Software Infrastructure for Natural Language Processing

We classify and review current approaches to software infrastructure for research, development and delivery of NLP systems. The task is motivated by a discussion of current trends in the field of NLP and Language Engineering. We describe a system called GATE (a General Architecture for Text Engineering) that provides a software infrastructure on top of which heterogeneous NLP processing modules may be evaluated and refined individually, or may be combined into larger application systems. GATE aims to support both researchers and developers working on component technologies (e.g. parsing, tagging, morphological analysis) and those working on developing end-user applications (e.g. information extraction, text summarisation, document generation, machine translation, and second language learning). GATE promotes reuse of component technology, permits specialisation and collaboration in large-scale projects, and allows for the comparison and evaluation of alternative technologies. The first release of GATE is now available - see http://www.dcs.shef.ac.uk/research/groups/nlp/gate/Comment: LaTeX, uses aclap.sty, 8 page

Visual Execution and Data Visualisation in Natural Language Processing

We describe GGI, a visual system that allows the user to execute an automatically generated data flow graph containing code modules that perform natural language processing tasks. These code modules operate on text documents. GGI has a suite of text visualisation tools that allows the user useful views of the annotation data that is produced by the modules in the executable graph. GGI forms part of the GATE natural language engineering system

Farm-gate phosphorus balances and soil phosphorus concentrations on intensive dairy farms in the south-west of Ireland

peer-reviewedThis project was part funded by the European Research and Development Fund under INTERREG IIIB: Green Dairy Project Number 100 and partly by the Dairy Levy. Financial support for post-graduate students involved in this study was provided by the Teagasc Walsh Fellowship Scheme.Phosphorus (P) loss to water is a significant threat to water quality in Ireland. Agriculture is an important source of this P. There is concern about balancing agronomic requirements and environmental protection in regulations prescribing P management on farms. This study examined farm-gate (P) balances and soil test P (STP) concentrations on 21 dairy farms in the south west of Ireland over four years, from 2003 to 2006 inclusive. Stocking density on the farms averaged 2.4 (s.d. = 0.4) livestock units (LU) per ha. Annual mean import of P onto farms was 21.6 (1.9) kg P/ha. Fertilizer P accounted for 47% (0.041), concentrates 35% (0.060) and organic manures 18% (0.034) of imported P. The mean annual P balance per farm was 9.4 (1.2) kg/ha, ranging from –3 to 47 kg/ha and mean P use efficiency was 0.71 (0.05) ranging from 0.24 to 1.37. The mean STP per farm following extraction using Morgan’s solution was 8.15 (2.9) mg/L of soil and ranged from 4.4 (2.2) to 14.7 (6.4) mg/L. There was a positive relationship (R2 = 0.34; P < 0.01) between STP and P balance; farms with a deficit of P tended to have agronomically sub-optimal STP and vice versa. The high between- and withinfarm variation in STP indicates that farmers were either unaware or were not making efficient use of STP results, and consequently there was agronomically sub-optimal soil P status in some fields and potentially environmentally damaging excesses on others (often within one farm). There was considerable potential to improve P management practices on these farms with clear agronomic and environmental benefits.European UnionTeagasc Walsh Fellowship ProgrammeDairy Levy Fun

GATE -- an Environment to Support Research and Development in Natural Language Engineering

We describe a software environment to support research and development in natural language (NL) engineering. This environment -- GATE (General Architecture for Text Engineering) -- aims to advance research in the area of machine processing of natural languages by providing a software infrastructure on top of which heterogeneous NL component modules may be evaluated and refined individually or may be combined into larger application systems. Thus, GATE aims to support both researchers and developers working on component technologies (e.g. parsing, tagging, morphological analysis) and those working on developing end-user applications (e.g. information extraction, text summarisation, document generation, machine translation, and second language learning). GATE will promote reuse of component technology, permit specialisation and collaboration in large-scale projects, and allow for the comparison and evaluation of alternative technologies. The first release of GATE is now available

Farm-gate nitrogen balances on intensive dairy farms in the south west of Ireland

peer-reviewedNitrogen management and farm-gate N balances were evaluated on 21 intensive dairy farms in the south west of Ireland for each of four years (2003 to 2006). The mean annual stocking density was equivalent to 202 kg/ha (s.d. 29.6) of N excreted by livestock on the farm. The mean annual farm-gate N surplus (imports – exports) declined between 2003 and 2006 (277 to 232 kg/ha, s.e. 6.8; P < 0.001) due to a decline in annual N imports (fertilizer, feed and imported manures; 335 to 288 kg/ha, s.e. 6.9; P < 0.001). Overall annual fertilizer N use on the farms decreased during the study period (266 to 223 kg/ha, s.e. 6.5; P < 0.001) mainly due to lower inputs for the first application in spring and for the production of first-cut silage. These decreases were partly offset by applying more slurry in spring for early grazing and for first-cut silage. The introduction of white clover resulted in lower N imports on four farms. Export of N from farms was unaffected by reductions in N imports. The mean efficiency of N use tended to increase over time (0.18 in 2003 to 0.20 in 2006). The large variation in quantities of fertilizer N applied on farms with similar stocking densities suggests potential for further improvements in the efficiency of N use. In terms of fertilizer N use, complying with S.I. No. 378 of 2006 did not require major changes in the N management practiceson 19 of the farms.This project was part-funded by the European Research and Development Fund under INTERREG IIIB: Green Dairy Project N° 100 and partly by the Dairy Levy. Financial support for post-graduate students involved in this study was provided by the Teagasc Walsh Fellowship Scheme

Nutrient management on intensive dairy farms in the southwest of Ireland

End of Project ReportIntensive grass-based dairy farming relies on high inputs of nutrients that are now regulated under SI 378, 2006 (Good Agricultural Practice for Protection of Waters). This project studied nutrient management practices on twenty-one intensive dairy farms in the south-west of Ireland between 2003 and 2006. Mean stocking rate was 202 kg organic-N/ha deposited by grazing livestock. Overall fertiliser-N use on the farms decreased from 266 to 223 kg N/ha/yr during the study, with the rate of fertiliser-N in the first application each year decreasing from 49 to 33 kg N/ha, while the rate of fertiliser-N applied for first cut silage production also fell from 106 to 96 kg N/ha. These decreases were partly achieved by applying more slurry in springtime and by the introduction of white clover on five of the farms. While the limits on fertiliser-N use under SI 378 were exceeded on ten farms in 2003, the limits were exceeded on only two farms in 2006. Fertiliser-P usage declined from 12.0 to 10.2 kg P/ha/yr, and complied with the limits of SI 378 on thirteen of the farms in 2006. Mean Morgan’s extractable soil P concentration (STP) exceeded 10 mg/l on five farms, while the mean concentration exceeded 8 mg/l on ten farms. Phosphorus management, therefore, was close to that required by SI 378 on most farms. Slurry storage capacity met or exceeded the minimum requirements of SI 378 on eight farms; substantial investment in slurry storage facilities was necessary on thirteen farms. The mean N surplus on the farms declined from 277 to 232 kg N/ha/yr during the study due to a decline in total N input from 335 to 288 kg N/ha/yr over the same period. The mean efficiency of N-use increased from 17.9 to 20.2 %. The large variation in rates of fertiliser-N applied on farms with similar stocking rates suggests potential for further improvements in N use efficiency on some farms. Decreases in nutrient input levels can be partly attributed to increased farmer awareness, due to advice and record keeping from this study and the introduction of SI 378, and the increasing cost of nutrient inputs relative to output prices. In terms of fertiliser N and P use and soil P concentrations, complying with the limits in SI 378 does not require major changes in nutrient management practices on the majority of these intensive dairy farms

Comparing Segmentation by Time and by Motion in Visual Search: An fMRI Investigation

Abstract Brain activity was recorded while participants engaged in a difficult visual search task for a target defined by the spatial configuration of its component elements. The search displays were segmented by time (a preview then a search display), by motion, or were unsegmented. A preparatory network showed activity to the preview display, in the time but not in the motion segmentation condition. A region of the precuneus showed (i) higher activation when displays were segmented by time or by motion, and (ii) correlated activity with larger segmentation benefits behaviorally, regardless of the cue. Additionally, the results revealed that success in temporal segmentation was correlated with reduced activation in early visual areas, including V1. The results depict partially overlapping brain networks for segmentation in search by time and motion, with both cue-independent and cue-specific mechanisms.</jats:p

Parallel distractor rejection as a binding mechanism in search

The relatively common experimental visual search task of finding a red X amongst red O’s and green X’s (conjunction search) presents the visual system with a binding problem. Illusory conjunctions (ICs) of features across objects must be avoided and only features present in the same object bound together. Correct binding into unique objects by the visual system may be promoted, and ICs minimized, by inhibiting the locations of distractors possessing non-target features (e.g., Treisman and Sato, 1990). Such parallel rejection of interfering distractors leaves the target as the only item competing for selection; thus solving the binding problem. In the present article we explore the theoretical and empirical basis of this process of active distractor inhibition in search. Specific experiments that provide strong evidence for a process of active distractor inhibition in search are highlighted. In the final part of the article we consider how distractor inhibition, as defined here, may be realized at a neurophysiological level (Treisman and Sato, 1990)

Parallel distractor rejection as a binding mechanism in search

The relatively common experimental visual search task of finding a red X amongst red O’s and green X’s (conjunction search) presents the visual system with a binding problem. Illusory conjunctions (ICs) of features across objects must be avoided and only features present in the same object bound together. Correct binding into unique objects by the visual system may be promoted, and ICs minimized, by inhibiting the locations of distractors possessing non-target features (e.g., Treisman and Sato, 1990). Such parallel rejection of interfering distractors leaves the target as the only item competing for selection; thus solving the binding problem. In the present article we explore the theoretical and empirical basis of this process of active distractor inhibition in search. Specific experiments that provide strong evidence for a process of active distractor inhibition in search are highlighted. In the final part of the article we consider how distractor inhibition, as defined here, may be realized at a neurophysiological level (Treisman and Sato, 1990)

Early Contrast Enhancement: a novel Magnetic Resonance Imaging biomarker of pleural malignancy

Introduction: Pleural Malignancy (PM) is often occult on subjective radiological assessment. We sought to define a novel, semi-objective Magnetic Resonance Imaging (MRI) biomarker of PM, targeted to increased tumour microvessel density (MVD) and applicable to minimal pleural thickening. Materials and methods: 60 consecutive patients with suspected PM underwent contrast-enhanced 3-T MRI then pleural biopsy. In 58/60, parietal pleura signal intensity (SI) was measured in multiple regions of interest (ROI) at multiple time-points, generating ROI SI/time curves and Mean SI gradient (MSIG: SI increment/time). The diagnostic performance of Early Contrast Enhancement (ECE; which was defined as a SI peak in at least one ROI at or before 4.5 min) was compared with subjective MRI and Computed Tomography (CT) morphology results. MSIG was correlated against tumour MVD (based on Factor VIII immunostain) in 31 patients with Mesothelioma. Results: 71% (41/58) patients had PM. Pleural thickening was &#60;10 mm in 49/58 (84%). ECE sensitivity was 83% (95% CI 61–94%), specificity 83% (95% CI 68–91%), positive predictive value 68% (95% CI 47–84%), negative predictive value 92% (78–97%). ECE performance was similar or superior to subjective CT and MRI. MSIG correlated with MVD (r = 0.4258, p = .02). Discussion: ECE is a semi-objective, perfusion-based biomarker of PM, measurable in minimal pleural thickening. Further studies are warranted