Linear Parsing Expression Grammars

PEGs were formalized by Ford in 2004, and have several pragmatic operators (such as ordered choice and unlimited lookahead) for better expressing modern programming language syntax. Since these operators are not explicitly defined in the classic formal language theory, it is significant and still challenging to argue PEGs' expressiveness in the context of formal language theory.Since PEGs are relatively new, there are several unsolved problems.One of the problems is revealing a subclass of PEGs that is equivalent to DFAs. This allows application of some techniques from the theory of regular grammar to PEGs. In this paper, we define Linear PEGs (LPEGs), a subclass of PEGs that is equivalent to DFAs. Surprisingly, LPEGs are formalized by only excluding some patterns of recursive nonterminal in PEGs, and include the full set of ordered choice, unlimited lookahead, and greedy repetition, which are characteristic of PEGs. Although the conversion judgement of parsing expressions into DFAs is undecidable in general, the formalism of LPEGs allows for a syntactical judgement of parsing expressions.Comment: Parsing expression grammars, Boolean finite automata, Packrat parsin

A JAFROC study of nodule detection performance in CT images of a thorax acquired during PET/CT

Purpose Two types of CT images (modalities) are acquired in PET/CT: for attenuation correction (AC) and diagnosis. The purpose of the study was to compare nodule detection and localization performance between these two modalities. Methods CT images, using both modalities, of an anthropomorphic chest phantom containing zero or more simulated spherical nodules of 5, 8, 10 and 12 mm diameters and contrasts −800, −630 and 100 HU were acquired. An observer performance study using nine observers interpreting 45 normal (zero nodules) images and 47 abnormal images (1–3 nodules; average 1.26) was conducted using the free-response receiver operating characteristic (FROC) paradigm. Data were analysed using an R software package implemented jackknife alternative FROC (JAFROC) analysis. Both empirical areas under the equally weighted AFROC curve (wAFROC) and under the highest rating inferred ROC (HR-ROC) curve were used as figures of merit (FOM). To control the probability of Type I error test alpha was set at 0.05. Results Nodule detection as measured by either FOM was significantly better on the diagnostic quality images (2nd modality), irrespective of the method of analysis, [reader averaged inter-modality wAFROC FOM difference = −0.07 (−0.11,−0.04); reader averaged inter-modality HR-ROC FOM difference = −0.05 (−0.09, −0.01)]. Conclusion Nodule detection was statistically worse on images acquired for AC; suggesting that images acquired for AC should not be used to evaluate pulmonary pathology. Keywords PET/CT; Nodule detection; JAFRO

The impact of simulated motion blur on lesion detection performance in full field digital mammography

Objective: Motion blur is a known phenomenon in full-field digital mammography, but the impact on lesion detection is unknown. This is the first study to investigate detection performance with varying magnitudes of simulated motion blur. Method: Seven observers (15±5 years’ reporting experience) evaluated 248 cases (62 containing malignant masses, 62 containing malignant microcalcifications and 124 normal cases) for three conditions: no blurring (0 mm) and two magnitudes of simulated blurring (0.7 mm and 1.5 mm). Abnormal cases were biopsy proven. Mathematical simulation was used to provide a pixel shift in order to simulate motion blur. A free-response observer study was conducted to compare lesion detection performance for the three conditions. The equally weighted jackknife alternative free-response receiver operating characteristic (wJAFROC) was used as the figure of merit. Test alpha was set at 0.05 to control probability of Type I error. Results: wJAFROC analysis found a statistically significant difference in lesion detection performance for both masses (F(2,22) = 6.01, P=0.0084) and microcalcifications (F(2,49) = 23.14, P<0.0001). The figures of merit reduced as the magnitude of simulated blurring increased. Statistical differences were found between some of the pairs investigated for the detection of masses (0.0mm v 0.7mm, and 0.0mm v 1.5mm) and all pairs for microcalcifications (0.0 mm v 0.7 mm, 0.0 mm v 1.5 mm, and 0.7 mm v 1.5 mm). No difference was detected between 0.7 mm and 1.5 mm for masses. Conclusion: Mathematical simulation of motion blur caused a statistically significant reduction in lesion detection performance. These false negative decisions could have implications for clinical practice. Advances in knowledge: This research demonstrates for the first time that motion blur has a negative and statistically significant impact on lesion detection performance digital mammography

Magnetars and pulsars: a missing link

There is growing evidence that soft gamma-ray repeaters (SGRs) and anomalous X-ray pulsars (AXPs) are isolated neutron stars with superstrong magnetic fields, i.e., magnetars, marking them a distinguished species from the conventional species of spindown-powered isolated neutron stars, i.e., radio pulsars. The current arguments in favor of the magnetar interpretation of SGR/AXP phenomenology will be outlined, and the two energy sources in magnetars, i.e. a magnetic dissipation energy and a spindown energy, will be reviewed. I will then discuss a missing link between magnetars and pulsars, i.e., lack of the observational evidence of the spindown-powered behaviors in known magnetars. Some recent theoretical efforts in studying such behaviors will be reviewed along with some predictions testable in the near future.Comment: Invited talk at the Sixth Pacific Rim Conference on Stellar Astrophysics, a tribute to Helmut A. Abt, July 11-17, 2002, Xi'an. To appear in the proceedings (eds. K. S. Cheng, K. C. Leung & T. P. Li

Effect of reconstruction methods and x-ray tube current-time product on nodule detection in an anthropomorphic thorax phantom : a crossed-modality JAFROC observer study

Purpose: To evaluate nodule detection in an anthropomorphic chest phantom in computed tomography (CT) images reconstructed with adaptive iterative dose reduction 3D (AIDR3D) and filtered back projection (FBP) over a range of tube current-time product (mAs). Methods: Two phantoms were used in this study: (i) an anthropomorphic chest phantom was loaded with spherical simulated nodules of 5, 8, 10 and 12mm in diameter and +100, -630 and -800 Hounsfied Units electron density; this would generate CT images for the observer study; (ii) a whole-body dosimetry verification phantom was used to ultimately estimate effective dose and risk according to the model of the BEIR VII committee. Both phantoms were scanned over a mAs range (10, 20, 30, and 40) while all other acquisition parameters remained constant. Images were reconstructed with both AIDR3D and FBP. 34 normal cases (no nodules) and 34 abnormal cases (containing 1-3 nodules, mean 1.35±0.54) cases were chosen for the observer study. Eleven observers evaluated images from all tube current-time product and reconstruction methods under the free-response paradigm. A crossed-modality jackknife alternative free-response operating characteristic (JAFROC) analysis method was developed for data analysis, averaging data over the two factors influencing nodule detection in this study: mAs and image reconstruction (AIDR3D or FBP). A Bonferroni correction was applied and the threshold for declaring significance was set at 0.025 to maintain the overall probability of Type I error at α = 0.05. Contrast-to-noise (CNR) was also measured for all nodules and evaluated by a linear least squares analysis. Results: For random-reader fixed-case crossed-modality JAFROC analysis there was no significant difference in nodule detection between AIDR3D and FBP when data was averaged over mAs (F(1,10) = 0.08, p = 0.789). However, when data was averaged over reconstruction methods, a significant difference was seen between multiple pairs of mAs settings (F(3,30) = 15.96, p<0.001). Measurements of effective dose and effective risk showed the expected linear dependence on mAs. Nodule CNR was statistically higher for simulated nodules on images reconstructed with AIDR3D (p<0.001). Conclusion: No significant difference in nodule detection performance was demonstrated between images reconstructed with FBP and AIDR3D. Tube current-time product was found to influence nodule detection, though further work is required for dose optimisation

Patient initiated clinics for patients with chronic or recurrent conditions managed in secondary care: a systematic review of patient reported outcomes and patient and clinician satisfaction

This is the final version of the article. Available from BioMed Central via the DOI in this record.BACKGROUND: The cost to the NHS of missed or inappropriate hospital appointments is considerable. Alternative methods of appointment scheduling might be more flexible to patients' needs without jeopardising health and service quality. The objective was to systematically review evidence of patient initiated clinics in secondary care on patient reported outcomes among patients with chronic/recurrent conditions. METHODS: Seven databases were searched from inception to June 2013. Hand searching of included studies references was also conducted. Studies comparing the effects of patient initiated clinics with traditional consultant led clinics in secondary care for patients with long term chronic or recurrent diseases on health related quality of life and/or patient satisfaction were included. Data was extracted by one reviewer and checked by a second. Results were synthesised narratively. RESULTS: Seven studies were included in the review, these covered a total of 1,655 participants across three conditions: breast cancer, inflammatory bowel disease and rheumatoid arthritis. Quality of reporting was variable. Results showed no significant differences between the intervention and control groups for psychological and health related quality of life outcomes indicating no evidence of harm. Some patients reported significantly more satisfaction using patient-initiated clinics than usual care (p < 0.001). CONCLUSIONS: The results show potential for patient initiated clinics to result in greater patient and clinician satisfaction. The patient-consultant relationship appeared to play an important part in patient satisfaction and should be considered an important area of future research as should the presence or absence of a guidebook to aid self-management. Patient initiated clinics fit the models of care suggested by policy makers and so further research into long term outcomes for patients and service use in this area of practice is both relevant and timely.This systematic review was funded by the National Institute of Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care (CLAHRC) for the South West. The views expressed in this publication are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health

The clinical effectiveness of patient initiated clinics for patients with chronic or recurrent conditions managed in secondary care: a systematic review

This is the final version of the article. Available from Public Library of Science via the DOI in this record.BACKGROUND: Missed or inappropriate hospital appointments cost the UK National Health Service millions of pounds each year and delay treatment for other patients. Innovative methods of appointment scheduling that are more flexible to patient needs, may improve service quality and preserve resources. METHODS: A systematic review of the evidence for the clinical effectiveness of patient initiated clinics in managing long term care for people with chronic or recurrent conditions in secondary care. Seven databases were searched including MEDLINE, Embase and PsycINFO (using the OVID interface), the Cochrane Library of Systematic Reviews and CENTRAL, Science Citation Index Expanded, Social Sciences Citation Index, and Conference Proceedings Citation Index (via the Web of Science interface) from inception to June 2013. Studies comparing patient initiated clinics with traditional consultant-led clinics in secondary care for people with long term chronic or recurrent diseases were included. Included studies had to provide data on clinical or resource use outcomes. Data were extracted and checked by two reviewers using a piloted, standardised data extraction form. RESULTS: Eight studies (n = 1927 individuals) were included. All were conducted in the UK. There were few significant differences in clinical outcomes between the intervention and control groups. In some instances, using the patient initiated clinics model was associated with savings in time and resource use. The risk of harm from using the patient initiated clinic model of organising outpatient care is low. Studies with longer follow-up periods are needed to assess the long term costs and the ongoing risk of potential harms. CONCLUSIONS: The UK policy context is ripe for evidence-based, patient-centred services to be implemented, especially where the use of health care resources can be optimised without reducing the quality of care. Implementation of patient initiated clinics should remain cautious, with importance placed on ongoing evaluation of long term outcomes and costs.This systematic review was funded by the National Institute of Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care for the South West. The views expressed in this publication are those of the author(s) and not necessarily those of the National Health Service, the NIHR or the Department of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

A Method for Serial Tissue Processing and Parallel Analysis of Aberrant Crypt Morphology, Mucin Depletion, and Beta-Catenin Staining in an Experimental Model of Colon Carcinogenesis

The use of architectural and morphological characteristics of cells for establishing prognostic indicators by which individual pathologies are assigned grade and stage is a well-accepted practice. Advances in automated micro- and macroscopic image acquisition and digital image analysis have created new opportunities in the field of prognostic assessment; but, one area in experimental pathology, animal models for colon cancer, has not taken advantage of these opportunities. This situation is primarily due to the methods available to evaluate the colon of the rodent for the presence of premalignant and malignant pathologies. We report a new method for the excision and processing of the entire colon of the rat and illustrate how this procedure permitted the quantitative assessment of aberrant crypt foci (ACF), a premalignant colon pathology, for characteristics consistent with progression to malignancy. ACF were detected by methylene blue staining and subjected to quantitative morphometric analysis. Colons were then restained with high iron diamine–alcian blue for assessment of mucin depletion using an image overlay to associate morphometric data with mucin depletion. The subsequent evaluation of ACF for beta-catenin staining is also demonstrated. The methods described are particularly relevant to the screening of compounds for cancer chemopreventive activity

Vascular tissue contractility changes following late gestational exposure to multi-walled carbon nanotubes or their dispersing vehicle in Sprague Dawley rats

Multi-walled carbon nanotubes (MWCNTs) are increasingly used in industry and in nanomedicine raising safety concerns, especially during unique life-stages such as pregnancy. We hypothesized that MWCNT exposure during pregnancy will increase vascular tissue contractile responses by increasing Rho kinase signaling. Pregnant (17-19 gestational days) and non-pregnant Sprague Dawley rats were exposed to 100 μg/kg of MWCNTs by intratracheal instillation or intravenous administration. Vasoactive responses of uterine, mesenteric, aortic and umbilical vessels were studied 24 hours post-exposure by wire myography. The contractile responses of the vessel segments were different between the pregnant and non-pregnant rats, following MWCNT exposure. Maximum stress generation in the uterine artery segments from the pregnant rats following pulmonary MWCNT exposure was increased in response to angiotensin II by 4.9 mN/mm2 (+118%), as compared to the naïve response and by 2.6 mN/mm2 (+40.7%) as compared to the vehicle exposed group. Following MWCNT exposure, serotonin induced approximately 4 mN/mm2 increase in stress generation of the mesenteric artery from both pregnant and non-pregnant rats as compared to the vehicle response. A significant contribution of the dispersion medium was identified as inducing changes in the contractile properties following both pulmonary and intravenous exposure to MWCNTs. Wire myographic studies in the presence of a Rho kinase inhibitor and RhoA and Rho kinase mRNA/protein expression of rat aortic endothelial cells were unaltered following exposure to MWCNTs, suggesting absent/minimal contribution of Rho kinase to the enhanced contractile responses following MWCNT exposure. The reactivity of the umbilical vein was not changed; however, mean fetal weight gain was reduced with dispersion media and MWCNT exposure by both routes. These results suggest a susceptibility of the vasculature during gestation to MWCNT and their dispersion media-induced vasoconstriction, predisposing reduced fetal growth during pregnancy

SHRIMP zircon geochronology of the Emeishan Large Igneous Province (SW China): implications for double mass extinctions in Late Permian

Abstract in http://www.lpi.usra.edu/meetings/gold2001/pdf/3519.pd