PAN AIR: A computer program for predicting subsonic or supersonic linear potential flows about arbitrary configurations using a higher order panel method. Volume 4: Maintenance document (version 3.0)

The Maintenance Document Version 3.0 is a guide to the PAN AIR software system, a system which computes the subsonic or supersonic linear potential flow about a body of nearly arbitrary shape, using a higher order panel method. The document describes the overall system and each program module of the system. Sufficient detail is given for program maintenance, updating, and modification. It is assumed that the reader is familiar with programming and CRAY computer systems. The PAN AIR system was written in FORTRAN 4 language except for a few CAL language subroutines which exist in the PAN AIR library. Structured programming techniques were used to provide code documentation and maintainability. The operating systems accommodated are COS 1.11, COS 1.12, COS 1.13, and COS 1.14 on the CRAY 1S, 1M, and X-MP computing systems. The system is comprised of a data base management system, a program library, an execution control module, and nine separate FORTRAN technical modules. Each module calculates part of the posed PAN AIR problem. The data base manager is used to communicate between modules and within modules. The technical modules must be run in a prescribed fashion for each PAN AIR problem. In order to ease the problem of supplying the many JCL cards required to execute the modules, a set of CRAY procedures (PAPROCS) was created to automatically supply most of the JCL cards. Most of this document has not changed for Version 3.0. It now, however, strictly applies only to PAN AIR version 3.0. The major changes are: (1) additional sections covering the new FDP module (which calculates streamlines and offbody points); (2) a complete rewrite of the section on the MAG module; and (3) strict applicability to CRAY computing systems

2-Aminoacetophenone as a potential breath biomarker for Pseudomonas aeruginosa in the cystic fibrosis lung

<p>Abstract</p> <p>Background</p> <p><it>Pseudomonas aeruginosa </it>infections are associated with progressive life threatening decline of lung function in cystic fibrosis sufferers. Growth of <it>Ps. aeruginosa </it>releases a "grape-like" odour that has been identified as the microbial volatile organic compound 2-aminoacetophenone (2-AA).</p> <p>Methods</p> <p>We investigated 2-AA for its specificity to <it>Ps. aeruginosa </it>and its suitability as a potential breath biomarker of colonisation or infection by Solid Phase Micro Extraction and Gas Chromatography-Mass Spectrometry (GC/MS).</p> <p>Results</p> <p>Cultures of 20 clinical strains of <it>Ps. aeruginosa </it>but not other respiratory pathogens had high concentrations of 2-AA in the head space of <it>in vitro </it>cultures when analysed by GC/MS. 2-AA was stable for 6 hours in deactivated glass sampling bulbs but was not stable in Tedlar^®bags. Optimisation of GC/MS allowed detection levels of 2-AA to low pico mol/mol range in breath. The 2-AA was detected in a significantly higher proportion of subjects colonised with <it>Ps. aeruginosa </it>15/16 (93.7%) than both the healthy controls 5/17 (29%) (p < 0.0002) and CF patients not colonised with <it>Ps. aeruginosa </it>4/13(30.7%) (p < 0.001). The sensitivity and specificity of the 2-AA breath test compared to isolation of <it>Ps. aeruginosa </it>in sputum and/or BALF was 93.8% (95% CI, 67-99) and 69.2% (95% CI, 38-89) respectively. The peak integration values for 2-AA analysis in the breath samples were significantly higher in <it>Ps. aeruginosa </it>colonised subjects (median 242, range 0-1243) than the healthy controls (median 0, range 0-161; p < 0.001) and CF subjects not colonised with <it>Ps. aeruginosa </it>(median 0, range 0-287; p < 0.003)</p> <p>Conclusions</p> <p>Our results report 2-AA as a promising breath biomarker for the detection of <it>Ps. aeruginosa </it>infections in the cystic fibrosis lung.</p

Visible-light-induced intramolecular charge transfer in the radical spirocyclisation of indole-tethered ynones

Indole-tethered ynones form an intramolecular electron donor-acceptor complex that can undergo visible-light-induced charge transfer to promote thiyl radical generation from thiols. This initiates a novel radical chain sequence, based on dearomatising spirocyclisation with concomitant C-S bond formation. Sulfur-containing spirocycles are formed in high yields using this simple and mild synthetic protocol, in which neither transition metal catalysts nor photocatalysts are required. The proposed mechanism is supported by various mechanistic studies, and the unusual radical initiation mode represents only the second report of the use of an intramolecular electron donor-acceptor complex in synthesis

Hand-rolled cigarette smoking patterns compared with factory-made cigarette smoking in New Zealand men

<p>Abstract</p> <p>Background</p> <p>Roll-your-own (RYO) cigarettes have increased in popularity, yet their comparative potential toxicity is uncertain. This study compares smoking of RYO and factory-made (FM) cigarettes on smoking pattern and immediate potential toxicity.</p> <p>Methods</p> <p>At a research clinic, 26 RYO and 22 FM volunteer male cigarette smokers, (addicted and overnight-tobacco-abstinent) each smoked 4 filter cigarettes, one half-hourly over 2 hours, either RYO or FM according to usual habit, using the CReSSMicro flowmeter. First cigarette smoked was their own brand. Subsequent cigarettes, all Holiday regular brand, were RYOs (0.5 g tobacco with filter), or FM with filter. Cravings on 100 mm visual analogue scale, and exhaled carbon monoxide (CO) were measured before and after each cigarette smoked.</p> <p>Results</p> <p>Smokers reported similar daily cigarette consumption (RYO 19.0, FM 17.4, p = 0.45), and similar time after waking to first cigarette. (RYO 6.1 minutes, FM 8.6 minutes, p = 0.113). First cigarette's RYO tobacco (0.45 g) weighed less than for FM (0.7 g, p < 0.001); less tobacco was burnt (0.36 g, FM 0.55 g, p < 0.001) but smoking patterns were no different. RYO smokers smoked subsequent cigarettes more intensively; inhaled 28% more smoke per cigarette (RYO 952 mL, FM 743 mL, p = 0.025); took 25% more puffs (RYO 16.9, FM 13.6, p = 0.035); puffed longer (RYO 28 seconds, FM 22 seconds, p = 0.012), taking similar puffs (RYO 57 mL, FM 59 mL). Over four cigarettes, RYOs boosted alveolar CO (RYO 13.8 ppm, FM 13.8 ppm), and reduced cravings (RYO 53%, FM 52%) no differently from FM cigarettes.</p> <p>Conclusion</p> <p>In these smokers, RYO smoking was associated with increased smoke exposure per cigarette, and similar CO breath levels, and even with filters is apparently no less and possibly more dangerous than FM smoking. Specific package warnings should warn of RYO smoking's true risk. RYOs are currently taxed much less than FM cigarettes in most countries; similar harm merits similar excise per cigarette.</p

The New Zealand 1986 very low birth weight cohort as young adults: mapping the road ahead

Background: Very low birth weight (less than 1500 g) is associated with increased morbidity and costs of health care in childhood. Emerging evidence suggests these infants face a range of health and social problems as young adults. We studied all New Zealand very low birth weight infants born in 1986 (when 58 % were exposed to antenatal corticosteroids) in infancy, with later follow-up at 7 to 8 years and 23 to 24 years. We now aim to assess the cohort at 26–28 years compared with controls. Methods/design The case sample will comprise a minimum of 250 members of the 1986 New Zealand national very low birth weight cohort (77 % of survivors). Outcomes will be compared with a control group of 100 young adults born at term in 1986. Following written informed consent, participants will travel to Christchurch for 2 days of assessments undertaken by experienced staff. Medical assessments include growth measures, vision, respiratory function, blood pressure and echocardiogram, renal function, dental examination and blood tests. Cognitive and neuropsychological functioning will be assessed with standard tests, and mental health and social functioning by participant interview. A telephone interview will be conducted with a parent or significant other person nominated by the respondent to gain a further perspective on the young person’s health and functioning. All those born at less than 28 weeks’ gestation, plus a random subset of the cohort to a total of 150 cases and 50 controls, will be offered cranial magnetic-resonance imaging. Statistical analysis will examine comparison with controls and long-term trajectories for the very low birth weight cohort. Discussion The research will provide crucial New Zealand data on the young adult outcomes for very low birth weight infants and address gaps in the international literature, particularly regarding cardiovascular, respiratory, visual and neurocognitive outcomes. These data will inform future neonatal care, provide evidence-based guidelines for care of preterm graduates transitioning to adult care, and help shape health education and social policies for this high risk group. Trial registration Australian New Zealand Clinical Trials Registry ACTRN12612000995875. Registered 1 October 2012 Electronic supplementary material The online version of this article (doi:10.1186/s12887-015-0413-9) contains supplementary material, which is available to authorized users

Individual and cumulative effects of GWAS susceptibility loci in lung cancer: associations after sub-phenotyping for COPD.

Epidemiological studies show that approximately 20-30% of chronic smokers develop chronic obstructive pulmonary disease (COPD) while 10-15% develop lung cancer. COPD pre-exists lung cancer in 50-90% of cases and has a heritability of 40-77%, much greater than for lung cancer with heritability of 15-25%. These data suggest that smokers susceptible to COPD may also be susceptible to lung cancer. This study examines the association of several overlapping chromosomal loci, recently implicated by GWA studies in COPD, lung function and lung cancer, in (n = 1400) subjects sub-phenotyped for the presence of COPD and matched for smoking exposure. Using this approach we show; the 15q25 locus confers susceptibility to lung cancer and COPD, the 4q31 and 4q22 loci both confer a reduced risk to both COPD and lung cancer, the 6p21 locus confers susceptibility to lung cancer in smokers with pre-existing COPD, the 5p15 and 1q23 loci both confer susceptibility to lung cancer in those with no pre-existing COPD. We also show the 5q33 locus, previously associated with reduced FEV(1), appears to confer susceptibility to both COPD and lung cancer. The 6p21 locus previously linked to reduced FEV(1) is associated with COPD only. Larger studies will be needed to distinguish whether these COPD-related effects may reflect, in part, associations specific to different lung cancer histology. We demonstrate that when the "risk genotypes" derived from the univariate analysis are incorporated into an algorithm with clinical variables, independently associated with lung cancer in multivariate analysis, modest discrimination is possible on receiver operator curve analysis (AUC = 0.70). We suggest that genetic susceptibility to lung cancer includes genes conferring susceptibility to COPD and that sub-phenotyping with spirometry is critical to identifying genes underlying the development of lung cancer

Monitoring chloramines and bromamines in a humid environment using selected ion flow tube mass spectrometry

The selectivity and sensitivity of selected ion flow tube mass spectrometry (SIFT-MS) for individual breath analysis of haloamines has been improved by heating the flow tube in a commercial instrument to around 106°C. Data is presented showing the marked reduction in the number density of water clusters of product ions of common breath metabolites that are isobaric with the product ions from monochloramine and monobromamine that are used to monitor the haloamine concentrations. These results have direct relevance to the real-time monitoring of chloramines in drinking water, swimming pools and food processing plants. However, once the isobaric overlaps from water cluster ions are reduced at the higher temperatures, there is no conclusive evidence showing the presence of haloamines on single breath exhalations in the mid parts per trillion range from examination of the breaths of volunteers