Influence of convective transport on tropospheric ozone and its precursors in a chemistry-climate model

The impact of convection on tropospheric O₃ and its precursors has been examined in a coupled chemistry-climate model. There are two ways that convection affects O₃. First, convection affects O₃ by vertical mixing of O₃ itself. Convection lifts lower tropospheric air to regions where the O₃ lifetime is longer, whilst mass-balance subsidence mixes O₃-rich upper tropospheric (UT) air downwards to regions where the O₃ lifetime is shorter. This tends to decrease UT O₃ and the overall tropospheric column of O₃. Secondly, convection affects O₃ by vertical mixing of O₃ precursors. This affects O₃ chemical production and destruction. Convection transports isoprene and its degradation products to the UT where they interact with lightning NO_x to produce PAN, at the expense of NO_x. In our model, we find that convection reduces UT NO_x through this mechanism; convective down-mixing also flattens our imposed profile of lightning emissions, further reducing UT NO_x. Over tropical land, which has large lightning NO_x emissions in the UT, we find convective lofting of NO_x from surface sources appears relatively unimportant. Despite UT NO_x decreases, UT O₃ production increases as a result of UT HO_x increases driven by isoprene oxidation chemistry. However, UT O₃ tends to decrease, as the effect of convective overturning of O₃ itself dominates over changes in O₃ chemistry. Convective transport also reduces UT O₃ in the mid-latitudes resulting in a 13% decrease in the global tropospheric O₃ burden. These results contrast with an earlier study that uses a model of similar chemical complexity. Differences in convection schemes as well as chemistry schemes – in particular isoprene-driven changes are the most likely causes of such discrepancies. Further modelling studies are needed to constrain this uncertainty range

Is query translation a distinct task from search?

INTRODUCTION The University of Sheffield participated in iCLEF 2002 using, as a test-bed, the prototype under development in the Clarity project. Clarity is an EU funded project aimed at developing a system for cross-language information retrieval for so-called low density languages, those with few translation resources. Currently translation between English and Finnish is supported; soon Swedish will be added and in the near future Latvian and Lithuanian. Clarity is being developed in a user-centred way with user involvement from the beginning. The design of the first user interface was based on current best practise, particular attention was paid to empirical evidence for a specific design choice. Six paper-based interface mock-ups representing important points in the cross-language search task were generated and presented for user assessment as a part of an extensive user study. The study (reported in Petrelli et al. 2002) was conducted to understand users and uses of cross-language information retrieval systems. Many different techniques were applied: contextual enquiry, interviews, questionnaires, informal evaluation of existing cross-language technology, and participatory design sessions with the interface mock-ups mentioned above. As a result, a user class profile was sketched and a long list of user requirements was compiled. As a followup, a redesign session took place and the new system was designed for users whoknow the language(s) they are searching (polyglots); • search for writing (journalists, translators business analysts); • have limited searching skills; • know the topic in advance or will learn/read on it while searching; • use many languages in the same search session and often swap between them. New system features were listed as important and the user interface was redesigned. Considering the result of the study the new interface allowed the user to dynamically change the language setting from query to query, hid the query translation and showed the retrieved set as ranked list primary. Despite the fact that this new design was considered to be more effective, a comparison between the first layout based on the relevant literature and the new one based on the user study was considered an important research question. In particular, the choice of hiding the query translation was considered an important design decision, against the common agreement to allow and support the user in controlling the system actions. Thus the participation of Sheffield in iCLEF was organized around the idea of checking if the user should validate the query translation before the search is run or instead if the system should perform the translation and search in a single step without any user’s supervision

Barriers to the use of a diagnostic oral microbiology laboratory by general dental practitioners

OBJECTIVE: To identify barriers on the use of diagnostic microbiology facilities in general dental practice. DESIGN: A cross-sectional survey using a postal questionnaire. SETTING: Primary/secondary care interface between the diagnostic oral microbiology laboratory, University of Glasgow Dental Hospital and School, Glasgow and dental practitioners within the surrounding health boards, 1998. SUBJECTS: All GDPs (797) within Argyll and Clyde, Ayrshire and Arran, Lanarkshire and Greater Glasgow Health Boards. MAIN OUTCOME MEASURES: The responses were expressed as both absolute and relative frequencies. RESULTS: Responses were received from 430 (55%). The most frequent reason for failure to use the service was lack of information, with more than half of the respondents claiming to be unaware of the facility. Lack of request forms and sampling equipment were also viewed as barriers to using the service. CONCLUSIONS: The laboratory is failing to successfully communicate its role in addressing the growing burden of antibiotic resistance in the community and must be more proactive in encouraging appropriate use and increasing accessibility of the service to GDPs

An evaluation resource for geographic information retrieval

In this paper we present an evaluation resource for geographic information retrieval developed within the Cross Language Evaluation Forum (CLEF). The GeoCLEF track is dedicated to the evaluation of geographic information retrieval systems. The resource encompasses more than 600,000 documents, 75 topics so far, and more than 100,000 relevance judgments for these topics. Geographic information retrieval requires an evaluation resource which represents realistic information needs and which is geographically challenging. Some experimental results and analysis are reported

Following basal stem rot in young oil palm plantings

The PCR primer GanET has previously been shown to be suitable for the specific amplification of DNA from Ganoderma boninense. A DNA extraction and PCR method has been developed that allows for the amplification of the G. boninense DNA from environmental samples of oil palm tissue. The GanET primer reaction was used in conjunction with a palm-sampling programme to investigate the possible infection of young palms through cut frond base surfaces. Ganoderma DNA was detected in frond base material at a greater frequency than would be expected by comparison with current infection levels. Comparisons are made between the height of the frond base infected, the number of frond bases infected, and subsequent development of basal stem rot. The preliminary results suggest that the development of basal stem rot may be more likely to occur when young lower frond bases are infected

Cross-lingual document retrieval categorisation and navigation based on distributed services

The widespread use of the Internet across countries has increased the need for access to document collections that are often written in languages different from a user’s native language. In this paper we describe Clarity, a Cross Language Information Retrieval (CLIR) system for English, Finnish, Swedish, Latvian and Lithuanian. Clarity is a fully-fledged retrieval system that supports the user during the whole process of query formulation, text retrieval and document browsing. We address four of the major aspects of Clarity: (i) the user-driven methodology that formed the basis for the iterative design cycle and framework in the project, (ii) the system architecture that was developed to support the interaction and coordination of Clarity’s distributed services, (iii) the data resources and methods for query translation, and (iv) the support for Baltic languages. Clarity is an example of a distributed CLIR system built with minimal translation resources and, to our knowledge, the only such system that currently supports Baltic languages

GeoCLEF 2007: the CLEF 2007 cross-language geographic information retrieval track overview

GeoCLEF ran as a regular track for the second time within the Cross Language Evaluation Forum (CLEF) 2007. The purpose of GeoCLEF is to test and evaluate cross-language geographic information retrieval (GIR): retrieval for topics with a geographic specification. GeoCLEF 2007 consisted of two sub tasks. A search task ran for the third time and a query classification task was organized for the first. For the GeoCLEF 2007 search task, twenty-five search topics were defined by the organizing groups for searching English, German, Portuguese and Spanish document collections. All topics were translated into English, Indonesian, Portuguese, Spanish and German. Several topics in 2007 were geographically challenging. Thirteen groups submitted 108 runs. The groups used a variety of approaches. For the classification task, a query log from a search engine was provided and the groups needed to identify the queries with a geographic scope and the geographic components within the local queries

A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum

Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large‐scale proteogenomics study of two important apicomplexan pathogens: Toxoplasma gondii and Neospora caninum. We queried proteomics data against a panel of official and alternate gene models generated directly from RNASeq data, using several newly generated and some previously published MS datasets for this meta‐analysis. We identified a total of 201 996 and 39 953 peptide‐spectrum matches for T. gondii and N. caninum, respectively, at a 1% peptide FDR threshold. This equated to the identification of 30 494 distinct peptide sequences and 2921 proteins (matches to official gene models) for T. gondii, and 8911 peptides/1273 proteins for N. caninum following stringent protein‐level thresholding. We have also identified 289 and 140 loci for T. gondii and N. caninum, respectively, which mapped to RNA‐Seq‐derived gene models used in our analysis and apparently absent from the official annotation (release 10 from EuPathDB) of these species. We present several examples in our study where the RNA‐Seq evidence can help in correction of the current gene model and can help in discovery of potential new genes

LoCuSS: The steady decline and slow quenching of star formation in cluster galaxies over the last four billion years

We present an analysis of the levels and evolution of star formation activity in a representative sample of 30 massive galaxy clusters at 0.15<z<0.30 from the Local Cluster Substructure Survey (LoCuSS), combining wide-field Spitzer 24um data with extensive spectroscopy of cluster members. The specific-SFRs of massive (M>10^10 M_sun) star-forming cluster galaxies within r200 are found to be systematically 28% lower than their counterparts in the field at fixed stellar mass and redshift, a difference significant at the 8.7-sigma level. This is the unambiguous signature of star formation in most (and possibly all) massive star-forming galaxies being slowly quenched upon accretion into massive clusters, their SFRs declining exponentially on quenching time-scales in the range 0.7-2.0 Gyr. We measure the mid-infrared Butcher-Oemler effect over the redshift range 0.0-0.4, finding rapid evolution in the fraction (f_SF) of massive (M_K3M_sun/yr, of the form f_SF (1+z)^7.6. We dissect the origins of the Butcher-Oemler effect, revealing it to be due to the combination of a ~3x decline in the mean specific-SFRs of star-forming cluster galaxies since z~0.3 with a ~1.5x decrease in number density. Two-thirds of this reduction in the specific-SFRs of star-forming cluster galaxies is due to the steady cosmic decline in the specific-SFRs among those field galaxies accreted into the clusters. The remaining one-third reflects an accelerated decline in the star formation activity of galaxies within clusters. The slow quenching of star-formation in cluster galaxies is consistent with a gradual shut down of star formation in infalling spiral galaxies as they interact with the intra-cluster medium via ram-pressure stripping or starvation mechanisms. We find no evidence for the build-up of cluster S0 bulges via major nuclear star-burst episodes.Comment: 24 pages, 12 figures. Accepted for publication in Ap