Ion-Atom/Argon - Calculation of ionization cross sections by fast ion impact for neutral target atoms ranging from hydrogen to argon

A FORTRAN 90 program is presented which calculates the total cross sections, and the electron energy spectra of the singly and doubly differential cross sections for the single target ionization of neutral atoms ranging from hydrogen up to and including argon. The code is applicable for the case of both high and low Z projectile impact in fast ion-atom collisions. The theoretical models provided for the program user are based on two quantum mechanical approximations which have proved to be very successful in the study of ionization in ion-atom collisions. These are the continuum-distorted-wave (CDW) and continuum-distorted-wave eikonal-initial-state (CDW-EIS) approximations. The codes presented here extend previously published. codes for single ionization of. target hydrogen [Crothers and McCartney, Comput. Phys. Commun. 72 (1992) 288], target helium [Nesbitt, O'Rourke and Crothers, Comput. Phys. Commun. 114 (1998) 385] and target atoms ranging from lithium to neon [O'Rourke, McSherry and Crothers, Comput. Phys. Commun. 131 (2000) 129]. Cross sections for all of these target atoms may be obtained as limiting cases from the present code. Title of program: ARGON Catalogue identifier: ADSE Program summary URL: http://cpc.cs.qub.ac.uk/cpc/summaries/ADSE Program obtainable from: CPC Program Library Queen's University of Belfast, N. Ireland Licensing provisions: none Computer for which the program is designed and others on which it is operable: Computers: Four by 200 MHz Pro Pentium Linux server, DEC Alpha 21164; Four by 400 MHz Pentium 2 Xeon 450 Linux server, IBM SP2 and SUN Enterprise 3500 Installations: Queen's University, Belfast Operating systems under which the program has been tested: Red-hat Linux 5.2, Digital UNIX Version 4.0d, AIX, Solaris SunOS 5.7 Compilers: PGI workstations, DEC CAMPUS Programming language used: FORTRAN 90 with MPI directives No. of bits in a word: 64, except on Linux servers 32 Number of processors used: any number Has the code been vectorized or parallelized? Parallelized using MPI No. of bytes in distributed program, including test data, etc.: 32 189 Distribution format: tar gzip file Keywords: Single ionization, cross sections, continuum-distorted-wave model, continuum- distorted-wave eikonal-initial-state model, target atoms, wave treatment Nature of physical problem: The code calculates total, and differential cross sections for the single ionization of target atoms ranging from hydrogen up to and including argon by both light and heavy ion impact. Method of solution: ARGON allows the user to calculate the cross sections using either the CDW or CDW-EIS [J. Phys. B 16 (1983) 3229] models within the wave treatment. Restrictions on the complexity of the program: Both the CDW and CDW-EIS models are two-state perturbative approximations. Typical running time: Times vary according to input data and number of processors. For one processor the test input data for double differential cross sections (40 points) took less than one second, whereas the test input for total cross sections (20 points) took 32 minutes. Unusual features of the program: none (C) 2003 Elsevier B.V All rights reserved.

Sensitivity and specificity of frequency-doubling technology, tendency-oriented perimetry, and Humphrey Swedish interactive threshold algorithm-fast perimetry in a glaucoma practice

PURPOSE: To evaluate the sensitivity and specificity of the screening mode of the Humphrey-Welch Allyn frequency-doubling technology (FDT), Octopus tendency-oriented perimetry (TOP), and the Humphrey Swedish Interactive Threshold Algorithm (SITA)-fast (HSF) in patients with glaucoma. DESIGN: A comparative consecutive case series. METHODS: This was a prospective study which took place in the glaucoma unit of an academic department of ophthalmology. One eye of 70 consecutive glaucoma patients and 28 age-matched normal subjects was studied. Eyes were examined with the program C-20 of FDT, G1-TOP, and 24-2 HSF in one visit and in random order. The gold standard for glaucoma was presence of a typical glaucomatous optic disk appearance on stereoscopic examination, which was judged by a glaucoma expert. The sensitivity and specificity, positive and negative predictive value, and receiver operating characteristic (ROC) curves of two algorithms for the FDT screening test, two algorithms for TOP, and three algorithms for HSF, as defined before the start of this study, were evaluated. The time required for each test was also analyzed. RESULTS: Values for area under the ROC curve ranged from 82.5%-93.9%. The largest area (93.9%) under the ROC curve was obtained with the FDT criteria, defining abnormality as presence of at least one abnormal location. Mean test time was 1.08 ± 0.28 minutes, 2.31 ± 0.28 minutes, and 4.14 ± 0.57 minutes for the FDT, TOP, and HSF, respectively. The difference in testing time was statistically significant (P <.0001). CONCLUSIONS: The C-20 FDT, G1-TOP, and 24-2 HSF appear to be useful tools to diagnose glaucoma. The test C-20 FDT and G1-TOP take approximately 1/4 and 1/2 of the time taken by 24 to 2 HSF. © 2002 by Elsevier Science Inc. All rights reserved.

Comparison of two fast strategies, SITA fast and TOP, for the assessment of visual fields in glaucoma patients

Purpose: To compare two fast threshold strategies of visual field assessment; SITA Fast (HSF) and Tendency Orientated Perimetry (TOP), in detecting visual field loss in patients with glaucoma. Methods: Seventy-six glaucoma, ocular hypertensive and normal patients had HSF and TOP performed in random order. Quantitative comparisons for the global visual field indices - mean deviation and defect (MD) for HSF and TOP, and pattern standard deviation (PSD) for HSF and loss variance (LV) for TOP - were made using correlation coefficients. Humphrey global parameters were converted to Octopus equivalents, and method comparison analysis was used to determine agreement between the two strategies. Test duration times were compared using t-test. Sensitivity and specificity for these two algorithms were determined according to predetermined criteria. Results: High correlation coefficient values were obtained for MD measurements between HSF and TOP (r=-0.89, P

Diagnostic accuracy of loop-mediated isothermal amplification as a near-patient test for meningococcal disease in children: An observational cohort study

Background: Diagnosis of meningococcal disease relies on recognition of clinical signs and symptoms that are notoriously non-specific, variable, and often absent in the early stages of the disease. Loop-mediated isothermal amplification (LAMP) has previously been shown to be fast and effective for the molecular detection of meningococcal DNA in clinical specimens. We aimed to assess the diagnostic accuracy of meningococcal LAMP as a near-patient test in the emergency department.

Methods: For this observational cohort study of diagnostic accuracy, children aged 0-13 years presenting to the emergency department of the Royal Belfast Hospital for Sick Children (Belfast, UK) with suspected meningococcal disease were eligible for inclusion. Patients underwent a standard meningococcal pack of investigations testing for meningococcal disease. Respiratory (nasopharyngeal swab) and blood specimens were collected from patients and tested with near-patient meningococcal LAMP and the results were compared with those obtained by reference laboratory tests (culture and PCR of blood and cerebrospinal fluid).

Findings: Between Nov 1, 2009, and Jan 31, 2012, 161 eligible children presenting at the hospital underwent the meningococcal pack of investigations and were tested for meningococcal disease, of whom 148 consented and were enrolled in the study. Combined testing of respiratory and blood specimens with use of LAMP was accurate (sensitivity 89% [95% CI 72-96], specificity 100% [97-100], positive predictive value 100% [85-100]; negative predictive value 98% [93-99]) and diagnostically useful (positive likelihood ratio 213 [95% CI 13-infinity] and negative likelihood ratio 0·11 [0·04-0·32]). The median time required for near-patient testing from sample to result was 1 h 26 min (IQR 1 h 20 min-1 h 32 min).

Interpretation: Meningococcal LAMP is straightforward enough for use in any hospital with basic laboratory facilities, and near-patient testing with this method is both feasible and effective. By contrast with existing UK National Institute of Health and Care Excellence guidelines, we showed that molecular testing of non-invasive respiratory specimens from children is diagnostically accurate and clinically useful.

Rapid quantification of microRNAs in plasma using a fast real time PCR system

The ability to rapidly detect circulating small RNAs, in particular microRNAs (miRNAs), would further increase their already established potential as biomarkers in a range of conditions. One rate-limiting factor is the time taken to perform quantitative real time PCR amplification. We therefore evaluated the ability of a novel thermal cycler to perform this step in less than 10 minutes. Quantitative PCR was performed on an xxpress® thermal cycler (BJS Biotechnologies, Perivale, UK), which employs a resistive heating system and forced air cooling to achieve thermal ramp rates of 10 °C/s, and a conventional peltier-controlled LightCycler 480 system (Roche, Basel, Switzerland) ramping at 4.8 °C/s. The threshold cycle (Ct) for detection of 18S rDNA from a standard genomic DNA sample was significantly more variable across the block (F-test, p=2.4x10-25) for the xxpress (20.01±0.47SD) than the LightCycler (19.87±0.04SD). RNA was extracted from human plasma, reverse transcribed and a panel of miRNAs amplified and detected using SYBR green (Kapa Biosystems, Wilmington, Ma, USA). The sensitivity of both systems was broadly comparable and both detected a panel of miRNAs reliably and indicated similar relative abundances. The xxpress thermal cycler facilitates rapid qPCR detection of small RNAs and brings point-of care diagnostics based upon circulating miRNAs a step closer to reality.

Test-retest variability in structural and functional parameters of glaucoma damage in the glaucoma imaging longitudinal study.

PURPOSE:

To determine the test-retest variability in perimetric, optic disc, and macular thickness parameters in a cohort of treated patients with established glaucoma.

PATIENTS AND METHODS:

In this cohort study, the authors analyzed the imaging studies and visual field tests at the baseline and 6-month visits of 162 eyes of 162 participant in the Glaucoma Imaging Longitudinal Study (GILS). They assessed the difference, expressed as the standard error of measurement, of Humphrey field analyzer II (HFA) Swedish Interactive Threshold Algorithm fast, Heidelberg retinal tomograph (HRT) II, and retinal thickness analyzer (RTA) parameters between the two visits and assumed that this difference was due to measurement variability, not pathologic change. A statistically significant change was defined as twice the standard error of measurement.

RESULTS:

In this cohort of treated glaucoma patients, it was found that statistically significant changes were 3.2 dB for mean deviation (MD), 2.2 for pattern standard deviation (PSD), 0.12 for cup shape measure, 0.26 mm for rim area, and 32.8 microm and 31.8 microm for superior and inferior macular thickness, respectively. On the basis of these values, it was estimated that the number of potential progression events detectable in this cohort by the parameters of MD, PSD, cup shape measure, rim area, superior macular thickness, and inferior macular thickness was 7.5, 6.0, 2.3, 5.7, 3.1, and 3.4, respectively.

CONCLUSIONS:

The variability of the measurements of MD, PSD, and rim area, relative to the range of possible values, is less than the variability of cup shape measure or macular thickness measurements. Therefore, the former measurements may be more useful global measurements for assessing progressive glaucoma damage.