A scientific approach to agent selection

The prioritisation of potential agents on the basis of likely efficacy is an important step in biological control because it can increase the probability of a successful biocontrol program, and reduce risks and costs. In this introductory paper we define success in biological control, review how agent selection has been approached historically, and outline the approach to agent selection that underpins the structure of this special issue on agent selection. Developing criteria by which to judge the success of a biocontrol agent (or program) provides the basis for agent selection decisions. Criteria will depend on the weed, on the ecological and management context in which that weed occurs, and on the negative impacts that biocontrol is seeking to redress. Predicting which potential agents are most likely to be successful poses enormous scientific challenges. 'Rules of thumb', 'scoring systems' and various conceptual and quantitative modelling approaches have been proposed to aid agent selection. However, most attempts have met with limited success due to the diversity and complexity of the systems in question. This special issue presents a series of papers that deconstruct the question of agent choice with the aim of progressively improving the success rate of biological control. Specifically they ask: (i) what potential agents are available and what should we know about them? (ii) what type, timing and degree of damage is required to achieve success? and (iii) which potential agent will reach the necessary density, at the right time, to exert the required damage in the target environment?

The scientific basis and development of a matrix metalloproteinase (MMP) -8 specific chair-side test for monitoring of periodontal health and disease from gingival crevicular fluid

Matrix metalloproteinase (MMP) -8, collagenase-2, is a key mediator of irreversible tissue destruction in chronic periodontitis and detectable in gingival crevicular fluid (GCF). MMP-8 mostly originates from neutrophil leukocytes, the first line of defence cells which exist abundantly in GCF, especially in inflammation. MMP-8 is capable of degrading almost all extra-cellular matrix and basement membrane components and is especially efficient against type I collagen. Thus the expression of MMP-8 in GCF could be valuable in monitoring the activity of periodontitis and possibly offers a diagnostic means to predict progression of periodontitis. In this study the value of MMP-8 detection from GCF in monitoring of periodontal health and disease was evaluated with special reference to its ability to differentiate periodontal health and different disease states of the periodontium and to recognise the progression of periodontitis, i.e. active sites. For chair-side detection of MMP-8 from the GCF or peri-implant sulcus fluid (PISF) samples, a dip-stick test based on immunochromatography involving two monoclonal antibodies was developed. The immunoassay for the detection of MMP-8 from GCF was found to be more suitable for monitoring of periodontitis than detection of GCF elastase concentration or activity. Periodontally healthy subjects and individuals suffering of gingivitis or of periodontitis could be differentiated by means of GCF MMP-8 levels and dipstick testing when the positive threshold value of the MMP-8 chair-side test was set at 1000 µg/l. MMP-8 dipstick test results from periodontally healthy and from subjects with gingivitis were mainly negative while periodontitis patients sites with deep pockets ( 5 mm) and which were bleeding on probing were most often test positive. Periodontitis patients GCF MMP-8 levels decreased with hygiene phase periodontal treatment (scaling and root planing, SRP) and even reduced during the three month maintenance phase. A decrease in GCF MMP-8 levels could be monitored with the MMP-8 test. Agreement between the test stick and the quantitative assay was very good (κ = 0.81) and the test provided a baseline sensitivity of 0.83 and specificity of 0.96. During the 12-month longitudinal maintenance phase, periodontitis patients progressing sites (sites with an increase in attachment loss ≥ 2 mm during the maintenance phase) had elevated GCF MMP-8 levels compared with stable sites. General mean MMP-8 concentrations in smokers (S) sites were lower than in non-smokers (NS) sites but in progressing S and NS sites concentrations were at an equal level. Sites with exceptionally and repeatedly elevated MMP-8 concentrations during the maintenance phase were clustered in smoking patients with poor response to SRP (refractory patients). These sites especially were identified by the MMP-8 test. Subgingival plaque samples from periodontitis patients deep periodontal pockets were examined by polymerase chain reaction (PCR) to find out if periodontal lesions may serve as a niche for Chlamydia pneumoniae. Findings were compared with the clinical periodontal parameters and GCF MMP-8 levels to determine the correlation with periodontal status. Traces of C. pneumoniae were identified from one periodontitis patient s pooled subgingival plaque sample by means of PCR. After periodontal treatment (SRP) the sample was negative for C. pneumoniae. Clinical parameters or biomarkers (MMP-8) of the patient with the positive C. pneumoniae finding did not differ from other study patients. In this study it was concluded that MMP-8 concentrations in GCF of sites from periodontally healthy individuals, subjects with gingivitis or with periodontitis are at different levels. The cut-off value of the developed MMP-8 test is at an optimal level to differentiate between these conditions and can possibly be utilised in identification of individuals at the risk of the transition of gingivitis to periodontitis. In periodontitis patients, repeatedly elevated GCF MMP-8 concentrations may indicate sites at risk of progression of periodontitis as well as patients with poor response to conventional periodontal treatment (SRP). This can be monitored by MMP-8 testing. Despite the lower mean GCF MMP-8 concentrations in smokers, a fraction of smokers sites expressed very high MMP-8 concentrations together with enhanced periodontal activity and could be identified with MMP-8 specific chair-side test. Deep periodontal lesions may be niches for non-periodontopathogenic micro-organisms with systemic effects like C. pneumoniae and possibly play a role in the transmission from one subject to another.

Australia’s present scientific capacity to progress the biological control of weeds

Australia has a very proud record of achievement in biological control of weeds and the underpinning science. From the earliest campaigns against prickly pear and lantana, weed biocontrol developed with major contributions from CSIRO and state governments to produce outstanding successes against weeds such as salvinia, rubber vine, Noogoora burr, bridal creeper and prickly pear. Maximum research activity occurred in the 1980s when some 30 scientists were working world wide on Australia’s weed problems. Activity declined gradually until the last few years when government divestment in agricultural research greatly diminished capacity. There are now approximately eight full-time scientist equivalents supporting Australia’s weed biocontrol effort. Australia may now need to adopt a team approach to tackle future major weed biological control projects.

Papers of the Jewish Theological Seminary and Scientific Institute

Digital image

High-quality polar UV measurements : scientific analyses and transfer of the irradiance scale

The Earth's ecosystems are protected from the dangerous part of the solar ultraviolet (UV) radiation by stratospheric ozone, which absorbs most of the harmful UV wavelengths. Severe depletion of stratospheric ozone has been observed in the Antarctic region, and to a lesser extent in the Arctic and midlatitudes. Concern about the effects of increasing UV radiation on human beings and the natural environment has led to ground based monitoring of UV radiation. In order to achieve high-quality UV time series for scientific analyses, proper quality control (QC) and quality assurance (QA) procedures have to be followed. In this work, practices of QC and QA are developed for Brewer spectroradiometers and NILU-UV multifilter radiometers, which measure in the Arctic and Antarctic regions, respectively. These practices are applicable to other UV instruments as well. The spectral features and the effect of different factors affecting UV radiation were studied for the spectral UV time series at Sodankylä. The QA of the Finnish Meteorological Institute's (FMI) two Brewer spectroradiometers included daily maintenance, laboratory characterizations, the calculation of long-term spectral responsivity, data processing and quality assessment. New methods for the cosine correction, the temperature correction and the calculation of long-term changes of spectral responsivity were developed. Reconstructed UV irradiances were used as a QA tool for spectroradiometer data. The actual cosine correction factor was found to vary between 1.08-1.12 and 1.08-1.13. The temperature characterization showed a linear temperature dependence between the instrument's internal temperature and the photon counts per cycle. Both Brewers have participated in international spectroradiometer comparisons and have shown good stability. The differences between the Brewers and the portable reference spectroradiometer QASUME have been within 5% during 2002-2010. The features of the spectral UV radiation time series at Sodankylä were analysed for the time period 1990-2001. No statistically significant long-term changes in UV irradiances were found, and the results were strongly dependent on the time period studied. Ozone was the dominant factor affecting UV radiation during the springtime, whereas clouds played a more important role during the summertime. During this work, the Antarctic NILU-UV multifilter radiometer network was established by the Instituto Nacional de Meteorogía (INM) as a joint Spanish-Argentinian-Finnish cooperation project. As part of this work, the QC/QA practices of the network were developed. They included training of the operators, daily maintenance, regular lamp tests and solar comparisons with the travelling reference instrument. Drifts of up to 35% in the sensitivity of the channels of the NILU-UV multifilter radiometers were found during the first four years of operation. This work emphasized the importance of proper QC/QA, including regular lamp tests, for the multifilter radiometers also. The effect of the drifts were corrected by a method scaling the site NILU-UV channels to those of the travelling reference NILU-UV. After correction, the mean ratios of erythemally-weighted UV dose rates measured during solar comparisons between the reference NILU-UV and the site NILU-UVs were 1.007±0.011 and 1.012±0.012 for Ushuaia and Marambio, respectively, when the solar zenith angle varied up to 80°. Solar comparisons between the NILU-UVs and spectroradiometers showed a ±5% difference near local noon time, which can be seen as proof of successful QC/QA procedures and transfer of irradiance scales. This work also showed that UV measurements made in the Arctic and Antarctic can be comparable with each other.

G.W. Leibniz and Scientific Societies

The famous philosopher Leibniz (1646-1716) was also active in the (cultural) politics of his time. His interest in forming scientific societies never waned and his efforts led to the founding of the Berlin Academy of Sciences. He also played a part in the founding of the Dresden Academy of Science and the St. Petersburg Academy of Science. Though Leibniz's models for the scientific society were the Royal Society and the Royal Science Academy of France, his pansophistic vision of scientific cooperation sometimes took on utopian dimensions. In this paper, I will present Leibniz's ideas of scientific cooperation as a kind of religious activity and discuss his various schemes for the founding of such scientific societies.

Lähteiden lumoamat : Henry Biaudet, Liisi Karttunen ja suomalainen historiantutkimus Roomassa 1900-luvun alussa

Enchanted by Sources. Henry Biaudet, Liisi Karttunen and Finnish Historical Research in Rome in the Early Twentieth Century This study traces the scholarly endeavours of Henry Biaudet (1870 1915) and Liisi Karttunen (1880 1957) and "La mission historique finlandaise à Rome" which they founded in 1909. They are forgotten in Finnish historiography, but remain internationally renowned for their contribution to the nunciature studies. By investigating their historical work on the Counter- Reformation era, their roles in the scientific communities of Helsinki and Rome as well as the intersection of politics and science in their scholarly practices the study explores the nature of historical research in general at the turn of the twentieth century. The work covers fields such as historiography, university history and the political use of history. Methodologically the research is based on the analysis and contextualization of published and unpublished sources (e.g. correspondences, university records, scholarly publications and reviews in academic journals). Henry Biaudet criticized the previous research on the Nordic Counter-Reformation for its narrow national scope and sources. He sought out a new approach, including the use of sources in archives all over Europe and the inclusion of the Catholic viewpoint. Accordingly, Biaudet and Karttunen searched for records in archives in Southern Europe. Their unorthodox interpretations were denounced in Finland since the picture they gave of late sixteenth-century Sweden was too different from the national narrative. Moreover, Finnish national identity was firmly rooted in Protestantism, and questioning the benevolence of the Reformation and its main actors was considered as an attack not only against historical truth but also national values. The comparison between Biaudet s and Karttunen s arguments and the accepted narrative in Finland shows how traditional interpretations of the Nordic Reformation were influenced by the Lutheran ethos and European anticlerical rhetoric. Historians have recently paid substantial attention to the political use of history, usually focusing on politicized constructions of the national past. This study shows how research that met the criteria of modern historiography also served political purposes. Conducting research in an international community of historians and publishing ambitious scholarly studies that interested an international audience were ways to create a positive image of Finland abroad. These were not uniquely Finnish ideas but rather ideas shared by the international community of historians in Rome. In this context, scientific pursuits were given a clear political meaning. This enhances our understanding of nineteenth-century historiography being firmly rooted between science and politics.

The Open Access Scientific Journal: An Empirical Study

The open access (OA) model for journals is compared to the open source principle for computer software. Since the early 1990s nearly 1,000 OA scientific journals have emerged – mostly as voluntary community efforts, although recently some professionally operating publishers have used author charges or institutional membership. This study of OA journals without author charges shows that their impact is still relatively small, but awareness of it is increasing. The average number of research articles per year is lower than for major scientific journals but the publication times are shorter.

Open Access to the Scientific Journal Literature: Situation 2009

Background: The Internet has recently made possible the free global availability of scientific journal articles. Open Access (OA) can occur either via OA scientific journals, or via authors posting manuscripts of articles published in subscription journals in open web repositories. So far there have been few systematic studies showing how big the extent of OA is, in particular studies covering all fields of science. Methodology/Principal Findings: The proportion of peer reviewed scholarly journal articles, which are available openly in full text on the web, was studied using a random sample of 1837 titles and a web search engine. Of articles published in 2008, 8,5% were freely available at the publishers’ sites. For an additional 11,9% free manuscript versions could be found using search engines, making the overall OA percentage 20,4%. Chemistry (13%) had the lowest overall share of OA, Earth Sciences (33%) the highest. In medicine, biochemistry and chemistry publishing in OA journals was more common. In all other fields author-posted manuscript copies dominated the picture. Conclusions/Significance: The results show that OA already has a significant positive impact on the availability of the scientific journal literature and that there are big differences between scientific disciplines in the uptake. Due to the lack of awareness of OA-publishing among scientists in most fields outside physics, the results should be of general interest to all scholars. The results should also interest academic publishers, who need to take into account OA in their business strategies and copyright policies, as well as research funders, who like the NIH are starting to require OA availability of results from research projects they fund. The method and search tools developed also offer a good basis for more in-depth studies as well as longitudinal studies.

Open Access to Scientific Publications – An Analysis of the Barriers to Change?

One of the effects of the Internet is that the dissemination of scientific publications in a few years has migrated to electronic formats. The basic business practices between libraries and publishers for selling and buying the content, however, have not changed much. In protest against the high subscription prices of mainstream publishers, scientists have started Open Access (OA) journals and e-print repositories, which distribute scientific information freely. Despite widespread agreement among academics that OA would be the optimal distribution mode for publicly financed research results, such channels still constitute only a marginal phenomenon in the global scholarly communication system. This paper discusses, in view of the experiences of the last ten years, the many barriers hindering a rapid proliferation of Open Access. The discussion is structured according to the main OA channels; peer-reviewed journals for primary publishing, subject- specific and institutional repositories for secondary parallel publishing. It also discusses the types of barriers, which can be classified as consisting of the legal framework, the information technology infrastructure, business models, indexing services and standards, the academic reward system, marketing, and critical mass.

Benchmarking Scientific Journals from the Submitting Author’s Viewpoint

Authors of scholarly papers to a large extent base the decision on where to submit their manuscripts on the prestige of journals, taking little account of other possible factors. Information concerning such factors is in fact often not available. This paper argues for the establishment of methods for benchmarking scientific journals, taking into account a wider range of journal performance parameters than is currently available. A model for how prospective authors determine the value of submitting to a particular journal is presented. The model includes eight factors that influence an author’s decision and 21 other underlying factors. The model is a qualitative one. The method proposes to benchmark groups of journals by application of the factors. Initial testing of the method has been undertaken in one discipline.

Scientific Journal Publishing – Yearly Volume and Open Access Availability

Introduction. We estimate the total yearly volume of peer-reviewed scientific journal articles published world-wide as well as the share of these articles available openly on the Web either directly or as copies in e-print repositories. Method. We rely on data from two commercial databases (ISI and Ulrich's Periodicals Directory) supplemented by sampling and Google searches. Analysis. A central issue is the finding that ISI-indexed journals publish far more articles per year (111) than non ISI-indexed journals (26), which means that the total figure we obtain is much lower than many earlier estimates. Our method of analysing the number of repository copies (green open access) differs from several earlier studies which have studied the number of copies in identified repositories, since we start from a random sample of articles and then test if copies can be found by a Web search engine. Results. We estimate that in 2006 the total number of articles published was approximately 1,350,000. Of this number 4.6% became immediately openly available and an additional 3.5% after an embargo period of, typically, one year. Furthermore, usable copies of 11.3% could be found in subject-specific or institutional repositories or on the home pages of the authors. Conclusions. We believe our results are the most reliable so far published and, therefore, should be useful in the on-going debate about Open Access among both academics and science policy makers. The method is replicable and also lends itself to longitudinal studies in the future.