Automatic measurement of propositional idea density from part-of-speech tagging

The original publication is available at www.springerlink.comThe Computerized Propositional Idea Density Rater (CPIDR, pronounced “spider”) is a computer program that determines the propositional idea density (P-density) of an English text automatically on the basis of partof-speech tags. The key idea is that propositions correspond roughly to verbs, adjectives, adverbs, prepositions, and conjunctions. After tagging the parts of speech using MontyLingua (Liu, 2004), CPIDR applies numerous rules to adjust the count, such as combining auxiliary verbs with the main verb. A “speech mode” is provided in which CPIDR rejects repetitions and a wider range of fillers. CPIDR is a user-friendly Windows .NET application distributed as open-source freeware under GPL. Tested against human raters, it agrees with the consensus of two human raters better than the team of five raters agree with each other [r(80) = .97 vs. r(10) = .82, respectively]

Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development

Transcript abundance of roughly a third of expressed Arabidopsis thaliana genes is circadian-regulated

Pre-analytical and analytical variables that influence urinary volatile organic compound measurements

There has been rapidly accelerating interest in the utilization of volatile organic compounds (VOCs) as non-invasive methods for rapid point-of-care medical diagnostics. There is widespread variation in analytical methods and protocols, with little understanding of the effects of sample storage on VOC profiles. This study aimed to determine the effects on VOC profiles of different storage times, at room temperature, prior to freezing, of sealed urine samples from healthy individuals. Analysis using Field Asymmetric Ion Motility Spectrometry (FAIMS) determined the alterations in VOC and total ion count profiles as a result of increasing room temperature storage times. Results indicated that increasing exposure time to room temperature prior to freezing had a threefold effect. Firstly, increased urinary VOC profile variability, with a plateau phase between 12 and 48 hours, before further degradation. Secondly, an increase in total ion count with time exposed to room temperature. Finally, a deterioration in VOCs with each sample run during the analysis process. This provides new insight into the effect of storage of urine samples for VOC analysis using FAIMS technology. Results of this study provide a recommendation for a 12-hour maximum duration at room temperature prior to storage

Minimal Gluten Exposure Alters Urinary Volatile Organic Compounds in Stable Coeliac Disease

Coeliac disease (CD) patients are distinguishable from healthy individuals via urinary volatile organic compounds (VOCs) analysis. We exposed 20 stable CD patients on gluten-free diet (GFDs) to a 14-day, 3 g/day gluten challenge (GCh), and assessed urinary VOC changes. A control cohort of 20 patients continued on GFD. Urine samples from Days 0, 7, 14, 28 and 56 were analysed using Lonestar FAIMS and Markes Gas Chromatography−Time of Flight−Mass Spectrometer (GC-TOF-MS). VOC signatures on D (day) 7−56 were compared with D0. Statistical analysis was performed using R. In GCh patients, FAIMS revealed significant VOC differences for all time points compared to D0. GC-TOF-MS revealed significant changes at D7 and D14 only. In control samples, FAIMS revealed significant differences at D7 only. GC-TOF-MS detected no significant differences. Chemical analysis via GC-MS-TOF revealed 12 chemicals with significantly altered intensities at D7 vs. D0 for GCh patients. The alterations persisted for six chemicals at D14 and one (N-methyltaurine) remained altered after D14. This low-dose, short-duration challenge was well tolerated. FAIMS and GC-TOF-MS detected VOC signature changes in CD patients when undergoing a minimal GCh. These findings suggest urinary VOCs could have a role in monitoring dietary compliance in CD patients

Breathomics—exhaled volatile organic compound analysis to detect hepatic encephalopathy : a pilot study

he current diagnostic challenge with diagnosing hepatic encephalopathy (HE) is identifying those with minimal HE as opposed to the more clinically apparent covert/overt HE. Rifaximin, is an effective therapy but earlier identification and treatment of HE could prevent liver disease progression and hospitalization. Our pilot study aimed to analyse breath samples of patients with different HE grades, and controls, using a portable electronic (e) nose. 42 patients were enrolled; 22 with HE and 20 controls. Bedside breath samples were captured and analysed using an uvFAIMS machine (portable e-nose). West Haven criteria applied and MELD scores calculated. We classify HE patients from controls with a sensitivity and specificity of 0.88 (0.73-0.95) and 0.68 (0.51-0.81) respectively, AUROC 0.84 (0.75-0.93). Minimal HE was distinguishable from covert/overt HE with sensitivity of 0.79 and specificity of 0.5, AUROC 0.71 (0.57-0.84). This pilot study has highlighted the potential of breathomics to identify VOCs signatures in HE patients for diagnostic purposes. Importantly this was performed utilizing a non-invasive, portable bedside device and holds potential for future early HE diagnosis

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day. Synchronized transcriptome cycling is driven through an extensive network of diurnal and clock-regulated transcription factors and their target cis-regulatory elements. Study of the cycling transcriptome in other plant species could thus help elucidate the similarities and differences and identify hubs of regulation common to monocot and dicot plants.Using a combination of oligonucleotide microarrays and data mining pipelines, we examined daily rhythms in gene expression in one monocotyledonous and one dicotyledonous plant, rice and poplar, respectively. Cycling transcriptomes were interrogated under different diurnal (driven) and circadian (free running) light and temperature conditions. Collectively, photocycles and thermocycles regulated about 60% of the expressed nuclear genes in rice and poplar. Depending on the condition tested, up to one third of oscillating Arabidopsis-poplar-rice orthologs were phased within three hours of each other suggesting a high degree of conservation in terms of rhythmic gene expression. We identified clusters of rhythmically co-expressed genes and searched their promoter sequences to identify phase-specific cis-elements, including elements that were conserved in the promoters of Arabidopsis, poplar, and rice.Our results show that the cycling patterns of many circadian clock genes are highly conserved across poplar, rice, and Arabidopsis. The expression of many orthologous genes in key metabolic and regulatory pathways is diurnal and/or circadian regulated and phased to similar times of day. Our results confirm previous findings in Arabidopsis of three major classes of cis-regulatory modules within the plant circadian network: the morning (ME, GBOX), evening (EE, GATA), and midnight (PBX/TBX/SBX) modules. Identification of identical overrepresented motifs in the promoters of cycling genes from different species suggests that the core diurnal/circadian cis-regulatory network is deeply conserved between mono- and dicotyledonous species

Interference effects in the photorecombination of argonlike Sc3+ ions: Storage-ring experiment and theory

Absolute total electron-ion recombination rate coefficients of argonlike Sc3+(3s2 3p6) ions have been measured for relative energies between electrons and ions ranging from 0 to 45 eV. This energy range comprises all dielectronic recombination resonances attached to 3p -> 3d and 3p -> 4s excitations. A broad resonance with an experimental width of 0.89 +- 0.07 eV due to the 3p5 3d2 2F intermediate state is found at 12.31 +- 0.03 eV with a small experimental evidence for an asymmetric line shape. From R-Matrix and perturbative calculations we infer that the asymmetric line shape may not only be due to quantum mechanical interference between direct and resonant recombination channels as predicted by Gorczyca et al. [Phys. Rev. A 56, 4742 (1997)], but may partly also be due to the interaction with an adjacent overlapping DR resonance of the same symmetry. The overall agreement between theory and experiment is poor. Differences between our experimental and our theoretical resonance positions are as large as 1.4 eV. This illustrates the difficulty to accurately describe the structure of an atomic system with an open 3d-shell with state-of-the-art theoretical methods. Furthermore, we find that a relativistic theoretical treatment of the system under study is mandatory since the existence of experimentally observed strong 3p5 3d2 2D and 3p5 3d 4s 2D resonances can only be explained when calculations beyond LS-coupling are carried out.Comment: 11 pages, 7 figures, 3 tables, Phys. Rev. A (in print), see also: http://www.strz.uni-giessen.de/~k