileh, Muchamad; Stojadinovic, Alexander; Avital, Itzhak; Gure, Ali Osmay; Halle, David; Nissan, Aviram

2015-01-01

Long non-coding RNAs (lncRNAs) have been shown to have functional roles in cancer biology and are dys-regulated in many tumors. Colon Cancer Associated Transcript -1 (CCAT1) is a lncRNA, previously shown to be significantly up-regulated in colon cancer. The aim of this study is to determine expression levels of CCAT1 in gastric carcinoma (GC). Tissue samples were obtained from patients undergoing resection for gastric carcinoma (n=19). For each patient, tumor tissue and normal appearing gastric mucosa were taken. Normal gastric tissues obtained from morbidly obese patients, undergoing laparoscopic sleeve gastrectomy served as normal controls (n=19). A human gastric carcinoma cell line (AGS) served as positive control. RNA was extracted from all tissue samples and CCAT1 expression was analyzed using quantitative real time-PCR (qRT-PCR). Low expression of CCAT1 was identified in normal gastric mucosa samples obtained from morbidly obese patients [mean Relative Quantity (RQ) = 1.95±0.4]. AGS human gastric carcinoma cell line showed an elevated level of CCAT1 expression (RQ=8.02). Expression levels of CCAT1 were approximately 10.8 fold higher in GC samples than in samples taken from the negative control group (RQ=21.1±5 vs. RQ=1.95±0.4, respectively, p<0.001). Interestingly, CCAT1 expression was significantly overexpressed in adjacent normal tissues when compared to the negative control group (RQ = 15.25±2 vs. RQ=1.95±0.4, respectively, p<0.001). Tissues obtained from recurrent GC cases showed the highest expression levels (RQ = 88.8±31; p<0.001). Expression levels increased with tumor stage (T4- 36.4±15, T3- 16.1±6, T2- 4.7±1), however this did not reach statistical significance (p=0.2). There was no difference in CCAT1 expression between intestinal and diffuse type GC (RQ=22.4±7 vs. 22.4±16, respectively, p=0.9). Within the normal gastric tissue samples, no significant difference in CCAT1 expression was observed in helicobacter pylori negative and positive patients (RQ= 2.4±0.9 vs. 0.93±0.2, respectively, p=0.13). CCAT1 is up-regulated in gastric cancer, and may serve as a potential bio-marker for early detection and surveillance.

Confocal Microscopy and Molecular-Specific Optical Contrast Agents for the Detection of Oral Neoplasia

PubMed Central

Carlson, Alicia L.; Gillenwater, Ann M.; Williams, Michelle D.; El-Naggar, Adel K.; Richards-Kortum, R. R.

2009-01-01

Using current clinical diagnostic techniques, it is difficult to visualize tumor morphology and architecture at the cellular level, which is necessary for diagnostic localization of pathologic lesions. Optical imaging techniques have the potential to address this clinical need by providing real-time, sub-cellular resolution images. This paper describes the use of dual mode confocal microscopy and optical molecular-specific contrast agents to image tissue architecture, cellular morphology, and sub-cellular molecular features of normal and neoplastic oral tissues. Fresh tissue slices were prepared from 33 biopsies of clinically normal and abnormal oral mucosa obtained from 14 patients. Reflectance confocal images were acquired after the application of 6% acetic acid, and fluorescence confocal images were acquired after the application of a fluorescence contrast agent targeting the epidermal growth factor receptor (EGFR). The dual imaging modes provided images similar to light microscopy of hematoxylin and eosin and immunohistochemistry staining, but from thick fresh tissue slices. Reflectance images provided information on the architecture of the tissue and the cellular morphology. The nuclear-to-cytoplasmic (N/C) ratio from the reflectance images was at least 7.5 times greater for the carcinoma than the corresponding normal samples, except for one case of highly keratinized carcinoma. Separation of carcinoma from normal and mild dysplasia was achieved using this ratio (p<0.01). Fluorescence images of EGFR expression yielded a mean fluorescence labeling intensity (FLI) that was at least 2.7 times higher for severe dysplasia and carcinoma samples than for the corresponding normal sample, and could be used to distinguish carcinoma from normal and mild dysplasia (p<0.01). Analyzed together, the N/C ratio and the mean FLI may improve the ability to distinguish carcinoma from normal squamous epithelium. PMID:17877424

Expression and localization of endocrine gland-derived vascular endothelial growth factor (EG-VEGF) in human pancreas and pancreatic adenocarcinoma.

PubMed

Morales, Angélica; Vilchis, Felipe; Chávez, Bertha; Chan, Carlos; Robles-Díaz, Guillermo; Díaz-Sánchez, Vicente

2007-10-01

Endocrine gland-derived vascular endothelial growth factor (EG-VEGF) was recently identified as the first tissue-specific angiogenic molecule. EG-VEGF (the gene product of PROK-1) appears to be expressed exclusively in steroid-producing organs such as the ovary, testis, adrenals and placenta. Since the human pancreatic cells retain steroidogenic activity, in the present study we ascertained whether this angiogenic factor is expressed in normal pancreas and pancreatic adenocarcinoma. Tissue samples from normal males (n=5), normal females (n=5) and from surgically resected adenocarcinomas (n=2) were processed for RT-PCR and immunohistochemical studies. Results from semi-quantitative analysis by RT-PCR suggest a distinct expression level for EG-VEGF in the different tissue samples. The relative amount of EG-VEGF mRNA in pancreas was more abundant in female adenocarcinoma (0.89) followed by male adenocarcinoma (0.71), than normal female (0.64) and normal male (0.38). The expression of mRNA for EG-VEGF in normal tissue was significantly higher in females than in males. All samples examined showed specific immunostaining for EG-VEGF. In male preparations, the positive labeling was localized predominantly within the pancreatic islets while in female preparations the main staining was detected towards the exocrine portion. Specific immunolabeling was also observed in endothelial cells of pancreatic blood vessels. Our data provide evidence that the human pancreas expresses the EG-VEGF, a highly specific mitogen which regulates proliferation and differentiation of the vascular endothelium. The significance of this finding could be interpreted as either, EG-VEGF is not exclusive of endocrine organs, or the pancreas should be considered as a functional steroidogenic tissue. The extent of the expression of EG-VEGF appears to have a dimorphic pattern in normal and tumoral pancreatic tissue.

Verification of three-microphone impedance tube method for measurement of transmission loss in aerogels

NASA Astrophysics Data System (ADS)

Connick, Robert J.

Accurate measurement of normal incident transmission loss is essential for the acoustic characterization of building materials. In this research, a method of measuring normal incidence sound transmission loss proposed by Salissou et al. as a complement to standard E2611-09 of the American Society for Testing and Materials [Standard Test Method for Measurement of Normal Incidence Sound Transmission of Acoustical Materials Based on the Transfer Matrix Method (American Society for Testing and Materials, New York, 2009)] is verified. Two sam- ples from the original literature are used to verify the method as well as a Filtros RTM sample. Following the verification, several nano-material Aerogel samples are measured.

Laser-induced fluorescence for the detection of esophageal and skin cancer

NASA Astrophysics Data System (ADS)

Vo-Dinh, Tuan; Panjehpour, Masoud; Overholt, Bergein F.; Julius, Clark E.; Overholt, Suzanne; Phan, Mary N.

2003-07-01

Laser-induced fluorescence (LIF) is used for in-vivo cancer diagnosis of the esophagus and skin cancer. For esophageal measurements a fiberoptic probe inserted through an endoscope was used. Autofluorescence of normal and malignant tissues were measured directly on patient skin without requiring an endoscope. Measurement of the fluorescence signal from the tissue was performed using laser excitation at 410 nm. The methodology was applied to differentiate normal and malignant tumors of the esophagus and malignant skin lesions. The results of this LIF approach were compared with histopathology results of the biopsy samples and indicated excellent agreement in the classification of normal and malignant tumors for the samples investigated.

EVALUATION OF A NEW MEAN SCALED AND MOMENT ADJUSTED TEST STATISTIC FOR SEM.

PubMed

Tong, Xiaoxiao; Bentler, Peter M

2013-01-01

Recently a new mean scaled and skewness adjusted test statistic was developed for evaluating structural equation models in small samples and with potentially nonnormal data, but this statistic has received only limited evaluation. The performance of this statistic is compared to normal theory maximum likelihood and two well-known robust test statistics. A modification to the Satorra-Bentler scaled statistic is developed for the condition that sample size is smaller than degrees of freedom. The behavior of the four test statistics is evaluated with a Monte Carlo confirmatory factor analysis study that varies seven sample sizes and three distributional conditions obtained using Headrick's fifth-order transformation to nonnormality. The new statistic performs badly in most conditions except under the normal distribution. The goodness-of-fit χ(2) test based on maximum-likelihood estimation performed well under normal distributions as well as under a condition of asymptotic robustness. The Satorra-Bentler scaled test statistic performed best overall, while the mean scaled and variance adjusted test statistic outperformed the others at small and moderate sample sizes under certain distributional conditions.

Concentration trends for lead and calcium-normalized lead in fish fillets from the Big River, a mining-contaminated stream in southeastern Missouri USA

USGS Publications Warehouse

Schmitt, Christopher J.; McKee, Michael J.

2016-01-01

Lead (Pb) and calcium (Ca) concentrations were measured in fillet samples of longear sunfish (Lepomis megalotis) and redhorse suckers (Moxostoma spp.) collected in 2005–2012 from the Big River, which drains a historical mining area in southeastern Missouri and where a consumption advisory is in effect due to elevated Pb concentrations in fish. Lead tends to accumulated in Ca-rich tissues such as bone and scale. Concentrations of Pb in fish muscle are typically low, but can become elevated in fillets from Pb-contaminated sites depending in part on how much bone, scale, and skin is included in the sample. We used analysis-of-covariance to normalize Pb concentration to the geometric mean Ca concentration (415 ug/g wet weight, ww), which reduced variation between taxa, sites, and years, as was the number of samples that exceeded Missouri consumption advisory threshold (300 ng/g ww). Concentrations of Pb in 2005–2012 were lower than in the past, especially after Ca-normalization, but the consumption advisory is still warranted because concentrations were >300 ng/g ww in samples of both taxa from contaminated sites. For monitoring purposes, a simple linear regression model is proposed for estimating Ca-normalized Pb concentrations in fillets from Pb:Ca molar ratios as a way of reducing the effects of differing preparation methods on fillet Pb variation.

Concentration Trends for Lead and Calcium-Normalized Lead in Fish Fillets from the Big River, a Mining-Contaminated Stream in Southeastern Missouri USA.

PubMed

Schmitt, Christopher J; McKee, Michael J

2016-11-01

Lead (Pb) and calcium (Ca) concentrations were measured in fillet samples of longear sunfish (Lepomis megalotis) and redhorse suckers (Moxostoma spp.) collected in 2005-2012 from the Big River, which drains a historical mining area in southeastern Missouri and where a consumption advisory is in effect due to elevated Pb concentrations in fish. Lead tends to accumulated in Ca-rich tissues such as bone and scale. Concentrations of Pb in fish muscle are typically low, but can become elevated in fillets from Pb-contaminated sites depending in part on how much bone, scale, and skin is included in the sample. We used analysis-of-covariance to normalize Pb concentration to the geometric mean Ca concentration (415 ug/g wet weight, ww), which reduced variation between taxa, sites, and years, as was the number of samples that exceeded Missouri consumption advisory threshold (300 ng/g ww). Concentrations of Pb in 2005-2012 were lower than in the past, especially after Ca-normalization, but the consumption advisory is still warranted because concentrations were >300 ng/g ww in samples of both taxa from contaminated sites. For monitoring purposes, a simple linear regression model is proposed for estimating Ca-normalized Pb concentrations in fillets from Pb:Ca molar ratios as a way of reducing the effects of differing preparation methods on fillet Pb variation.

Aspartate aminotransferase (AST) blood test

MedlinePlus

The normal range is 10 to 34 U/L (0.17 to 0.57 µkat/L). Normal value ranges may vary slightly among different laboratories. Some labs use different measurements or may test different samples. Talk to your health ...

File format for normalizing radiological concentration exposure rate and dose rate data for the effects of radioactive decay and weathering processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kraus, Terrence D.

2017-04-01

This report specifies the electronic file format that was agreed upon to be used as the file format for normalized radiological data produced by the software tool developed under this TI project. The NA-84 Technology Integration (TI) Program project (SNL17-CM-635, Normalizing Radiological Data for Analysis and Integration into Models) investigators held a teleconference on December 7, 2017 to discuss the tasks to be completed under the TI program project. During this teleconference, the TI project investigators determined that the comma-separated values (CSV) file format is the most suitable file format for the normalized radiological data that will be outputted frommore » the normalizing tool developed under this TI project. The CSV file format was selected because it provides the requisite flexibility to manage different types of radiological data (i.e., activity concentration, exposure rate, dose rate) from other sources [e.g., Radiological Assessment and Monitoring System (RAMS), Aerial Measuring System (AMS), Monitoring and Sampling). The CSV file format also is suitable for the file format of the normalized radiological data because this normalized data can then be ingested by other software [e.g., RAMS, Visual Sampling Plan (VSP)] used by the NA-84’s Consequence Management Program.« less

Detection of septicemia in chicken livers by spectroscopy,.

PubMed

Dey, B P; Chen, Y R; Hsieh, C; Chan, D E

2003-02-01

To establish a procedure for differentiating normal chickens from chickens with septicemia/toxemia (septox) by machine inspection under the Hazard Analysis and Critical Control Point-Based Inspection Models Project, spectral measurements of 300 chicken livers, of which half were normal and half were condemned due to septox conditions, were collected and analyzed. Neural network classification of the spectral data after principal component analysis (PCA) indicated that normal and septox livers were correctly differentiated by spectroscopy at a rate of 96%. Analysis of the data established 100% correlation between the spectroscopic identification and the subset of samples, both normal and septox, that were histopathologically diagnosed. In an attempt to establish the microbiological etiology of the diseased livers, isolates from 30 livers indicated that the poultry carcasses were contaminated mostly with coliforms present in the environment, hindering the isolation of pathogenic microorganisms. Therefore, to establish the cause of diseased livers, a strictly aseptic environment and procedure for sample collection is required.

Low prevalence of high risk human papillomavirus in normal oral mucosa by hybrid capture 2

PubMed Central

González-Losa, Maria del Refugio; Manzano-Cabrera, Luis; Rueda-Gordillo, Florencio; Hernández-Solís, Sandra E.; Puerto-Solís, Luis

2008-01-01

High risk human papillomavirus (HR-HPV) are recognized as a necessary factor to development cervical cancer. During the last decade many studies have found HR-HPV in oral squamous cell carcinoma (OSCC) and normal oral mucosa, however the association between HR-HPV and OSCC is still uncertain. The aim of the study was to determine DNA HR-HPV in normal oral cavity of healthy adults. A cross-sectional study was performed; samples from 77 patients with normal oral cavity were collected at the Dentistry school, Autonomous University of Yucatan, Merida, Yucatan, México. HR-HPV was detected by hybrid capture 2. One sample out of 77(1.2%) was positive for HR-PVH. It was from a man of 50 years old. HRHPV is present in low rate among healthy oral mucosa. Hybrid capture 2 could be a good methodology for large epidemiology studies. PMID:24031173

Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data.

PubMed

Reisetter, Anna C; Muehlbauer, Michael J; Bain, James R; Nodzenski, Michael; Stevens, Robert D; Ilkayeva, Olga; Metzger, Boyd E; Newgard, Christopher B; Lowe, William L; Scholtens, Denise M

2017-02-02

Metabolomics offers a unique integrative perspective for health research, reflecting genetic and environmental contributions to disease-related phenotypes. Identifying robust associations in population-based or large-scale clinical studies demands large numbers of subjects and therefore sample batching for gas-chromatography/mass spectrometry (GC/MS) non-targeted assays. When run over weeks or months, technical noise due to batch and run-order threatens data interpretability. Application of existing normalization methods to metabolomics is challenged by unsatisfied modeling assumptions and, notably, failure to address batch-specific truncation of low abundance compounds. To curtail technical noise and make GC/MS metabolomics data amenable to analyses describing biologically relevant variability, we propose mixture model normalization (mixnorm) that accommodates truncated data and estimates per-metabolite batch and run-order effects using quality control samples. Mixnorm outperforms other approaches across many metrics, including improved correlation of non-targeted and targeted measurements and superior performance when metabolite detectability varies according to batch. For some metrics, particularly when truncation is less frequent for a metabolite, mean centering and median scaling demonstrate comparable performance to mixnorm. When quality control samples are systematically included in batches, mixnorm is uniquely suited to normalizing non-targeted GC/MS metabolomics data due to explicit accommodation of batch effects, run order and varying thresholds of detectability. Especially in large-scale studies, normalization is crucial for drawing accurate conclusions from non-targeted GC/MS metabolomics data.

A large-scale measurement of dielectric properties of normal and malignant colorectal tissues obtained from cancer surgeries at Larmor frequencies.

PubMed

Li, Zhou; Deng, Guanhua; Li, Zhe; Xin, Sherman Xuegang; Duan, Song; Lan, Maoying; Zhang, Sa; Gao, Yixin; He, Jun; Zhang, Songtao; Tang, Hongming; Wang, Weiwei; Han, Shuai; Yang, Qing X; Zhuang, Ling; Hu, Jiani; Liu, Feng

2016-11-01

Knowledge of dielectric properties of malignant human tissues is necessary for the recently developed magnetic resonance (MR) technique called MR electrical property tomography. This technique may be used in early tumor detection based on the obvious differentiation of the dielectric properties between normal and malignant tissues. However, the dielectric properties of malignant human tissues in the scale of the Larmor frequencies are not completely available in the literature. In this study, the authors focused only on the dielectric properties of colorectal tumor tissue. The dielectric properties of 504 colorectal malignant samples excised from 85 patients in the scale of the Larmor frequencies were measured using the precision open-ended coaxial probe method. The obtained complex-permittivity data were fitted to the single-pole Cole-Cole model. The median permittivity and conductivity for the malignant tissue sample were 79.3 and 0.881 S/m at 128 MHz, which were 14.6% and 17.0% higher, respectively, than those of normal tissue samples. Significant differences between normal and malignant tissues were found for the dielectric properties (p < 0.05). Experimental results indicated that the dielectric properties were significantly different between normal and malignant tissues for colorectal tissue. This large-scale clinical measurement provides more subtle base data to validate the technique of MR electrical property tomography.

Vaginal lactobacilli profile in pregnant women with normal & abnormal vaginal flora.

PubMed

Yeruva, Thirupathaiah; Rajkumar, Hemalatha; Donugama, Vasundhara

2017-10-01

Lactobacilli species that are better adapted to vaginal environment of women may colonize better and offer protection against vaginal pathogenic bacteria. In this study, the distribution of common Lactobacillus species was investigated in pregnant women. Sixty seven pregnant women were included in the study and vaginal samples were collected for Gram staining. Women were classified as normal vaginal flora, intermediate flora and bacterial vaginosis (BV) based on Nugent's score. Vaginal samples were also collected for the identification of Lactobacillus spp. by multiplex polymerase chain reaction (PCR) profiling of 16S rDNA amplification method. Lactobacillus crispatus (100%) was the most predominant Lactobacillus spp. present in pregnant women with normal flora, followed by L. iners (77%), L. jensenii (74%) and L. helveticus (60%). While, L. iners was commonly present across groups in women with normal, intermediate or BV flora, L. crispatus, L. jensenii and L. helveticus decreased significantly as the vaginal flora changed to intermediate and BV. In women with BV, except L. iners other species of lactobacilli was less frequently prevalent. Species such as L. rhamnosus, L. fermentum, L. paracasei and L. casei were not detected in any vaginal sample. L. crispatus, L. jensinii and L. helveticus were predominant species in women with normal flora. L. crispatus alone or in combination with L. jensinii and L. helveticus may be evaluated for probiotic properties for the prevention and treatment of BV.

Constant strain rate experiments and constitutive modeling for a class of bitumen

NASA Astrophysics Data System (ADS)

Reddy, Kommidi Santosh; Umakanthan, S.; Krishnan, J. Murali

2012-08-01

The mechanical properties of bitumen vary with the nature of the crude source and the processing methods employed. To understand the role of the processing conditions played in the mechanical properties, bitumen samples derived from the same crude source but processed differently (blown and blended) are investigated. The samples are subjected to constant strain rate experiments in a parallel plate rheometer. The torque applied to realize the prescribed angular velocity for the top plate and the normal force applied to maintain the gap between the top and bottom plate are measured. It is found that when the top plate is held stationary, the time taken by the torque to be reduced by a certain percentage of its maximum value is different from the time taken by the normal force to decrease by the same percentage of its maximum value. Further, the time at which the maximum torque occurs is different from the time at which the maximum normal force occurs. Since the existing constitutive relations for bitumen cannot capture the difference in the relaxation times for the torque and normal force, a new rate type constitutive model, incorporating this response, is proposed. Although the blended and blown bitumen samples used in this study correspond to the same grade, the mechanical responses of the two samples are not the same. This is also reflected in the difference in the values of the material parameters in the model proposed. The differences in the mechanical properties between the differently processed bitumen samples increase further with aging. This has implications for the long-term performance of the pavement.

Sample Size Determination for One- and Two-Sample Trimmed Mean Tests

ERIC Educational Resources Information Center

Luh, Wei-Ming; Olejnik, Stephen; Guo, Jiin-Huarng

2008-01-01

Formulas to determine the necessary sample sizes for parametric tests of group comparisons are available from several sources and appropriate when population distributions are normal. However, in the context of nonnormal population distributions, researchers recommend Yuen's trimmed mean test, but formulas to determine sample sizes have not been…

On the relative frequencies of spectroscopically normal and peculiar type Ia supernovae

NASA Technical Reports Server (NTRS)

Branch, David; Fisher, Adam; Nugent, Peter

1993-01-01

After defining what we mean by spectroscopically 'normal' and 'peculiar' Type Ia supernove, we report the results of an attempt to subclassify 84 SNe Ia either as normal or as like one of the recent, peculiar SNe Ia: 1991T, 1991bg, or 1986G. Only SNe 1957A and 1960H are found to have been certifiably abnormal, with SN 1957A; appearing to have been like SN 1991bg, and SN 1960H having been like SN 1991bg or SN 1988G; SNe 1971I and 1980I are under suspicion of having been like SN 1986G, and SN 1988G of having been like SN 1991T. Of the SNe Ia we have been able to classify either as normal or as peculiar, 89% (or 83%, counting those under suspicion as peculiar) are normal. Our main conclusion is that the observational sample of SNe Ia is strongly peaked at 'spectroscopically normal.' We further conclude that when arranged in the photometric sequence of Phillips (1993) SNe Ia also form a spectroscopic sequence, and that peculiar SNe Ia are over-represented in the Phillips sample.

Overcoming Heparin-Associated RT-qPCR Inhibition and Normalization Issues for microRNA Quantification in Patients with Acute Myocardial Infarction.

PubMed

Coelho-Lima, Jose; Mohammed, Ashfaq; Cormack, Suzanne; Jones, Samuel; Das, Rajiv; Egred, Mohaned; Panahi, Pedram; Ali, Simi; Spyridopoulos, Ioakim

2018-06-11

 Cardiac-enriched micro ribonucleic acids (miRNAs) are released into the circulation following ST-elevation myocardial infarction (STEMI). Lack of standardized approaches for reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) data normalization and presence of RT-qPCR inhibitors (e.g. heparin) in patient blood samples have prevented reproducible miRNA quantification in this cohort and subsequent translation of these biomarkers to clinical practice.  Using a RT-qPCR miRNA screening platform, we identified and validated an endogenous circulating miRNA as a normalization control. In addition, we assessed the effects of in vivo and in vitro anticoagulant drugs administration (heparin and bivalirudin) on three RT-qPCR normalization strategies (global miRNA mean, exogenous spike-in control [cel-miR-39] and endogenous miRNA control). Finally, we evaluated the effect of heparin and its in vitro inhibition with heparinase on the quantification of cardiac-enriched miRNAs in STEMI patients.  miR-425-5p was validated as an endogenous miRNA control. Heparin administration in vitro and in vivo inhibited all RT-qPCR normalization strategies. In contrast, bivalirudin had no effects on cel-miR-39 or miR-425-5p quantification. In vitro RNA sample treatment with 0.3 U of heparinase overcame heparin-induced over-estimation of cardiac-enriched miRNA levels and improved their correlation with high-sensitivity troponin T.  miRNA quantification in STEMI patients receiving heparin is jeopardized by its effect on all RT-qPCR normalization approaches. Use of samples from bivalirudin-treated patients or in vitro treatment of heparin-contaminated samples with heparinase are suitable alternatives for miRNA quantification in this cohort. Finally, we reinforce the evidence that cardiac-enriched miRNAs early after myocardial reperfusion reflect the severity of cardiac injury. Schattauer GmbH Stuttgart.

Radio emission from dusty galaxies observed by AKARI

NASA Astrophysics Data System (ADS)

Pepiak, A.; Pollo, A.; Takeuchi, T. T.; Solarz, A.; Jurusik, W.

2014-10-01

We probe radio-infrared correlation for two samples of extragalactic sources from the local Universe from the AKARI All-Sky Catalogue. The first, smaller sample (1053 objects) was constructed by the cross-correlation of the AKARI/FIS All-Sky Survey Bright Source Catalogue, the AKARI IRC All-Sky Survey Point Source Catalogue and the NRAO VLA Sky Survey, i.e. it consists of sources detected in the mid- and far-infrared by AKARI, and at the 1.4 GHz radio frequency by NRAO. The second, larger sample (13,324 objects) was constructed by the cross-correlation of only the AKARI/FIS All-Sky Survey Bright Source Catalogue and the NRAO VLA Sky Survey, i.e. it consists of sources detected in the far-infrared and radio, without a condition to be detected in the mid-infrared. Additionally, all objects in both samples were identified as galaxies in the NED and/or SIMBAD databases, and a part of them is known to host active galactic nuclei (AGNs). For the present analysis, we have restricted our samples only to sources with known redshift z. In this paper, we analyse the far-infrared-radio correlation for both of these samples. We compare the ratio of infrared and radio emission from normal star-forming dusty galaxies and AGNs in both samples. For the smaller sample we obtained =2.14 for AGNs and =2.27 for normal galaxies, while for the larger sample =2.15 for AGNs and =2.22 for normal galaxies. An average value of the slope in both samples is ~2.2, which is consistent with the previous measurements from the literature.

Evaluation of sampling plans to detect Cry9C protein in corn flour and meal.

PubMed

Whitaker, Thomas B; Trucksess, Mary W; Giesbrecht, Francis G; Slate, Andrew B; Thomas, Francis S

2004-01-01

StarLink is a genetically modified corn that produces an insecticidal protein, Cry9C. Studies were conducted to determine the variability and Cry9C distribution among sample test results when Cry9C protein was estimated in a bulk lot of corn flour and meal. Emphasis was placed on measuring sampling and analytical variances associated with each step of the test procedure used to measure Cry9C in corn flour and meal. Two commercially available enzyme-linked immunosorbent assay kits were used: one for the determination of Cry9C protein concentration and the other for % StarLink seed. The sampling and analytical variances associated with each step of the Cry9C test procedures were determined for flour and meal. Variances were found to be functions of Cry9C concentration, and regression equations were developed to describe the relationships. Because of the larger particle size, sampling variability associated with cornmeal was about double that for corn flour. For cornmeal, the sampling variance accounted for 92.6% of the total testing variability. The observed sampling and analytical distributions were compared with the Normal distribution. In almost all comparisons, the null hypothesis that the Cry9C protein values were sampled from a Normal distribution could not be rejected at 95% confidence limits. The Normal distribution and the variance estimates were used to evaluate the performance of several Cry9C protein sampling plans for corn flour and meal. Operating characteristic curves were developed and used to demonstrate the effect of increasing sample size on reducing false positives (seller's risk) and false negatives (buyer's risk).

Interpreting the concordance statistic of a logistic regression model: relation to the variance and odds ratio of a continuous explanatory variable

PubMed Central

2012-01-01

Background When outcomes are binary, the c-statistic (equivalent to the area under the Receiver Operating Characteristic curve) is a standard measure of the predictive accuracy of a logistic regression model. Methods An analytical expression was derived under the assumption that a continuous explanatory variable follows a normal distribution in those with and without the condition. We then conducted an extensive set of Monte Carlo simulations to examine whether the expressions derived under the assumption of binormality allowed for accurate prediction of the empirical c-statistic when the explanatory variable followed a normal distribution in the combined sample of those with and without the condition. We also examine the accuracy of the predicted c-statistic when the explanatory variable followed a gamma, log-normal or uniform distribution in combined sample of those with and without the condition. Results Under the assumption of binormality with equality of variances, the c-statistic follows a standard normal cumulative distribution function with dependence on the product of the standard deviation of the normal components (reflecting more heterogeneity) and the log-odds ratio (reflecting larger effects). Under the assumption of binormality with unequal variances, the c-statistic follows a standard normal cumulative distribution function with dependence on the standardized difference of the explanatory variable in those with and without the condition. In our Monte Carlo simulations, we found that these expressions allowed for reasonably accurate prediction of the empirical c-statistic when the distribution of the explanatory variable was normal, gamma, log-normal, and uniform in the entire sample of those with and without the condition. Conclusions The discriminative ability of a continuous explanatory variable cannot be judged by its odds ratio alone, but always needs to be considered in relation to the heterogeneity of the population. PMID:22716998

Increased Steady-State Mutant Huntingtin mRNA in Huntington's Disease Brain.

PubMed

Liu, Wanzhao; Chaurette, Joanna; Pfister, Edith L; Kennington, Lori A; Chase, Kathryn O; Bullock, Jocelyn; Vonsattel, Jean Paul G; Faull, Richard L M; Macdonald, Douglas; DiFiglia, Marian; Zamore, Phillip D; Aronin, Neil

2013-01-01

Huntington's disease is caused by expansion of CAG trinucleotide repeats in the first exon of the huntingtin gene, which is essential for both development and neurogenesis. Huntington's disease is autosomal dominant. The normal allele contains 6 to 35 CAG triplets (average, 18) and the mutant, disease-causing allele contains >36 CAG triplets (average, 42). We examined 279 postmortem brain samples, including 148 HD and 131 non-HD controls. A total of 108 samples from 87 HD patients that are heterozygous at SNP rs362307, with a normal allele (18 to 27 CAG repeats) and a mutant allele (39 to 73 CAG repeats) were used to measure relative abundance of mutant and wild-type huntingtin mRNA. We used allele-specific, quantitative RT-PCR based on SNP heterozygosity to estimate the relative amount of mutant versus normal huntingtin mRNA in postmortem brain samples from patients with Huntington's disease. In the cortex and striatum, the amount of mRNA from the mutant allele exceeds that from the normal allele in 75% of patients. In the cerebellum, no significant difference between the two alleles was evident. Brain tissues from non-HD controls show no significant difference between two alleles of huntingtin mRNAs. Allelic differences were more pronounced at early neuropathological grades (grades 1 and 2) than at late grades (grades 3 and 4). More mutant HTT than normal could arise from increased transcription of mutant HTT allele, or decreased clearance of mutant HTT mRNA, or both. An implication is that equimolar silencing of both alleles would increase the mutant HTT to normal HTT ratio.

High-resolution microendoscope imaging of inverted papilloma and normal sinonasal mucosa: evaluation of interobserver concordance.

PubMed

Parasher, Arjun K; Kidwai, Sarah M; Schorn, Victor J; Goljo, Erden; Weinberg, Alan D; Richards-Kortum, Rebecca; Sikora, Andrew G; Iloreta, Alfred Marc; Govindaraj, Satish; Miles, Brett A

2015-12-01

High-resolution microendoscopy (HRME) enables real-time imaging of epithelial tissue. The utility of this novel imaging modality for inverted papilloma has not been previously described. This study examines the ability of otolaryngologists to differentiate between images of inverted papilloma and normal sinonasal mucosa obtained with a HRME. Inverted papilloma and normal sinonasal mucosa specimens were stained with a contrast agent, proflavine. HRME images were subsequently captured. Histopathological diagnosis was obtained for each sample. Quality-controlled images were used to assemble a training set. After reviewing the training images, 6 otolaryngologists without prior HRME experience reviewed and classified test images. Five samples of inverted papilloma and 2 normal sinonasal mucosa samples were collected. Four representative images from each specimen were used for the 28-image test set. The mean accuracy among all reviewers was 89.9% (95% confidence interval [CI], 84.3% to 94.0%). The sensitivity to correctly identify inverted papilloma was 86.7% (95% CI, 79.2% to 92.2%), and the specificity was 92.9% (95% CI, 89.0% to 100.0%). The Fleiss kappa interrater reliability score was 0.80 (95% CI, 0.70 to 0.89). Inverted papilloma and normal sinonasal mucosa have distinct HRME imaging characteristics. Otolaryngologists can be successfully trained to distinguish between inverted papilloma and normal sinonasal mucosa. HRME is a feasible tool for identification of inverted papilloma. By conducting future in vivo trials, HRME potentially may enable real-time surgical margin determination during surgical excision of inverted papilloma. © 2015 ARS-AAOA, LLC.

Comprehensive Analysis of Genome Rearrangements in Eight Human Malignant Tumor Tissues

PubMed Central

Wang, Chong

2016-01-01

Carcinogenesis is a complex multifactorial, multistage process, but the precise mechanisms are not well understood. In this study, we performed a genome-wide analysis of the copy number variation (CNV), breakpoint region (BPR) and fragile sites in 2,737 tumor samples from eight tumor entities and in 432 normal samples. CNV detection and BPR identification revealed that BPRs tended to accumulate in specific genomic regions in tumor samples whereas being dispersed genome-wide in the normal samples. Hotspots were observed, at which segments with similar alteration in copy number were overlapped along with BPRs adjacently clustered. Evaluation of BPR occurrence frequency showed that at least one was detected in about and more than 15% of samples for each tumor entity while BPRs were maximal in 12% of the normal samples. 127 of 2,716 tumor-relevant BPRs (termed ‘common BPRs’) exhibited also a noticeable occurrence frequency in the normal samples. Colocalization assessment identified 20,077 CNV-affecting genes and 169 of these being known tumor-related genes. The most noteworthy genes are KIAA0513 important for immunologic, synaptic and apoptotic signal pathways, intergenic non-coding RNA RP11-115C21.2 possibly acting as oncogene or tumor suppressor by changing the structure of chromatin, and ADAM32 likely importance in cancer cell proliferation and progression by ectodomain-shedding of diverse growth factors, and the well-known tumor suppressor gene p53. The BPR distributions indicate that CNV mutations are likely non-random in tumor genomes. The marked recurrence of BPRs at specific regions supports common progression mechanisms in tumors. The presence of hotspots together with common BPRs, despite its small group size, imply a relation between fragile sites and cancer-gene alteration. Our data further suggest that both protein-coding and non-coding genes possessing a range of biological functions might play a causative or functional role in tumor biology. This research enhances our understanding of the mechanisms for tumorigenesis and progression. PMID:27391163

Evaluation of NKX3.1 and C-MYC expression in canine prostatic cancer.

PubMed

Fonseca-Alves, Carlos Eduardo; Kobayashi, Priscila Emiko; Laufer-Amorim, Renée

2018-06-01

NKX3.1/C-MYC cross-regulation has been reported in the normal human prostate, and loss of NKX3.1 and gain of C-MYC seem to be important events in prostate cancer development and progression. The dog can be an interesting model for human prostatic disease, and yet only one previous research study has shown deregulation of NKX3.1 and MYC in the canine prostate. To address the expression of NKX3.1 and C-MYC in different canine prostatic lesions, this study verified the gene and protein expression of NKX3.1 and C-MYC in normal canine prostatic tissues. We identified a 26 kDa band that corresponded to the NKX3.1 protein, while C-MYC showed a 50 kDa band on Western blotting analysis of all prostatic tissues. We observed that NKX3.1 protein and transcript were down-regulated in prostate cancer (PC) samples compared with non-neoplastic samples. We also observed that C-MYC protein was overexpressed in PC samples compared with normal (P = .001) and proliferative inflammatory atrophy (PIA) samples (P = .003). We found a positive correlation between NKX3.1 and C-MYC protein expression in normal and PIA samples. Interestingly, a negative correlation (NKX3.1 downregulation and MYC overexpression) was observed between NKX3.1 and MYC transcripts in PC. Thus, samples with higher C-MYC expression also exhibited higher NKX3.1 expression, which indicates the regulation of C-MYC by NKX3.1 protein. As in humans, these two genes and proteins were found to be related to canine prostate cancer. However, in contrast from what is observed in humans, in canine PC samples, the downregulation of NKX3.1 cannot be explained by DNA hypermethylation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Mammary stem cell and macrophage markers are enriched in normal tissue adjacent to inflammatory breast cancer.

PubMed

Reddy, Jay P; Atkinson, Rachel L; Larson, Richard; Burks, Jared K; Smith, Daniel; Debeb, Bisrat G; Ruffell, Brian; Creighton, Chad J; Bambhroliya, Arvind; Reuben, James M; Van Laere, Steven J; Krishnamurthy, Savitri; Symmans, William F; Brewster, Abenaa M; Woodward, Wendy A

2018-06-01

We hypothesized that breast tissue not involved by tumor in inflammatory breast cancer (IBC) patients contains intrinsic differences, including increased mammary stem cells and macrophage infiltration, which may promote the IBC phenotype. Normal breast parenchyma ≥ 5 cm away from primary tumors was obtained from mastectomy specimens. This included an initial cohort of 8 IBC patients and 60 non-IBC patients followed by a validation cohort of 19 IBC patients and 25 non-IBC patients. Samples were immunostained for either CD44 + CD49f + CD133/2 + mammary stem cell markers or the CD68 macrophage marker and correlated with IBC status. Quantitation of positive cells was determined using inForm software from PerkinElmer. We also examined the association between IBC status and previously published tumorigenic stem cell and IBC tumor signatures in the validation cohort samples. 8 of 8 IBC samples expressed isolated CD44 + CD49f + CD133/2 + stem cell marked cells in the initial cohort as opposed to 0/60 non-IBC samples (p = 0.001). Similarly, the median number of CD44 + CD49f + CD133/2 + cells was significantly higher in the IBC validation cohort as opposed to the non-IBC validation cohort (25.7 vs. 14.2, p = 0.007). 7 of 8 IBC samples expressed CD68 + histologically confirmed macrophages in initial cohort as opposed to 12/48 non-IBC samples (p = 0.001). In the validation cohort, the median number of CD68 + cells in IBC was 3.7 versus 1.0 in the non-IBC cohort (p = 0.06). IBC normal tissue was positively associated with a tumorigenic stem cell signature (p = 0.02) and with a 79-gene IBC signature (p < 0.001). Normal tissue from IBC patients is enriched for both mammary stem cells and macrophages and has higher association with both a tumorigenic stem cell signature and IBC-specific tumor signature. Collectively, these data suggest that IBC normal tissue differs from non-IBC tissue. Whether these changes occur before the tumor develops or is induced by tumor warrants further investigation.

Three distinct pneumotypes characterize the microbiome of the lung in BALB/cJ mice.

PubMed

Scheiermann, Julia; Klinman, Dennis M

2017-01-01

Bacteria can rarely be isolated from normal healthy lungs using conventional culture techniques, supporting the traditional belief that the lungs are sterile. Yet recent studies using next generation sequencing report that bacterial DNA commonly found in the upper respiratory tract (URT) is present at lower levels in the lungs. Interpretation of that finding is complicated by the technical limitations and potential for contamination introduced when dealing with low biomass samples. The current work sought to overcome those limitations to clarify the number, type and source of bacteria present in the lungs of normal mice. Results showed that the oral microbiome is diverse and highly conserved whereas murine lung samples fall into three distinct patterns. 33% of the samples were sterile, as they lacked culturable bacteria and their bacterial DNA content did not differ from background. 9% of samples contained comparatively higher amounts of bacterial DNA whose composition mimicked that detected in the URT. A final group (58%) contained smaller amounts of microbial DNA whose composition was correlating to that of rodent chow and cage bedding, likely acquired by inspiration of food and bedding fragments. By analyzing each sample independently rather than working with group averages, this work eliminated the bias introduced by aspiration-contaminated samples to establish that three distinct microbiome pneumotypes are present in normal murine lungs.

Metabolic profiles of the Flos Abelmoschus manihot extract by intestinal bacteria from the normal and CKD model rats based on UPLC-Q-TOF/MS.

PubMed

Du, Le-Yue; Tao, Jin-Hua; Jiang, Shu; Qian, Da-Wei; Guo, Jian-Ming; Duan, Jin-Ao

2017-02-01

Flos Abelmoschus manihot is a traditional herbal medicine widely used in clinical practice to tackle chronic kidney disease (CKD) for thousands of years. Nowadays, many studies indicate that gut bacteria are closely related to the progression of CKD and CKD-related complications. In this study, a UPLC-Q-TOF/MS method coupled with the MetaboLynx™ software was established and successfully applied to investigate the metabolites and metabolic profile of Flos A. manihot extract by intestinal bacteria from normal and CKD rats. Eight parent components and eight metabolites were characterized by their protonated ions. Among these compounds, 15 were detected in the two group samples while M16 was only determined in the CKD model samples. Compared with the quercetin-type glycosides, fewer myricetin-type and gossypetin-type metabolites were obtained in the two group samples. These metabolites suggested that deglycosylation and methylation are the major metabolic pathways of Flos A. manihot extract. Few differences of metabolite classes were observed in the two group samples. However, the concentrations of aglycones such as quercetin, myricetin and gossypetin in the normal samples were notably higher than those in the CKD model samples. The results are important in unravelling the pharmacological effects of A. manihot and clarifying its mechanism of action in vivo. Copyright © 2016 John Wiley & Sons, Ltd.

Specific heat in KFe2As2 in zero and applied magnetic field

NASA Astrophysics Data System (ADS)

Kim, J. S.; Kim, E. G.; Stewart, G. R.; Chen, X. H.; Wang, X. F.

2011-05-01

The specific heat down to 0.08 K of the iron pnictide superconductor KFe2As2 was measured on a single-crystal sample with a residual resistivity ratio of ˜650, with a Tconset determined by a specific heat of 3.7 K. The zero-field normal-state specific heat divided by temperature, C/T, was extrapolated from above Tc to T=0 by insisting on agreement between the extrapolated normal-state entropy at Tc, Snextrap(Tc), and the measured superconducting-state entropy at Tc, Ssmeas(Tc), since for a second-order phase transition the two entropies must be equal. This extrapolation would indicate that this rather clean sample of KFe2As2 exhibits non-Fermi-liquid behavior; i.e., C/T increases at low temperatures, in agreement with the reported non-Fermi-liquid behavior in the resistivity. However, specific heat as a function of magnetic field shows that the shoulder feature around 0.7 K, which is commonly seen in KFe2As2 samples, is not evidence for a second superconducting gap as has been previously proposed but instead is due to an unknown magnetic impurity phase, which can affect the entropy balance and the extrapolation of the normal-state specific heat. This peak (somewhat larger in magnitude) with similar field dependence is also found in a less pure sample of KFe2As2, with a residual resistivity ratio of only 90 and Tconset=3.1 K. These data, combined with the measured normal-state specific heat in field to suppress superconductivity, allow the conclusion that an increase in the normal-state specific heat as T→0 is in fact not seen in KFe2As2; i.e., Fermi-liquid behavior is observed.

Average of delta: a new quality control tool for clinical laboratories.

PubMed

Jones, Graham R D

2016-01-01

Average of normals is a tool used to control assay performance using the average of a series of results from patients' samples. Delta checking is a process of identifying errors in individual patient results by reviewing the difference from previous results of the same patient. This paper introduces a novel alternate approach, average of delta, which combines these concepts to use the average of a number of sequential delta values to identify changes in assay performance. Models for average of delta and average of normals were developed in a spreadsheet application. The model assessed the expected scatter of average of delta and average of normals functions and the effect of assay bias for different values of analytical imprecision and within- and between-subject biological variation and the number of samples included in the calculations. The final assessment was the number of patients' samples required to identify an added bias with 90% certainty. The model demonstrated that with larger numbers of delta values, the average of delta function was tighter (lower coefficient of variation). The optimal number of samples for bias detection with average of delta was likely to be between 5 and 20 for most settings and that average of delta outperformed average of normals when the within-subject biological variation was small relative to the between-subject variation. Average of delta provides a possible additional assay quality control tool which theoretical modelling predicts may be more valuable than average of normals for analytes where the group biological variation is wide compared with within-subject variation and where there is a high rate of repeat testing in the laboratory patient population. © The Author(s) 2015.

Characterizations of linear sufficient statistics

NASA Technical Reports Server (NTRS)

Peters, B. C., Jr.; Reoner, R.; Decell, H. P., Jr.

1977-01-01

A surjective bounded linear operator T from a Banach space X to a Banach space Y must be a sufficient statistic for a dominated family of probability measures defined on the Borel sets of X. These results were applied, so that they characterize linear sufficient statistics for families of the exponential type, including as special cases the Wishart and multivariate normal distributions. The latter result was used to establish precisely which procedures for sampling from a normal population had the property that the sample mean was a sufficient statistic.

Relationships between equine airway reactivity measured by flowmetric plethysmography and specific indicators of airway inflammation in horses with suspected inflammatory airway disease.

PubMed

Wichtel, M; Gomez, D; Burton, S; Wichtel, J; Hoffman, A

2016-07-01

Agreement between airway reactivity measured by flowmetric plethysmography and histamine bronchoprovocation, and lower airway inflammation measured by bronchoalveolar lavage (BAL) cytology, has not been studied in horses with suspected inflammatory airway disease (IAD). We tested the hypothesis that airway reactivity is associated with BAL cytology in horses presenting for unexplained poor performance and/or chronic cough. Prospective clinical study. Forty-five horses, predominantly young Standardbred racehorses, presenting for unexplained poor performance or chronic cough, underwent endoscopic evaluation, tracheal wash, flowmetric plethysmography with histamine bronchoprovocation and BAL. Histamine response was measured by calculating PC35, the concentration of nebulised histamine eliciting an increase in Δflow of 35%. In this population, there was no significant correlation between histamine response and cell populations in BAL cytology. When airway hyperreactivity (AHR) was defined as ≥35% increase in Δflow at a histamine concentration of <6 mg/ml, 24 of the 45 horses (53%) were determined to have AHR. Thirty-three (73%) had either abnormal BAL cytology or AHR, and were diagnosed with IAD on this basis. Of horses diagnosed with IAD, 9 (27%) had an abnormal BAL, 11 (33%) had AHR and 13 (39%) had both. Airway reactivity and BAL cytology did not show concordance in this population of horses presenting for unexplained poor performance and/or chronic cough. Failure to include tests of airway reactivity may lead to underdiagnosis of IAD in young Standardbred racehorses that present with clinical signs suggestive of IAD. © 2015 EVJ Ltd.

Effects of NaCl stress on seed germination and seedling development of Brassica insularis Moris (Brassicaceae).

PubMed

Santo, A; Mattana, E; Frigau, L; Marzo Pastor, A; Picher Morelló, M C; Bacchetta, G

2017-05-01

Brassica insularis is a protected plant that grows on both coastal and inland cliffs in the western Mediterranean Basin. The objective of this study was to test if any variability exists in the salt stress response during seed germination and seedling development in this species relative to its provenance habitat. Variability among three populations in the salt stress effects on seed germination and recovery under different temperatures was evaluated. The effect of nebulisation of a salt solution on seedling development was evaluated between populations growing at different distances from the sea. Seeds of B. insularis could germinate at NaCl concentrations up to 200 mm. Seed viability was negatively affected by salt, and recovery ability decreased with increasing temperature or salinity. Inter-population variability was detected in salt response during the seed germination phase, as well as in seedling salt spray tolerance. The inland population seedlings had drastically decreased survival and life span and failed to survive to the end of the experiment. In contrast, at least 90% of the coastal seedlings survived, even when sprayed at the highest frequency with salt solution. This study allowed investigation of two natural factors, soil salinity and marine aerosols, widely present in the B. insularis habitat, and provided the first insights into ecology of this protected species and its distribution in the Mediterranean. These results might be useful in understanding the actual distributions of other species with the same ecology that experience these same abiotic parameters. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

High spatial resolution analysis of ferromanganese concretions by LA-ICP-MS†

PubMed Central

Axelsson, Mikael D; Rodushkin, Ilia; Baxter, Douglas C; Ingri, Johan; Öhlander, Björn

2002-01-01

A procedure was developed for the determination of element distributions in cross-sections of ferromanganese concretions using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The effects of carrier flow rates, rf forward power, ablation energy, ablation spot size, repetition rate and number of shots per point on analyte intensity were studied. It is shown that different carrier gas flow rates are required in order to obtain maximum sensitivities for different groups of elements, thus complicating the optimisation of ICP parameters. On the contrary, LA parameters have very similar effects on almost all elements studied, thus providing a common optimum parameter set for the entire mass range. However, for selected LA parameters, the use of compromise conditions was necessary in order to compensate for relatively slow data acquisition by ICP-MS and maintain high spatial resolution without sacrificing the multielemental capabilities of the technique. Possible variations in ablation efficiency were corrected for mathematically using the sum of Fe and Mn intensities. Quantification by external calibration against matrix-matched standards was successfully used for more than 50 elements. These standards, in the form of pressed pellets (no binder), were prepared in-house using ferromanganese concentrates from a deep-sea nodule reference material as well as from shallow-marine concretions varying in size and having different proportions of three major phases: aluminosilicates, Fe- and Mn-oxyhydroxides. Element concentrations in each standard were determined by means of conventional solution nebulisation ICP-MS following acid digestion. Examples of selected inter-element correlations in distribution patterns along the cross-section of a concretion are given.

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.

PubMed

Lehmann, Kjong-Van; Kahles, André; Kandoth, Cyriac; Lee, William; Schultz, Nikolaus; Stegle, Oliver; Rätsch, Gunnar

2015-01-01

We present a genome-wide analysis of splicing patterns of 282 kidney renal clear cell carcinoma patients in which we integrate data from whole-exome sequencing of tumor and normal samples, RNA-seq and copy number variation. We proposed a scoring mechanism to compare splicing patterns in tumor samples to normal samples in order to rank and detect tumor-specific isoforms that have a potential for new biomarkers. We identified a subset of genes that show introns only observable in tumor but not in normal samples, ENCODE and GEUVADIS samples. In order to improve our understanding of the underlying genetic mechanisms of splicing variation we performed a large-scale association analysis to find links between somatic or germline variants with alternative splicing events. We identified 915 cis- and trans-splicing quantitative trait loci (sQTL) associated with changes in splicing patterns. Some of these sQTL have previously been associated with being susceptibility loci for cancer and other diseases. Our analysis also allowed us to identify the function of several COSMIC variants showing significant association with changes in alternative splicing. This demonstrates the potential significance of variants affecting alternative splicing events and yields insights into the mechanisms related to an array of disease phenotypes.

Recurrent cis-SAGe chimeric RNA, D2HGDH-GAL3ST2, in prostate cancer.

PubMed

Qin, Fujun; Song, Zhenguo; Chang, Maxwell; Song, Yansu; Frierson, Henry; Li, Hui

2016-09-28

Neighboring genes transcribing in the same direction can form chimeric RNAs via cis-splicing (cis-SAGe). Previously, we reported 16 novel cis-SAGe chimeras in prostate cancer cell lines, and performed in silico validation on 14 pairs of normal and tumor samples from Chinese patients. However, whether these fusions exist in different populations, as well as their clinical implications, remains unclear. To investigate, we developed a bioinformatics pipeline using modified Spliced Transcripts Alignment to a Reference (STAR) to quantify these fusion RNAs simultaneously in silico. From RNA-Seq data of 100 paired normal and prostate cancer samples from TCGA, we find that most fusions are not specific to cancer. However, D2HGDH-GAL3ST2 is more frequently seen in cancer samples, and seems to be enriched in the African American group. Further validation with our own collection as well as from commercial sources did not detect this fusion RNA in 29 normal prostate samples, but in 19 of 93 prostate cancer samples. It is more frequently detected in late stage cancer, suggesting a role in cancer progression. Consistently, silencing this fusion resulted in dramatic reduction of cell proliferation rate and cell motility. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A Third Moment Adjusted Test Statistic for Small Sample Factor Analysis.

PubMed

Lin, Johnny; Bentler, Peter M

2012-01-01

Goodness of fit testing in factor analysis is based on the assumption that the test statistic is asymptotically chi-square; but this property may not hold in small samples even when the factors and errors are normally distributed in the population. Robust methods such as Browne's asymptotically distribution-free method and Satorra Bentler's mean scaling statistic were developed under the presumption of non-normality in the factors and errors. This paper finds new application to the case where factors and errors are normally distributed in the population but the skewness of the obtained test statistic is still high due to sampling error in the observed indicators. An extension of Satorra Bentler's statistic is proposed that not only scales the mean but also adjusts the degrees of freedom based on the skewness of the obtained test statistic in order to improve its robustness under small samples. A simple simulation study shows that this third moment adjusted statistic asymptotically performs on par with previously proposed methods, and at a very small sample size offers superior Type I error rates under a properly specified model. Data from Mardia, Kent and Bibby's study of students tested for their ability in five content areas that were either open or closed book were used to illustrate the real-world performance of this statistic.

Revisiting the incidence of Mg II absorbers along the blazar sightlines

NASA Astrophysics Data System (ADS)

Mishra, Sapna; Chand, Hum; Gopal-Krishna; Joshi, Ravi

2018-04-01

It is believed that the cool gas clouds traced by Mg II absorption, within a velocity offset of 5000 km/s from the background quasar, are associated with the quasar itself, whereas the absorbers seen at larger velocity offsets towards us are intervening systems and hence their existence is completely independent of the background quasar. Recent evidence by Bergeron et al. 2011 (hereafter BBM), however, seriously questions this canonical view, by showing that the number density of intervening Mg II absorbers along the sightlines towards 45 blazars is, on average, 2 times the expectation based on the Mg II absorption systems seen on the sightlines to normal QSOs. Given the serious implications of this finding, it becomes important to revisit this issue by enlarging the source sample and subjecting it to an independent analysis. Here, we first report our results based on a re-analysis of the spectroscopic data for the BBM sample; this has reproduced their factor 2 excess in dN/dz along blazar sightlines, vis-a-vis the normal QSOs. Next, we assemble a 6 times larger sample of blazar sightlines, albeit with lower SNR. Using this enlarged sample together with the BBM sample, our analysis shows that the dN/dz of Mg II absorbers statistically matches that known for normal QSO sightlines.

XMM-Newton Proposal 03060602

NASA Astrophysics Data System (ADS)

Strickland, David

2004-10-01

We propose to observe 3 edge-on Milky-Way-like normal spiral galaxies in order to constrain the presence, properties and physical origin of hot gas in their halos, a topic about which relatively little is currently known. These observations will complete our sample of 8 edge-on normal spirals for which we have a wide range of existing observational data, so that all galaxies will have deep XMM-Newton and/or Chandra observations. With this sample we can assess the relative contribution to the halo X-ray emission of normal spirals from SNII-driven galactic fountains, accretion of primordial gas, and SNIa-driven outflows. The observations will robustly detect NGC 891-like hot halos, broadly quantify their properties, and can be used to constrain the efficiency of mechanical energy feedback.

In-vivo cancer diagnosis of the esophagus using laser-induced fluorescence

NASA Astrophysics Data System (ADS)

Vo-Dinh, Tuan; Panjehpour, Masoud; Overholt, Bergein F.; Buckley, Paul F., II; Edwards, Donna H.

1995-04-01

Laser-induced fluorescence (LIF) was used for direct in-vivo cancer diagnosis of the esophagus without requiring biopsy. The methodology was applied to differentiate normal and malignant tumors of the esophagus. Endogenous fluorescence of normal and malignant tissues were measured directly using a fiberoptic probe inserted through an endoscope. The measurements were performed in vivo during routine endoscopy. Detection of the fluorescence signal from the tissue was performed using laser excitation. The results of this LIF approach were compared with histopathology results of the biopsy samples and indicated excellent agreement in the classification of normal and malignant tumors for the samples investigated. The LIF procedure could lead to the development of a rapid and cost-effective technique for cancer diagnosis.

Distribution of the Determinant of the Sample Correlation Matrix: Monte Carlo Type One Error Rates.

ERIC Educational Resources Information Center

Reddon, John R.; And Others

1985-01-01

Computer sampling from a multivariate normal spherical population was used to evaluate the type one error rates for a test of sphericity based on the distribution of the determinant of the sample correlation matrix. (Author/LMO)

Reversal and Rotation Errors by Normal and Retarded Readers

ERIC Educational Resources Information Center

Black, F. William

1973-01-01

Reports an investigation of the incidence of and relationships among word and letter reversals in writing and Bender-Gestalt rotation errors in matched samples of normal and retarded readers. No significant diffenences were found in the two groups. (TO)

Sampling intensity and normalizations: Exploring cost-driving factors in nationwide mapping of tree canopy cover

Treesearch

John Tipton; Gretchen Moisen; Paul Patterson; Thomas A. Jackson; John Coulston

2012-01-01

There are many factors that will determine the final cost of modeling and mapping tree canopy cover nationwide. For example, applying a normalization process to Landsat data used in the models is important in standardizing reflectance values among scenes and eliminating visual seams in the final map product. However, normalization at the national scale is expensive and...

On the efficacy of procedures to normalize Ex-Gaussian distributions.

PubMed

Marmolejo-Ramos, Fernando; Cousineau, Denis; Benites, Luis; Maehara, Rocío

2014-01-01

Reaction time (RT) is one of the most common types of measure used in experimental psychology. Its distribution is not normal (Gaussian) but resembles a convolution of normal and exponential distributions (Ex-Gaussian). One of the major assumptions in parametric tests (such as ANOVAs) is that variables are normally distributed. Hence, it is acknowledged by many that the normality assumption is not met. This paper presents different procedures to normalize data sampled from an Ex-Gaussian distribution in such a way that they are suitable for parametric tests based on the normality assumption. Using simulation studies, various outlier elimination and transformation procedures were tested against the level of normality they provide. The results suggest that the transformation methods are better than elimination methods in normalizing positively skewed data and the more skewed the distribution then the transformation methods are more effective in normalizing such data. Specifically, transformation with parameter lambda -1 leads to the best results.

Assessing Amide Proton Transfer (APT) MRI Contrast Origins in 9 L Gliosarcoma in the Rat Brain Using Proteomic Analysis.

PubMed

Yan, Kun; Fu, Zongming; Yang, Chen; Zhang, Kai; Jiang, Shanshan; Lee, Dong-Hoon; Heo, Hye-Young; Zhang, Yi; Cole, Robert N; Van Eyk, Jennifer E; Zhou, Jinyuan

2015-08-01

To investigate the biochemical origin of the amide photon transfer (APT)-weighted hyperintensity in brain tumors. Seven 9 L gliosarcoma-bearing rats were imaged at 4.7 T. Tumor and normal brain tissue samples of equal volumes were prepared with a coronal rat brain matrix and a tissue biopsy punch. The total tissue protein and the cytosolic subproteome were extracted from both samples. Protein samples were analyzed using two-dimensional gel electrophoresis, and the proteins with significant abundance changes were identified by mass spectrometry. There was a significant increase in the cytosolic protein concentration in the tumor, compared to normal brain regions, but the total protein concentrations were comparable. The protein profiles of the tumor and normal brain tissue differed significantly. Six cytosolic proteins, four endoplasmic reticulum proteins, and five secreted proteins were considerably upregulated in the tumor. Our experiments confirmed an increase in the cytosolic protein concentration in tumors and identified several key proteins that may cause APT-weighted hyperintensity.

[Role of placental apoptosis in fetal growth restriction].

PubMed

Liu, Yuan; Gao, Peng; Xie, Yingbo; Wang, Shuyun; Dai, Minsheng; Jiang, Sen

2002-12-01

To determine the relationship of placental cellular apoptosis and pathophysiology of fetal growth restriction (FGR). Placental samples were obtained from 18 pregnancies complicated by FGR and 14 normal pregnancies. Terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end labeling (TUNEL) and transmission electron microscopy were used to confirm the occurrence of apoptosis. In FGR group the placental apoptosis rate was (n = 18) 12.1 per thousand, the average placental weight was (236 +/- 24) g, the average birth weight was (2,071 +/- 428) g; In normal group (n = 14), the placental apoptosis rate was 7.3 per thousand, the average placental weight was (354 +/- 63) g, the average birth weight was (3,411 +/- 588) g (P < 0.05). The incidence of apoptosis was significantly higher in placental samples from pregnancies with FGR compared with normal placental samples (P < 0.05). Under transmission election microscopy, apoptosis was obviously compact and the chromatins were formed as mass. These results suggest that apoptosis may play a role in the pathophysiologic mechanisms of FGR.

Prenatal diagnosis of LAD-I on cord blood by flowcytometry.

PubMed

Madkaikar, Manisha Rajan; Gupta, Maya; Rao, Meghana; Ghosh, Kanjaksha

2012-12-01

To optimize a simple flowcytometric technique for Prenatal diagnosis (PND) for Leukocyte adhesions defect (LAD-I) on cordocentesis sample at 18 wk gestation. Normal reference ranges for expression of CD18/CD11-integrins in neutrophils and lymphocytes at 18 wk of gestation were established by flowcytometry. PND for LAD-I was then performed on the cordocentesis samples in three 'at risk' pregnancies after ruling out maternal contamination. CD18 and CD11a expression on fetal lymphocytes were found to be the most useful parameters for PND of LAD-I. All the three fetuses tested showed normal expression of CD18/CD11-integrins and thus were unaffected. This was confirmed by testing the cord blood (CB) samples after delivery and normal growth and absence of serious infections on follow-up. Flowcytometry offers a rapid and sensitive technique for PND of LAD-I in the absence of facilities for molecular diagnosis. Obstetricians, even in developing countries with modest facilities, can offer considerable relief for the families.

Microarray expression profiling in adhesion and normal peritoneal tissues.

PubMed

Ambler, Dana R; Golden, Alicia M; Gell, Jennifer S; Saed, Ghassan M; Carey, David J; Diamond, Michael P

2012-05-01

To identify molecular markers associated with adhesion and normal peritoneal tissue using microarray expression profiling. Comparative study. University hospital. Five premenopausal women. Adhesion and normal peritoneal tissue samples were obtained from premenopausal women. Ribonucleic acid was extracted using standard protocols and processed for hybridization to Affymetrix Whole Transcript Human Gene Expression Chips. Microarray data were obtained from five different patients, each with adhesion tissue and normal peritoneal samples. Real-time polymerase chain reaction was performed for confirmation using standard protocols. Gene expression in postoperative adhesion and normal peritoneal tissues. A total of 1,263 genes were differentially expressed between adhesion and normal tissues. One hundred seventy-three genes were found to be up-regulated and 56 genes were down-regulated in the adhesion tissues compared with normal peritoneal tissues. The genes were sorted into functional categories according to Gene Ontology annotations. Twenty-six up-regulated genes and 11 down-regulated genes were identified with functions potentially relevant to the pathophysiology of postoperative adhesions. We evaluated and confirmed expression of 12 of these specific genes via polymerase chain reaction. The pathogenesis, natural history, and optimal treatment of postoperative adhesive disease remains unanswered. Microarray analysis of adhesions identified specific genes with increased and decreased expression when compared with normal peritoneum. Knowledge of these genes and ontologic pathways with altered expression provide targets for new therapies to treat patients who have or are at risk for postoperative adhesions. Copyright © 2012 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Contact Quotient of Female Singers Singing Four Pitches for Five Vowels in Normal and Pressed Phonations.

PubMed

Ong Tan, Kendrich Graemer

2017-09-01

The present study aimed to investigate the contact quotient (CQ) values of breathy, normal, and pressed phonation types in four different sections of the female singing range. Electroglottography (EGG) and acoustic signals were recorded from 10 female singing teachers. Five vowels were sung for 1-3 seconds each, in three phonation types-normal, breathy, and pressed, in four pitches representing registration change points in the singing range. CQ values were automatically generated from the EGG signal using VoceVista at 35% threshold level. Sound pressure levels were checked in Praat. Unianova and correlations were performed using an SPSS program. CQ values of female participants in the study yielded ranges of 0.25-0.62 in normal and 0.34-0.73 in pressed. Normal and pressed CQ differed significantly from each other at P < 0.00. Breathy samples were not viable for analysis. A concentration of CQ values from 0.5 to 0.6 of both pressed low and pressed break samples was noted, but CQ values across the pitch range showed no significant trend. Normal and pressed phonation CQ values beyond the speaking pitch varied among the subjects. Pressed phonation CQ values were mostly higher, but the values were only relative to the corresponding normal phonation on the same pitch. Other measurements may be more suitable for measuring vocal fold impact stress in higher frequencies, thus, distinguishing normal from pressed singing. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Association between dental caries and body mass in preschool children.

PubMed

Pikramenou, V; Dimitraki, D; Zoumpoulakis, M; Verykouki, E; Kotsanos, N

2016-06-01

This was to explore the association between dental caries and body mass index (BMI) by conducting a cross-sectional study of a sample of preschool children from a major Greek city. The sample consisted of 2180 children aged 2.5-5.9 years from 33 private day care centres of Thessaloniki. The examinations were performed on site in ample day light by one examiner using disposable dental mirrors and a penlight. Oral examinations included recording of dental caries by dmfs index. Subject's height and weight were measured using a portable measuring unit and a digital scale, respectively. The overall prevalence of underweight, normal weight, overweight and obese children in each BMI-based weight category was 11.8, 72.2, 12.8, and 3.2 %, respectively. The mean age of the total sample was 50.09 (±10.28) months, mean dmfs was 0.36 (±1.9) and the caries-free children were 90.0 %. Overweight children were 1.36 times and obese children 1.99 times more likely to have higher dmfs than normal weight children. The mean dmfs values of underweight children did not significantly differ than that of children with normal weight. The relatively higher dmfs of the obese and overweight children was mostly evident in the older (60-71 months) age group. Caries prevalence in this sample of Greek children attending private day care centres was low. Overweight and obese preschool children were at higher risk of dental caries than normal- and underweight children.

Activation of RAS family genes in urothelial carcinoma.

PubMed

Boulalas, I; Zaravinos, A; Karyotis, I; Delakas, D; Spandidos, D A

2009-05-01

Bladder cancer is the fifth most common malignancy in men in Western society. We determined RAS codon 12 and 13 point mutations and evaluated mRNA expression levels in transitional cell carcinoma cases. Samples from 30 human bladder cancers and 30 normal tissues were analyzed by polymerase chain reaction/restriction fragment length polymorphism and direct sequencing to determine the occurrence of mutations in codons 12 and 13 of RAS family genes. Moreover, we used real-time reverse transcriptase-polymerase chain reaction to evaluate the expression profile of RAS genes in bladder cancer specimens compared to that in adjacent normal tissues. Overall H-RAS mutations in codon 12 were observed in 9 tumor samples (30%). Two of the 9 patients (22%) had invasive bladder cancer and 7 (77%) had noninvasive bladder cancer. One H-RAS mutation (11%) was homozygous and the remaining 89% were heterozygous. All samples were WT for K and N-RAS oncogenes. Moreover, 23 of 30 samples (77%) showed over expression in at least 1 RAS family gene compared to adjacent normal tissue. K and N-RAS had the highest levels of over expression in bladder cancer specimens (50%), whereas 27% of transitional cell carcinomas demonstrated H-RAS over expression relative to paired normal tissues. Our results underline the importance of H-RAS activation in human bladder cancer by codon 12 mutations. Moreover, they provide evidence that increased expression of all 3 RAS genes is a common event in bladder cancer that is associated with disease development.

Emittance measurements of Space Shuttle orbiter reinforced carbon-carbon

NASA Technical Reports Server (NTRS)

Caram, Jose M.; Bouslog, Stanley A.; Cunnington, George R., Jr.

1992-01-01

The spectral and total normal emittance of the Reinforced Carbon-Carbon (RCC) used on Space Shuttle nose cap and wing leading edges has been measured at room temperature and at surface temperatures of 1200 to 2100 K. These measurements were made on virgin and two flown RCC samples. Room temperature directional emittance data were also obtained and were used to determine the total hemispherical emittance of RCC as a function of temperature. Results of the total normal emittance for the virgin samples showed good agreement with the current RCC emittance design curve; however, the data from the flown samples showed an increase in the emittance at high temperature possibly due to exposure from flight environments.

Far-infrared properties of cluster galaxies

NASA Technical Reports Server (NTRS)

Bicay, M. D.; Giovanelli, R.

1987-01-01

Far-infrared properties are derived for a sample of over 200 galaxies in seven clusters: A262, Cancer, A1367, A1656 (Coma), A2147, A2151 (Hercules), and Pegasus. The IR-selected sample consists almost entirely of IR normal galaxies, with Log of L(FIR) = 9.79 solar luminosities, Log of L(FIR)/L(B) = 0,79, and Log of S(100 microns)/S(60 microns) = 0.42. None of the sample galaxies has Log of L(FIR) greater than 11.0 solar luminosities, and only one has a FIR-to-blue luminosity ratio greater than 10. No significant differences are found in the FIR properties of HI-deficient and HI-normal cluster galaxies.

Extreme Mean and Its Applications

NASA Technical Reports Server (NTRS)

Swaroop, R.; Brownlow, J. D.

1979-01-01

Extreme value statistics obtained from normally distributed data are considered. An extreme mean is defined as the mean of p-th probability truncated normal distribution. An unbiased estimate of this extreme mean and its large sample distribution are derived. The distribution of this estimate even for very large samples is found to be nonnormal. Further, as the sample size increases, the variance of the unbiased estimate converges to the Cramer-Rao lower bound. The computer program used to obtain the density and distribution functions of the standardized unbiased estimate, and the confidence intervals of the extreme mean for any data are included for ready application. An example is included to demonstrate the usefulness of extreme mean application.

LIMS for Lasers 2015 for achieving long-term accuracy and precision of δ2H, δ17O, and δ18O of waters using laser absorption spectrometry

USGS Publications Warehouse

Coplen, Tyler B.; Wassenaar, Leonard I

2015-01-01

RationaleAlthough laser absorption spectrometry (LAS) instrumentation is easy to use, its incorporation into laboratory operations is not easy, owing to extensive offline manipulation of comma-separated-values files for outlier detection, between-sample memory correction, nonlinearity (δ-variation with water amount) correction, drift correction, normalization to VSMOW-SLAP scales, and difficulty in performing long-term QA/QC audits.MethodsA Microsoft Access relational-database application, LIMS (Laboratory Information Management System) for Lasers 2015, was developed. It automates LAS data corrections and manages clients, projects, samples, instrument-sample lists, and triple-isotope (δ17O, δ18O, and δ2H values) instrumental data for liquid-water samples. It enables users to (1) graphically evaluate sample injections for variable water yields and high isotope-delta variance; (2) correct for between-sample carryover, instrumental drift, and δ nonlinearity; and (3) normalize final results to VSMOW-SLAP scales.ResultsCost-free LIMS for Lasers 2015 enables users to obtain improved δ17O, δ18O, and δ2H values with liquid-water LAS instruments, even those with under-performing syringes. For example, LAS δ2HVSMOW measurements of USGS50 Lake Kyoga (Uganda) water using an under-performing syringe having ±10 % variation in water concentration gave +31.7 ± 1.6 ‰ (2-σ standard deviation), compared with the reference value of +32.8 ± 0.4 ‰, after correction for variation in δ value with water concentration, between-sample memory, and normalization to the VSMOW-SLAP scale.ConclusionsLIMS for Lasers 2015 enables users to create systematic, well-founded instrument templates, import δ2H, δ17O, and δ18O results, evaluate performance with automatic graphical plots, correct for δ nonlinearity due to variable water concentration, correct for between-sample memory, adjust for drift, perform VSMOW-SLAP normalization, and perform long-term QA/QC audits easily. Published in 2015. This article is a U.S. Government work and is in the public domain in the USA.

Normalization and microbial differential abundance strategies depend upon data characteristics.

PubMed

Weiss, Sophie; Xu, Zhenjiang Zech; Peddada, Shyamal; Amir, Amnon; Bittinger, Kyle; Gonzalez, Antonio; Lozupone, Catherine; Zaneveld, Jesse R; Vázquez-Baeza, Yoshiki; Birmingham, Amanda; Hyde, Embriette R; Knight, Rob

2017-03-03

Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data contains many zeros. Although we are typically interested in comparing relative abundance of taxa in the ecosystem of two or more groups, we can only measure the taxon relative abundance in specimens obtained from the ecosystems. Because the comparison of taxon relative abundance in the specimen is not equivalent to the comparison of taxon relative abundance in the ecosystems, this presents a special challenge. Second, because the relative abundance of taxa in the specimen (as well as in the ecosystem) sum to 1, these are compositional data. Because the compositional data are constrained by the simplex (sum to 1) and are not unconstrained in the Euclidean space, many standard methods of analysis are not applicable. Here, we evaluate how these challenges impact the performance of existing normalization methods and differential abundance analyses. Effects on normalization: Most normalization methods enable successful clustering of samples according to biological origin when the groups differ substantially in their overall microbial composition. Rarefying more clearly clusters samples according to biological origin than other normalization techniques do for ordination metrics based on presence or absence. Alternate normalization measures are potentially vulnerable to artifacts due to library size. Effects on differential abundance testing: We build on a previous work to evaluate seven proposed statistical methods using rarefied as well as raw data. Our simulation studies suggest that the false discovery rates of many differential abundance-testing methods are not increased by rarefying itself, although of course rarefying results in a loss of sensitivity due to elimination of a portion of available data. For groups with large (~10×) differences in the average library size, rarefying lowers the false discovery rate. DESeq2, without addition of a constant, increased sensitivity on smaller datasets (<20 samples per group) but tends towards a higher false discovery rate with more samples, very uneven (~10×) library sizes, and/or compositional effects. For drawing inferences regarding taxon abundance in the ecosystem, analysis of composition of microbiomes (ANCOM) is not only very sensitive (for >20 samples per group) but also critically the only method tested that has a good control of false discovery rate. These findings guide which normalization and differential abundance techniques to use based on the data characteristics of a given study.

Atomic force microscopy contact, tapping, and jumping modes for imaging biological samples in liquids

NASA Astrophysics Data System (ADS)

Moreno-Herrero, F.; Colchero, J.; Gómez-Herrero, J.; Baró, A. M.

2004-03-01

The capabilities of the atomic force microscope for imaging biomolecules under physiological conditions has been systematically investigated. Contact, dynamic, and jumping modes have been applied to four different biological systems: DNA, purple membrane, Alzheimer paired helical filaments, and the bacteriophage φ29. These samples have been selected to cover a wide variety of biological systems in terms of sizes and substrate contact area, which make them very appropriate for the type of comparative studies carried out in the present work. Although dynamic mode atomic force microscopy is clearly the best choice for imaging soft samples in air, in liquids there is not a leading technique. In liquids, the most appropriate imaging mode depends on the sample characteristics and preparation methods. Contact or dynamic modes are the best choices for imaging molecular assemblies arranged as crystals such as the purple membrane. In this case, the advantage of image acquisition speed predominates over the disadvantage of high lateral or normal force. For imaging individual macromolecules, which are weakly bonded to the substrate, lateral and normal forces are the relevant factors, and hence the jumping mode, an imaging mode which minimizes lateral and normal forces, is preferable to other imaging modes.

Alu-derived cis-element regulates tumorigenesis-dependent gastric expression of GASDERMIN B (GSDMB).

PubMed

Komiyama, Hiromitsu; Aoki, Aya; Tanaka, Shigekazu; Maekawa, Hiroshi; Kato, Yoriko; Wada, Ryo; Maekawa, Takeo; Tamura, Masaru; Shiroishi, Toshihiko

2010-02-01

GASDERMIN B (GSDMB) belongs to the novel gene family GASDERMIN (GSDM). All GSDM family members are located in amplicons, genomic regions often amplified during cancer development. Given that GSDMB is highly expressed in cancerous cells and the locus resides in an amplicon, GSDMB may be involved in cancer development and/or progression. However, only limited information is available on GSDMB expression in tissues, normal and cancerous, from cancer patients. Furthermore, the molecular mechanisms that regulate GSDMB expression in gastric tissues are poorly understood. We investigated the spatiotemporal expression patterns of GSDMB in gastric cancer patients and the 5' regulatory sequences upstream of GSDMB. GSDMB was not expressed in the majority of normal gastric-tissue samples, and the expression level was very low in the few normal samples with GSDMB expression. Most pre-cancer samples showed moderate GSDMB expression, and most cancerous samples showed augmented GSDMB expression. Analysis of genome sequences revealed that an Alu element resides in the 5' region upstream of GSDMB. Reporter assays using intact, deleted, and mutated Alu elements clearly showed that this Alu element positively regulates GSDMB expression and that a putative IKZF binding motif in this element is crucial to upregulate GSDMB expression.

Asymptotic confidence intervals for the Pearson correlation via skewness and kurtosis.

PubMed

Bishara, Anthony J; Li, Jiexiang; Nash, Thomas

2018-02-01

When bivariate normality is violated, the default confidence interval of the Pearson correlation can be inaccurate. Two new methods were developed based on the asymptotic sampling distribution of Fisher's z' under the general case where bivariate normality need not be assumed. In Monte Carlo simulations, the most successful of these methods relied on the (Vale & Maurelli, 1983, Psychometrika, 48, 465) family to approximate a distribution via the marginal skewness and kurtosis of the sample data. In Simulation 1, this method provided more accurate confidence intervals of the correlation in non-normal data, at least as compared to no adjustment of the Fisher z' interval, or to adjustment via the sample joint moments. In Simulation 2, this approximate distribution method performed favourably relative to common non-parametric bootstrap methods, but its performance was mixed relative to an observed imposed bootstrap and two other robust methods (PM1 and HC4). No method was completely satisfactory. An advantage of the approximate distribution method, though, is that it can be implemented even without access to raw data if sample skewness and kurtosis are reported, making the method particularly useful for meta-analysis. Supporting information includes R code. © 2017 The British Psychological Society.

Gene Expression Profiling of Multiple Leiomyomata Uteri and Matched Normal Tissue from a Single Patient

PubMed Central

Dimitrova, Irina K.; Richer, Jennifer K.; Rudolph, Michael C.; Spoelstra, Nicole S.; Reno, Elaine M.; Medina, Theresa M.; Bradford, Andrew P.

2009-01-01

Objective To identify differentially expressed genes between fibroid and adjacent normal myometrium in an identical hormonal and genetic background. Design Array analysis of 3 leiomyomata and matched adjacent normal myometrium in a single patient. Setting University of Colorado Hospital. Patient(s) A single female undergoing medically indicated hysterectomy for symptomatic fibroids. Interventions(s) mRNA isolation and microarray analysis, reverse-transcriptase polymerase chain reaction, western blotting and immunohistochemistry. Main Outcome Measure(s) Changes in mRNA and protein levels in leiomyomata and matched normal myometrium. Result(s) Expression of 197 genes was increased and 619 decreased, significantly by at least 2 fold, in leiomyomata relative to normal myometrium. Expression profiles between tumors were similar and normal myometrial samples showed minimal variation. Changes in, and variation of, expression of selected genes were confirmed in additional normal and leiomyoma samples from multiple patients. Conclusion(s) Analysis of multiple tumors from a single patient confirmed changes in expression of genes described in previous, apparently disparate, studies and identified novel targets. Gene expression profiles in leiomyomata are consistent with increased activation of mitogenic pathways and inhibition of apoptosis. Down-regulation of genes implicated in invasion and metastasis, of cancers, was observed in fibroids. This expression pattern may underlie the benign nature of uterine leiomyomata and may aid in the differential diagnosis of leiomyosarcoma. PMID:18672237

Characteristics of cold-induced dark, firm, dry broiler chicken breast meat.

PubMed

Dadgar, S; Lee, E S; Crowe, T G; Classen, H L; Shand, P J

2012-01-01

1. A study was designed to characterise dark, firm, dry (DFD) breast meat resulting from cold exposure of broilers and compare its properties with normal breast meat from cold-stressed and control birds. 2. A total of 140 broilers were selected from 5- and 6-week-old birds exposed to cold temperatures ranging from -18 to -4°C, or a control temperature of +20°C for 3 h in an environmental chamber. Half of these birds were slaughtered immediately following the cold exposure and the other half were given 2 h of lairage. 3. Breast meat samples were categorised based on ultimate pH (pH(u)) and colour L* (lightness) values into normal (5·7 ≤ pH(u)≤ 6·1; 46 ≤ L* ≤ 53) breast meat from control (control-normal) or cold-stressed (cold-normal) birds, and DFD (pH(u) > 6·1; L* < 46) breast meat, which only occurred in cold-stressed birds (cold-DFD). 4. Residual glycogen was not different between cold-DFD and control-normal breast meat. Lactate concentration was lower in cold-DFD compared with control-normal breast meat. Lactate concentration almost tripled for all the samples by 30 h post-mortem, which resulted in a drop in pH of normal meat, but did not have any effect on pH of DFD breast meat. Glycolytic potential at both 5 min and 30 h post-mortem was lower in DFD breast meat compared with the normal breast meat from both cold-stressed and control birds. 5. Cold-DFD breast meat was significantly darker, with higher pH(u), lower cook loss, higher water-binding capacity and processing cook yield than cold-normal and control-normal breast meat, which were not different from each other.

Epigenetic Silencing of the MLH1 Promoter in Relation to the Development of Gastric Cancer and its use as a Biomarker for Patients with Microsatellite Instability: a Systematic Analysis.

PubMed

Hu, Guimei; Qin, Lijun; Zhang, Xinjun; Ye, Guoliang; Huang, Tao

2018-01-01

Human mutL homolog 1 (MLH1) promoter methylation was reported in gastric cancer (GC). This study determined the clinicopathological, prognostic, and diagnostic effects of MLH1 promoter methylation in GC. The combined odds ratio (OR) or hazard ratio (HR) and their corresponding 95% confidence intervals (95% CI) were calculated. The pooled sensitivity, specificity, and area under the curve (AUC) were analyzed. A total of 4654 GC patients and 3669 non-malignant controls were identified in this systematic analysis. MLH1 promoter methylation was significantly higher in GC samples than in gastric adenomas, chronic gastritis, adjacent tissues, normal gastric mucosa, and normal healthy blood samples, but it exhibited a similar frequency in GC vs. intestinal metaplasia and dysplasia samples. MLH1 promoter methylation correlated with age and microsatellite instability (MSI), but it was not associated with gender, H. pylori infection, smoking, drinking behaviors, pathological histology, tumor differentiation, clinical stage, lymph node status, distant metastasis, or overall survival of GC. MLH1 promoter methylation exhibited a poor sensitivity value (< 0.5) in patients with GC compared with adjacent tissues, gastric adenomas, chronic gastritis, normal gastric mucosa, and normal healthy blood samples. The pooled sensitivity, specificity, and AUC of MLH1 promoter methylation in GC with MSI vs. GC with microsatellite stability (MSS) samples were 0.64, 0.96, and 0.90, respectively. Our results suggest that the detection of MLH1 promoter methylation may be a potential prognostic biomarker for GC patients with MSI. © 2018 The Author(s). Published by S. Karger AG, Basel.

Validation of reference genes aiming accurate normalization of qRT-PCR data in Dendrocalamus latiflorus Munro.

PubMed

Liu, Mingying; Jiang, Jing; Han, Xiaojiao; Qiao, Guirong; Zhuo, Renying

2014-01-01

Dendrocalamus latiflorus Munro distributes widely in subtropical areas and plays vital roles as valuable natural resources. The transcriptome sequencing for D. latiflorus Munro has been performed and numerous genes especially those predicted to be unique to D. latiflorus Munro were revealed. qRT-PCR has become a feasible approach to uncover gene expression profiling, and the accuracy and reliability of the results obtained depends upon the proper selection of stable reference genes for accurate normalization. Therefore, a set of suitable internal controls should be validated for D. latiflorus Munro. In this report, twelve candidate reference genes were selected and the assessment of gene expression stability was performed in ten tissue samples and four leaf samples from seedlings and anther-regenerated plants of different ploidy. The PCR amplification efficiency was estimated, and the candidate genes were ranked according to their expression stability using three software packages: geNorm, NormFinder and Bestkeeper. GAPDH and EF1α were characterized to be the most stable genes among different tissues or in all the sample pools, while CYP showed low expression stability. RPL3 had the optimal performance among four leaf samples. The application of verified reference genes was illustrated by analyzing ferritin and laccase expression profiles among different experimental sets. The analysis revealed the biological variation in ferritin and laccase transcript expression among the tissues studied and the individual plants. geNorm, NormFinder, and BestKeeper analyses recommended different suitable reference gene(s) for normalization according to the experimental sets. GAPDH and EF1α had the highest expression stability across different tissues and RPL3 for the other sample set. This study emphasizes the importance of validating superior reference genes for qRT-PCR analysis to accurately normalize gene expression of D. latiflorus Munro.

Cytologic comparison of the percentage of mast cells in lymph node aspirate samples from clinically normal dogs versus dogs with allergic dermatologic disease and dogs with cutaneous mast cell tumors.

PubMed

Mutz, Melanie L; Boudreaux, Bonnie B; Royal, Angela; Merchant, Sandra; Pucheu-Haston, Cherie; Griffith, Emily H; Gieger, Tracy L

2017-08-15

OBJECTIVE To compare percentages of mast cells in lymph node (LN) aspirate samples from clinically normal dogs, dogs with allergic dermatologic disease (ADD), and dogs with cutaneous mast cell tumors (MCTs). DESIGN Prospective cross-sectional study. ANIMALS 20 healthy dogs (group 1), 20 dogs with ADD (group 2), and 20 dogs with an MCT on the head or limbs (group 3). PROCEDURES LN aspirate samples were obtained from easily accessible LNs in group 1, affected skin regions in group 2, and the likely draining LN or LNs of the MCT in group 3; the percentage of mast cells was manually determined for each LN. For group 3, LNs were cytologically categorized with a modified version of a published metastasis categorization scheme. RESULTS Median (range) percentage of mast cells in aspirate samples was 0% (0% to 0.1%) for group 1, 0.05% (0% to 0.55%) for group 2, and 0.4% (0% to 77.4%) for group 3. In group 3, 16 LNs (13 dogs) were palpably normal in size; 6 of these had evidence of possible or certain metastasis. Seven LNs (7 dogs) in group 3 were palpably enlarged, and 5 of these had evidence of certain metastasis. CONCLUSIONS AND CLINICAL RELEVANCE This study provided evidence to support the use of a uniform cytologic grading system to further define nodal metastasis in dogs with MCTs as well as estimates of the percentage of mast cells in LN aspirate samples for healthy dogs and dogs with ADD. Palpably normal LNs in dogs with cutaneous MCT may contain metastasis.

Viability and Burden of Leishmania in Extralesional Sites during Human Dermal Leishmaniasis

PubMed Central

Romero, Ibeth; Téllez, Jair; Suárez, Yazmín; Cardona, Maria; Figueroa, Roger; Zelazny, Adrian; Gore Saravia, Nancy

2010-01-01

Background The clinical and epidemiological significance of Leishmania DNA in extralesional sites is obscured by uncertainty of whether the DNA derives from viable parasites. To examine dissemination of Leishmania during active disease and the potential participation of human infection in transmission, Leishmania 7SLRNA was exploited to establish viability and estimate parasite burden in extralesional sites of dermal leishmaniasis patients. Methods The feasibility of discriminating parasite viability by PCR of Leishmania 7SLRNA was evaluated in relation with luciferase activity of luc transfected intracellular amastigotes in dose-response assays of Glucantime cytotoxicity. Monocytes, tonsil swabs, aspirates of normal skin and lesions of 28 cutaneous and 2 mucocutaneous leishmaniasis patients were screened by kDNA amplification/Southern blot. Positive samples were analyzed by quantitative PCR of Leishmania 7SLRNA genes and transcripts. Results 7SLRNA amplification coincided with luciferase activity, confirming discrimination of parasite viability. Of 22 patients presenting kDNA in extralesional samples, Leishmania 7SLRNA genes or transcripts were detected in one or more kDNA positive samples in 100% and 73% of patients, respectively. Gene and transcript copy number amplified from extralesional tissues were comparable to lesions. 7SLRNA transcripts were detected in 13/19 (68%) monocyte samples, 5/12 (42%) tonsil swabs, 4/11 (36%) normal skin aspirates, and 22/25 (88%) lesions; genes were quantifiable in 15/19 (79%) monocyte samples, 12/13 (92%) tonsil swabs, 8/11 (73%) normal skin aspirates. Conclusion Viable parasites are present in extralesional sites, including blood monocytes, tonsils and normal skin of dermal leishmaniasis patients. Leishmania 7SLRNA is an informative target for clinical and epidemiologic investigations of human leishmaniasis. PMID:20856851

Molecular Survey of Bacterial Communities Associated with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers

PubMed Central

Jiang, Tieshan; Mandal, Rabindra K.; Wideman, Robert F.; Khatiwara, Anita; Pevzner, Igal; Min Kwon, Young

2015-01-01

Bacterial chondronecrosis with osteomyelitis (BCO) is recognized as an important cause of lameness in commercial broiler chickens (meat-type chickens). Relatively little is known about the microbial communities associated with BCO. This study was conducted to increase our understanding of the microbial factors associated with BCO using a culture-independent approach. Using Illumina sequencing of the hyper-variable region V6 in the 16S rRNA gene, we characterized the bacterial communities in 97 femoral or tibial heads from normal and lame broilers carefully selected to represent diverse variations in age, line, lesion type, floor type, clinical status and bone type. Our in-depth survey based on 14 million assembled sequence reads revealed that complex bacterial communities exist in all samples, including macroscopically normal bones from clinically healthy birds. Overall, Proteobacteria (mean 90.9%) comprised the most common phylum, followed by Firmicutes (6.1%) and Actinobacteria (2.6%), accounting for more than 99% of all reads. Statistical analyses demonstrated that there are differences in bacterial communities in different types of bones (femur vs. tibia), lesion types (macroscopically normal femora or tibiae vs. those with pathognomonic BCO lesions), and among individual birds. This analysis also showed that BCO samples overrepresented genera Staphylococcus, whose species have been frequently isolated in BCO samples in previous studies. Rarefaction analysis demonstrated the general tendency that increased severities of BCO lesions were associated with reduced species diversity in both femoral and tibial samples when compared to macroscopically normal samples. These observations suggest that certain bacterial subgroups are preferentially selected in association with the development of BCO lesions. Understanding the microbial species associated with BCO will identify opportunities for understanding and modulating the pathogenesis of this form of lameness in broilers. PMID:25881241

Human respiratory syncytial virus load normalized by cell quantification as predictor of acute respiratory tract infection.

PubMed

Gómez-Novo, Miriam; Boga, José A; Álvarez-Argüelles, Marta E; Rojo-Alba, Susana; Fernández, Ana; Menéndez, María J; de Oña, María; Melón, Santiago

2018-05-01

Human respiratory syncytial virus (HRSV) is a common cause of respiratory infections. The main objective is to analyze the prediction ability of viral load of HRSV normalized by cell number in respiratory symptoms. A prospective, descriptive, and analytical study was performed. From 7307 respiratory samples processed between December 2014 to April 2016, 1019 HRSV-positive samples, were included in this study. Low respiratory tract infection was present in 729 patients (71.54%). Normalized HRSV load was calculated by quantification of HRSV genome and human β-globin gene and expressed as log10 copies/1000 cells. HRSV mean loads were 4.09 ± 2.08 and 4.82 ± 2.09 log10 copies/1000 cells in the 549 pharyngeal and 470 nasopharyngeal samples, respectively (P < 0.001). The viral mean load was 4.81 ± 1.98 log10 copies/1000 cells for patients under the age of 4-year-old (P < 0.001). The viral mean loads were 4.51 ± 2.04 cells in patients with low respiratory tract infection and 4.22 ± 2.28 log10 copies/1000 cells with upper respiratory tract infection or febrile syndrome (P < 0.05). A possible cut off value to predict LRTI evolution was tentatively established. Normalization of viral load by cell number in the samples is essential to ensure an optimal virological molecular diagnosis avoiding that the quality of samples affects the results. A high viral load can be a useful marker to predict disease progression. © 2018 Wiley Periodicals, Inc.

Isolating RNA from precursor and mature melanocytes from human vitiligo and normal skin using laser capture microdissection.

PubMed

Goldstein, Nathaniel B; Koster, Maranke I; Hoaglin, Laura G; Wright, Michael J; Robinson, Steven E; Robinson, William A; Roop, Dennis R; Norris, David A; Birlea, Stanca A

2016-10-01

To characterize the gene expression profile of regenerated melanocytes in the narrow band UVB (NBUVB)-treated vitiligo epidermis and their precursors in the hair follicle, we present here a strategy of RNA isolation from in situ melanocytes using human frozen skin. We developed a rapid immunostaining protocol using the NKI-beteb antibody, which labels differentiated and precursor melanocytes, followed by fluorescent laser capture microdissection. This technique enabled the direct isolation, from melanocyte and adjacent keratinocyte populations, of satisfactory quality RNA that was successfully amplified and analysed by qRT-PCR. The melanocyte-specific gene transcripts TYR, DCT, TYRP1 and PMEL were significantly upregulated in our NBUVB-treated melanocyte samples as compared with the keratinocyte samples, while keratinocyte-specific genes (KRT5 and KRT14) were expressed significantly higher in the keratinocyte samples as compared with the melanocyte samples. Furthermore, in both NBUVB-treated vitiligo skin and normal skin, when bulge melanocytes were compared with epidermal melanocytes, we found significantly lower expression of melanocyte-specific genes and significantly higher expression of three melanocytic stem cell genes (SOX9, WIF1 and SFRP1), while ALCAM and ALDH1A1 transcripts did not show significant variation. We found significantly higher expression of melanocyte-specific genes in the epidermis of NBUVB-treated vitiligo, as compared to the normal skin. When comparing bulge melanocyte samples from untreated vitiligo, NBUVB-treated vitiligo and normal skin, we did not find significant differences in the expression of melanocyte-specific genes or melanocytic stem cell genes. These techniques offer valuable opportunities to study melanocytes and their precursors in vitiligo and other pigmentation disorders. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Learning with sublexical information from emerging reading vocabularies in exceptionally early and normal reading development.

PubMed

Thompson, G Brian; Fletcher-Flinn, Claire M; Wilson, Kathryn J; McKay, Michael F; Margrain, Valerie G

2015-03-01

Predictions from theories of the processes of word reading acquisition have rarely been tested against evidence from exceptionally early readers. The theories of Ehri, Share, and Byrne, and an alternative, Knowledge Sources theory, were so tested. The former three theories postulate that full development of context-free letter sounds and awareness of phonemes are required for normal acquisition, while the claim of the alternative is that with or without such, children can use sublexical information from their emerging reading vocabularies to acquire word reading. Results from two independent samples of children aged 3-5, and 5 years, with mean word reading levels of 7 and 9 years respectively, showed underdevelopment of their context-free letter sounds and phoneme awareness, relative to their word reading levels and normal comparison samples. Despite such underdevelopment, these exceptional readers engaged in a form of phonological recoding that enabled pseudoword reading, at the level of older-age normal controls matched on word reading level. Moreover, in the 5-year-old sample further experiments showed that, relative to normal controls, they had a bias toward use of sublexical information from their reading vocabularies for phonological recoding of heterophonic pseudowords with irregular consistent spelling, and were superior in accessing word meanings independently of phonology, although only if the readers were without exposure to explicit phonics. The three theories were less satisfactory than the alternative theory in accounting for the learning of the exceptionally early readers. Copyright © 2014 Elsevier B.V. All rights reserved.

Substitutions of aspartic acid for glycine-220 and of arginine for glycine-664 in the triple helix of the pro alpha 1(I) chain of type I procollagen produce lethal osteogenesis imperfecta and disrupt the ability of collagen fibrils to incorporate crystalline hydroxyapatite.

PubMed Central

Culbert, A A; Lowe, M P; Atkinson, M; Byers, P H; Wallis, G A; Kadler, K E

1995-01-01

We identified two infants with lethal (type II) osteogenesis imperfecta (OI) who were heterozygous for mutations in the COL1A1 gene that resulted in substitutions of aspartic acid for glycine at position 220 and arginine for glycine at position 664 in the product of one COL1A1 allele in each individual. In normal age- and site-matched bone, approximately 70% (by number) of the collagen fibrils were encrusted with plate-like crystallites of hydroxyapatite. In contrast, approximately 5% (by number) of the collagen fibrils in the probands' bone contained crystallites. In contrast with normal bone, the c-axes of hydroxyapatite crystallites were sometimes poorly aligned with the long axis of fibrils obtained from OI bone. Chemical analysis showed that the OI samples contained normal amounts of calcium. The probands' bone samples contained type I collagen, overmodified type I collagen and elevated levels of type III and V collagens. On the basis of biochemical and morphological data, the fibrils in the OI samples were co-polymers of normal and mutant collagen. The results are consistent with a model of fibril mineralization in which the presence of abnormal type I collagen prevents normal collagen in the same fibril from incorporating hydroxyapatite crystallites. Images Figure 1 Figure 2 Figure 3 PMID:7487936

Expression of the cytoskeleton regulatory protein Mena in human gastric carcinoma and its prognostic significance

PubMed Central

Xu, Lihua; Tan, Huo; Liu, Ruiming; Huang, Qungai; Zhang, Nana; Li, Xi; Wang, Jiani

2017-01-01

The cytoskeleton regulatory protein Mena is reportedly overexpressed in breast cancer; however, data regarding its expression level and clinical significance in gastric carcinoma (GC) is limited. The aim of the present study was to investigate Mena expression levels and prognostic significance in GC. Mena mRNA expression level was determined by reverse transcription-quantitative polymerase chain reaction in 10 paired GC and adjacent normal tissues. The Mena protein expression level was analyzed in paraffin-embedded GC samples and adjacent normal tissues by immunohistochemistry. Statistical analyses were also performed to evaluate the clinicopathological significance of Mena. The results revealed that the mRNA expression level of Mena was significantly higher in G Ct issues compared with in adjacent normal tissues from10 paired samples. In the paraffin-embedded tissue samples, the protein expression level of Mena was higher in G Ct issues compared with in adjacent normal tissues. Compared with adjacent normal tissues, Mena overexpression was observed in 52.83% (56/106) of patients. The overexpression of Mena was significantly associated with the T stage (P=0.033), tumor-node-metastasis (TNM) stage (P<0.001) and decreased overall survival (P<0.001). Based on a multivariate analysis, Mena expression level was an independent prognostic factor for overall survival time. In conclusion, Mena wasoverexpressed in G C tissues and significantly associated with the T stage, TNM stage and overall survival time. Mena may therefore be suitable as a prognostic indicator for patients with GC. PMID:29113241

Expression of the cytoskeleton regulatory protein Mena in human gastric carcinoma and its prognostic significance.

PubMed

Xu, Lihua; Tan, Huo; Liu, Ruiming; Huang, Qungai; Zhang, Nana; Li, Xi; Wang, Jiani

2017-11-01

The cytoskeleton regulatory protein Mena is reportedly overexpressed in breast cancer; however, data regarding its expression level and clinical significance in gastric carcinoma (GC) is limited. The aim of the present study was to investigate Mena expression levels and prognostic significance in GC. Mena mRNA expression level was determined by reverse transcription-quantitative polymerase chain reaction in 10 paired GC and adjacent normal tissues. The Mena protein expression level was analyzed in paraffin-embedded GC samples and adjacent normal tissues by immunohistochemistry. Statistical analyses were also performed to evaluate the clinicopathological significance of Mena. The results revealed that the mRNA expression level of Mena was significantly higher in G Ct issues compared with in adjacent normal tissues from10 paired samples. In the paraffin-embedded tissue samples, the protein expression level of Mena was higher in G Ct issues compared with in adjacent normal tissues. Compared with adjacent normal tissues, Mena overexpression was observed in 52.83% (56/106) of patients. The overexpression of Mena was significantly associated with the T stage (P=0.033), tumor-node-metastasis (TNM) stage (P<0.001) and decreased overall survival (P<0.001). Based on a multivariate analysis, Mena expression level was an independent prognostic factor for overall survival time. In conclusion, Mena wasoverexpressed in G C tissues and significantly associated with the T stage, TNM stage and overall survival time. Mena may therefore be suitable as a prognostic indicator for patients with GC.

Colon Cancer Associated Transcript-1 (CCAT1) Expression in Adenocarcinoma of the Stomach

PubMed Central

Mizrahi, Ido; Mazeh, Haggi; Grinbaum, Ronit; Beglaibter, Nahum; Wilschanski, Michael; Pavlov, Vera; Adileh, Muchamad; Stojadinovic, Alexander; Avital, Itzhak; Gure, Ali Osmay; Halle, David; Nissan, Aviram

2015-01-01

Background: Long non-coding RNAs (lncRNAs) have been shown to have functional roles in cancer biology and are dys-regulated in many tumors. Colon Cancer Associated Transcript -1 (CCAT1) is a lncRNA, previously shown to be significantly up-regulated in colon cancer. The aim of this study is to determine expression levels of CCAT1 in gastric carcinoma (GC). Methods: Tissue samples were obtained from patients undergoing resection for gastric carcinoma (n=19). For each patient, tumor tissue and normal appearing gastric mucosa were taken. Normal gastric tissues obtained from morbidly obese patients, undergoing laparoscopic sleeve gastrectomy served as normal controls (n=19). A human gastric carcinoma cell line (AGS) served as positive control. RNA was extracted from all tissue samples and CCAT1 expression was analyzed using quantitative real time-PCR (qRT-PCR). Results: Low expression of CCAT1 was identified in normal gastric mucosa samples obtained from morbidly obese patients [mean Relative Quantity (RQ) = 1.95±0.4]. AGS human gastric carcinoma cell line showed an elevated level of CCAT1 expression (RQ=8.02). Expression levels of CCAT1 were approximately 10.8 fold higher in GC samples than in samples taken from the negative control group (RQ=21.1±5 vs. RQ=1.95±0.4, respectively, p<0.001). Interestingly, CCAT1 expression was significantly overexpressed in adjacent normal tissues when compared to the negative control group (RQ = 15.25±2 vs. RQ=1.95±0.4, respectively, p<0.001). Tissues obtained from recurrent GC cases showed the highest expression levels (RQ = 88.8±31; p<0.001). Expression levels increased with tumor stage (T4- 36.4±15, T3- 16.1±6, T2- 4.7±1), however this did not reach statistical significance (p=0.2). There was no difference in CCAT1 expression between intestinal and diffuse type GC (RQ=22.4±7 vs. 22.4±16, respectively, p=0.9). Within the normal gastric tissue samples, no significant difference in CCAT1 expression was observed in helicobacter pylori negative and positive patients (RQ= 2.4±0.9 vs. 0.93±0.2, respectively, p=0.13). Conclusion: CCAT1 is up-regulated in gastric cancer, and may serve as a potential bio-marker for early detection and surveillance. PMID:25561974

Personality dimensions in bulimia nervosa, binge eating disorder, and obesity.

PubMed

Peterson, Carol B; Thuras, Paul; Ackard, Diann M; Mitchell, James E; Berg, Kelly; Sandager, Nora; Wonderlich, Stephen A; Pederson, Melissa W; Crow, Scott J

2010-01-01

The purpose of this investigation was to examine differences in personality dimensions among individuals with bulimia nervosa, binge eating disorder, non-binge eating obesity, and a normal-weight comparison group as well as to determine the extent to which these differences were independent of self-reported depressive symptoms. Personality dimensions were assessed using the Multidimensional Personality Questionnaire in 36 patients with bulimia nervosa, 54 patients with binge eating disorder, 30 obese individuals who did not binge eat, and 77 normal-weight comparison participants. Participants with bulimia nervosa reported higher scores on measures of stress reaction and negative emotionality compared to the other 3 groups and lower well-being scores compared to the normal-weight comparison and the obese samples. Patients with binge eating disorder scored lower on well-being and higher on harm avoidance than the normal-weight comparison group. In addition, the bulimia nervosa and binge eating disorder groups scored lower than the normal-weight group on positive emotionality. When personality dimensions were reanalyzed using depression as a covariate, only stress reaction remained higher in the bulimia nervosa group compared to the other 3 groups and harm avoidance remained higher in the binge eating disorder than the normal-weight comparison group. The higher levels of stress reaction in the bulimia nervosa sample and harm avoidance in the binge eating disorder sample after controlling for depression indicate that these personality dimensions are potentially important in the etiology, maintenance, and treatment of these eating disorders. Although the extent to which observed group differences in well-being, positive emotionality, and negative emotionality reflect personality traits, mood disorders, or both, is unclear, these features clearly warrant further examination in understanding and treating bulimia nervosa and binge eating disorder.

Molecular Targeting of Prostate Cancer During Androgen Ablation: Inhibition of CHES1/FOXN3

DTIC Science & Technology

2011-05-01

activity (Firefly luciferase) was normalized to Renilla luciferase activity. Results are presented as fold-change in PSA reporter activity...reporter (DLR) assays performed. In each sample, the CHES1-RR1/3.5 reporter activity (Firefly luciferase) was normalized to Renilla luciferase...4.0) reporter activity (Firefly luciferase) was normalized to Renilla luciferase activity. Results are presented as fold-change in BNIP3 reporter

XFM demonstrates preferential accumulation of a vanadyl-based MRI contrast agent in murine colonic tumors

PubMed Central

Mustafi, Devkumar; Ward, Jesse; Dougherty, Urszula; Bissonnette, Marc; Hart, John; Vogt, Stefan; Karczmar, Gregory S.

2016-01-01

Contrast agents that specifically enhance cancers on MRI would allow earlier detection. Vanadyl-based chelates (VCs) selectively enhance rodent cancers on MRI, suggesting selective uptake of VCs by cancers. Here we report X-ray fluorescence microscopy (XFM) of VC uptake by murine colon cancer. Colonic tumors in mice treated with azoxymethane/dextran sulfate sodium were identified by MRI. Then a gadolinium-based contrast agent and a VC were injected I.V.; mice were sacrificed and colons sectioned. VC distribution was sampled at 120 minutes after injection to evaluate the long term accumulation. Gadolinium distribution was sampled at 10 minutes after injection due to its rapid washout. XFM was performed on 72 regions of normal and cancerous colon from 5 normal mice and 4 cancer-bearing mice. XFM showed that all gadolinium was extracellular with similar concentrations in colon cancers and normal colon. In contrast, the average VC concentration was 2-fold higher in cancers vs. normal tissue (p<0.002). Cancers also contained numerous ‘hot spots’ with intracellular VC concentrations 6-fold higher than the concentration in normal colon (p<0.0001). No ‘hot spots’ were detected in normal colon. This is the first direct demonstration that VCs selectively accumulate in cancer cells, and thus may improve cancer detection. PMID:25813904

Differential expression of glucose transporters in normal and pathologic thyroid tissue.

PubMed

Matsuzu, Kenichi; Segade, Fernando; Matsuzu, Utako; Carter, Aaron; Bowden, Donald W; Perrier, Nancy D

2004-10-01

Malignant cells demonstrate increased glucose uptake and utilization. Immunohistochemical studies have suggested that enhanced glucose uptake in cancer cells may be caused by the overexpression of glucose transporters (GLUTs), in most cases GLUT1 and/or GLUT3. The aim of this study was to examine in detail the expression pattern and levels of GLUT genes in normal and pathologic thyroid tissues and to evaluate the clinical significance of GLUT mRNA levels. One hundred fifty-two surgically resected thyroid tissue samples from 103 patients were evaluated. Samples included: normal thyroid tissue (n = 58), benign thyroid disease (n = 61), and thyroid carcinoma (n = 33). Expression of the GLUT1, GLUT2, GLUT3, GLUT4, and GLUT10 genes were examined by reverse transcription-polymerase chain reaction (RT-PCR) and mRNA levels were quantitated by real-time RT-PCR. All thyroid parenchymal cells expressed GLUT1, GLUT3, GLUT4, and GLUT10. GLUT1 showed increased expression in carcinoma cases (p < 0.0001) and also in comparison with paired normal tissue samples from the same patient (p < 0.0001). Other GLUTs were statistically unchanged in pathologic tissues. These results are consistent with the theory that GLUT1 is upregulated during carcinogenesis and may play a major role in enhanced glucose uptake in thyroid cancer cells.

The phonatory deviation diagram: a novel objective measurement of vocal function.

PubMed

Madazio, Glaucya; Leão, Sylvia; Behlau, Mara

2011-01-01

To identify the discriminative characteristics of the phonatory deviation diagram (PDD) in rough, breathy and tense voices. One hundred and ninety-six samples of normal and dysphonic voices from adults were submitted to perceptual auditory evaluation, focusing on the predominant vocal quality and the degree of deviation. Acoustic analysis was performed with the VoxMetria (CTS Informatica). Significant differences were observed between the dysphonic and normal groups (p < 0.001), and also between the breathy and rough samples (p = 0.044) and the breathy and tense samples (p < 0.001). All normal voices were positioned in the inferior left quadrant, 45% of the rough voices in the inferior right quadrant, 52.6% of the breathy voices in the superior right quadrant and 54.3% of the tense voices in the inferior left quadrant of the PDD. In the inferior left quadrant, 93.8% of voices with no deviation were located and 72.7% of voices with mild deviation; voices with moderate deviation were distributed in the inferior and superior right quadrants, the latter ones containing the most deviant voices and 80% of voices with severe deviation. The PDD was able to discriminate normal from dysphonic voices, and the distribution was related to the type and degree of voice alteration. Copyright © 2011 S. Karger AG, Basel.

Improved ultrasonic TV images achieved by use of Lamb-wave orientation technique

NASA Technical Reports Server (NTRS)

Berger, H.

1967-01-01

Lamb-wave sample orientation technique minimizes the interference from standing waves in continuous wave ultrasonic television imaging techniques used with thin metallic samples. The sample under investigation is oriented such that the wave incident upon it is not normal, but slightly angled.

Observing Behavior and Atypically Restricted Stimulus Control

ERIC Educational Resources Information Center

Dube, William V.; Dickson, Chata A.; Balsamo, Lyn M.; O'Donnell, Kristin Lombard; Tomanari, Gerson Y.; Farren, Kevin M.; Wheeler, Emily E.; McIlvane, William J.

2010-01-01

Restricted stimulus control refers to discrimination learning with atypical limitations in the range of controlling stimuli or stimulus features. In the study reported here, 4 normally capable individuals and 10 individuals with intellectual disabilities (ID) performed two-sample delayed matching to sample. Sample-stimulus observing was recorded…

Pedagogical Simulation of Sampling Distributions and the Central Limit Theorem

ERIC Educational Resources Information Center

Hagtvedt, Reidar; Jones, Gregory Todd; Jones, Kari

2007-01-01

Students often find the fact that a sample statistic is a random variable very hard to grasp. Even more mysterious is why a sample mean should become ever more Normal as the sample size increases. This simulation tool is meant to illustrate the process, thereby giving students some intuitive grasp of the relationship between a parent population…

On the incidence of Mg II absorbers along the blazar sightlines

NASA Astrophysics Data System (ADS)

Mishra, S.; Chand, H.; Krishna, Gopal-; Joshi, R.; Shchekinov, Y. A.; Fatkhullin, T. A.

2018-02-01

It is widely believed that the cool gas clouds traced by Mg II absorption, within a velocity offset of 5000 km s-1 relative to the background quasar are mostly associated with the quasar itself, whereas the absorbers seen at larger velocity offsets towards us are intervening absorber systems and hence their existence is completely independent of the background quasar. Recent evidence by Bergeron et al. (hereinafter BBM) has seriously questioned this paradigm, by showing that the number density of intervening Mg II absorbers towards the 45 blazars in their sample is nearly two times the expectation based on the Mg II absorption systems seen towards normal quasars (QSOs). Given its serious implications, it becomes important to revisit this finding, by enlarging the blazar sample and subjecting it to an independent analysis. Here, we first report the outcome of our re-analysis of the available spectroscopic data for the BBM sample itself. Our analysis of the BBM sample reproduces their claimed factor of 2 excess of dN/dz along blazar sightlines, vis-à-vis normal QSOs. We have also assembled an approxmately three times larger sample of blazars, albeit with moderately sensitive optical spectra. Using this sample together with the BBM sample, our analysis shows that the dN/dz of the Mg II absorbers statistically matches that known for normal QSO sightlines. Further, the analysis indicates that associated absorbers might be contributing significantly to the estimated dN/dz up to offset speeds Δv ∼ 0.2c relative to the blazar.

Sampling and storage of blood for pH and blood gas analysis.

PubMed

Haskins, S C

1977-02-15

Techniques used in sampling and storage of a blood sample for pH and gas measurements can have an important effect on the measured values. Observation of these techniques and principles will minimize in vitro alteration of the pH and blood gas values. To consider that a significant change has occurred in a pH or blood gas measurement from previous values, the change must exceed 0.015 for pH, 3 mm Hg for PCO2, 5 mm Hg for PO2, and 2 mEq/L for [HCO-3] or base excess/deficit. In vitro dilution of the blood sample with anticoagulant should be avoided because it will alter the measured PCO2 and base excess/deficit values. Arterial samples should be collected for meaningful pH and blood gas values. Central venous and free-flowing capillary blood can be used for screening procedures in normal patients but are subject to considerable error. A blood sample can be stored for up to 30 minutes at room temperature without significant change in acid-base values but only up to 12 minutes before significant changes occur in PO2. A blood sample can be stored for up to 3.5 hours in an ice-water bath without significant change in pH and for 6 hours without significant change in PCO2 or PO2. Variations of body temperatures from normal will cause a measurable change in pH and blood gas values when the blood is exposed to the normal water bath temperatures of the analyzer.

Evaluation of Normalization Methods on GeLC-MS/MS Label-Free Spectral Counting Data to Correct for Variation during Proteomic Workflows

NASA Astrophysics Data System (ADS)

Gokce, Emine; Shuford, Christopher M.; Franck, William L.; Dean, Ralph A.; Muddiman, David C.

2011-12-01

Normalization of spectral counts (SpCs) in label-free shotgun proteomic approaches is important to achieve reliable relative quantification. Three different SpC normalization methods, total spectral count (TSpC) normalization, normalized spectral abundance factor (NSAF) normalization, and normalization to selected proteins (NSP) were evaluated based on their ability to correct for day-to-day variation between gel-based sample preparation and chromatographic performance. Three spectral counting data sets obtained from the same biological conidia sample of the rice blast fungus Magnaporthe oryzae were analyzed by 1D gel and liquid chromatography-tandem mass spectrometry (GeLC-MS/MS). Equine myoglobin and chicken ovalbumin were spiked into the protein extracts prior to 1D-SDS- PAGE as internal protein standards for NSP. The correlation between SpCs of the same proteins across the different data sets was investigated. We report that TSpC normalization and NSAF normalization yielded almost ideal slopes of unity for normalized SpC versus average normalized SpC plots, while NSP did not afford effective corrections of the unnormalized data. Furthermore, when utilizing TSpC normalization prior to relative protein quantification, t-testing and fold-change revealed the cutoff limits for determining real biological change to be a function of the absolute number of SpCs. For instance, we observed the variance decreased as the number of SpCs increased, which resulted in a higher propensity for detecting statistically significant, yet artificial, change for highly abundant proteins. Thus, we suggest applying higher confidence level and lower fold-change cutoffs for proteins with higher SpCs, rather than using a single criterion for the entire data set. By choosing appropriate cutoff values to maintain a constant false positive rate across different protein levels (i.e., SpC levels), it is expected this will reduce the overall false negative rate, particularly for proteins with higher SpCs.

Electron Micrographs of Quail Limb Bones formed in microgravity

NASA Technical Reports Server (NTRS)

2003-01-01

Electron micrographs of quail limb bones that formed under the influence of microgravity show decreased mineralization compared to bones formed in normal gravity. The letters B and C indicate bone and cartilage sides of the sample, respectively, with the arrows marking the junction between bone and cartilage cells. The asterisks indicate where mineralization begins. The bone that developed during spaceflight (top) shows less mineral compared to the control sample (bottom); the control sample clearly shows mineral deposits (dark spots) that are absent in the flight sample. Quail eggs are small and develop quickly, making them ideal for space experiments. In late 2001, the Avian Development Facility (ADF) made its first flight and carried eggs used in two investigations, development and function of the irner-ear balance system in normal and altered gravity environments, and skeletal development in embryonic quail.

Case report of unexplained hypocalcaemia in a slightly haemolysed sample.

PubMed

Cornes, Michael

2017-06-15

The case presented highlights a common pre-analytical problem identified in the laboratory that was initially missed. It concerns a young, generally healthy adult patient with no significant medical history and no significant family history. They presented with common flu like symptoms to their primary care clinician who considered this was most likely a viral problem that would pass with time. The clinician, however, did some routine bloods to reassure the patient despite a lack of clinical indication. When the sample was analysed the sample was haemolysed with strikingly low calcium. This led to the patient being called into hospital for urgent repeat investigations, all of which turned out to be within normal ranges. On further investigation the original sample was found to be contaminated. This result would normally have been flagged but was missed due to the complication of haemolysis.

Method performance and multi-laboratory assessment of a normal phase high pressure liquid chromatography-fluorescence detection method for the quantitation of flavanols and procyanidins in cocoa and chocolate containing samples.

PubMed

Robbins, Rebecca J; Leonczak, Jadwiga; Johnson, J Christopher; Li, Julia; Kwik-Uribe, Catherine; Prior, Ronald L; Gu, Liwei

2009-06-12

The quantitative parameters and method performance for a normal-phase HPLC separation of flavanols and procyanidins in chocolate and cocoa-containing food products were optimized and assessed. Single laboratory method performance was examined over three months using three separate secondary standards. RSD(r) ranged from 1.9%, 4.5% to 9.0% for cocoa powder, liquor and chocolate samples containing 74.39, 15.47 and 1.87 mg/g flavanols and procyanidins, respectively. Accuracy was determined by comparison to the NIST Standard Reference Material 2384. Inter-lab assessment indicated that variability was quite low for seven different cocoa-containing samples, with a RSD(R) of less than 10% for the range of samples analyzed.

Selection of reference genes for gene expression studies in heart failure for left and right ventricles.

PubMed

Li, Mengmeng; Rao, Man; Chen, Kai; Zhou, Jianye; Song, Jiangping

2017-07-15

Real-time quantitative reverse transcriptase-PCR (qRT-PCR) is a feasible tool for determining gene expression profiles, but the accuracy and reliability of the results depends on the stable expression of selected housekeeping genes in different samples. By far, researches on stable housekeeping genes in human heart failure samples are rare. Moreover the effect of heart failure on the expression of housekeeping genes in right and left ventricles is yet to be studied. Therefore we aim to provide stable housekeeping genes for both ventricles in heart failure and normal heart samples. In this study, we selected seven commonly used housekeeping genes as candidates. By using the qRT-PCR, the expression levels of ACTB, RAB7A, GAPDH, REEP5, RPL5, PSMB4 and VCP in eight heart failure and four normal heart samples were assessed. The stability of candidate housekeeping genes was evaluated by geNorm and Normfinder softwares. GAPDH showed the least variation in all heart samples. Results also indicated the difference of gene expression existed in heart failure left and right ventricles. GAPDH had the highest expression stability in both heart failure and normal heart samples. We also propose using different sets of housekeeping genes for left and right ventricles respectively. The combination of RPL5, GAPDH and PSMB4 is suitable for the right ventricle and the combination of GAPDH, REEP5 and RAB7A is suitable for the left ventricle. Copyright © 2017 Elsevier B.V. All rights reserved.

A survey of FRAXE allele sizes in three populations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhong, N.; Ju, W.; Curley, D.

1996-08-09

FRAXE is a fragile site located at Xq27-8, which contains polymorphic triplet GCC repeats associated with a CpG island. Similar to FRAXA, expansion of the GCC repeats results in an abnormal methylation of the CpG island and is associated with a mild mental retardation syndrome (FRAXE-MR). We surveyed the GCC repeat alleles of FRAXE from 3 populations. A total of 665 X chromosomes including 416 from a New York Euro-American sample (259 normal and 157 with FRAXA mutations), 157 from a Chinese sample (144 normal and 13 FRAXA), and 92 from a Finnish sample (56 normal and 36 FRAXA) weremore » analyzed by polymerase chain reaction. Twenty-seven alleles, ranging from 4 to 39 GCC repeats, were observed. The modal repeat number was 16 in the New York and Finnish samples and accounted for 24% of all the chromosomes tested (162/665). The modal repeat number in the Chinese sample was 18. A founder effect for FRAXA was suggested among the Finnish FRAXA samples in that 75% had the FRAXE 16 repeat allele versus only 30% of controls. Sequencing of the FRAXE region showed no imperfections within the GCC repeat region, such as those commonly seen in FRAXA. The smaller size and limited range of repeats and the lack of imperfections suggests the molecular mechanisms underlying FRAXE triplet mutations may be different from those underlying FRAXA. 27 refs., 4 figs., 1 tab.« less

TGF-Alpha Expression During Breast Tumorigenesis

DTIC Science & Technology

1999-07-01

contributors to breast tumorigenesis. Therefore, we examined TGFa expression in normal and transformed epithelium. We also examined TOFa and EGFR protein in...patient samples it is difficult to determine what effect tissue culture has on normal T(3Fa protein synthesis and processing. TOFa protein expression

Reducing Bias and Error in the Correlation Coefficient Due to Nonnormality.

PubMed

Bishara, Anthony J; Hittner, James B

2015-10-01

It is more common for educational and psychological data to be nonnormal than to be approximately normal. This tendency may lead to bias and error in point estimates of the Pearson correlation coefficient. In a series of Monte Carlo simulations, the Pearson correlation was examined under conditions of normal and nonnormal data, and it was compared with its major alternatives, including the Spearman rank-order correlation, the bootstrap estimate, the Box-Cox transformation family, and a general normalizing transformation (i.e., rankit), as well as to various bias adjustments. Nonnormality caused the correlation coefficient to be inflated by up to +.14, particularly when the nonnormality involved heavy-tailed distributions. Traditional bias adjustments worsened this problem, further inflating the estimate. The Spearman and rankit correlations eliminated this inflation and provided conservative estimates. Rankit also minimized random error for most sample sizes, except for the smallest samples ( n = 10), where bootstrapping was more effective. Overall, results justify the use of carefully chosen alternatives to the Pearson correlation when normality is violated.

Gene expression profiling of human breast tissue samples using SAGE-Seq.

PubMed

Wu, Zhenhua Jeremy; Meyer, Clifford A; Choudhury, Sibgat; Shipitsin, Michail; Maruyama, Reo; Bessarabova, Marina; Nikolskaya, Tatiana; Sukumar, Saraswati; Schwartzman, Armin; Liu, Jun S; Polyak, Kornelia; Liu, X Shirley

2010-12-01

We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification of differentially expressed genes. We find that the diversity of cancer transcriptomes is significantly higher than that of normal cells. Our analysis indicates that transcript discovery plateaus at 10 million reads/sample, and suggests a minimum desired sequencing depth around five million reads. Comparison of SAGE-Seq and traditional SAGE on normal and cancerous breast tissues reveals higher sensitivity of SAGE-Seq to detect less-abundant genes, including those encoding for known breast cancer-related transcription factors and G protein-coupled receptors (GPCRs). SAGE-Seq is able to identify genes and pathways abnormally activated in breast cancer that traditional SAGE failed to call. SAGE-Seq is a powerful method for the identification of biomarkers and therapeutic targets in human disease.

Reducing Bias and Error in the Correlation Coefficient Due to Nonnormality

PubMed Central

Hittner, James B.

2014-01-01

It is more common for educational and psychological data to be nonnormal than to be approximately normal. This tendency may lead to bias and error in point estimates of the Pearson correlation coefficient. In a series of Monte Carlo simulations, the Pearson correlation was examined under conditions of normal and nonnormal data, and it was compared with its major alternatives, including the Spearman rank-order correlation, the bootstrap estimate, the Box–Cox transformation family, and a general normalizing transformation (i.e., rankit), as well as to various bias adjustments. Nonnormality caused the correlation coefficient to be inflated by up to +.14, particularly when the nonnormality involved heavy-tailed distributions. Traditional bias adjustments worsened this problem, further inflating the estimate. The Spearman and rankit correlations eliminated this inflation and provided conservative estimates. Rankit also minimized random error for most sample sizes, except for the smallest samples (n = 10), where bootstrapping was more effective. Overall, results justify the use of carefully chosen alternatives to the Pearson correlation when normality is violated. PMID:29795841

Dye-Enhanced Multimodal Confocal Imaging of Brain Cancers

NASA Astrophysics Data System (ADS)

Wirth, Dennis; Snuderl, Matija; Sheth, Sameer; Curry, William; Yaroslavsky, Anna

2011-04-01

Background and Significance: Accurate high resolution intraoperative detection of brain tumors may result in improved patient survival and better quality of life. The goal of this study was to evaluate dye enhanced multimodal confocal imaging for discriminating normal and cancerous brain tissue. Materials and Methods: Fresh thick brain specimens were obtained from the surgeries. Normal and cancer tissues were investigated. Samples were stained in methylene blue and imaged. Reflectance and fluorescence signals were excited at 658nm. Fluorescence emission and polarization were registered from 670 nm to 710 nm. The system provided lateral resolution of 0.6 μm and axial resolution of 7 μm. Normal and cancer specimens exhibited distinctively different characteristics. H&E histopathology was processed from each imaged sample. Results and Conclusions: The analysis of normal and cancerous tissues indicated clear differences in appearance in both the reflectance and fluorescence responses. These results confirm the feasibility of multimodal confocal imaging for intraoperative detection of small cancer nests and cells.

Spectral analysis of tissues from patients with cancer using a portable spectroscopic diagnostic ratiometer unit

NASA Astrophysics Data System (ADS)

Sordillo, Laura A.; Pu, Yang; Sordillo, Peter P.; Budansky, Yury; Alfano, R. R.

2014-05-01

Spectral profiles of tissues from patients with breast carcinoma, malignant carcinoid and non-small cell lung carcinoma were acquired using native fluorescence spectroscopy. A novel spectroscopic ratiometer device (S3-LED) with selective excitation wavelengths at 280 nm and 335 nm was used to produce the emission spectra of the key biomolecules, tryptophan and NADH, in the tissue samples. In each of the samples, analysis of emission intensity peaks from biomolecules showed increased 340 nm/440 nm and 340 nm/460 nm ratios in the malignant samples compared to their paired normal samples. This most likely represented increased tryptophan to NADH ratios in the malignant tissue samples compared to their paired normal samples. Among the non-small cell lung carcinoma and breast carcinomas, it appeared that tumors of very large size or poor differentiation had an even greater increase in the 340 nm/440 nm and 340 nm/460 nm ratios. In the samples of malignant carcinoid, which is known to be a highly metabolically active tumor, a marked increase in these ratios was also seen.

The establishment and external validation of NIR qualitative analysis model for waste polyester-cotton blend fabrics.

PubMed

Li, Feng; Li, Wen-Xia; Zhao, Guo-Liang; Tang, Shi-Jun; Li, Xue-Jiao; Wu, Hong-Mei

2014-10-01

A series of 354 polyester-cotton blend fabrics were studied by the near-infrared spectra (NIRS) technology, and a NIR qualitative analysis model for different spectral characteristics was established by partial least squares (PLS) method combined with qualitative identification coefficient. There were two types of spectrum for dying polyester-cotton blend fabrics: normal spectrum and slash spectrum. The slash spectrum loses its spectral characteristics, which are effected by the samples' dyes, pigments, matting agents and other chemical additives. It was in low recognition rate when the model was established by the total sample set, so the samples were divided into two types of sets: normal spectrum sample set and slash spectrum sample set, and two NIR qualitative analysis models were established respectively. After the of models were established the model's spectral region, pretreatment methods and factors were optimized based on the validation results, and the robustness and reliability of the model can be improved lately. The results showed that the model recognition rate was improved greatly when they were established respectively, the recognition rate reached up to 99% when the two models were verified by the internal validation. RC (relation coefficient of calibration) values of the normal spectrum model and slash spectrum model were 0.991 and 0.991 respectively, RP (relation coefficient of prediction) values of them were 0.983 and 0.984 respectively, SEC (standard error of calibration) values of them were 0.887 and 0.453 respectively, SEP (standard error of prediction) values of them were 1.131 and 0.573 respectively. A series of 150 bounds samples reached used to verify the normal spectrum model and slash spectrum model and the recognition rate reached up to 91.33% and 88.00% respectively. It showed that the NIR qualitative analysis model can be used for identification in the recycle site for the polyester-cotton blend fabrics.

Controlled alignment of carbon nanofibers in a large-scale synthesis process

NASA Astrophysics Data System (ADS)

Merkulov, Vladimir I.; Melechko, A. V.; Guillorn, M. A.; Simpson, M. L.; Lowndes, D. H.; Whealton, J. H.; Raridon, R. J.

2002-06-01

Controlled alignment of catalytically grown carbon nanofibers (CNFs) at a variable angle to the substrate during a plasma-enhanced chemical vapor deposition process is achieved. The CNF alignment is controlled by the direction of the electric field lines during the synthesis process. Off normal CNF orientations are achieved by positioning the sample in the vicinity of geometrical features of the sample holder, where bending of the electric field lines occurs. The controlled growth of kinked CNFs that consist of two parts aligned at different angles to the substrate normal also is demonstrated.

System for determining position of normal shock in supersonic flow

NASA Technical Reports Server (NTRS)

Iverson, Jr., Donald G. (Inventor); Daiber, Troy D. (Inventor)

1991-01-01

Light from a plurality of light emitting diodes is transmitted through optical cables (12) to a lens system. The lenses (56, 58) expand and collimate the light and project it in a sheet (16) across the supersonic inlet of an aircraft power plant perpendicular to incoming airflow. A normal shock bends a portion of the sheet of light (16). A linear array of a multiplicity of optical fiber ends collects discrete samples of light. The samples are processed and compared to a predetermined profile to determine the shock location.

Tensile testing apparatus

NASA Technical Reports Server (NTRS)

Blackburn, L. B.; Ellingsworth, J. R. (Inventor)

1985-01-01

An improved mechanical extensometer is described for use with a constant load creep test machine. The dead weight of the extensometer is counterbalanced by two pairs of weights connected through a pulley system and to rod extension and leading into the furnace where the test sample is undergoing elevated temperature (above 500 F.) tensile testing. Novel gripper surfaces, conical tip and flat surface are provided in each sampling engaging platens to reduce the grip pressure normally required for attachment of the extensometer to the specimen and reduce initial specimen bending normally associated with foil-gage metal testing.

Detection of equine herpesvirus in horses with idiopathic keratoconjunctivitis and comparison of three sampling techniques.

PubMed

Hollingsworth, Steven R; Pusterla, Nicola; Kass, Philip H; Good, Kathryn L; Brault, Stephanie A; Maggs, David J

2015-09-01

To determine the role of equine herpesvirus (EHV) in idiopathic keratoconjunctivitis in horses and to determine whether sample collection method affects detection of EHV DNA by quantitative polymerase chain reaction (qPCR). Twelve horses with idiopathic keratoconjunctivitis and six horses without signs of ophthalmic disease. Conjunctival swabs, corneal scrapings, and conjunctival biopsies were collected from 18 horses: 12 clinical cases with idiopathic keratoconjunctivitis and six euthanized controls. In horses with both eyes involved, the samples were taken from the eye judged to be more severely affected. Samples were tested with qPCR for EHV-1, EHV-2, EHV-4, and EHV-5 DNA. Quantity of EHV DNA and viral replicative activity were compared between the two populations and among the different sampling techniques; relative sensitivities of the sampling techniques were determined. Prevalence of EHV DNA as assessed by qPCR did not differ significantly between control horses and those with idiopathic keratoconjunctivitis. Sampling by conjunctival swab was more likely to yield viral DNA as assessed by qPCR than was conjunctival biopsy. EHV-1 and EHV-4 DNA were not detected in either normal or IKC-affected horses; EHV-2 DNA was detected in two of 12 affected horses but not in normal horses. EHV-5 DNA was commonly found in ophthalmically normal horses and horses with idiopathic keratoconjunctivitis. Because EHV-5 DNA was commonly found in control horses and in horses with idiopathic keratoconjunctivitis, qPCR was not useful for the etiological diagnosis of equine keratoconjunctivitis. Conjunctival swabs were significantly better at obtaining viral DNA samples than conjunctival biopsy in horses in which EHV-5 DNA was found. © 2015 American College of Veterinary Ophthalmologists.

Influence of color on dielectric properties of marinated poultry breast meat.

PubMed

Samuel, D; Trabelsi, S

2012-08-01

The dielectric behavior of foods when exposed to radio-frequency and microwave electric fields is highly influenced by moisture content and the degree of water binding with constituents of the food materials. The ability to correlate specific food quality characteristics with the dielectric properties can lead to the development of rapid, nondestructive techniques for such quality measurements. Water-holding capacity is a critical attribute in meat quality. Up to 50% of raw poultry meat in the United States is marinated with mixtures of water, salts, and phosphates. The objective of this study was to determine if variations in breast meat color would affect the dielectric properties of marinated poultry meat over a broad frequency range from 500 MHz to 50 GHz. Poultry meat was obtained from a local commercial plant in Georgia (USA). Color and pH measurements were taken on the breast filets. Groups of breast filets were sorted into classes of pale and normal before adding marination pickup percentages of 0, 5, 10, and 15. Breast filets were vacuum-tumbled and weighed for pickup percentages. Dielectric properties of the filets were measured with a coaxial open-ended probe on samples equilibrated to 25°C. Samples from pale meat exhibited higher dielectric properties than samples from normal meat. No differences could be observed between samples from pale and normal meat after marination of the samples. Overall, dielectric properties increased as the marination pickup increased (α=0.05). Marination pickup strongly influenced the dielectric loss factor. Differences between samples marinated at different pickup levels were more pronounced at lower frequencies for the dielectric loss factor. As frequency increased, the differences between samples decreased. Differences in dielectric constant between samples were not as consistent as those seen with the dielectric loss factor.

Adipogenesis in thyroid eye disease.

PubMed

Crisp, M; Starkey, K J; Lane, C; Ham, J; Ludgate, M

2000-10-01

Adipogenesis contributes to the pathogenesis of thyroid eye disease (TED). Thyrotropin receptor (TSHR) transcripts are present in orbital fat. This study was conducted to determine whether they are expressed as functional protein, and if so, whether this is restricted to TED orbits or to a particular stage in adipocyte differentiation. Samples of fat were obtained from 18 TED-affected orbits and 4 normal orbits, and 9 were obtained from nonorbital locations. Frozen sections were examined by immunocytochemistry using monoclonal antibodies specific for the human TSHR. Samples were disaggregated and the preadipocytes separated from the mature by differential centrifugation and cultured in serum-free or DM and examined for morphologic changes, oil red O and TSHR staining, and TSH-induced cyclic adenosine monophosphate (cAMP) production. Marked immunoreactivity was observed in frozen sections from all three TED samples and faint staining in both normal orbital fat samples. In vitro, 1% to 5% of preadipocytes displayed TSHR immunoreactivity in five of six TED and two of three normal orbital samples and in three of five nonorbital samples. Differentiation, was induced in all 14 orbital samples. Three of four nonorbital samples contained occasional differentiated cells. Fifty percent to 70% of differentiating cells demonstrated receptor immunoreactivity. Two of three TED and four of four nonorbital preadipocytes in DM and/or mature adipocytes displayed a TSH-mediated increase in cAMP. The results indicate that orbital fat TSHR transcripts are expressed as protein, which can be functional. This is not aberrant in TED orbits, although expression may be upregulated. The majority of preadipocytes undergoing differentiation express the receptor, indicating a key role for this population in one mechanism for increasing orbital volume.

Superficial and deep changes of histology, texture and particle size distribution in broiler wooden breast muscle during refrigerated storage.

PubMed

Soglia, Francesca; Gao, Jingxian; Mazzoni, Maurizio; Puolanne, Eero; Cavani, Claudio; Petracci, Massimiliano; Ertbjerg, Per

2017-09-01

Recently the poultry industry faced an emerging muscle abnormality termed wooden breast (WB), the prevalence of which has dramatically increased in the past few years. Considering the incomplete knowledge concerning this condition and the lack of information on possible variations due to the intra-fillet sampling locations (superficial vs. deep position) and aging of the samples, this study aimed at investigating the effect of 7-d storage of broiler breast muscles on histology, texture, and particle size distribution, evaluating whether the sampling position exerts a relevant role in determining the main features of WB. With regard to the histological observations, severe myodegeneration accompanied by accumulation of connective tissue was observed within the WB cases, irrespective of the intra-fillet sampling position. No changes in the histological traits took place during the aging in either the normal or the WB samples. As to textural traits, although a progressive tenderization process took place during storage (P ≤ 0.001), the differences among the groups were mainly detected when raw meat rather than cooked was analyzed, with the WB samples exhibiting the highest (P ≤ 0.001) 80% compression values. In spite of the increased amount of connective tissue components in the WB cases, their thermally labile cross-links will account for the similar compression and shear-force values as normal breast cases when measured on cooked samples. Similarly, the enlargement of extracellular matrix and fibrosis might contribute in explaining the different fragmentation patterns observed between the superficial and the deep layer in the WB samples, with the superficial part exhibiting a higher amount of larger particles and an increase in particles with larger size during storage, compared to normal breasts. © 2017 Poultry Science Association Inc.

Emissivity measurements of shocked tin using a multi-wavelength integrating sphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seifter, A; Holtkamp, D B; Iverson, A J

Pyrometric measurements of radiance to determine temperature have been performed on shock physics experiments for decades. However, multi-wavelength pyrometry schemes sometimes fail to provide credible temperatures in experiments, which incur unknown changes in sample emissivity, because an emissivity change also affects the spectral radiance. Hence, for shock physics experiments using pyrometry to measure temperatures, it is essential to determine the dynamic sample emissivity. The most robust way to determine the normal spectral emissivity is to measure the spectral normal-hemispherical reflectance using an integrating sphere. In this paper we describe a multi-wavelength (1.6–5.0 μm) integrating sphere system that utilizes a “reversed”more » scheme, which we use for shock physics experiments. The sample to be shocked is illuminated uniformly by scattering broadband light from inside a sphere onto the sample. A portion of the light reflected from the sample is detected at a point 12° from normal to the sample surface. For this experiment, we used the system to measure emissivity of shocked tin at four wavelengths for shock stress values between 17 and 33 GPa. The results indicate a large increase in effective emissivity upon shock release from tin when the shock is above 24–25 GPa, a shock stress that partially melts the sample. We also recorded an IR image of one of the shocked samples through the integrating sphere, and the emissivity inferred from the image agreed well with the integrating-sphere, pyrometer-detector data. Here, we discuss experimental data, uncertainties, and a data analysis process. We also describe unique emissivity-measurement problems arising from shock experiments and methods to overcome such problems.« less

Physical Properties of Normal Grade Biodiesel and Winter Grade Biodiesel

PubMed Central

Sadrolhosseini, Amir Reza; Moksin, Mohd Maarof; Nang, Harrison Lau Lik; Norozi, Monir; Yunus, W. Mahmood Mat; Zakaria, Azmi

2011-01-01

In this study, optical and thermal properties of normal grade and winter grade palm oil biodiesel were investigated. Surface Plasmon Resonance and Photopyroelectric technique were used to evaluate the samples. The dispersion curve and thermal diffusivity were obtained. Consequently, the variation of refractive index, as a function of wavelength in normal grade biodiesel is faster than winter grade palm oil biodiesel, and the thermal diffusivity of winter grade biodiesel is higher than the thermal diffusivity of normal grade biodiesel. This is attributed to the higher palmitic acid C16:0 content in normal grade than in winter grade palm oil biodiesel. PMID:21731429

Influence of population versus convenience sampling on sample characteristics in studies of cognitive aging.

PubMed

Brodaty, Henry; Mothakunnel, Annu; de Vel-Palumbo, Melissa; Ames, David; Ellis, Kathryn A; Reppermund, Simone; Kochan, Nicole A; Savage, Greg; Trollor, Julian N; Crawford, John; Sachdev, Perminder S

2014-01-01

We examined whether differences in findings of studies examining mild cognitive impairment (MCI) were associated with recruitment methods by comparing sample characteristics in two contemporaneous Australian studies, using population-based and convenience sampling. The Sydney Memory and Aging Study invited participants randomly from the electoral roll in defined geographic areas in Sydney. The Australian Imaging, Biomarkers and Lifestyle Study of Ageing recruited cognitively normal (CN) individuals via media appeals and MCI participants via referrals from clinicians in Melbourne and Perth. Demographic and cognitive variables were harmonized, and similar diagnostic criteria were applied to both samples retrospectively. CN participants recruited via convenience sampling were younger, better educated, more likely to be married and have a family history of dementia, and performed better cognitively than those recruited via population-based sampling. MCI participants recruited via population-based sampling had better memory performance and were less likely to carry the apolipoprotein E ε4 allele than clinically referred participants but did not differ on other demographic variables. A convenience sample of normal controls is likely to be younger and better functioning and that of an MCI group likely to perform worse than a purportedly random sample. Sampling bias should be considered when interpreting findings. Copyright © 2014 Elsevier Inc. All rights reserved.

Comparisons between gouge and bare surface friction of serpentinite at seismic slip velocities: Implications for dynamic weakening of gouge-bearing faults

NASA Astrophysics Data System (ADS)

Proctor, B.; Mitchell, T. M.; Hirth, G.; Goldsby, D. L.; Di Toro, G.; Zorzi, F.

2013-12-01

High-velocity friction (HVF) experiments on bare rock surfaces have revealed various dynamic weakening processes (e.g., flash weakening, gel weakening, melt lubrication) that likely play a fundamental role in coseismic fault weakening. However, faults generally contain a thin layer of gouge separating the solid wallrocks, thus it is important to understand how the presence of gouge modifies the efficiency of these weakening processes at seismic slip rates. We explored the frictional behavior of bare surfaces and powdered samples of an antigorite-rich serpentinite (ARS) and a lizardite-rich serpentinite (LRS) at earthquake slip rates. HVF experiments were conducted with slip displacements ranging from ~0.5 to 2m, at velocities ranging from 0.002m/s to 6.5 m/s, and with normal stresses ranging from 2-22 MPa for gouge and 5-100MPa for bare surfaces. Our results demonstrate that the friction coefficient (μ) of powdered serpentine is significantly larger than that of bare surfaces under otherwise identical conditions. Bare surface friction decreases over a weakening distance of a few centimeters to a nominally steady-state value of ~0.1 at velocities greater than 0.1m/s. The nominal steady-state friction decreases non-linearly with increasing normal stress from 0.14 to 0.045 at 5 and ~100MPa respectfully at a slip velocity of 1m/s. Additionally, the recovery of frictional strength during deceleration depends on total displacement; samples slipped for ~50mm recover faster than samples slipped for ~0.5m. Microstructural analysis of bare surfaces deformed at the highest normal stresses revealed translucent glass-like material on the slip surfaces and XRD analysis of wear material revealed an increasing presence of olivine and enstatite with increasing normal stress. In contrast, gouge requires an order of magnitude higher velocity than bare surfaces to induce frictional weakening, has a larger weakening distance and higher steady state friction values for equivalent deformation conditions. Furthermore, we observe a strong normal stress dependence of the nominal steady state friction and the weakening distance of ARS and LRS gouge from 0.51 to 0.39 and from 25-10cm at 4MPa and 22MPa, respectfully, for at a slip velocity of 1m/s. Strain was localized onto a shear surface in the range of 100-300 microns wide in all gouge samples deformed at >10cm/s and XRD analyses revealed the presence of olivine and enstatite in samples with the most weakening and none in samples with no weakening. Our results indicate that dynamic weakening occurs in gouge at low normal stress in response to strain localization and shear heating of the slip surface. However, because more initial displacement is required to localize strain, weakening initiates at higher velocities and after larger weakening distances than bare surfaces. At higher normal stress, localization occurs after less displacement and the differences between gouge and bare-surface friction diminish; extrapolation of our data suggests that the behavior of serpentine gouge will approach that of bare surfaces at normal stresses ≥60 MPa.

Unsupervised Ensemble Anomaly Detection Using Time-Periodic Packet Sampling

NASA Astrophysics Data System (ADS)

Uchida, Masato; Nawata, Shuichi; Gu, Yu; Tsuru, Masato; Oie, Yuji

We propose an anomaly detection method for finding patterns in network traffic that do not conform to legitimate (i.e., normal) behavior. The proposed method trains a baseline model describing the normal behavior of network traffic without using manually labeled traffic data. The trained baseline model is used as the basis for comparison with the audit network traffic. This anomaly detection works in an unsupervised manner through the use of time-periodic packet sampling, which is used in a manner that differs from its intended purpose — the lossy nature of packet sampling is used to extract normal packets from the unlabeled original traffic data. Evaluation using actual traffic traces showed that the proposed method has false positive and false negative rates in the detection of anomalies regarding TCP SYN packets comparable to those of a conventional method that uses manually labeled traffic data to train the baseline model. Performance variation due to the probabilistic nature of sampled traffic data is mitigated by using ensemble anomaly detection that collectively exploits multiple baseline models in parallel. Alarm sensitivity is adjusted for the intended use by using maximum- and minimum-based anomaly detection that effectively take advantage of the performance variations among the multiple baseline models. Testing using actual traffic traces showed that the proposed anomaly detection method performs as well as one using manually labeled traffic data and better than one using randomly sampled (unlabeled) traffic data.

A Third Moment Adjusted Test Statistic for Small Sample Factor Analysis

PubMed Central

Lin, Johnny; Bentler, Peter M.

2012-01-01

Goodness of fit testing in factor analysis is based on the assumption that the test statistic is asymptotically chi-square; but this property may not hold in small samples even when the factors and errors are normally distributed in the population. Robust methods such as Browne’s asymptotically distribution-free method and Satorra Bentler’s mean scaling statistic were developed under the presumption of non-normality in the factors and errors. This paper finds new application to the case where factors and errors are normally distributed in the population but the skewness of the obtained test statistic is still high due to sampling error in the observed indicators. An extension of Satorra Bentler’s statistic is proposed that not only scales the mean but also adjusts the degrees of freedom based on the skewness of the obtained test statistic in order to improve its robustness under small samples. A simple simulation study shows that this third moment adjusted statistic asymptotically performs on par with previously proposed methods, and at a very small sample size offers superior Type I error rates under a properly specified model. Data from Mardia, Kent and Bibby’s study of students tested for their ability in five content areas that were either open or closed book were used to illustrate the real-world performance of this statistic. PMID:23144511

Structure-Preserving Color Normalization and Sparse Stain Separation for Histological Images.

PubMed

Vahadane, Abhishek; Peng, Tingying; Sethi, Amit; Albarqouni, Shadi; Wang, Lichao; Baust, Maximilian; Steiger, Katja; Schlitter, Anna Melissa; Esposito, Irene; Navab, Nassir

2016-08-01

Staining and scanning of tissue samples for microscopic examination is fraught with undesirable color variations arising from differences in raw materials and manufacturing techniques of stain vendors, staining protocols of labs, and color responses of digital scanners. When comparing tissue samples, color normalization and stain separation of the tissue images can be helpful for both pathologists and software. Techniques that are used for natural images fail to utilize structural properties of stained tissue samples and produce undesirable color distortions. The stain concentration cannot be negative. Tissue samples are stained with only a few stains and most tissue regions are characterized by at most one effective stain. We model these physical phenomena that define the tissue structure by first decomposing images in an unsupervised manner into stain density maps that are sparse and non-negative. For a given image, we combine its stain density maps with stain color basis of a pathologist-preferred target image, thus altering only its color while preserving its structure described by the maps. Stain density correlation with ground truth and preference by pathologists were higher for images normalized using our method when compared to other alternatives. We also propose a computationally faster extension of this technique for large whole-slide images that selects an appropriate patch sample instead of using the entire image to compute the stain color basis.

Proteomic Profiling of Paraffin-Embedded Samples Identifies Metaplasia-Specific and Early-Stage Gastric Cancer Biomarkers

PubMed Central

Sousa, Josane F.; Ham, Amy-Joan L.; Whitwell, Corbin; Nam, Ki Taek; Lee, Hyuk-Joon; Yang, Han-Kwang; Kim, Woo Ho; Zhang, Bing; Li, Ming; LaFleur, Bonnie; Liebler, Daniel C.; Goldenring, James R.

2013-01-01

Early diagnosis and curative resection are the predominant factors associated with increased survival in patients with gastric cancer. However, most gastric cancer cases are still diagnosed at later stages. Since most pathologic specimens are archived as FFPE samples, the ability to use them to generate expression profiles can greatly improve cancer biomarker discovery. We sought to uncover new biomarkers for stomach preneoplastic metaplasias and neoplastic lesions by generating proteome profiles using FFPE samples. We combined peptide isoelectric focusing and liquid chromatography–tandem mass spectrometry analysis to generate proteomic profiles from FFPE samples of intestinal-type gastric cancer, metaplasia, and normal mucosa. The expression patterns of selected proteins were analyzed by immunostaining first in single tissue sections from normal stomach, metaplasia, and gastric cancer and later in larger tissue array cohorts. We detected 60 proteins up-regulated and 87 proteins down-regulated during the progression from normal mucosa to metaplasia to gastric cancer. Two of the up-regulated proteins, LTF and DMBT1, were validated as specific markers for spasmolytic polypeptide–expressing metaplasia and intestinal metaplasia, respectively. In cancers, significantly lower levels of DMBT1 or LTF correlated with more advanced disease and worse prognosis. Thus, proteomic profiling using FFPE samples has led to the identification of two novel markers for stomach metaplasias and gastric cancer prognosis. PMID:22944598

Multivariate classification of infrared spectra of cell and tissue samples

DOEpatents

Haaland, David M.; Jones, Howland D. T.; Thomas, Edward V.

1997-01-01

Multivariate classification techniques are applied to spectra from cell and tissue samples irradiated with infrared radiation to determine if the samples are normal or abnormal (cancerous). Mid and near infrared radiation can be used for in vivo and in vitro classifications using at least different wavelengths.

Robust Bayesian Factor Analysis

ERIC Educational Resources Information Center

Hayashi, Kentaro; Yuan, Ke-Hai

2003-01-01

Bayesian factor analysis (BFA) assumes the normal distribution of the current sample conditional on the parameters. Practical data in social and behavioral sciences typically have significant skewness and kurtosis. If the normality assumption is not attainable, the posterior analysis will be inaccurate, although the BFA depends less on the current…

Coccidioides complement fixation

MedlinePlus

... antibodies are detected in the blood sample. Normal value ranges may vary slightly among different laboratories. Some labs use different measurements or test different samples. Talk to your health care provider about the meaning of your specific test results.

Is Middle-Upper Arm Circumference "normally" distributed? Secondary data analysis of 852 nutrition surveys.

PubMed

Frison, Severine; Checchi, Francesco; Kerac, Marko; Nicholas, Jennifer

2016-01-01

Wasting is a major public health issue throughout the developing world. Out of the 6.9 million estimated deaths among children under five annually, over 800,000 deaths (11.6 %) are attributed to wasting. Wasting is quantified as low Weight-For-Height (WFH) and/or low Mid-Upper Arm Circumference (MUAC) (since 2005). Many statistical procedures are based on the assumption that the data used are normally distributed. Analyses have been conducted on the distribution of WFH but there are no equivalent studies on the distribution of MUAC. This secondary data analysis assesses the normality of the MUAC distributions of 852 nutrition cross-sectional survey datasets of children from 6 to 59 months old and examines different approaches to normalise "non-normal" distributions. The distribution of MUAC showed no departure from a normal distribution in 319 (37.7 %) distributions using the Shapiro-Wilk test. Out of the 533 surveys showing departure from a normal distribution, 183 (34.3 %) were skewed (D'Agostino test) and 196 (36.8 %) had a kurtosis different to the one observed in the normal distribution (Anscombe-Glynn test). Testing for normality can be sensitive to data quality, design effect and sample size. Out of the 533 surveys showing departure from a normal distribution, 294 (55.2 %) showed high digit preference, 164 (30.8 %) had a large design effect, and 204 (38.3 %) a large sample size. Spline and LOESS smoothing techniques were explored and both techniques work well. After Spline smoothing, 56.7 % of the MUAC distributions showing departure from normality were "normalised" and 59.7 % after LOESS. Box-Cox power transformation had similar results on distributions showing departure from normality with 57 % of distributions approximating "normal" after transformation. Applying Box-Cox transformation after Spline or Loess smoothing techniques increased that proportion to 82.4 and 82.7 % respectively. This suggests that statistical approaches relying on the normal distribution assumption can be successfully applied to MUAC. In light of this promising finding, further research is ongoing to evaluate the performance of a normal distribution based approach to estimating the prevalence of wasting using MUAC.

Nitric oxide synthase 2 (NOS2) expression in histologically normal margins of oral squamous cell carcinoma.

PubMed

Morelatto, Rosana; Itoiz, María-Elina; Guiñazú, Natalia; Piccini, Daniel; Gea, Susana; López-de Blanc, Silvia

2014-05-01

The activity of Nitric Oxide Synthase 2 (NOS2) was found in oral squamous cell carcinomas (OSCC) but not in normal mucosa. Molecular changes associated to early carcinogenesis have been found in mucosa near carcinomas, which is considered a model to study field cancerization. The aim of the present study is to analyze NOS2 expression at the histologically normal margins of OSCC. Eleven biopsy specimens of OSCC containing histologically normal margins (HNM) were analyzed. Ten biopsies of normal oral mucosa were used as controls. The activity of NOS2 was determined by immunohistochemistry. Salivary nitrate and nitrite as well as tobacco and alcohol consumption were also analyzed. The Chi-squared test was applied. Six out of the eleven HNM from carcinoma samples showed positive NOS2 activity whereas all the control group samples yielded negative (p=0.005). No statistically significant association between enzyme expression and tobacco and/or alcohol consumption and salivary nitrate and nitrite was found. NOS2 expression would be an additional evidence of alterations that may occur in a state of field cancerization before the appearance of potentially malignant morphological changes.

Shoulder strength value differences between genders and age groups.

PubMed

Balcells-Diaz, Eudald; Daunis-I-Estadella, Pepus

2018-03-01

The strength of a normal shoulder differs according to gender and decreases with age. Therefore, the Constant score, which is a shoulder function measurement tool that allocates 25% of the final score to strength, differs from the absolute values but likely reflects a normal shoulder. To compare group results, a normalized Constant score is needed, and the first step to achieving normalization involves statistically establishing the gender differences and age-related decline. In this investigation, we sought to verify the gender difference and age-related decline in strength. We obtained a randomized representative sample of the general population in a small to medium-sized Spanish city. We then invited this population to participate in our study, and we measured their shoulder strength. We performed a statistical analysis with a power of 80% and a P value < .05. We observed a statistically significant difference between the genders and a statistically significant decline with age. To the best of our knowledge, this is the first investigation to study a representative sample of the general population from which conclusions can be drawn regarding Constant score normalization. Copyright © 2017 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Trace elemental analysis in cancer-afflicted tissues of penis and testis by PIXE technique

NASA Astrophysics Data System (ADS)

Naga Raju, G. J.; John Charles, M.; Bhuloka Reddy, S.; Sarita, P.; Seetharami Reddy, B.; Rama Lakshmi, P. V. B.; Vijayan, V.

2005-04-01

PIXE technique was employed to estimate the trace elemental concentrations in the biological samples of cancerous penis and testis. A 3 MeV proton beam was employed to excite the samples. From the present results it can be seen that the concentrations of Cl, Fe and Co are lower in the cancerous tissue of the penis when compared with those in normal tissue while the concentrations of Cu, Zn and As are relatively higher. The concentrations of K, Ca, Ti, Cr, Mn, Br, Sr and Pb are in agreement within standard deviations in both cancerous and normal tissues. In the cancerous tissue of testis, the concentrations of K, Cr and Cu are higher while the concentrations of Fe, Co and Zn are lower when compared to those in normal tissue of testis. The concentrations of Cl, Ca, Ti and Mn are in agreement in both cancerous and normal tissues of testis. The higher levels of Cu lead to the development of tumor. Our results also support the underlying hypothesis of an anticopper, antiangiogenic approach to cancer therapy. The Cu/Zn ratios of both penis and testis were higher in cancer tissues compared to that of normal.

Contact resistance and normal zone formation in coated yttrium barium copper oxide superconductors

NASA Astrophysics Data System (ADS)

Duckworth, Robert Calvin

2001-11-01

This project presents a systematic study of contact resistance and normal zone formation in silver coated YBa2CU3Ox (YBCO) superconductors. A unique opportunity exists in YBCO superconductors because of the ability to use oxygen annealing to influence the interfacial properties and the planar geometry of this type of superconductor to characterize the contact resistance between the silver and YBCO. The interface represents a region that current must cross when normal zones form in the superconductor and a high contact resistance could impede the current transfer or produce excess Joule heating that would result in premature quench or damage of the sample. While it has been shown in single-crystalline YBCO processing methods that the contact resistance of the silver/YBCO interface can be influenced by post-process oxygen annealing, this has not previously been confirmed for high-density films, nor for samples with complete layers of silver deposited on top of the YBCO. Both the influence of contact resistance and the knowledge of normal zone formation on conductor sized samples is essential for their successful implementation into superconducting applications such as transmission lines and magnets. While normal zone formation and propagation have been studied in other high temperature superconductors, the amount of information with respect to YBCO has been very limited. This study establishes that the processing method for the YBCO does not affect the contact resistance and mirrors the dependence of contact resistance on oxygen annealing temperature observed in earlier work. It has also been experimentally confirmed that the current transfer length provides an effective representation of the contact resistance when compared to more direct measurements using the traditional four-wire method. Finally for samples with low contact resistance, a combination of experiments and modeling demonstrate an accurate understanding of the key role of silver thickness and substrate thickness on the stability of silver-coated YBCO Rolling Assisted Bi-Axially Textured Substrates conductors. Both the experimental measurements and the one-dimensional model show that increasing the silver thickness results in an increased thermal runaway current; that is, the current above which normal zones continue to grow due to insufficient local cooling.

Anomalous waveforms observed in laboratory-formed gas hydrate-bearing and ice-bearing sediments

PubMed Central

Lee, Myung W.; Waite, William F.

2011-01-01

Acoustic transmission measurements of compressional, P, and shear, S, wave velocities rely on correctly identifying the P- and S-body wave arrivals in the measured waveform. In cylindrical samples for which the sample is much longer than the acoustic wavelength, these body waves can be obscured by high-amplitude waveform features arriving just after the relatively small-amplitude P-body wave. In this study, a normal mode approach is used to analyze this type of waveform, observed in sediment containing gas hydrate or ice. This analysis extends an existing normal-mode waveform propagation theory by including the effects of the confining medium surrounding the sample, and provides guidelines for estimating S-wave velocities from waveforms containing multiple large-amplitude arrivals. PMID:21476628

Matuyama/Brunhes Polarity Transition in Owens Lake, CA, Sediment

NASA Astrophysics Data System (ADS)

Liddicoat, Joseph; Kravchinsky, Vadim

2014-05-01

The complexity of the Matuyama/Brunhes (M/B) polarity transition is becoming better understood from investigations of volcanic rocks (Coe et al., 2004), loess (Jin et al., 2012; Evans et al., 2011; Kravchinsky, 2013), and marine (Clement and Opdyke, 1982; Hartl and Tauxe, 1996; Macri et al., 2010) and lacustrine (Valet et al., 1988; Sagnotti et al., 2013) sediments. The transition appears to include a brief interval of normal polarity prior to the entry into the Brunhes Normal Chron (Coe et al., 2004; Jin et al., 2012; Evans et al., 2011), and the transition has Virtual Geomagnetic Poles rapidly moving from the Southern Hemisphere to the Northern Hemisphere (Coe et al., 2004; Jin et al., 2012; Evans et al., 2011; Sagnotti et al., 2013). The M/B polarity transition is recorded in exposed Pleistocene lake sediments near Bishop, CA, where the brief interval of normal polarity noted above is present and the change from full reverse to full normal polarity occurs rapidly. The brief interval of normal polarity is recorded at two sites separated laterally by about 150 m and is in single hand samples measured at vertical spacing of 2.0-2.5 cm using six samples per measured level and alternating field demagnetization at 20 mT (Liddicoat, 1993, Table 1 and Fig. 8). The siltstone is unweathered glacial flour from the Sierra Nevada that borders the western side of Owens Valley where the sediments were deposited in Owens Lake. In the siltstone, the majority of the samples have a percentage of about 60 percent where the grain diameter is less than 63 micrometres, and in those samples there is about a five percent fraction when the diameter is two micrometres or less. The Total Inorganic Carbon in most samples is about 0.25 percent (Bergeron, 2013), and magnetite is the dominant carrier of the magnetization (Liddicoat, 1993). The palaeomagnetic directions recording the terminus of the full M/B transition, which occurs before the field intensity is completely recovered, spans no more than 35 cm of siltstone at each of two localities about a km apart. We will present the results of a continuing palaeomagnetic investigation of the M/B transition at this locality.

Biostatistics Series Module 3: Comparing Groups: Numerical Variables.

PubMed

Hazra, Avijit; Gogtay, Nithya

2016-01-01

Numerical data that are normally distributed can be analyzed with parametric tests, that is, tests which are based on the parameters that define a normal distribution curve. If the distribution is uncertain, the data can be plotted as a normal probability plot and visually inspected, or tested for normality using one of a number of goodness of fit tests, such as the Kolmogorov-Smirnov test. The widely used Student's t-test has three variants. The one-sample t-test is used to assess if a sample mean (as an estimate of the population mean) differs significantly from a given population mean. The means of two independent samples may be compared for a statistically significant difference by the unpaired or independent samples t-test. If the data sets are related in some way, their means may be compared by the paired or dependent samples t-test. The t-test should not be used to compare the means of more than two groups. Although it is possible to compare groups in pairs, when there are more than two groups, this will increase the probability of a Type I error. The one-way analysis of variance (ANOVA) is employed to compare the means of three or more independent data sets that are normally distributed. Multiple measurements from the same set of subjects cannot be treated as separate, unrelated data sets. Comparison of means in such a situation requires repeated measures ANOVA. It is to be noted that while a multiple group comparison test such as ANOVA can point to a significant difference, it does not identify exactly between which two groups the difference lies. To do this, multiple group comparison needs to be followed up by an appropriate post hoc test. An example is the Tukey's honestly significant difference test following ANOVA. If the assumptions for parametric tests are not met, there are nonparametric alternatives for comparing data sets. These include Mann-Whitney U-test as the nonparametric counterpart of the unpaired Student's t-test, Wilcoxon signed-rank test as the counterpart of the paired Student's t-test, Kruskal-Wallis test as the nonparametric equivalent of ANOVA and the Friedman's test as the counterpart of repeated measures ANOVA.

On the efficacy of procedures to normalize Ex-Gaussian distributions

PubMed Central

Marmolejo-Ramos, Fernando; Cousineau, Denis; Benites, Luis; Maehara, Rocío

2015-01-01

Reaction time (RT) is one of the most common types of measure used in experimental psychology. Its distribution is not normal (Gaussian) but resembles a convolution of normal and exponential distributions (Ex-Gaussian). One of the major assumptions in parametric tests (such as ANOVAs) is that variables are normally distributed. Hence, it is acknowledged by many that the normality assumption is not met. This paper presents different procedures to normalize data sampled from an Ex-Gaussian distribution in such a way that they are suitable for parametric tests based on the normality assumption. Using simulation studies, various outlier elimination and transformation procedures were tested against the level of normality they provide. The results suggest that the transformation methods are better than elimination methods in normalizing positively skewed data and the more skewed the distribution then the transformation methods are more effective in normalizing such data. Specifically, transformation with parameter lambda -1 leads to the best results. PMID:25709588

Empirical evaluation of data normalization methods for molecular classification.

PubMed

Huang, Huei-Chung; Qin, Li-Xuan

2018-01-01

Data artifacts due to variations in experimental handling are ubiquitous in microarray studies, and they can lead to biased and irreproducible findings. A popular approach to correct for such artifacts is through post hoc data adjustment such as data normalization. Statistical methods for data normalization have been developed and evaluated primarily for the discovery of individual molecular biomarkers. Their performance has rarely been studied for the development of multi-marker molecular classifiers-an increasingly important application of microarrays in the era of personalized medicine. In this study, we set out to evaluate the performance of three commonly used methods for data normalization in the context of molecular classification, using extensive simulations based on re-sampling from a unique pair of microRNA microarray datasets for the same set of samples. The data and code for our simulations are freely available as R packages at GitHub. In the presence of confounding handling effects, all three normalization methods tended to improve the accuracy of the classifier when evaluated in an independent test data. The level of improvement and the relative performance among the normalization methods depended on the relative level of molecular signal, the distributional pattern of handling effects (e.g., location shift vs scale change), and the statistical method used for building the classifier. In addition, cross-validation was associated with biased estimation of classification accuracy in the over-optimistic direction for all three normalization methods. Normalization may improve the accuracy of molecular classification for data with confounding handling effects; however, it cannot circumvent the over-optimistic findings associated with cross-validation for assessing classification accuracy.

Copy Number Variations of TBK1 in Australian Patients With Primary Open-Angle Glaucoma

PubMed Central

AWADALLA, MONA S.; FINGERT, JOHN H.; ROOS, BENJAMIN E.; CHEN, SIMON; HOLMES, RICHARD; GRAHAM, STUART L.; CHEHADE, MARK; GALANOPOLOUS, ANNA; RIDGE, BRONWYN; SOUZEAU, EMMANUELLE; ZHOU, TIGER; SIGGS, OWEN M.; HEWITT, ALEX W.; MACKEY, DAVID A.; BURDON, KATHRYN P.; CRAIG, JAMIE E.

2015-01-01

PURPOSE To investigate the presence of TBK1 copy number variations in a large, well-characterized Australian cohort of patients with glaucoma comprising both normal-tension glaucoma and high-tension glaucoma cases. DESIGN A retrospective cohort study. METHODS DNA samples from patients with normal-tension glaucoma and high-tension glaucoma and unaffected controls were screened for TBK1 copy number variations using real-time quantitative polymerase chain reaction. Samples with additional copies of the TBK1 gene were further tested using custom comparative genomic hybridization arrays. RESULTS Four out of 334 normal-tension glaucoma cases (1.2%) were found to carry TBK1 copy number variations using quantitative polymerase chain reaction. One extra dose of the TBK1 gene (duplication) was detected in 3 normal-tension glaucoma patients, while 2 extra doses of the gene (triplication) were detected in a fourth normal-tension glaucoma patient. The results were further confirmed by custom comparative genomic hybridization arrays. Further, the TBK1 copy number variation segregated with normal-tension glaucoma in the family members of the probands, showing an autosomal dominant pattern of inheritance. No TBK1 copy number variations were detected in 1045 Australian patients with high-tension glaucoma or in 254 unaffected controls. CONCLUSION We report the presence of TBK1 copy number variations in our Australian normal-tension glaucoma cohort, including the first example of more than 1 extra copy of this gene in glaucoma patients (gene triplication). These results confirm TBK1 to be an important cause of normal-tension glaucoma, but do not suggest common involvement in high-tension glaucoma. PMID:25284765

Quantifying Normal Craniofacial Form and Baseline Craniofacial Asymmetry in the Pediatric Population.

PubMed

Cho, Min-Jeong; Hallac, Rami R; Ramesh, Jananie; Seaward, James R; Hermann, Nuno V; Darvann, Tron A; Lipira, Angelo; Kane, Alex A

2018-03-01

Restoring craniofacial symmetry is an important objective in the treatment of many craniofacial conditions. Normal form has been measured using anthropometry, cephalometry, and photography, yet all of these modalities have drawbacks. In this study, the authors define normal pediatric craniofacial form and craniofacial asymmetry using stereophotogrammetric images, which capture a densely sampled set of points on the form. After institutional review board approval, normal, healthy children (n = 533) with no known craniofacial abnormalities were recruited at well-child visits to undergo full head stereophotogrammetric imaging. The children's ages ranged from 0 to 18 years. A symmetric three-dimensional template was registered and scaled to each individual scan using 25 manually placed landmarks. The template was deformed to each subject's three-dimensional scan using a thin-plate spline algorithm and closest point matching. Age-based normal facial models were derived. Mean facial asymmetry and statistical characteristics of the population were calculated. The mean head asymmetry across all pediatric subjects was 1.5 ± 0.5 mm (range, 0.46 to 4.78 mm), and the mean facial asymmetry was 1.2 ± 0.6 mm (range, 0.4 to 5.4 mm). There were no significant differences in the mean head or facial asymmetry with age, sex, or race. Understanding the "normal" form and baseline distribution of asymmetry is an important anthropomorphic foundation. The authors present a method to quantify normal craniofacial form and baseline asymmetry in a large pediatric sample. The authors found that the normal pediatric craniofacial form is asymmetric, and does not change in magnitude with age, sex, or race.

Individual A-Scan Signal Normalization Between Two Spectral Domain Optical Coherence Tomography Devices

PubMed Central

Chen, Chieh-Li; Ishikawa, Hiroshi; Wollstein, Gadi; Ling, Yun; Bilonick, Richard A.; Kagemann, Larry; Sigal, Ian A.; Schuman, Joel S.

2013-01-01

Purpose. We developed a method to normalize optical coherence tomography (OCT) signal profiles from two spectral-domain (SD) OCT devices so that the comparability between devices increases. Methods. We scanned 21 eyes from 14 healthy and 7 glaucoma subjects with two SD-OCT devices on the same day, with equivalent cube scan patterns centered on the fovea (Cirrus HD-OCT and RTVue). Foveola positions were selected manually and used as the center for registration of the corresponding images. A-scan signals were sampled 1.8 mm from the foveola in the temporal, superior, nasal, and inferior quadrants. After oversampling and rescaling RTVue data along the Z-axis to match the corresponding Cirrus data format, speckle noise reduction and amplitude normalization were applied. For comparison between normalized A-scan profiles, mean absolute difference in amplitude in percentage was measured at each sampling point. As a reference, the mean absolute difference between two Cirrus scans on the same eye also was measured. Results. The mean residual of the A-scan profile amplitude was reduced significantly after signal normalization (12.7% vs. 6.2%, P < 0.0001, paired t-test). All four quadrants also showed statistically significant reduction (all P < 0.0001). Mean absolute difference after normalization was smaller than the one between two Cirrus scans. No performance difference was detected between health and glaucomatous eyes. Conclusions. The reported signal normalization method successfully reduced the A-scan profile differences between two SD-OCT devices. This signal normalization processing may improve the direct comparability of OCT image analysis and measurement on various devices. PMID:23611992

Effect of the callipyge phenotype and cooking method on tenderness of several major lamb muscles.

PubMed

Shackelford, S D; Wheeler, T L; Koohmaraie, M

1997-08-01

We conducted three experiments to determine the effects of the callipyge phenotype on the tenderness of several major lamb muscles and to determine the effect of method of cookery on the tenderness of callipyge lamb at 7 d postmortem. In Exp. 1, chops from normal (n = 23) and callipyge (n = 16) carcasses were open-hearth-broiled. Warner-Bratzler shear force values of longissimus, gluteus medius, semimembranosus, biceps femoris, semitendinosus, adductor, and quadriceps femoris were 123, 44, 28, 26, 19, 16, and 13% greater, respectively, for callipyge (P < .05). In Exp. 2, muscles from normal (n = 18) and callipyge (n = 18) carcasses were oven-roasted. Shear force of triceps brachii was 11% greater for callipyge (P < .001); however, phenotype did not affect shear force of supraspinatus (P = .87) or psoas major (P = .64). In Exp. 3, a trained sensory panel evaluated leg roasts and open-hearth-broiled leg chops from normal (n = 60) and callipyge lamb carcasses (n = 60). Callipyge chops were less tender than normal chops (P < .05). Regardless of callipyge phenotype, muscles were more (P < .05) tender when roasted; however, the effect of method of cookery on tenderness scores was greater for callipyge muscles than for normal muscles. Callipyge roasts and normal roasts had similar tenderness (P = .58), and callipyge roasts were more tender than normal chops (P < .05). Regardless of cooking method, callipyge samples were less juicy than normal samples (P < .05). These data demonstrate that the callipyge phenotype will likely reduce consumer satisfaction due to reduced tenderness and juiciness; however, reduced tenderness in callipyge leg muscles could be prevented by ovenroasting.

Language Sampling for Preschoolers With Severe Speech Impairments

PubMed Central

Ragsdale, Jamie; Bustos, Aimee

2016-01-01

Purpose The purposes of this investigation were to determine if measures such as mean length of utterance (MLU) and percentage of comprehensible words can be derived reliably from language samples of children with severe speech impairments and if such measures correlate with tools that measure constructs assumed to be related. Method Language samples of 15 preschoolers with severe speech impairments (but receptive language within normal limits) were transcribed independently by 2 transcribers. Nonparametric statistics were used to determine which measures, if any, could be transcribed reliably and to determine if correlations existed between language sample measures and standardized measures of speech, language, and cognition. Results Reliable measures were extracted from the majority of the language samples, including MLU in words, mean number of syllables per utterance, and percentage of comprehensible words. Language sample comprehensibility measures were correlated with a single word comprehensibility task. Also, language sample MLUs and mean length of the participants' 3 longest sentences from the MacArthur–Bates Communicative Development Inventory (Fenson et al., 2006) were correlated. Conclusion Language sampling, given certain modifications, may be used for some 3-to 5-year-old children with normal receptive language who have severe speech impairments to provide reliable expressive language and comprehensibility information. PMID:27552110

Assessment the impact of samplers change on the uncertainty related to geothermalwater sampling

NASA Astrophysics Data System (ADS)

Wątor, Katarzyna; Mika, Anna; Sekuła, Klaudia; Kmiecik, Ewa

2018-02-01

The aim of this study is to assess the impact of samplers change on the uncertainty associated with the process of the geothermal water sampling. The study was carried out on geothermal water exploited in Podhale region, southern Poland (Małopolska province). To estimate the uncertainty associated with sampling the results of determinations of metasilicic acid (H2SiO3) in normal and duplicate samples collected in two series were used (in each series the samples were collected by qualified sampler). Chemical analyses were performed using ICP-OES method in the certified Hydrogeochemical Laboratory of the Hydrogeology and Engineering Geology Department at the AGH University of Science and Technology in Krakow (Certificate of Polish Centre for Accreditation No. AB 1050). To evaluate the uncertainty arising from sampling the empirical approach was implemented, based on double analysis of normal and duplicate samples taken from the same well in the series of testing. The analyses of the results were done using ROBAN software based on technique of robust statistics analysis of variance (rANOVA). Conducted research proved that in the case of qualified and experienced samplers uncertainty connected with the sampling can be reduced what results in small measurement uncertainty.

Language Sampling for Preschoolers With Severe Speech Impairments.

PubMed

Binger, Cathy; Ragsdale, Jamie; Bustos, Aimee

2016-11-01

The purposes of this investigation were to determine if measures such as mean length of utterance (MLU) and percentage of comprehensible words can be derived reliably from language samples of children with severe speech impairments and if such measures correlate with tools that measure constructs assumed to be related. Language samples of 15 preschoolers with severe speech impairments (but receptive language within normal limits) were transcribed independently by 2 transcribers. Nonparametric statistics were used to determine which measures, if any, could be transcribed reliably and to determine if correlations existed between language sample measures and standardized measures of speech, language, and cognition. Reliable measures were extracted from the majority of the language samples, including MLU in words, mean number of syllables per utterance, and percentage of comprehensible words. Language sample comprehensibility measures were correlated with a single word comprehensibility task. Also, language sample MLUs and mean length of the participants' 3 longest sentences from the MacArthur-Bates Communicative Development Inventory (Fenson et al., 2006) were correlated. Language sampling, given certain modifications, may be used for some 3-to 5-year-old children with normal receptive language who have severe speech impairments to provide reliable expressive language and comprehensibility information.

Irradiation Does Not Increase the Penetration Depth of Doxorubicin in Normal Tissue After Pressurized Intra-peritoneal Aerosol Chemotherapy (PIPAC) in an Ex Vivo Model.

PubMed

Khosrawipour, Veria; Bellendorf, Alexander; Khosrawipour, Carolina; Hedayat-Pour, Yousef; Diaz-Carballo, David; Förster, Eckart; Mücke, Ralph; Kabakci, Burak; Adamietz, Irenäus Anton; Fakhrian, Khashayar

To compare the impact of single fractional with bi-fractional irradiation on the depth of doxorubicin penetration into the normal tissue after pressurized intra-peritoneal aerosol chemotherapy (PIPAC) in our ex vivo model. Fresh post mortem swine peritoneum was cut into 12 proportional sections. Two control samples were treated with PIPAC only (no irradiation), one sample on day 1, the other on day 2. Five samples were irradiated with 1, 2, 4, 7 or 14 Gy followed by PIPAC. Four samples were treated on day one with 0.5, 1, 2, 3.5 or 7 Gy and with the same radiation dose 24 h later followed by PIPAC. Doxorubicin was aerosolized in an ex vivo PIPAC model at 12 mmHg/36°C. In-tissue doxorubicin penetration was measured using fluorescence microscopy on frozen thin sections. Doxorubicin penetration (DP) after PIPAC for the control samples was 407 μm and 373 μm, respectively. DP for samples with single fraction irradiation was 396 μm after 1 Gy, 384 μm after 2 Gy, 327 μm after 4 Gy, 280 μm after 7 Gy and 243 μm after 14 Gy. DP for samples with 2 fractions of irradiation was 376 μm after 0.5+0.5 Gy, 363 μm after 1+1 Gy, 372 μm after 2+2 Gy, 341 μm after 3.5+3.5 and 301 μm after 7+7 Gy irradiation. Fractionating of the irradiation did not significantly change DP into normal tissue. Irradiation does not increase the penetration depth of doxorubicin into the normal tissue but might have a limiting impact on penetration and distribution of doxorubicin. Further studies are warranted to investigate the impact of addition of irradiation to PIPAC of tumor cells and to find out if irradiation can be used safely as chemopotenting agent for patients with peritoneal metastases treated with PIPAC. Copyright © 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

MET amplification, expression, and exon 14 mutations in colorectal adenocarcinoma.

PubMed

Zhang, Meng; Li, Guichao; Sun, Xiangjie; Ni, Shujuan; Tan, Cong; Xu, Midie; Huang, Dan; Ren, Fei; Li, Dawei; Wei, Ping; Du, Xiang

2018-04-08

MET amplification, expression, and splice mutations at exon 14 result in dysregulation of the MET signaling pathway. The aim of this study was to identify the relationship between MET amplification, protein or mRNA expression, and mutations in colorectal cancer (CRC). MET immunohistochemistry (IHC) was used for MET protein expression analysis and fluorescence in situ hybridization (FISH) was used for MET amplification detection. Both analyses were performed in tissue microarrays (TMA) containing 294 of colorectal adenocarcinoma tissue samples and 131 samples of adjacent normal epithelial tissue. MET mRNA expression was examined by real-time quantitative polymerase chain reaction (qRT-PCR) in 72 fresh colorectal adenocarcinoma tissue samples and adjacent normal colon tissue. PCR sequencing was performed to screen for MET exon 14 splice mutations in 59 fresh CRC tissue samples. Our results showed that MET protein expression was higher in colorectal tumor tissue than in adjacent normal intestinal epithelium. Positive MET protein expression was associated with significantly poorer overall survival (OS) and disease-free survival (DFS). Multivariate analysis revealed that positive MET protein expression was an independent risk factor for DFS, but not for OS. MET mRNA expression was upregulated in tumor tissues compared with the adjacent normal tissues. The incidence of MET amplification was 4.4%. None of the patients was positive for MET mutation. Collectively, MET was overexpressed in colorectal adenocarcinoma, and its positive protein expression predicted a poorer outcome in CRC patients. Furthermore, according to our results, MET amplification and 14 exon mutation are extremely rare events in colorectal adenocarcinoma. Copyright © 2018. Published by Elsevier Inc.

Sialidase activity in aerobic vaginitis is equal to levels during bacterial vaginosis.

PubMed

Marconi, C; Donders, G G G; Bellen, G; Brown, D R; Parada, C M G L; Silva, M G

2013-04-01

To evaluate levels of proinflammatory cytokines and sialidase activity in aerobic vaginitis (AV) in relation to normal vaginal flora and bacterial vaginosis (BV). In this cross-sectional study, a total of 682 consecutive non-pregnant women attending the gynecology service were assessed and 408 women were included. Vaginal rinsing samples were collected from 223 women with microscopic finding of BV (n=98), aerobic vaginitis (n=25) and normal flora (n=100). Samples were tested for interleukin (IL)-1β, IL-6, IL-8, tumor necrosis factor (TNF)-α, and sialidase activity. Compared to women with normal flora, vaginal levels of IL-1β were highly increased in both BV and AV (p<0.0001). Significantly higher vaginal IL-6 was detected in AV (p<0.0001) but not in BV, in relation to normal flora. Women with AV also presented increased IL-8 levels (p<0.001), while those with BV presented levels similar to normal flora. Sialidase was increased in BV and AV compared with the normal group (p<0.0001) but no difference in sialidase activity was observed between BV and AV. A more intense inflammatory host response occurs for AV than for BV when compared with normal flora. Furthermore, the increased sialidase activity in AV and BV indicates that both abnormal vaginal flora types can be harmful to the maintenance of a healthy vaginal environment. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Sibling Conflict Resolution Skills: Assessment and Training

ERIC Educational Resources Information Center

Thomas, Brett W.; Roberts, Mark W.

2009-01-01

Sibling conflict can rise to the level of a clinical problem. In Phase 1 a lengthy behavioral role-play analog sampling child reactions to normal sibling conflicts was successfully shortened. In Phase 2 normal children who lacked sibling conflict resolution skills were randomly assigned to a Training or Measurement Only condition. Training…

A State-trait Analysis of Alpha Density and Personality Variables in a Normal Population

ERIC Educational Resources Information Center

Degood, Douglas E.; Valle, Ronald S.

1975-01-01

This paper examined the relationship of some selected trait measures of personality with resting samples of alpha density in a normal population and the implications of such data for a state-trait approach to alpha and the experiential states associated with alpha. (Author/RK)

Logistic Approximation to the Normal: The KL Rationale

ERIC Educational Resources Information Center

Savalei, Victoria

2006-01-01

A rationale is proposed for approximating the normal distribution with a logistic distribution using a scaling constant based on minimizing the Kullback-Leibler (KL) information, that is, the expected amount of information available in a sample to distinguish between two competing distributions using a likelihood ratio (LR) test, assuming one of…

A Comparison of Normal and Elliptical Estimation Methods in Structural Equation Models.

ERIC Educational Resources Information Center

Schumacker, Randall E.; Cheevatanarak, Suchittra

Monte Carlo simulation compared chi-square statistics, parameter estimates, and root mean square error of approximation values using normal and elliptical estimation methods. Three research conditions were imposed on the simulated data: sample size, population contamination percent, and kurtosis. A Bentler-Weeks structural model established the…

Rate of Visual Information Pick-Up in Learning Disabled and Normal Boys.

ERIC Educational Resources Information Center

Bryant, Susan K.; And Others

1983-01-01

A span-of-apprehension task and a backward masking technique were combined to allow measurement of the apprehension span of a sample of 34 learning disabled and normal boys about 8 to 13 years old at various time intervals following stimulus presentation. (Author/SW)

Normal and Reversed-Phase Thin Layer Chromatography of Green Leaf Extracts

ERIC Educational Resources Information Center

Sjursnes, Birte Johanne; Kvittingen, Lise; Schmid, Rudolf

2015-01-01

Introductory experiments of chromatography are often conducted by separating colored samples, such as inks, dyes, and plant extracts, using filter paper, chalk, or thin layer chromatography (TLC) plates with various solvent systems. Many simple experiments have been reported. The relationship between normal chromatography and reversed-phase…

The Best and the Rest: Revisiting the Norm of Normality of Individual Performance

ERIC Educational Resources Information Center

O'Boyle, Ernest, Jr.; Aguinis, Herman

2012-01-01

We revisit a long-held assumption in human resource management, organizational behavior, and industrial and organizational psychology that individual performance follows a Gaussian (normal) distribution. We conducted 5 studies involving 198 samples including 633,263 researchers, entertainers, politicians, and amateur and professional athletes.…

Analytical Fingerprint of Wolframite Ore Concentrates.

PubMed

Gäbler, Hans-Eike; Schink, Wilhelm; Goldmann, Simon; Bahr, Andreas; Gawronski, Timo

2017-07-01

Ongoing violent conflicts in Central Africa are fueled by illegal mining and trading of tantalum, tin, and tungsten ores. The credibility of document-based traceability systems can be improved by an analytical fingerprint applied as an independent method to confirm or doubt the documented origin of ore minerals. Wolframite (Fe,Mn)WO 4 is the most important ore mineral for tungsten and is subject to artisanal mining in Central Africa. Element concentrations of wolframite grains analyzed by laser ablation-inductively coupled plasma-mass spectrometry are used to establish the analytical fingerprint. The data from ore concentrate samples are multivariate, not normal or log-normal distributed. The samples cannot be regarded as representative aliquots of a population. Based on the Kolmogorov-Smirnov distance, a measure of similarity between a sample in question and reference samples from a database is determined. A decision criterion is deduced to recognize samples which do not originate from the declared mine site. © 2017 American Academy of Forensic Sciences.

A 57-year follow-up of occlusal changes, oral health, and attitudes toward teeth.

PubMed

Stenvik, Arild; Espeland, Lisen; Berg, Rolf E

2011-04-01

Very few studies have addressed long-term development and risks associated with untreated malocclusion. The purpose of this study was to examine changes in occlusion in a lifelong perspective and to compare oral health and attitudes toward teeth among persons with malocclusion with those having normal occlusion. In 1950 an epidemiologic survey of 2349 8-year-olds was conducted and included 4 intraoral photographs. Three selected samples with different malocclusions (deep bite, crossbite, or irregular teeth) and 1 sample with normal occlusion (a total of 183 subjects) were, 57 years later, invited for examination and an extensive interview about dental experiences and attitudes. Sixty-nine responded (38%) and constitute the subjects studied. Malocclusion remained the same or worsened except in subjects having deep bite in childhood, which in some improved and in others became worse. Crowding generally increased. Sixteen persons reported moderate or severe temporomandular joint (TMJ) problems, and of these 7 belonged to the group with crossbite in childhood. With few exceptions, the subjects in all samples had good oral hygiene, visited the dentist regularly, and had well-preserved dentitions. Mean number of missing teeth was significantly lower among those with normal occlusion compared with the malocclusion groups. Individuals with normal occlusion responded favorably to all questions related to attitudes and experiences about their teeth, while responses in the malocclusion groups varied. Persons with the particular malocclusions examined experienced more problems related to teeth later in life compared with those having normal occlusion in childhood. Copyright © 2011 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Stone former urine proteome demonstrates a cationic shift in protein distribution compared to normal.

PubMed

Kolbach-Mandel, Ann M; Mandel, Neil S; Hoffmann, Brian R; Kleinman, Jack G; Wesson, Jeffrey A

2017-08-01

Many urine proteins are found in calcium oxalate stones, yet decades of research have failed to define the role of urine proteins in stone formation. This urine proteomic study compares the relative amounts of abundant urine proteins between idiopathic calcium oxalate stone forming and non-stone forming (normal) cohorts to identify differences that might correlate with disease. Random mid-morning urine samples were collected following informed consent from 25 stone formers and 14 normal individuals. Proteins were isolated from urine using ultrafiltration. Urine proteomes for each sample were characterized using label-free spectral counting mass spectrometry, so that urine protein relative abundances could be compared between the two populations. A total of 407 unique proteins were identified with the 38 predominant proteins accounting for >82% of all sample spectral counts. The most highly abundant proteins were equivalent in stone formers and normals, though significant differences were observed in a few moderate abundance proteins (immunoglobulins, transferrin, and epidermal growth factor), accounting for 13 and 10% of the spectral counts, respectively. These proteins contributed to a cationic shift in protein distribution in stone formers compared to normals (22% vs. 18%, p = 0.04). Our data showing only small differences in moderate abundance proteins suggest that no single protein controls stone formation. Observed increases in immunoglobulins and transferrin suggest increased inflammatory activity in stone formers, but cannot distinguish cause from effect in stone formation. The observed cationic shift in protein distribution would diminish protein charge stabilization, which could lead to protein aggregation and increased risk for crystal aggregation.

Parametric modelling of cost data in medical studies.

PubMed

Nixon, R M; Thompson, S G

2004-04-30

The cost of medical resources used is often recorded for each patient in clinical studies in order to inform decision-making. Although cost data are generally skewed to the right, interest is in making inferences about the population mean cost. Common methods for non-normal data, such as data transformation, assuming asymptotic normality of the sample mean or non-parametric bootstrapping, are not ideal. This paper describes possible parametric models for analysing cost data. Four example data sets are considered, which have different sample sizes and degrees of skewness. Normal, gamma, log-normal, and log-logistic distributions are fitted, together with three-parameter versions of the latter three distributions. Maximum likelihood estimates of the population mean are found; confidence intervals are derived by a parametric BC(a) bootstrap and checked by MCMC methods. Differences between model fits and inferences are explored.Skewed parametric distributions fit cost data better than the normal distribution, and should in principle be preferred for estimating the population mean cost. However for some data sets, we find that models that fit badly can give similar inferences to those that fit well. Conversely, particularly when sample sizes are not large, different parametric models that fit the data equally well can lead to substantially different inferences. We conclude that inferences are sensitive to choice of statistical model, which itself can remain uncertain unless there is enough data to model the tail of the distribution accurately. Investigating the sensitivity of conclusions to choice of model should thus be an essential component of analysing cost data in practice. Copyright 2004 John Wiley & Sons, Ltd.

Hookah-Related Twitter Chatter: A Content Analysis

PubMed Central

Sowles, Shaina J.; Moreno, Megan; Zewdie, Kidist; Grucza, Richard A.; Bierut, Laura J.; Cavazos-Rehg, Patricia A.

2015-01-01

Introduction Hookah smoking is becoming increasingly popular among young adults and is often perceived as less harmful than cigarette use. Prior studies show that it is common for youth and young adults to network about substance use behaviors on social media. Social media messages about hookah could influence its use among young people. We explored normalization or discouragement of hookah smoking, and other common messages about hookah on Twitter. Methods From the full stream of tweets posted on Twitter from April 12, 2014, to May 10, 2014 (approximately 14.5 billion tweets), all tweets containing the terms hookah, hooka, shisha, or sheesha were collected (n = 358,523). The hookah tweets from Twitter users (tweeters) with high influence and followers were identified (n = 39,824) and a random sample of 5,000 tweets was taken (13% of tweets with high influence and followers). The sample of tweets was qualitatively coded for normalization (ie, makes hookah smoking seem common and normal or portrays positive experiences with smoking hookah) or discouragement of hookah smoking, and other common themes using crowdsourcing. Results Approximately 87% of the sample of tweets normalized hookah use, and 7% were against hookah or discouraged its use. Nearly half (46%) of tweets that normalized hookah indicated that the tweeter was smoking hookah or wanted to smoke hookah, and 19% were advertisements/promotions for hookah bars or products. Conclusion Educational campaigns about health harms from hookah use and policy changes regarding smoke-free air laws and tobacco advertising on the Internet may be useful to help offset the influence of pro-hookah messages seen on social media. PMID:26226068

No Evidence of Human Papilloma Virus Infection in Basal Cell Carcinoma

PubMed Central

Nahidi, Yalda; Meibodi, Naser Tayyebi; Meshkat, Zahra; Esmaili, Habibollah; Jahanfakhr, Samaneh

2015-01-01

Background: Basal cell carcinoma (BCC) is the most common skin cancer among whites, and several risk factors have been discussed in itsdevelopment and progress. Detection of human papilloma virus (HPV) deoxyribonucleic acid (DNA) BCCs in some studies suggests that the virus may play a role in the pathogenesis of this disease. Several molecular studies showed conflicting reports. Aims: The purpose of this study was to investigate the association between HPV and BCC using polymerase chain reaction (PCR). Materials and Methods: HPV DNA detection was done for 42 paraffin-embedded tissue specimens of BCC and 42 normal skin samples around the lesions by PCR using GP5+/GP6+ primers. Results: HPV DNA was not found in any of the 42 samples of BCC, and only one normal skin sample around the lesions was positive for HPV DNA by PCR. Conclusion: In this study, no statistically significant difference was seen between the presence of HPV DNA in BCC and normal skin around the lesion, and HPV is not likely to have an important role in pathogenesis of BCC. PMID:26288402

Dose estimation and dating of pottery from Turkey

NASA Astrophysics Data System (ADS)

Altay Atlıhan, M.; Şahiner, Eren; Soykal Alanyalı, Feriştah

2012-06-01

The luminescence method is a widely used technique for environmental dosimetry and dating archaeological, geological materials. In this study, equivalent dose (ED) and annual dose rate (AD) of an archaeological sample were measured. The age of the material was calculated by means of equivalent dose divided by the annual dose rate. The archaeological sample was taken from Antalya, Turkey. Samples were prepared by the fine grain technique and equivalent dose was found using multiple-aliquot-additive-dose (MAAD) and single aliquot regeneration (SAR) techniques. Also the short shine normalization-MAAD and long shine normalization-MAAD were applied and the results of the methods were compared with each other. The optimal preheat temperature was found to be 200 °C for 10 min. The annual doses of concentrations of the major radioactive isotopes were determined using a high-purity germanium detector and a low-level alpha counter. The age of the sample was found to be 510±40 years.

Signs of neurobehavioral dysfunction in a sample of learning disabled children: stability and concurrent validity.

PubMed

Morrison, D C; Hinshaw, S P; Carte, E T

1985-12-01

Of 270 learning disabled children with average intelligence and significant delays in reading comprehension a sample of 37 were evaluated for signs of neurobehavioral dysfunction. All such signs--primitive reflexes, equilibrium reactions, and postrotary nystagmus--were reliably assessed. A subsample of 19 children was compared with developmentally normal and mentally retarded samples for the occurrence of tonic neck reflexes and equilibrium reactions. The learning disabled children consistently showed deviancies like those of the retarded children; both of these groups differed from the normal children on most measures. These deviant responses persisted over a 9-mo. period for the learning disabled group. Compared with norms, the total learning disabled sample displayed hyponystagmus, and this depressed nystagmus persisted for 11 mo. Results are discussed in relation to the lack of correlation among the various signs of neurobehavioral dysfunction in the learning disabled children.

Changes in Abundance of Oral Microbiota Associated with Oral Cancer

PubMed Central

Schmidt, Brian L.; Kuczynski, Justin; Bhattacharya, Aditi; Huey, Bing; Corby, Patricia M.; Queiroz, Erica L. S.; Nightingale, Kira; Kerr, A. Ross; DeLacure, Mark D.; Veeramachaneni, Ratna; Olshen, Adam B.; Albertson, Donna G.

2014-01-01

Individual bacteria and shifts in the composition of the microbiome have been associated with human diseases including cancer. To investigate changes in the microbiome associated with oral cancers, we profiled cancers and anatomically matched contralateral normal tissue from the same patient by sequencing 16S rDNA hypervariable region amplicons. In cancer samples from both a discovery and a subsequent confirmation cohort, abundance of Firmicutes (especially Streptococcus) and Actinobacteria (especially Rothia) was significantly decreased relative to contralateral normal samples from the same patient. Significant decreases in abundance of these phyla were observed for pre-cancers, but not when comparing samples from contralateral sites (tongue and floor of mouth) from healthy individuals. Weighted UniFrac principal coordinates analysis based on 12 taxa separated most cancers from other samples with greatest separation of node positive cases. These studies begin to develop a framework for exploiting the oral microbiome for monitoring oral cancer development, progression and recurrence. PMID:24887397

Measurement uncertainty of ester number, acid number and patchouli alcohol of patchouli oil produced in Yogyakarta

NASA Astrophysics Data System (ADS)

Istiningrum, Reni Banowati; Saepuloh, Azis; Jannah, Wirdatul; Aji, Didit Waskito

2017-03-01

Yogyakarta is one of patchouli oil distillation center in Indonesia. The quality of patchouli oil greatly affect its market price. Therefore, testing quality of patchouli oil parameters is an important concern, one through determination of the measurement uncertainty. This study will determine the measurement uncertainty of ester number, acid number and content of patchouli alcohol through a bottom up approach. Source contributor to measurement uncertainty of ester number is a mass of the sample, a blank and sample titration volume, the molar mass of KOH, HCl normality, and replication. While the source contributor of the measurement uncertainty of acid number is the mass of the sample, the sample titration volume, the relative mass and normality of KOH, and repetition. Determination of patchouli alcohol by Gas Chromatography considers the sources of measurement uncertainty only from repeatability because reference materials are not available.

Fragile X protein in newborn dried blood spots.

PubMed

Adayev, Tatyana; LaFauci, Giuseppe; Dobkin, Carl; Caggana, Michele; Wiley, Veronica; Field, Michael; Wotton, Tiffany; Kascsak, Richard; Nolin, Sarah L; Glicksman, Anne; Hosmer, Nicole; Brown, W Ted

2014-10-28

The fragile X syndrome (FXS) results from mutation of the FMR1 gene that prevents expression of its gene product, FMRP. We previously characterized 215 dried blood spots (DBS) representing different FMR1 genotypes and ages with a Luminex-based immunoassay (qFMRP). We found variable FMRP levels in the normal samples and identified affected males by the drastic reduction of FMRP. Here, to establish the variability of expression of FMRP in a larger random population we quantified FMRP in 2,000 anonymous fresh newborn DBS. We also evaluated the effect of long term storage on qFMRP by retrospectively assaying 74 aged newborn DBS that had been stored for 7-84 months that included normal and full mutation individuals. These analyses were performed on 3 mm DBS disks. To identify the alleles associated with the lowest FMRP levels in the fresh DBS, we analyzed the DNA in the samples that were more than two standard deviations below the mean. Analysis of the fresh newborn DBS revealed a broad distribution of FMRP with a mean approximately 7-fold higher than that we previously reported for fresh DBS in normal adults and no samples whose FMRP level indicated FXS. DNA analysis of the lowest FMRP DBS showed that this was the low extreme of the normal range and included a female carrying a 165 CGG repeat premutation. In the retrospective study of aged newborn DBS, the FMRP mean of the normal samples was less than 30% of the mean of the fresh DBS. Despite the degraded signal from these aged DBS, qFMRP identified the FXS individuals. The assay showed that newborn DBS contain high levels of FMRP that will allow identification of males and potentially females, affected by FXS. The assay is also an effective screening tool for aged DBS stored for up to four years.

Aberrant Expression of the Cell Polarity Regulator aPKCλ/ι is Associated With Disease Progression in Cervical Intraepithelial Neoplasia (CIN): A Possible Marker for Predicting CIN Prognosis.

PubMed

Mizushima, Taichi; Asai-Sato, Mikiko; Akimoto, Kazunori; Nagashima, Yoji; Taguri, Masataka; Sasaki, Kazunori; Nakaya, Masa-aki; Asano, Ryoko; Tokinaga, Aya; Kiyono, Tohru; Hirahara, Fumiki; Ohno, Shigeo; Miyagi, Etsuko

2016-03-01

Atypical protein kinase C λ/ι (aPKCλ/ι) is a regulator of epithelial cellular polarity. It is also overexpressed in several cancers and functions in cell proliferation and invasion. Therefore, we hypothesized that aPKCλ/ι may be involved in development and progression of cervical intraepithelial neoplasia (CIN), the precancerous disease of cervical cancer induced by human papillomavirus. To do this, we investigated the relationship between aPKCλ/ι expression and CIN. aPKCλ/ι expression level and subcellular localization were assessed in 192 CIN biopsy samples and 13 normal epithelial samples using immunohistochemistry. aPKCλ/ι overexpression (normal epithelium, 7.7%; CIN1, 41.7%; CIN2/3, 76.4%) and aPKCλ/ι nuclear localization (normal epithelium, 0.0%; CIN1, 36.9%; CIN2/3, 78.7%) were higher in CIN samples than normal samples (P<0.05), suggesting that CIN grade is related to aPKCλ/ι overexpression and nuclear localization. Then, 140 CIN cases were retrospectively analyzed for 4-yr cumulative disease progression and regression rates using the Cox proportional hazards model. CIN1 cases with aPKCλ/ι overexpression or aPKCλ/ι nuclear localization had a higher progression rate than CIN1 cases with normal aPKCλ/ι expression levels or cytoplasmic localization (62.5% vs. 9.7% and 63.1% vs. 9.4%, respectively; P<0.001). Multivariate analysis indicated that human papillomavirus types 16 and 18, aPKCλ/ι overexpression (hazard ratio=4.26; 95% confidence interval, 1.50-12.1; P=0.007), and aPKCλ/ι nuclear localization (hazard ratio=3.59; 95% confidence interval, 1.24-10.4; P=0.019) were independent risk factors for CIN1 progression. In conclusion, aPKCλ/ι could be useful for the therapeutic management of patients with CIN, particularly those with non-human papillomavirus 16/18 types.

[The value of alpha-methylacyl-CoA racemase expression in the progression of colonic carcinoma].

PubMed

López-Valdivia, Cecilia M; González-Matea, Manuel; Mayordomo, Empar; Hervás, David; Ramos, David

Alpha-methylacyl-CoA racemase (AMACR) expression has been demonstrated in several normal tissues and in diverse types of carcinoma. Our aim was to analyze the immunohistochemical expression of AMACR in the sequence-progression of colonic cancer. We studied 237 cases, including samples of normal mucosa of the colon, adenomas with different degrees of dysplasia, colonic carcinomas, lymph nodes and liver metastases of colonic carcinomas. A scale of intensity and percentage of expression was used to analyze the AMACR immunohistochemical profile. The expression was nearly absent in samples of normal mucosa, increased in both adenomas and carcinomas, decreased in lymph node metastases but was significantly increased in liver metastases. Copyright © 2016 Sociedad Española de Anatomía Patológica. Publicado por Elsevier España, S.L.U. All rights reserved.

Perceived health status and cardiometabolic risk among a sample of youth in Mexico

PubMed Central

Flores, Yvonne N.; Shaibi, Gabriel Q.; Morales, Leo S.; Salmerón, Jorge; Skalicky, Anne M.; Edwards, Todd C.; Gallegos-Carrillo, Katia; Patrick, Donald L.

2015-01-01

Purpose To examine differences in self-reported perceived mental and physical health status (PHS), as well as known cardiometabolic risk factors in a sample of normal weight, overweight, and obese Mexican youths. Methods Cross-sectional analysis of 164 youths aged 11-18 years recruited in Cuernavaca, Mexico. Participants completed a self-administered questionnaire that included measures of generic and weight-specific quality of life (QoL), perceived health, physical function, depressive symptoms, and body shape satisfaction. Height, weight and waist circumference were measured and body mass index (BMI) was determined. Fasting blood samples from participants yielded levels of glucose, triglycerides, and cholesterol (total, HDL and LDL). Results Nearly 50% of participants were female, 21% had a normal BMI, 39% were overweight, and 40% were obese. Obese youths reported significantly lower measures of PHS and showed an increase in cardiometabolic risk, compared to normal weight youths. Physical functioning, generic and weight-specific QoL were inversely associated with BMI, waist circumference and glucose. Depressive symptoms were positively correlated with BMI, waist circumference, glucose levels and HDL cholesterol. No correlation was found between PHS and cardiometabolic risk measures after controlling for BMI. Conclusions In this sample of Mexican youths, obesity was associated with a significantly lower PHS and increased cardiometabolic risk. PMID:25648756

Thyroid peroxidase (TPO) expressed in thyroid and breast tissues shows similar antigenic properties.

PubMed

Godlewska, Marlena; Arczewska, Katarzyna D; Rudzińska, Magdalena; Łyczkowska, Anna; Krasuska, Wanda; Hanusek, Karolina; Ruf, Jean; Kiedrowski, Mirosław; Czarnocka, Barbara

2017-01-01

Thyroid peroxidase (TPO) is essential for physiological function of the thyroid gland. The high prevalence of thyroid peroxidase antibodies (TPOAbs) in patients with breast cancer and their protective role had previously been demonstrated, indicating a link between breast cancer and thyroid autoimmunity. Recently, TPO was shown to be present in breast cancer tissue samples but its antigenicity has not been analyzed. In this study, we investigated TPO expression levels in a series of fifty-six breast cancer samples paired with normal (peri-tumoral) tissue and its antigenic activity using a panel of well-characterized murine anti-human TPOAbs. We have shown that TPO transcripts were present in both normal and cancer tissue samples, although the amounts in the latter were reduced. Additionally, we observed that TPO levels are lower in more advanced cancers. TPO protein expression was confirmed in all tissue samples, both normal and cancerous. We also found that the antigenicity of the immunodominant regions (IDRs) in breast TPO resembles that of thyroid TPO, which is crucial for effective interactions with human TPOAbs. Expression of TPO in breast cancer together with its antigenic activity may have beneficial effects in TPOAb-positive breast cancer patients. However, further studies are needed to confirm the beneficial role of TPOAbs and to better understand the underlying mechanism.

High Rhodotorula sequences in skin transcriptome of patients with diffuse systemic sclerosis

PubMed Central

Arron, Sarah T.; Dimon, Michelle T.; Li, Zhenghui; Johnson, Michael E.; Wood, Tammara; Feeney, Luzviminda; Angeles, Jorge Gil; Lafyatis, Robert; Whitfield, Michael L.

2014-01-01

Previous studies have suggested a role for pathogens as a trigger of systemic sclerosis (SSc), though neither a pathogen nor a mechanism of pathogenesis is known. Here we show enrichment of Rhodotorula sequences in the skin of patients with early, diffuse SSc compared to normal controls. RNA-seq was performed on four SSc and four controls, to a depth of 200 million reads per patient. Data were analyzed to quantify the non-human sequence reads in each sample. We found little difference between bacterial microbiome and viral read counts, but found a significant difference between the read counts for a mycobiome component, R. glutinis. Normal samples contained almost no detected R. glutinis or other Rhodotorula sequence reads (mean score 0.021 for R. glutinis, 0.024 for all Rhodotorula). In contrast, SSc samples had a mean score of 5.039 for R. glutinis (5.232 for Rhodotorula). We were able to assemble the D1–D2 hypervariable region of the 28S rRNA of R. glutinis from each of the SSc samples. Taken together, these results suggest R. glutinis may be present in the skin of early SSc patients at higher levels than normal skin, raising the possibility that it may be triggering the inflammatory response found in SSc. PMID:24608988

High Rhodotorula sequences in skin transcriptome of patients with diffuse systemic sclerosis.

PubMed

Arron, Sarah T; Dimon, Michelle T; Li, Zhenghui; Johnson, Michael E; Wood, Tammara A; Feeney, Luzviminda; Angeles, Jorge G; Lafyatis, Robert; Whitfield, Michael L

2014-08-01

Previous studies have suggested a role for pathogens as a trigger of systemic sclerosis (SSc), although neither a pathogen nor a mechanism of pathogenesis is known. Here we show enrichment of Rhodotorula sequences in the skin of patients with early, diffuse SSc compared with that in normal controls. RNA-seq was performed on four SSc patients and four controls, to a depth of 200 million reads per patient. Data were analyzed to quantify the nonhuman sequence reads in each sample. We found little difference between bacterial microbiome and viral read counts, but found a significant difference between the read counts for a mycobiome component, R. glutinis. Normal samples contained almost no detected R. glutinis or other Rhodotorula sequence reads (mean score 0.021 for R. glutinis, 0.024 for all Rhodotorula). In contrast, SSc samples had a mean score of 5.039 for R. glutinis (5.232 for Rhodotorula). We were able to assemble the D1-D2 hypervariable region of the 28S ribosomal RNA (rRNA) of R. glutinis from each of the SSc samples. Taken together, these results suggest that R. glutinis may be present in the skin of early SSc patients at higher levels than in normal skin, raising the possibility that it may be triggering the inflammatory response found in SSc.

contamDE: differential expression analysis of RNA-seq data for contaminated tumor samples.

PubMed

Shen, Qi; Hu, Jiyuan; Jiang, Ning; Hu, Xiaohua; Luo, Zewei; Zhang, Hong

2016-03-01

Accurate detection of differentially expressed genes between tumor and normal samples is a primary approach of cancer-related biomarker identification. Due to the infiltration of tumor surrounding normal cells, the expression data derived from tumor samples would always be contaminated with normal cells. Ignoring such cellular contamination would deflate the power of detecting DE genes and further confound the biological interpretation of the analysis results. For the time being, there does not exists any differential expression analysis approach for RNA-seq data in literature that can properly account for the contamination of tumor samples. Without appealing to any extra information, we develop a new method 'contamDE' based on a novel statistical model that associates RNA-seq expression levels with cell types. It is demonstrated through simulation studies that contamDE could be much more powerful than the existing methods that ignore the contamination. In the application to two cancer studies, contamDE uniquely found several potential therapy and prognostic biomarkers of prostate cancer and non-small cell lung cancer. An R package contamDE is freely available at http://homepage.fudan.edu.cn/zhangh/softwares/ zhanghfd@fudan.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

[Exposure of normal Tenon's capsule fibroblasts from pterygium to 5-fluorouracil and mitomycin C].

PubMed

Viveiros, Magda Massae Hata; Schellini, Silvana Artioli; Candeias, João; Padovani, Carlos Roberto

2007-01-01

To evaluate the fibroblast proliferation activity of normal Tenon's capsule from primary and recurrent patients with pterygium. A randomized prospective study was performed with 41 normal Tenon's capsule fragments from 21 primary and 20 recurrent patients with pterygium. The sample was collected from the inferior cul-de-sac. Proliferation rate from fibroblasts were evaluated after mitomycin C and 5-fluorouracil exposition. Data were submitted to statistical analysis. Of the 41 cultivated normal Tenon's capsules, only 1 from primary and 2 from recurrent pterygium patients proliferated. After antimitotic exposition, the proliferation rate was similar with both drugs. Mitomycin and 5-fluorouracil promote similar inhibition regarding proliferation of normal Tenon's fibroblast cultures.

Diffusion phenomenon at the interface of Cu-brass under a strong gravitational field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogata, Yudai; Tokuda, Makoto; Januszko, Kamila

2015-03-28

To investigate diffusion phenomenon at the interface between Cu and brass under a strong gravitational field generated by ultracentrifuge apparatus, we performed gravity experiments on samples prepared by electroplating with interfaces normal and parallel to the direction of gravity. For the parallel-mode sample, for which sedimentation cannot occur thorough the interface, the concentration change was significant within the lower gravity region; many pores were observed in this region. Many vacancies arising from crystal strain due to the strong gravitational field moved into the lower gravity region, and enhanced the atoms mobilities. For the two normal-mode samples, which have interface normalmore » to the direction of gravity, the composition gradient of the brass-on-Cu sample was steeper than that for Cu-on-brass. This showed that the atoms of denser Cu diffuse in the direction of gravity, whereas Zn atoms diffuse in the opposite direction by sedimentation. The interdiffusion coefficients became higher in the Cu-on-brass sample, and became lower in the brass-on-Cu sample. This rise may be related to the behavior of the vacancies.« less

Early detection of disease: The correlation of the volatile organic profiles from patients with upper respiratory infections with subjects of normal profiles

NASA Technical Reports Server (NTRS)

Zlatkis, A.

1979-01-01

A method is described whereby a transevaporator is used for sampling 60-100 microns of aqueous sample. Volatiles are stripped from the sample either by a stream of helium and collection on a porous polymer, Tenax, or by 0.8 ml of 2-chloropropane and collected on glass beads. The volatiles are thermally desorbed into a precolumn which is connected to a capillary gas chromatographic column for analysis. The technique is shown to be reproducible and suitable for determining chromatographic profiles for a wide variety of sample types. Using a transevaporator sampling technique, the volatile profiles from 70 microns of serum were obtained by capillary column gas chromatography. The complex chromatograms were interpreted by a combination of manual and computer techniques and a two peak ratio method devised for the classification of normal and virus infected sera. Using the K-Nearest Neighbor approach, 85.7 percent of the unknown samples were classified correctly. Some preliminary results indicate the possible use of the method for the assessment of virus susceptibility.

Profiling of adrenocorticotropic hormone and arginine vasopressin in human pituitary gland and tumor thin tissue sections using droplet-based liquid-microjunction surface-sampling-HPLC–ESI-MS–MS

DOE PAGES

Kertesz, Vilmos; Calligaris, David; Feldman, Daniel R.; ...

2015-06-18

Described here are the results from the profiling of the proteins arginine vasopressin (AVP) and adrenocorticotropic hormone (ACTH) from normal human pituitary gland and pituitary adenoma tissue sections using a fully automated droplet-based liquid microjunction surface sampling-HPLC-ESI-MS/MS system for spatially resolved sampling, HPLC separation, and mass spectral detection. Excellent correlation was found between the protein distribution data obtained with this droplet-based liquid microjunction surface sampling-HPLC-ESI-MS/MS system and those data obtained with matrix assisted laser desorption ionization (MALDI) chemical imaging analyses of serial sections of the same tissue. The protein distributions correlated with the visible anatomic pattern of the pituitary gland.more » AVP was most abundant in the posterior pituitary gland region (neurohypophysis) and ATCH was dominant in the anterior pituitary gland region (adenohypophysis). The relative amounts of AVP and ACTH sampled from a series of ACTH secreting and non-secreting pituitary adenomas correlated with histopathological evaluation. ACTH was readily detected at significantly higher levels in regions of ACTH secreting adenomas and in normal anterior adenohypophysis compared to non-secreting adenoma and neurohypophysis. AVP was mostly detected in normal neurohypophysis as anticipated. This work demonstrates that a fully automated droplet-based liquid microjunction surface sampling system coupled to HPLC-ESI-MS/MS can be readily used for spatially resolved sampling, separation, detection, and semi-quantitation of physiologically-relevant peptide and protein hormones, such as AVP and ACTH, directly from human tissue. In addition, the relative simplicity, rapidity and specificity of the current methodology support the potential of this basic technology with further advancement for assisting surgical decision-making.« less

Vitamin D Receptor Expression in Normal, Premalignant, and Malignant Human Lung Tissue

PubMed Central

Menezes, Ravi J.; Cheney, Richard T.; Husain, Aliya; Tretiakova, Maria; Loewen, Gregory; Johnson, Candace S.; Jayaprakash, Vijay; Moysich, Kirsten B.; Salgia, Ravi; Reid, Mary E.

2009-01-01

Background There is a strong interest in identifying chemopreventive agents that might help decrease the burden of lung cancer. The active metabolite of vitamin D, 1,25-dihydroxycholecalciferol (calcitriol), has been shown to have antiproliferative effects in several tumor types, mediated by the vitamin D receptor (VDR). This is the first comprehensive survey of VDR expression in a series of human lung tissues, including normal and premalignant central airway biopsies and lung tumors. Methods Immunohistochemical expression of nuclear and cytoplasmic VDR was examined in 180 premalignant or malignant bronchial biopsies from bronchoscopy of 78 high-risk individuals at the Roswell Park Cancer Institute and also in 63 tumor samples from 35 lung cancer patients from the University of Chicago Hospitals. Associations between clinicopathologic data and VDR expression were examined. Results VDR expression was present in many samples. In biopsies, VDR was commonly detected throughout the full epithelial layer. Most histologically normal (60%, 53 of 88) and metaplastic (61%, 39 of 64) samples had moderate to high nuclear intensity; dysplastic samples mostly had low nuclear intensity (10 of 18, 55%). In tumor samples, 62% (38 of 61) were lacking cytoplasmic VDR, with nuclear expression present in 79%(49 of 62). Analysis of all samples revealed a positive linear trend between proportion of samples with greater nuclear than cytoplasmic intensity and increasing histologic grade (P < 0.01). Conclusions VDR expression spanned the lung carcinogenesis spectrum. Nuclear expression was similar across various histologies, whereas cytoplasmic expression decreased with increasing histologic grade. These results indicate that there is potential for the use of calcitriol as a chemopreventive agent against the development of lung cancer. (Cancer Epidemiol Bio-markers Prev 2008;17(5):1104–10) PMID:18483332

Profiling of adrenocorticotropic hormone and arginine vasopressin in human pituitary gland and tumor thin tissue sections using droplet-based liquid-microjunction surface-sampling-HPLC–ESI-MS–MS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kertesz, Vilmos; Calligaris, David; Feldman, Daniel R.

Described here are the results from the profiling of the proteins arginine vasopressin (AVP) and adrenocorticotropic hormone (ACTH) from normal human pituitary gland and pituitary adenoma tissue sections using a fully automated droplet-based liquid microjunction surface sampling-HPLC-ESI-MS/MS system for spatially resolved sampling, HPLC separation, and mass spectral detection. Excellent correlation was found between the protein distribution data obtained with this droplet-based liquid microjunction surface sampling-HPLC-ESI-MS/MS system and those data obtained with matrix assisted laser desorption ionization (MALDI) chemical imaging analyses of serial sections of the same tissue. The protein distributions correlated with the visible anatomic pattern of the pituitary gland.more » AVP was most abundant in the posterior pituitary gland region (neurohypophysis) and ATCH was dominant in the anterior pituitary gland region (adenohypophysis). The relative amounts of AVP and ACTH sampled from a series of ACTH secreting and non-secreting pituitary adenomas correlated with histopathological evaluation. ACTH was readily detected at significantly higher levels in regions of ACTH secreting adenomas and in normal anterior adenohypophysis compared to non-secreting adenoma and neurohypophysis. AVP was mostly detected in normal neurohypophysis as anticipated. This work demonstrates that a fully automated droplet-based liquid microjunction surface sampling system coupled to HPLC-ESI-MS/MS can be readily used for spatially resolved sampling, separation, detection, and semi-quantitation of physiologically-relevant peptide and protein hormones, such as AVP and ACTH, directly from human tissue. In addition, the relative simplicity, rapidity and specificity of the current methodology support the potential of this basic technology with further advancement for assisting surgical decision-making.« less

Metabolic differences between short children with GH peak levels in the lower normal range and healthy children of normal height.

PubMed

Tidblad, Anders; Gustafsson, Jan; Marcus, Claude; Ritzén, Martin; Ekström, Klas

2017-06-01

Severe growth hormone deficiency (GHD) leads to several metabolic effects in the body ranging from abnormal body composition to biochemical disturbances. However, less is known regarding these parameters in short children with GH peak levels in the lower normal range during provocation tests. Our aim was to study the metabolic profile of this group and compare it with that of healthy children of normal height. Thirty-five pre-pubertal short children (<-2.5 SDS) aged between 7 and 10years, with peak levels of GH between 7 and 14μg/L in an arginine insulin tolerance test (AITT), were compared with twelve age- and sex-matched children of normal height. The metabolic profile of the subjects was analysed by blood samples, DEXA, frequently sampled intravenous glucose tolerance test, microdialysis and stable isotope examinations of rates of glucose production and lipolysis. There were no overall significant metabolic differences between the groups. However, in the subgroup analysis, the short children with GH peaks <10μg/L had significantly lower fasting insulin levels which also correlated to other metabolic parameters. The short pre-pubertal children with GH peak levels between 7 and 14μg/L did not differ significantly from healthy children of normal height but subpopulations within this group show significant metabolic differences. Copyright © 2017 Elsevier Ltd. All rights reserved.

Incidence and Determinants of Port Occlusions in Cancer Outpatients: A Prospective Cohort Study.

PubMed

Milani, Alessandra; Mazzocco, Ketti; Gandini, Sara; Pravettoni, Gabriella; Libutti, Livio; Zencovich, Claudia; Sbriglia, Ada; Pari, Chiara; Magon, Giorgio; Saiani, Luisa

Normal saline is considered a safe alternative for heparin as a locking solution in totally implantable venous access devices. The incidence rate of partial occlusion with the use of normal saline (easy injection, impossible aspiration) is estimated at 4%. The aim of this study was to investigate determinants of partial occlusions with the use of normal saline solution and the maintenance of positive pressure in the catheter. We enrolled 218 patients with different solid tumors who underwent pharmacologic treatment through the port with different frequencies: from once every week to at least once every month. The port was flushed with normal saline solution keeping a positive pressure in the catheter. We performed 4111 observations and documented normal port functioning in 99% of observations (n = 4057) and partial occlusions in 1% of observations (n = 54). Partial occlusions were significantly associated with frequency of port flushing (P < .05), chemotherapy (P < .001), and blood sample collection (P < .001). The use of positive pressure in addition to normal saline reduces the incidence rate of partial occlusions. The type of treatment, blood sample collection, and treatment schedule are important determinants of partial occlusions. Nurses play a key role in maintaining a functioning port using positive pressure during the flushing techniques. Certain risk factors must be monitored to prevent partial occlusions, and certain patients are more likely to present with port-related problems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, David Robert; Fensin, Saryu Jindal; Dippo, Olivia

Here, we present a study on the spall strength of additive manufactured (AM) Ti-6Al-4V. Samples were obtained from two pieces of selective laser melted (SLM, a powder bed fusion technique) Ti-6Al-4V such that the response to dynamic tensile loading could be investigated as a function of the orientation between the build layers and the loading direction. A sample of wrought bar-stock Ti-6Al-4V was also tested to act as a baseline representing the traditionally manufactured material response. A single-stage light gas-gun was used to launch a thin flyer plate into the samples, generating a region of intense tensile stress on amore » plane normal to the impact direction. The rear free surface velocity time history of each sample was recorded with laser-based velocimetry to allow the spall strength to be calculated. The samples were also soft recovered to enable post-mortem characterization of the spall damage evolution. Results showed that when the tensile load was applied normal to the interfaces between the build layers caused by the SLM fabrication process the spall strength was drastically reduced, dropping to 60% of that of the wrought material. However, when loaded parallel to the AM build layer interfaces the spall strength was found to remain at 95% of the wrought control, suggesting that when loading normal to the AM layer interfaces, void nucleation is facilitated more readily due to weaknesses along these boundaries. Quasi-static testing of the same sample orientations revealed a much lower degree of anisotropy, demonstrating the importance of rate-dependent studies for damage evolution in AM materials.« less

Power and temperature dependent photoluminescence investigation of the linear polarization at normal and inverted interface transitions in InP/InAlAs and InGaAsP/InAlAs QW structures

NASA Astrophysics Data System (ADS)

Esmaielpour, Hamidreza; Whiteside, Vincent R.; Hirst, Louise C.; Forbes, David V.; Walters, Robert J.; Sellers, Ian R.

We present an investigation of the interface effects for InGaAsP/InAlAs QW and InP/InAlAs QW structures capped with an InP layer. Continuous wave photoluminescence (PL) spectroscopy of these samples at 4 K shows features associated with the interfaces of an InAlAs layer grown on an InP layer (normal interface) and an InP layer grown on an InAlAs material (inverted interface). Power dependent PL of the InGaAsP QW indicates that there are two features related to the inverted interface, whereby the linear polarization of one increases and for the other decreases. In addition, a temperature dependent study of this sample shows that as the temperature increases: the linear polarization for both features decreases; at room temperature, there is negligible polarization effect. A power dependent PL study of the InP QW structure shows both normal and inverted interface transitions have opposing trends in linear polarization. Notably, the temperature dependent PL investigation displays a reduction of polarization degree for the inverted interface: as expected; while an increase of polarization for the normal interface was observed. In addition, power and temperature dependence of peak energy of the interface transitions for both samples will be presented.

Estimates and Standard Errors for Ratios of Normalizing Constants from Multiple Markov Chains via Regeneration

PubMed Central

Doss, Hani; Tan, Aixin

2017-01-01

In the classical biased sampling problem, we have k densities π1(·), …, πk(·), each known up to a normalizing constant, i.e. for l = 1, …, k, πl(·) = νl(·)/ml, where νl(·) is a known function and ml is an unknown constant. For each l, we have an iid sample from πl,·and the problem is to estimate the ratios ml/ms for all l and all s. This problem arises frequently in several situations in both frequentist and Bayesian inference. An estimate of the ratios was developed and studied by Vardi and his co-workers over two decades ago, and there has been much subsequent work on this problem from many different perspectives. In spite of this, there are no rigorous results in the literature on how to estimate the standard error of the estimate. We present a class of estimates of the ratios of normalizing constants that are appropriate for the case where the samples from the πl’s are not necessarily iid sequences, but are Markov chains. We also develop an approach based on regenerative simulation for obtaining standard errors for the estimates of ratios of normalizing constants. These standard error estimates are valid for both the iid case and the Markov chain case. PMID:28706463

Estimates and Standard Errors for Ratios of Normalizing Constants from Multiple Markov Chains via Regeneration.

PubMed

Doss, Hani; Tan, Aixin

2014-09-01

In the classical biased sampling problem, we have k densities π 1 (·), …, π k (·), each known up to a normalizing constant, i.e. for l = 1, …, k , π l (·) = ν l (·)/ m l , where ν l (·) is a known function and m l is an unknown constant. For each l , we have an iid sample from π l , · and the problem is to estimate the ratios m l /m s for all l and all s . This problem arises frequently in several situations in both frequentist and Bayesian inference. An estimate of the ratios was developed and studied by Vardi and his co-workers over two decades ago, and there has been much subsequent work on this problem from many different perspectives. In spite of this, there are no rigorous results in the literature on how to estimate the standard error of the estimate. We present a class of estimates of the ratios of normalizing constants that are appropriate for the case where the samples from the π l 's are not necessarily iid sequences, but are Markov chains. We also develop an approach based on regenerative simulation for obtaining standard errors for the estimates of ratios of normalizing constants. These standard error estimates are valid for both the iid case and the Markov chain case.

Investigating the relationship between FMR1 allele length and cognitive ability in children: a subtle effect of the normal allele range on the normal ability range?

PubMed

Loat, C S; Craig, G; Plomin, R; Craig, I W

2006-09-01

The FMR1 gene contains a trinucleotide repeat tract which can expand from a normal size of around 30 repeats to over 200 repeats, causing mental retardation (Fragile X Syndrome). Evidence suggests that premutation males (55-200 repeats) are susceptible to a late-onset tremor/ataxia syndrome and females to premature ovarian failure, and that intermediate alleles ( approximately 41-55 repeats) and premutations may be in excess in samples with special educational needs. We explored the relationship between FMR1 allele length and cognitive ability in 621 low ability and control children assessed at 4 and 7 years, as well as 122 students with high IQ. The low and high ability and control samples showed no between-group differences in incidence of longer alleles. In males there was a significant negative correlation between allele length and non-verbal ability at 4 years (p = 0.048), academic achievement in maths (p = 0.003) and English (p = 0.011) at 7 years, and IQ in the high ability group (p = 0.018). There was a significant negative correlation between allele length and a standardised score for IQ and general cognitive ability at age 7 in the entire male sample (p = 0.002). This suggests that, within the normal spectrum of allele length, increased repeat numbers may have a limiting influence on cognitive performance.

On the asymptotic improvement of supervised learning by utilizing additional unlabeled samples - Normal mixture density case

NASA Technical Reports Server (NTRS)

Shahshahani, Behzad M.; Landgrebe, David A.

1992-01-01

The effect of additional unlabeled samples in improving the supervised learning process is studied in this paper. Three learning processes. supervised, unsupervised, and combined supervised-unsupervised, are compared by studying the asymptotic behavior of the estimates obtained under each process. Upper and lower bounds on the asymptotic covariance matrices are derived. It is shown that under a normal mixture density assumption for the probability density function of the feature space, the combined supervised-unsupervised learning is always superior to the supervised learning in achieving better estimates. Experimental results are provided to verify the theoretical concepts.

Cases of type C botulism in broiler chickens.

PubMed

Dohms, J E; Allen, P H; Rosenberger, J K

1982-01-01

Twenty-seven cases of type C botulism were studied in integrated broiler operations on the Delmarva Peninsula. Single and repeated outbreaks in broiler flocks were observed. No botulinum toxin was found in litter and feed samples despite repeated testing. Clostridium botulinum type C was cultured from litter, feed, and tissues of morbid and clinically normal chickens sampled from farms in which flocks experienced botulism. Clostridium botulinum type C could not be cultured from tissues of clinically normal chickens taken from a farm without a flock history of botulism or from caged broilers reared in semi-isolation.

Small angle scattering polarization biopsy: a comparative analysis of various skin diseases

NASA Astrophysics Data System (ADS)

Zimnyakov, D. A.; Alonova, M. V.; Yermolenko, S. B.; Ivashko, P. V.; Reshetnikova, E. M.; Galkina, E. M.; Utz, S. R.

2013-12-01

An approach to differentiation of the morphological features of normal and pathological human epidermis on the base of statistical analysis of the local polarization states of laser light forward scattered by in-vitro tissue samples is discussed. The eccentricity and the azimuth angle of local polarization ellipses retrieved for various positions of the focused laser beam on the tissue surface, and the coefficient of collimated transmittance are considered as the diagnostic parameters for differentiation. The experimental data obtained with the psoriasis, discoid lupus erythematosus, alopecia, lichen planus, scabies, demodex, and normal skin samples are presented.

Validity of the WISC-IV Spanish for a clinically referred sample of Hispanic children.

PubMed

San Miguel Montes, Liza E; Allen, Daniel N; Puente, Antonio E; Neblina, Cris

2010-06-01

The Wechsler Intelligence Scale for Children (WISC) is the most commonly used intelligence test for children. Five years ago, a Spanish version of the WISC-IV was published (WISC-IV Spanish; Wechsler, 2005), but a limited amount of published information is available regarding its utility when assessing clinical samples. The current study included 107 children who were Spanish speaking and of Puerto Rican descent that had been administered the WISC-IV Spanish. They were subdivided into a clinical sample of 35 children with diagnoses of various forms of brain dysfunction (primarily learning disability, attention-deficit/hyperactivity disorder, and epilepsy) and a comparison group made up of 72 normal children who were part of the WISC-IV Spanish version standardization sample. Comparisons between these groups and the standardization sample were performed for the WISC-IV Spanish index and subtest scores. Results indicated that the clinical sample performed worse than the comparison samples on the Working Memory and Processing Speed Indexes, although findings varied to some extent depending on whether the clinical group was compared with the normal comparison group or the standardization sample. These findings provide support for the criterion validity of the WISC-IV Spanish when it is used to assess a clinically referred sample with brain dysfunction.

Liquid and gel electrodes for transverse free flow electrophoresis

DOEpatents

Jung, Byoungsok; Rose, Klint A; Shusteff, Maxim; Persat, Alexandre; Santiago, Juan

2015-04-07

The present invention provides a mechanism for separating or isolating charged particles under the influence of an electric field without metal electrodes being in direct contact with the sample solution. The metal electrodes normally in contact with the sample are replaced with high conductivity fluid electrodes situated parallel and adjacent to the sample. When the fluid electrodes transmit the electric field across the sample, particles within the sample migrate according to their electrophoretic mobility.

Automated PCR setup for forensic casework samples using the Normalization Wizard and PCR Setup robotic methods.

PubMed

Greenspoon, S A; Sykes, K L V; Ban, J D; Pollard, A; Baisden, M; Farr, M; Graham, N; Collins, B L; Green, M M; Christenson, C C

2006-12-20

Human genome, pharmaceutical and research laboratories have long enjoyed the application of robotics to performing repetitive laboratory tasks. However, the utilization of robotics in forensic laboratories for processing casework samples is relatively new and poses particular challenges. Since the quantity and quality (a mixture versus a single source sample, the level of degradation, the presence of PCR inhibitors) of the DNA contained within a casework sample is unknown, particular attention must be paid to procedural susceptibility to contamination, as well as DNA yield, especially as it pertains to samples with little biological material. The Virginia Department of Forensic Science (VDFS) has successfully automated forensic casework DNA extraction utilizing the DNA IQ(trade mark) System in conjunction with the Biomek 2000 Automation Workstation. Human DNA quantitation is also performed in a near complete automated fashion utilizing the AluQuant Human DNA Quantitation System and the Biomek 2000 Automation Workstation. Recently, the PCR setup for casework samples has been automated, employing the Biomek 2000 Automation Workstation and Normalization Wizard, Genetic Identity version, which utilizes the quantitation data, imported into the software, to create a customized automated method for DNA dilution, unique to that plate of DNA samples. The PCR Setup software method, used in conjunction with the Normalization Wizard method and written for the Biomek 2000, functions to mix the diluted DNA samples, transfer the PCR master mix, and transfer the diluted DNA samples to PCR amplification tubes. Once the process is complete, the DNA extracts, still on the deck of the robot in PCR amplification strip tubes, are transferred to pre-labeled 1.5 mL tubes for long-term storage using an automated method. The automation of these steps in the process of forensic DNA casework analysis has been accomplished by performing extensive optimization, validation and testing of the software methods.

Effects of Sampling and Spatio/Temporal Granularity in Traffic Monitoring on Anomaly Detectability

NASA Astrophysics Data System (ADS)

Ishibashi, Keisuke; Kawahara, Ryoichi; Mori, Tatsuya; Kondoh, Tsuyoshi; Asano, Shoichiro

We quantitatively evaluate how sampling and spatio/temporal granularity in traffic monitoring affect the detectability of anomalous traffic. Those parameters also affect the monitoring burden, so network operators face a trade-off between the monitoring burden and detectability and need to know which are the optimal paramter values. We derive equations to calculate the false positive ratio and false negative ratio for given values of the sampling rate, granularity, statistics of normal traffic, and volume of anomalies to be detected. Specifically, assuming that the normal traffic has a Gaussian distribution, which is parameterized by its mean and standard deviation, we analyze how sampling and monitoring granularity change these distribution parameters. This analysis is based on observation of the backbone traffic, which exhibits spatially uncorrelated and temporally long-range dependence. Then we derive the equations for detectability. With those equations, we can answer the practical questions that arise in actual network operations: what sampling rate to set to find the given volume of anomaly, or, if the sampling is too high for actual operation, what granularity is optimal to find the anomaly for a given lower limit of sampling rate.

Efficacy of Influenza Vaccination and Tamiflu® Treatment – Comparative Studies with Eurasian Swine Influenza Viruses in Pigs

PubMed Central

Duerrwald, Ralf; Schlegel, Michael; Bauer, Katja; Vissiennon, Théophile; Wutzler, Peter; Schmidtke, Michaela

2013-01-01

Recent epidemiological developments demonstrated that gene segments of swine influenza A viruses can account for antigenic changes as well as reduced drug susceptibility of pandemic influenza A viruses. This raises questions about the efficacy of preventive measures against swine influenza A viruses. Here, the protective effect of vaccination was compared with that of prophylactic Tamiflu® treatment against two Eurasian swine influenza A viruses. 11-week-old pigs were infected by aerosol nebulisation with high doses of influenza virus A/swine/Potsdam/15/1981 (H1N1/1981, heterologous challenge to H1N1 vaccine strain) and A/swine/Bakum/1832/2000 (H1N2/2000, homologous challenge to H1N2 vaccine strain) in two independent trials. In each trial (i) 10 pigs were vaccinated twice with a trivalent vaccine (RESPIPORC® FLU3; 28 and 7 days before infection), (ii) another 10 pigs received 150 mg/day of Tamiflu® for 5 days starting 12 h before infection, and (iii) 12 virus-infected pigs were left unvaccinated and untreated and served as controls. Both viruses replicated efficiently in porcine respiratory organs causing influenza with fever, dyspnoea, and pneumonia. Tamiflu® treatment as well as vaccination prevented clinical signs and significantly reduced virus shedding. Whereas after homologous challenge with H1N2/2000 no infectious virus in lung and hardly any lung inflammation were detected, the virus titre was not and the lung pathology was only partially reduced in H1N1/1981, heterologous challenged pigs. Tamiflu® application did not affect these study parameters. In conclusion, all tested preventive measures provided protection against disease. Vaccination additionally prevented virus replication and histopathological changes in the lung of homologous challenged pigs. PMID:23630601

Efficacy of influenza vaccination and tamiflu® treatment--comparative studies with Eurasian Swine influenza viruses in pigs.

PubMed

Duerrwald, Ralf; Schlegel, Michael; Bauer, Katja; Vissiennon, Théophile; Wutzler, Peter; Schmidtke, Michaela

2013-01-01

Recent epidemiological developments demonstrated that gene segments of swine influenza A viruses can account for antigenic changes as well as reduced drug susceptibility of pandemic influenza A viruses. This raises questions about the efficacy of preventive measures against swine influenza A viruses. Here, the protective effect of vaccination was compared with that of prophylactic Tamiflu® treatment against two Eurasian swine influenza A viruses. 11-week-old pigs were infected by aerosol nebulisation with high doses of influenza virus A/swine/Potsdam/15/1981 (H1N1/1981, heterologous challenge to H1N1 vaccine strain) and A/swine/Bakum/1832/2000 (H1N2/2000, homologous challenge to H1N2 vaccine strain) in two independent trials. In each trial (i) 10 pigs were vaccinated twice with a trivalent vaccine (RESPIPORC® FLU3; 28 and 7 days before infection), (ii) another 10 pigs received 150 mg/day of Tamiflu® for 5 days starting 12 h before infection, and (iii) 12 virus-infected pigs were left unvaccinated and untreated and served as controls. Both viruses replicated efficiently in porcine respiratory organs causing influenza with fever, dyspnoea, and pneumonia. Tamiflu® treatment as well as vaccination prevented clinical signs and significantly reduced virus shedding. Whereas after homologous challenge with H1N2/2000 no infectious virus in lung and hardly any lung inflammation were detected, the virus titre was not and the lung pathology was only partially reduced in H1N1/1981, heterologous challenged pigs. Tamiflu® application did not affect these study parameters. In conclusion, all tested preventive measures provided protection against disease. Vaccination additionally prevented virus replication and histopathological changes in the lung of homologous challenged pigs.

A spray technique for preparing uniform large-area PIXE calibration standards from aqueous solutions

NASA Astrophysics Data System (ADS)

Menzel, N.; Hietel, B.; Leirer, M.; Szymczak, W.; Wittmaack, K.

1999-04-01

We describe a procedure for preparing reference standards that can be used to calibrate PIXE spectra of aerosol deposits collected on suitable backing films made, for example, of synthesised polymers (polypropylene, polycarbonate etc.) or chemically modified biopolymers (e.g., cellulose actetate). Aqueous solutions of well defined concentration were prepared from metal salts. The solutions were spray-deposited on cellulose acetate backings using a nebuliser. Lateral uniformity of the deposited layer over areas ranging from several mm to several cm was accomplished by raster scanning the table on which the backing was mounted. By optimising the experimental parameters, deposition could be accomplished without any detectable wetting of delicate substrates like paper. The areal density of the deposited material was calculated from the concentration of the solute, the volume of the consumed solution and the raster scanned area. The reference standards were analysed by PIXE using an external beam chamber backfilled with helium. The Si(Li) based detection system contained a thin funny filter so that X-ray spectra could be measured down to 1 keV. The proton energy on impact was 1.1 MeV. This relatively low probe energy has the advantage of producing favourable elemental X-ray peak heights relative to the bremsstrahlung-background, notably at energies between 2 and 7 keV. Under the same conditions sufficiently high X-ray yields were achieved for heavy elements like Zn and Pb. Using large area beams, bombardment-induced stress in the backing films could be kept at a low level so that very reproducible background spectra were obtained. Hence a straightforward background subtraction routine could be employed. Sensitivities were determined for 23 elements ranging from Na to Pb. Advantages and problems associated with the different metal salts are discussed briefly.

Effects of aerosolised substance P on lung resistance in guinea-pigs: a comparison between inhibition of neutral endopeptidase and angiotensin-converting enzyme.

PubMed

Lötvall, J O; Skoogh, B E; Barnes, P J; Chung, K F

1990-05-01

1. We have examined in guinea-pigs, in vivo, the effects of inhibition of neutral endopeptidase (NEP) and angiotensin-converting enzyme (ACE) on the airway response to aerosolised substance P (SP). We aerosolised captopril (4.6 mM, 60 breaths; 210 nmol) to inhibit ACE and acetorphan (0.3, 1 and 3 mM, 60 breaths; 9 nmol, 33 nmol and 110 nmol respectively) to inhibit NEP. We also examined the effect of the highest dose of acetorphan (110 nmol) on the response to aerosolised acetylcholine (ACh). 2. Responsiveness to SP (or ACh) was measured as the change in lung resistance (RL) induced by nebulisation of increasing concentrations of SP (or ACh) before and after treatment with the inhibitor. PC200, defined as the provocative concentration inducing an increase in RL of 200% above baseline was calculated for each challenge. 3. Administration of acetorphan before the second SP-challenge induced a dose-dependent decrease in PC200 for SP amounting to 1.8 (+/- 0.3) log units after treatment with 11 nmol acetorphan. Treatment with vehicle before the second SP-challenge or with 3 mM acetorphan before the second ACh-challenge had no significant effect on PC200. 4. Treatment with captopril (21 nmol) induced only a small, nonsignificant leftward shift of PC200 to SP (0.3 +/- 0.2 log units). 5. We conclude that a NEP-like enzyme, but not ACE, regulates the response to aerosolised SP. We suggest that the same is true for SP released endogenously from sensory nerve endings in the airway epithelial layer.

Effects of aerosolised substance P on lung resistance in guinea-pigs: a comparison between inhibition of neutral endopeptidase and angiotensin-converting enzyme.

PubMed Central

Lötvall, J. O.; Skoogh, B. E.; Barnes, P. J.; Chung, K. F.

1990-01-01

1. We have examined in guinea-pigs, in vivo, the effects of inhibition of neutral endopeptidase (NEP) and angiotensin-converting enzyme (ACE) on the airway response to aerosolised substance P (SP). We aerosolised captopril (4.6 mM, 60 breaths; 210 nmol) to inhibit ACE and acetorphan (0.3, 1 and 3 mM, 60 breaths; 9 nmol, 33 nmol and 110 nmol respectively) to inhibit NEP. We also examined the effect of the highest dose of acetorphan (110 nmol) on the response to aerosolised acetylcholine (ACh). 2. Responsiveness to SP (or ACh) was measured as the change in lung resistance (RL) induced by nebulisation of increasing concentrations of SP (or ACh) before and after treatment with the inhibitor. PC200, defined as the provocative concentration inducing an increase in RL of 200% above baseline was calculated for each challenge. 3. Administration of acetorphan before the second SP-challenge induced a dose-dependent decrease in PC200 for SP amounting to 1.8 (+/- 0.3) log units after treatment with 11 nmol acetorphan. Treatment with vehicle before the second SP-challenge or with 3 mM acetorphan before the second ACh-challenge had no significant effect on PC200. 4. Treatment with captopril (21 nmol) induced only a small, nonsignificant leftward shift of PC200 to SP (0.3 +/- 0.2 log units). 5. We conclude that a NEP-like enzyme, but not ACE, regulates the response to aerosolised SP. We suggest that the same is true for SP released endogenously from sensory nerve endings in the airway epithelial layer. PMID:1695534

DNase and atelectasis in non-cystic fibrosis pediatric patients

PubMed Central

Hendriks, Tom; de Hoog, Matthijs; Lequin, Maarten H; Devos, Annick S; Merkus, Peter JFM

2005-01-01

Introduction No evidence based treatment is available for atelectasis. We aimed to evaluate the clinical and radiologic changes in pediatric patients who received DNase for persistent atelectasis that could not be attributed to cardiovascular causes, and who were unresponsive to treatment with inhaled bronchodilators and physiotherapy. Methods All non-cystic fibrosis pediatric patients who received nebulised or endotracheally instilled DNase for atelectasis between 1998 and 2002, with and without mechanical ventilation, were analysed in a retrospective descriptive study. The endpoints were the blood pCO2, the heart rate, the respiratory rate, the FiO2 and the chest X-ray scores before and after treatment. Results In 25 of 30 patients (median [range] age, 1.6 [0.1–11] years) who met inclusion criteria, paired data of at least three endpoints were available. All clinical parameters improved significantly within 2 hours (P < 0.01), except for the heart rate (P = 0.06). Chest X-ray scores improved significantly within 24 hours after DNase treatment (P < 0.001). Individual improvement was observed in 17 patients and no clinical change was observed in five patients. Temporary deterioration (n = 3) was associated with increased airway obstruction and desaturations. No other complications were observed. Conclusion After treatment with DNase for atelectasis of presumably infectious origin in non-cystic fibrosis pediatric patients, rapid clinical improvement was observed within 2 hours and radiologic improvement was documented within 24 hours in the large majority of children, and increased airway obstruction and ventilation–perfusion mismatch occurred in three children, possibly due to rapid mobilisation of mucus. DNase may be an effective treatment for infectious atelectasis in non-cystic fibrosis pediatric patients. PMID:16137347

Note: Microelectrode-shielding tip for scanning probe electron energy spectroscopy

NASA Astrophysics Data System (ADS)

Huang, Wei; Li, Zhean; Xu, Chunkai; Liu, Jian; Xu, Chunye; Chen, Xiangjun

2018-04-01

We report a novel microelectrode-shielding tip (ME tip) for scanning probe electron energy spectroscopy (SPEES). The shielding effect of this tip is studied through comparing the detection efficiency with the normal tip by both experiment and simulation. The results show that the backscattering count rate detected by the SPEES instrument using the normal tip begins to decrease as the tip approaches to the sample surface within 21 μm, while that using the ME tip only starts to drop off within 1 μm. This indicates that the electron energy spectra can be measured with the ME tip at a much closer tip-sample distance. Furthermore, it is also demonstrated that the ME tip can be used to obtain topography of the sample surface in situ simultaneously.

Anomalous waveforms observed in laboratory-formed gas hydrate-bearing and ice-bearing sediments

USGS Publications Warehouse

Lee, M.W.; Waite, W.F.

2011-01-01

Acoustic transmission measurements of compressional, P, and shear, S, wave velocities rely on correctly identifying the P- and S-body wave arrivals in the measured waveform. In cylindrical samples for which the sample is much longer than the acoustic wavelength, these body waves can be obscured by high-amplitude waveform features arriving just after the relatively small-amplitude P-body wave. In this study, a normal mode approach is used to analyze this type of waveform, observed in sediment containing gas hydrate or ice. This analysis extends an existing normal-mode waveform propagation theory by including the effects of the confining medium surrounding the sample, and provides guidelines for estimating S-wave velocities from waveforms containing multiple large-amplitude arrivals. ?? 2011 Acoustical Society of America.

In vivo classification of human skin burns using machine learning and quantitative features captured by optical coherence tomography

NASA Astrophysics Data System (ADS)

Singla, Neeru; Srivastava, Vishal; Singh Mehta, Dalip

2018-02-01

We report the first fully automated detection of human skin burn injuries in vivo, with the goal of automatic surgical margin assessment based on optical coherence tomography (OCT) images. Our proposed automated procedure entails building a machine-learning-based classifier by extracting quantitative features from normal and burn tissue images recorded by OCT. In this study, 56 samples (28 normal, 28 burned) were imaged by OCT and eight features were extracted. A linear model classifier was trained using 34 samples and 22 samples were used to test the model. Sensitivity of 91.6% and specificity of 90% were obtained. Our results demonstrate the capability of a computer-aided technique for accurately and automatically identifying burn tissue resection margins during surgical treatment.

Novel Sample-handling Approach for XRD Analysis with Minimal Sample Preparation

NASA Technical Reports Server (NTRS)

Sarrazin, P.; Chipera, S.; Bish, D.; Blake, D.; Feldman, S.; Vaniman, D.; Bryson, C.

2004-01-01

Sample preparation and sample handling are among the most critical operations associated with X-ray diffraction (XRD) analysis. These operations require attention in a laboratory environment, but they become a major constraint in the deployment of XRD instruments for robotic planetary exploration. We are developing a novel sample handling system that dramatically relaxes the constraints on sample preparation by allowing characterization of coarse-grained material that would normally be impossible to analyze with conventional powder-XRD techniques.

Computer program determines exact two-sided tolerance limits for normal distributions

NASA Technical Reports Server (NTRS)

Friedman, H. A.; Webb, S. R.

1968-01-01

Computer program determines by numerical integration the exact statistical two-sided tolerance limits, when the proportion between the limits is at least a specified number. The program is limited to situations in which the underlying probability distribution for the population sampled is the normal distribution with unknown mean and variance.

Confidence bounds for normal and lognormal distribution coefficients of variation

Treesearch

Steve Verrill

2003-01-01

This paper compares the so-called exact approach for obtaining confidence intervals on normal distribution coefficients of variation to approximate methods. Approximate approaches were found to perform less well than the exact approach for large coefficients of variation and small sample sizes. Web-based computer programs are described for calculating confidence...

Normalization Regression Estimation With Application to a Nonorthogonal, Nonrecursive Model of School Learning.

ERIC Educational Resources Information Center

Bulcock, J. W.; And Others

Advantages of normalization regression estimation over ridge regression estimation are demonstrated by reference to Bloom's model of school learning. Theoretical concern centered on the structure of scholastic achievement at grade 10 in Canadian high schools. Data on 886 students were randomly sampled from the Carnegie Human Resources Data Bank.…

Self-Regulation during Pretend Play in Children with Intellectual Disability and in Normally Developing Children

ERIC Educational Resources Information Center

Vieillevoye, Sandrine; Nader-Grosbois, Nathalie

2008-01-01

This study investigated the symbolic behavior and the self-regulation in dyads of children with intellectual disability and of normally developing children. Specifically, these processes were studied in link with the children's characteristics (mental age, linguistic level, individual pretend play level). The sample included 80 participants, 40…

Normalization of mass cytometry data with bead standards

PubMed Central

Finck, Rachel; Simonds, Erin F.; Jager, Astraea; Krishnaswamy, Smita; Sachs, Karen; Fantl, Wendy; Pe’er, Dana; Nolan, Garry P.; Bendall, Sean C.

2013-01-01

Mass cytometry uses atomic mass spectrometry combined with isotopically pure reporter elements to currently measure as many as 40 parameters per single cell. As with any quantitative technology, there is a fundamental need for quality assurance and normalization protocols. In the case of mass cytometry, the signal variation over time due to changes in instrument performance combined with intervals between scheduled maintenance must be accounted for and then normalized. Here, samples were mixed with polystyrene beads embedded with metal lanthanides, allowing monitoring of mass cytometry instrument performance over multiple days of data acquisition. The protocol described here includes simultaneous measurements of beads and cells on the mass cytometer, subsequent extraction of the bead-based signature, and the application of an algorithm enabling correction of both short- and long-term signal fluctuations. The variation in the intensity of the beads that remains after normalization may also be used to determine data quality. Application of the algorithm to a one-month longitudinal analysis of a human peripheral blood sample reduced the range of median signal fluctuation from 4.9-fold to 1.3-fold. PMID:23512433

Effect of rapid rigor mortis processes on protein functionality in pectoralis major muscle of domestic turkeys.

PubMed

Pietrzak, M; Greaser, M L; Sosnicki, A A

1997-08-01

The pale, soft, exudative (PSE) phenomenon in turkey pectoralis major (breast) muscle was studied using a combination of biochemical, meat quality, microscopic, and gel electrophoresis techniques. Breast muscle samples were collected from turkeys characterized by slow vs fast postmortem glycolysis assessed by muscle pH at 20 min after death. The PSE group was characterized by lower muscle ATP (P < .05) and higher lactate levels (P < .05) compared with the normal group. Excess water-holding capacity and cooking yield were significantly lower (P < .05) in the PSE group than in normal turkeys. Breast muscle of the PSE group was also lighter (P < .05) than that in the normal group as determined by Minolta L* values. The SDS-PAGE, Western blotting, and immunofluorescence microscopy revealed that phosphorylase, a soluble enzyme, became tightly associated with the myofibrils in muscle from the PSE group. Also, less myosin could be solubilized from PSE vs normal myofibril samples. The results indicate that irreversible myosin insolubility due to low pH and high-temperature conditions is decisive in the development of PSE turkey breast muscle.

Comparing the social skills of students addicted to computer games with normal students.

PubMed

Zamani, Eshrat; Kheradmand, Ali; Cheshmi, Maliheh; Abedi, Ahmad; Hedayati, Nasim

2010-01-01

This study aimed to investigate and compare the social skills of studentsaddicted to computer games with normal students. The dependentvariable in the present study is the social skills. The study population included all the students in the second grade ofpublic secondary school in the city of Isfahan at the educational year of2009-2010. The sample size included 564 students selected using thecluster random sampling method. Data collection was conducted usingQuestionnaire of Addiction to Computer Games and Social SkillsQuestionnaire (The Teenage Inventory of Social Skill or TISS). The results of the study showed that generally, there was a significantdifference between the social skills of students addicted to computer gamesand normal students. In addition, the results indicated that normal studentshad a higher level of social skills in comparison with students addicted tocomputer games. As the study results showed, addiction to computer games may affectthe quality and quantity of social skills. In other words, the higher theaddiction to computer games, the less the social skills. The individualsaddicted to computer games have less social skills.).

Comparing the Social Skills of Students Addicted to Computer Games with Normal Students

PubMed Central

Zamani, Eshrat; Kheradmand, Ali; Cheshmi, Maliheh; Abedi, Ahmad; Hedayati, Nasim

2010-01-01

Background This study aimed to investigate and compare the social skills of studentsaddicted to computer games with normal students. The dependentvariable in the present study is the social skills. Methods The study population included all the students in the second grade ofpublic secondary school in the city of Isfahan at the educational year of2009-2010. The sample size included 564 students selected using thecluster random sampling method. Data collection was conducted usingQuestionnaire of Addiction to Computer Games and Social SkillsQuestionnaire (The Teenage Inventory of Social Skill or TISS). Findings The results of the study showed that generally, there was a significantdifference between the social skills of students addicted to computer gamesand normal students. In addition, the results indicated that normal studentshad a higher level of social skills in comparison with students addicted tocomputer games. Conclusion As the study results showed, addiction to computer games may affectthe quality and quantity of social skills. In other words, the higher theaddiction to computer games, the less the social skills. The individualsaddicted to computer games have less social skills.). PMID:24494102

Empirical evaluation of data normalization methods for molecular classification

PubMed Central

Huang, Huei-Chung

2018-01-01

Background Data artifacts due to variations in experimental handling are ubiquitous in microarray studies, and they can lead to biased and irreproducible findings. A popular approach to correct for such artifacts is through post hoc data adjustment such as data normalization. Statistical methods for data normalization have been developed and evaluated primarily for the discovery of individual molecular biomarkers. Their performance has rarely been studied for the development of multi-marker molecular classifiers—an increasingly important application of microarrays in the era of personalized medicine. Methods In this study, we set out to evaluate the performance of three commonly used methods for data normalization in the context of molecular classification, using extensive simulations based on re-sampling from a unique pair of microRNA microarray datasets for the same set of samples. The data and code for our simulations are freely available as R packages at GitHub. Results In the presence of confounding handling effects, all three normalization methods tended to improve the accuracy of the classifier when evaluated in an independent test data. The level of improvement and the relative performance among the normalization methods depended on the relative level of molecular signal, the distributional pattern of handling effects (e.g., location shift vs scale change), and the statistical method used for building the classifier. In addition, cross-validation was associated with biased estimation of classification accuracy in the over-optimistic direction for all three normalization methods. Conclusion Normalization may improve the accuracy of molecular classification for data with confounding handling effects; however, it cannot circumvent the over-optimistic findings associated with cross-validation for assessing classification accuracy. PMID:29666754

Improved Discovery of Molecular Interactions in Genome-Scale Data with Adaptive Model-Based Normalization

PubMed Central

Brown, Patrick O.

2013-01-01

Background High throughput molecular-interaction studies using immunoprecipitations (IP) or affinity purifications are powerful and widely used in biology research. One of many important applications of this method is to identify the set of RNAs that interact with a particular RNA-binding protein (RBP). Here, the unique statistical challenge presented is to delineate a specific set of RNAs that are enriched in one sample relative to another, typically a specific IP compared to a non-specific control to model background. The choice of normalization procedure critically impacts the number of RNAs that will be identified as interacting with an RBP at a given significance threshold – yet existing normalization methods make assumptions that are often fundamentally inaccurate when applied to IP enrichment data. Methods In this paper, we present a new normalization methodology that is specifically designed for identifying enriched RNA or DNA sequences in an IP. The normalization (called adaptive or AD normalization) uses a basic model of the IP experiment and is not a variant of mean, quantile, or other methodology previously proposed. The approach is evaluated statistically and tested with simulated and empirical data. Results and Conclusions The adaptive (AD) normalization method results in a greatly increased range in the number of enriched RNAs identified, fewer false positives, and overall better concordance with independent biological evidence, for the RBPs we analyzed, compared to median normalization. The approach is also applicable to the study of pairwise RNA, DNA and protein interactions such as the analysis of transcription factors via chromatin immunoprecipitation (ChIP) or any other experiments where samples from two conditions, one of which contains an enriched subset of the other, are studied. PMID:23349766

77 FR 6666 - Airworthiness Directives; CFM International, S.A. Turbofan Engines

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-09

... International, S.A. model CFM56-5B series turbofan engines. This AD was prompted by a normal quality sampling at... quality sampling at CFM International. S.A. that isolated a production batch of fan blades with...

Predicting the toxicity of sediment-associated trace metals with simultaneously extracted trace metal: Acid-volatile sulfide concentrations and dry weight-normalized concentrations: A critical comparison

USGS Publications Warehouse

Long, E.R.; MacDonald, D.D.; Cubbage, J.C.; Ingersoll, C.G.

1998-01-01

The relative abilities of sediment concentrations of simultaneously extracted trace metal: acid-volatile sulfide (SEM: AVS) and dry weight-normalized trace metals to correctly predict both toxicity and nontoxicity were compared by analysis of 77 field-collected samples. Relative to the SEM:AVS concentrations, sediment guidelines based upon dry weight-normalized concentrations were equally or slightly more accurate in predicting both nontoxic and toxic results in laboratory tests.

Effect of Elicitation Variables on Analysis of Language Samples for Normal and Language-Disordered Children.

ERIC Educational Resources Information Center

Fields, Thomas A.; Ashmore, Lear L.

1980-01-01

Expressive language samples were obtained from 20 children in four location-stimulus combinations and from wireless radio telemetry. No significant differences existed between the locations of home and clinic, but significant differences were noted among samples elicited using pictures as opposed to open-ended questions as compared to telemetry…

An Investigation of the Sample Performance of Two Nonnormality Corrections for RMSEA

ERIC Educational Resources Information Center

Brosseau-Liard, Patricia E.; Savalei, Victoria; Li, Libo

2012-01-01

The root mean square error of approximation (RMSEA) is a popular fit index in structural equation modeling (SEM). Typically, RMSEA is computed using the normal theory maximum likelihood (ML) fit function. Under nonnormality, the uncorrected sample estimate of the ML RMSEA tends to be inflated. Two robust corrections to the sample ML RMSEA have…

7 CFR 42.123 - Flow diagram for skip lot sampling and inspection.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 2 2014-01-01 2014-01-01 false Flow diagram for skip lot sampling and inspection. 42.123 Section 42.123 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING... Procedures § 42.123 Flow diagram for skip lot sampling and inspection. EC02SE91.000 Notes: 1. Only normal...