bluuebunny/crossref_metadata_2025 huggingface dataset:
Semantic determinism and the grammaticalisation of have to in English
Authors: Ziegeler Debra
Published: March 2010

The traditionally held view that grammaticalisation should be a semantically-motivated process (as discussed, for example, in Hopper and Traugott 2003: 75, summarising Bybee 1985; Bybee and Dahl 1989; Heine, Claudi and Hünnemeyer 1991; Heine et al. 1993; and Heine and Kuteva 2002) has not been without its critics. One particular area of study, so far for the most part unchallenged, is Fi­scher’s (1994, 1997, 2007) treatment of the grammaticalising periphrastic modal of obligation, have to, in English. She provides a syntactically-led grammaticalisation account in which it is believed that the present-day, developing modal form had links with an earlier, Middle English expression in which the transitive object of the infinitive was located in pre-infinitival position, shared by both the infinitive and have. The syntactically-determined explanation for the grammaticalisation of this modal expression also takes account of the fact that many of the visible grammaticalisation effects are demonstrated to have taken place following the general shift in word order during the Middle English period, from an SOV to an SVO order. In the present study, the alternative viewpoint (first proposed by Brinton 1991) in which the syntactic word order shift is seen to be most frequently associated with transitive objects that referred to entities incapable of acting as possessors is expanded to suggest a context-induced path of grammaticalisation (Heine, Claudi and Hünnemeyer 1991; Heine 2002). In addition, the shift of the object to post-infinitival position is seen to be unavoidably linked to the prior development of obligation senses in the older construction, so necessitating a semantically-motivated explanation of the grammaticalisation route for have to.
Auxiliary selection and the role of transitivity in grammaticalisation
Authors: Shin Keun Young
Published: March 2010

This paper provides an examination and analysis of two roughly synonymous aspectual markers in Korean, pelita and malta, that developed from the transitive verbs ‘throw away’ and ‘stop’, respectively. Based on electronic corpora, it is shown that these markers are distributed divergently: malta is strongly preferred to pelita in passive, non-volitional and resistant contexts. The divergent distributions of pelita and malta can be more clearly understood in terms of transitivity. I propose that the transitivity difference of their lexical sources is reflected in constraints on their grammaticalisation and contemporary uses. The low vs. high transitivity of the lexical verbs malta and pelita has persisted in grammaticalisation and brought about differences between their grammaticalised forms. This paper suggests that the gradient notion of transitivity can be used as an explanatory principle that generalises differences between synonymous grammatical words that developed from different lexical verbs.
Mathematics learners and mathematics textbooks: a question of identity? Whose curriculum? Whose mathematics?
Authors: Macintyre Tom , Hamilton Sheila
Published: March 2010

One of the challenges for policy‐makers and educationalists today is to increase participation levels and success rates within the study of mathematics. Patterns of inclusion and exclusion in mathematics education are difficult to tie down but it is widely recognised that there are issues about ‘maths’ that affect participation. For learners, textbooks are a key element in both mathematical teaching and learning, and there is evidence that a reliance on textbooks can be a feature of classroom practice. The current study draws on a recent analysis of two schemes of mathematics textbooks used to deliver the curriculum in Scottish secondary schools. This small‐scale study explores learners' responses to different mathematics textbooks, with the focus of the study being on the relationship between perceptions of the mathematics curriculum and perceptions of identity. Using textual analysis and focus group discussions, we explored the research question: ‘Are learners able to see “self”, or their interests, represented within the textbook, curriculum content and examples chosen to contextualise it?’ The findings indicate that content selection and presentation of materials appear to influence learners' participation and success in mathematics, although a larger scale study would further illuminate these findings. In particular, findings indicated that in order to maximise learners' engagement with the subject, content selection should be realistic and relevant to their experiences and aspirations for future employment and career paths. The study also sets out a conceptual framework for the analysis of mathematics textbooks, to inform practitioners and publishers of key issues related to learners' identity with the subject matter.
Developing students' ability to engage critically with science in the news: identifying elements of the ‘media awareness’ dimension
Authors: Jarman Ruth , McClune Billy
Published: March 2010

Worldwide, science education reform movements are stressing the need to promote ‘scientific literacy’ among young people. Increasingly, this is taken to include empowering students to engage critically with science‐related news reporting. Despite this requirement now featuring in statutory curricula throughout the UK, there has, to date, been a dearth of research‐informed advice to assist science teachers as they identify appropriate instructional objectives in this regard and design relevant learning activities through which these might be achieved. In this study, prominent science communication scholars, science journalists, science educators and media educators were interviewed to determine what knowledge, skills and habits of mind they judged valuable for individuals reading science‐related news stories. Teachers of science and of English from nine secondary schools in Northern Ireland addressed the same issue. A striking – and significant – finding of the study was the very substantial number of statements of knowledge, skill and disposition offered by participants that relate to ‘media awareness’, an issue largely overlooked in the science education literature. The school‐focused phase of the research suggests that cross‐curricular approaches involving teachers of science collaborating with those of English/media education or media studies may best serve to address this important curricular goal.
Implementing a new science National Curriculum for England: how trainee teachers see the How Science Works strand in schools
Authors: Toplis Rob , Golabek Charles , Cleaves Anna
Published: March 2010

This article reports empirical work conducted by three university teacher education providers into how a major revision of the science curriculum in England, the How Science Works strand, has been translated into practice for 14–16 year olds in schools. Data were collected from pre‐service teachers about their understanding, experiences, perceived challenges and resourcing of How Science Works during their final school experience. The results indicate that implementation of How Science Works in schools lies on a spectrum between two extremes referred to as creative implementation and restricted implementation; a recognition that success with this new approach requires a fuller engagement in higher order thinking skills; and that the importance of differentiation is paramount if all pupils are to connect with the new curriculum. The article concludes that support is needed for major transitions in pedagogy with both serving and trainee teachers. This needs to start with teacher education and encompass teacher development, with greater involvement both in school and university programmes.
Some reflections on the philosophical and pedagogical challenges of transforming education
Authors: Hipkins Rosemary , Reid Alan , Bull Ally
Published: March 2010

This paper responds to the articles in the recent special edition of The Curriculum Journal (Volume 20, Number 3). The special edition discusses an ‘archaeological’ approach to student enquiry, with associated ideas of personalisation, competency development, and building learning power. We argue that the papers both raise and omit complex issues that need to be addressed if their transformative agenda is to be realized. For example, it is important to reconsider traditional assumptions about the nature of knowledge, so that teachers' practice and students' learning can become more appropriately aligned to twenty‐first century conditions of knowing and being. Similarly, the wider political contexts that frame practice need to be addressed, in part by rethinking connections between pedagogy, curriculum and assessment to provide a more satisfactory theoretical rationale for competencies and personalization, and by re‐theorising related ideas such as ‘equity’. We fear that lack of attention to such issues will simply mean the new pedagogies will continue to reproduce the status quo.
Use of fluorimetry to evaluate atrazine toxicity to phytoplankton communities
Authors: Zananski Tiffany J. , Twiss Michael R. , Mihuc Timothy B.
Published: March 2010

Toxicity of atrazine was determined for natural phytoplankton communities in lake water samples from Missisquoi Bay (Lake Champlain, CA, US) at monthly intervals from May to August 2005 in order to assess how this herbicide could affect phytoplankton dynamics. Atrazine was added at 0, 5, 20, and 50 μ g L− 1 in 14 L treatments and incubated under simulated ambient light conditions (43 μ mol m− 2 s− 1). Phytoplankton community composition changes in the treatments were followed using a phytoplankton-specific fluorometer (FluoroProbe) and size fractionated filtration and analysis of extracted chlorophyll-a. Phycocyanin-rich Cyanobacteria decreased with increasing atrazine concentration in June and July and increased with atrazine concentration in August. Further experimentation utilizing a fast repetition rate fluorometer revealed that atrazine impacts on phytoplankton autofluorescence can impair FluoroProbe measurements over the short term (1 h to < 7 days).
Are the fish captured from Kor River, Fars (Iran), safe to eat?
Authors: Ebrahimi Mansour , Taherianfard Mahnaz
Published: March 2010

A total of 75 samples of two species of cyprinid fishes, Cyprinus carpio and Capoeta sp., were collected from three sections of the upper, middle and lower parts of the Kor River in the Fars province, and were analyzed for the determination of Pb, Hg, Cd and As concentrations by the Induction Coupled Plasma method. The average concentrations of Pb in muscle tissues of male Cyprinus carpio and Capoeta sp. were 0.77 ± 0.19, 0.41 ± 0.14 (mg kg− 1); while they were 1.03 ± 0.66, 0.42 ± 0.45 (mg kg− 1) for Hg, 0.08 ± 0.01, 0.08 ± 0.01(mg kg− 1) for Cd and 0.51 ± 0.06, 0.36 ± 0.11 (mg kg− 1) for As (Mean ± SE), respectively. In female Cyprinus carpio and Capoeta sp., the concentrations of Pb were 0.66 ± 0.20 and 0.41 ± 0.15 (mg kg− 1), Hg were 0.49 ± 0.45 and 0.32 ± 30 (mg kg− 1), Cd were 0.24 ± 0.01 and 0.26 ± 0.02 (mg kg− 1) and As were 0.39 ± 0.12 and 0.42 ± 0.13 (mg kg− 1), respectively. The concentrations of heavy metals in mid sampling zone were significantly (P < 0.05) higher than the two other zones; while no significant differences (P > 0.05) were seen in heavy metals assay between the two sexes and species.

The results showed industrial activities around the mid sampling zone of Kor River have polluted the River and the maximum concentrations of Pb, Hg and As residues in fish muscles were 1.46, 0.64 and 1.34 mg kg− 1, which are higher than the maximum levels allowed in fish filets by Environment Protection Agency (EPA) (2, 1 and 5 mg kg− 1), and are therefore not suitable for human consumption.
Combining biodiversity conservation with poverty alleviation - a case study in the Mekong Delta, Vietnam
Authors: Triet Tran
Published: March 2010

In many developing countries there is a prevailing conflict between biodiversity conservation and the need for poverty alleviation. One possible solution for solving that conflict is to find ways that help poor people directly benefit from conservation activities. This approach has been tested in a wetland conservation project in Phu My village, Kien Luong District, Kien Giang Province in Vietnam. The 2,000-hectare seasonally inundated grassland, dominated by the sedge Lepironia articulata (Cyperaceae), in Phu My Village is the last of its kind remaining in the Mekong Delta. In November 2004, a new model of protected area was therefore established. Unlike other protected areas in Vietnam where resource exploitation is prohibited, this is an “open” protected area in the sense that the local Khmer ethnic minority people are still allowed to harvest Lepironia as they have been doing for hundreds of years. The project provides local people with skills training and production equipment so that they can make fine handicrafts from the Lepironia they harvest. The project also helps with marketing handicraft products to higher profitable export markets. After three years of operating, the daily income of people who participated was on average twice as much as it was before the project began. The unique remnant wetland is protected, which would otherwise have been turned into a rice cultivation area according to the previous land use planning of Kien Giang Province.
Chemical composition of wetland sediments as an integrator of trophic state
Authors: de Vicente Inmaculada , Guerrero Francisco , Cruz-Pizarro Luis
Published: March 2010

Because eutrophication constitutes a key problem in limnology, evaluation of trophic state is a preliminary and essential step for the conservation and management of aquatic ecosystems. Frequently, lake trophic state is expressed by using parameters measured in the water column such as water transparency, total phosphorus or chlorophyll-a concentrations. The application of these indices usually requires repeated seasonal monitoring of the system for obtaining the annual mean values. Considering that lake sediments reflect lake trophic state, in this work we show the relevance of using sediment composition (total N and organic matter content) for obtaining quantitative data related to lake trophic state (bio-production number, BPN). Our results show that the estimated values obtained with BPN (ranging from 5.23 to 6.33), in a lake with relatively low organic matter content, reflected the trophic state as estimated by traditional water-column methods. Furthermore, the reproducibility of the BPN method, which is reflected by the constant BPN values along time, means that only one sampling including the spatial heterogeneity of the surface sediment, can provide a reasonable composite measure of trophic condition in a wetland. Finally, and as it represents a less time-consuming index, we propose the BPN as an appropriate trophic state indicator for wetlands, shallow lakes, and aquatic systems showing large temporal variability.
Freshwater fishes of Bangladesh: Fisheries, biodiversity and habitat
Authors: Hussain M.G.
Published: March 2010

Fisheries play an important role in nutrition, income, employment and export earnings in Bangladesh. Fishes contribute to 63% of animal protein intake, about 5% of gross domestic product and 5% of export earnings; approximately 1.4 million people are directly engaged in fishing, 11 million in part-time fishing and another 3 million in aquaculture activities. The fisheries are highly diversified and comprised of inland open water capture fisheries, inland closed water culture fisheries and marine fisheries, which contribute respectively 35%, 44% and 21% to total fish production of 2.1 million tonnes. The major environmental factors having negative impacts on fisheries development are mainly: human impacts on riverine morphology, disruption of ecology, intensive agriculture, and modern developments. Fish conservation acts and regulations exist, but enforcement is difficult because of prevailing socio-economic conditions. Few regulatory mechanisms presently exist for protecting aquaculture environments.

Production from inland openwater capture fisheries is declining due to over-exploitation and habitat degradation. However, aquaculture production, which mostly follows traditional practices, has been steadily increasing. Fisheries research has made significant contributions to the large growth of aquaculture through generating a number of economically viable, socially acceptable and environmentally compatible technologies being used by different categories of farmers, large and small. Presently, formulation and implementation of strategies and policies for conservation and sustainable management of degraded aquatic habitats have been immensely effective along with the generation and wider application/dissemination of suitable aquaculture and management technologies, which are expected to ensure the conservation of aquatic genetic resources. This paper reviews all these subjects and emphasizes future needs for development and implementation of policies/regulations at the national level, before it becomes too late to conserve valuable aquatic biodiversity and their habitats.
Emerging resource use conflicts between Kenyan fishermen, pastoralists and tribesmen of Lake Turkana
Authors: Yongo E. O. , Abila R. O. , Lwenya C.
Published: March 2010

Frequent droughts over the years causing partial or total loss of livestock caused the community to take up fishing in Lake Turkana as an alternative activity for survival. The objective of the study was to get baseline information on the socio-economic situation in Lake Turkana area. Survey revealed that in recent years there have been increased incidences of insecurity and cattle rustling, which has driven more pastoralists into fishing. Most respondents indicated they were primarily fishers, followed by pastoralists. Most fished in the shallow inshore areas using mainly gillnets and purse seine nets. The greatest concern of the fishers is the conflict with the tribesmen of southern Ethiopia. The fishing offers an opportunity for the pastoral communities to settle down to a sedentary lifestyle, making it easier to access health, educational and other essential services. Women are also involved, though in low numbers, some of whom own boats and gears. Currently, fishery resources in offshore areas are unexploited, but there is a need to control pressure in inshore shallow areas.
Long-term changes in the Changjiang Estuary plankton community related to anthropogenic eutrophication
Authors: Li Yun , Li Daoji , Tang Jingliang , Wang Yiming , Liu Zhigang , He Songqin
Published: March 2010

The Changjiang River is well-known to channel significant anthropogenic influences to the estuary. However, long-term changes in plankton community related to anthropogenic eutrophication in the estuarine water are not well documented. In this paper, data from a nine year study (1996, 1998–2005) on suspended matter, chemical oxygen demand, nutrients and plankton community were collected and analyzed by principal component analysis. These data reveal that N/P ratio was always much higher than 40 and Si/N ratio decreased from 1.35 to 0.94 between 1996 and 2005. As an ecological consequence to such nutrient balance changes, phytoplankton species diversity and the dominance of diatoms decreased, dinoflagellates increasingly dominated the phytoplankton population, and the frequency of harmful algal blooms caused by dinoflagellates also increased. Furthermore, due to the reduced diatom availability, the dominance of copepods decreased, zooplankton diversity increased, and medusae increasingly dominated the zooplankton population. Water column nutrient ratios, therefore, are also important factors affecting anthropogenic eutrophication, as are the contamination loadings from land.
Changes in the numbers of dominating parasites as indicators of the condition of roach, Rutilus rutilus lacustris, and dace Leuciscus leuciscus baicalensis (Pisces: Cyprinidae) populations in the transect Selenga River – River Delta – Lake Baikal
Authors: Pronin N.M. , Batueva M.D. , Sondueva L.D. , Burdukovskaya T.G. , Dugarov Zh.N. , Pronina S.V.
Published: March 2010

Changes in the numbers of 10 species of parasites belonging to 5 classes of roach and Siberian dace were investigated in the transect “Selenga River – Delta – Lake Baikal” in 2001–2006. The numbers either increased along this transect (myxosporea Myxobolus bramae, monogeneans of genus Dactylogyrus, diplostomatids metacercariae and Rhipidocotyle campanula, parasitic copepodes Ergasilus sieboldi and E. briani) or decreased (myxosporea Myxidium rhodei, cestoda Caryophyllaeides fennica, trematoda Allocreadium isoporum). Differences in the infection rates of fishes in the transect are explained by features of the parasite morphology and biology, and by levels of water contamination.
From Mfangano to Madrid: The global commodity chain for Kenyan Nile perch
Authors: Johnson Jennifer Lee
Published: March 2010

Lake Victoria is the world's second largest freshwater body and home to one of the most dramatic speciation of indigenous cichlids in the world. Bordered by Kenya, Tanzania and Uganda in East Africa, the Lake Victoria Basin (LVB) provides food, water and livelihoods for over 30 million people around its shores, with 10 million engaged in the fisheries sector. The Colonial Era introduction of the invasive Nile perch (Lates niloticus) in the 1950's, combined with the introduction of industrialized fish processing in the 1980's, transformed fishing throughout the Basin. The introduction and commercial harvesting of the Nile perch, subsequent human population growth, and the looming problems of climate change continue to compromise the health of this important fishery. This paper applies a global commodity chain framework with an ethnographic approach to the case of the export-oriented Nile perch from the Kenyan island of Mfangano in July 2007. Unless otherwise noted, all price and empirical data are based on interviews, market surveys, and participant observation conducted by the author in Kenya in June, July, and August of 2007. In 2007, prices paid to local Kenyan fishermen, boat owners, and agents represent 24% of the total value from the fishery (∼ 3% to each fisherman, 14% to boat owners and 4% to agents); prices paid to processors represent 36% of the value, and 39% of the value accrues to international seafood wholesalers and retailers.
The effect of intensive fishing on two cichlids (Oreochromis niloticusandAstatotilapia burtoni) in Nyangara wetland at the north end of Lake Tanganyika (D. R. Congo) with fishery management implications
Authors: Mulimbwa N'sibula , Sarvala Jouko , van der Knaap Martin
Published: March 2010

The Nyangara wetland, also known as Laguna, in the fluvial plain of Rusizi River at the northern end of Lake Tanganyika, harbours a fish fauna which offers food and income for 500 people directly or indirectly associated with fisheries. Fishing focuses mainly on two cichlids (Oreochromis niloticus and Astatotilapia burtoni) and the marbled lungfish (Protopterus aethiopicus).

Studies of population structure were based on length-frequency distributions of fish in catch samples. The size at first maturation was estimated using total length and state of gonad maturity estimated macroscopically. Minimum and maximum sizes in catches ranged from 10 to 100 mm total length in A. burtoni and from 20 to 180 mm in O. niloticus. Sizes at first maturation were 65 mm total length for female and 70 mm for male in A. burtoni and 130 mm in O. niloticus. Immature fish comprised 95 % of the catch. The majority of harvesting thus took place before the onset of maturity. In both species, the dominance of very small fish in the population structure, the reduced maximal size, and the early maturation of fish, indicated high fishing mortality.

Although further studies are needed to properly understand the effects of intensive fishing on fish populations in the Nyangara wetland, the present study suggests that the fishing community would be well-advised to follow the precautionary approach and pay more attention to the numbers and types of fishing gear, and to appropriate mesh sizes to ensure successful spawning of fish. To reduce fishing pressure, alternative sources of protein should be sought, such as pond aquaculture, agriculture and animal husbandry for example.
Cargo- and adaptor-specific mechanisms regulate clathrin-mediated endocytosis
Authors: Mettlen Marcel , Loerke Dinah , Yarar Defne , Danuser Gaudenz , Schmid Sandra L.
Published: March 2010

Clathrin-mediated endocytosis of surface receptors and their bound ligands (i.e., cargo) is highly regulated, including by the cargo itself. One of the possible sources of the observed heterogeneous dynamics of clathrin-coated pits (CCPs) might be the different cargo content. Consistent with this, we show that CCP size and dynamic behavior varies with low density lipoprotein receptor (LDLR) expression levels in a manner dependent on the LDLR-specific adaptors, Dab2 and ARH. In Dab2-mCherry–expressing cells, varying LDLR expression leads to a progressive increase in CCP size and to the appearance of nonterminal endocytic events. In LDLR and ARH-mCherry–expressing cells in addition to an increase in CCP size, turnover of abortive CCPs increases, and the rate of CCP maturation decreases. Altogether, our results underscore the highly dynamic and cargo-responsive nature of CCP assembly and suggest that the observed heterogeneity is, in part, related to compositional differences (e.g., cargo and adaptors) between CCPs.
Asymmetric Intrahousehold Allocation of Calories in China
Authors: Shimokawa Satoru
Published: March 2010

To analyze intrahousehold calorie allocation, we propose a new framework that takes into account asymmetric consumption behavior due to liquidity constraints and loss aversion. We find that intrahousehold calorie allocation responds asymmetrically to expected declines and increases in household food availability in China. Compared with previous studies based on symmetric consumption behavior, our framework provides stronger evidence of gender bias in intrahousehold calorie allocation among children in urban areas and among elderly people in rural areas, and of demographic bias between girls and prime‐age adults in both urban and rural areas. Implications for demographic targeting in nutrition programs are discussed.
Pathway discovery in metabolic networks by subgraph extraction
Authors: Faust Karoline , Dupont Pierre , Callut Jérôme , van Helden Jacques
Published: March 2010

Motivation: Subgraph extraction is a powerful technique to predict pathways from biological networks and a set of query items (e.g. genes, proteins, compounds, etc.). It can be applied to a variety of different data types, such as gene expression, protein levels, operons or phylogenetic profiles. In this article, we investigate different approaches to extract relevant pathways from metabolic networks. Although these approaches have been adapted to metabolic networks, they are generic enough to be adjusted to other biological networks as well.

Results: We comparatively evaluated seven sub-network extraction approaches on 71 known metabolic pathways from Saccharomyces cerevisiae and a metabolic network obtained from MetaCyc. The best performing approach is a novel hybrid strategy, which combines a random walk-based reduction of the graph with a shortest paths-based algorithm, and which recovers the reference pathways with an accuracy of ∼77%.

Availability: Most of the presented algorithms are available as part of the network analysis tool set (NeAT). The kWalks method is released under the GPL3 license.

Contact:  kfaust@ulb.ac.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
Proximate composition and energy content of forage species from the Bay of Biscay: high- or low-quality food?
Authors: Spitz Jérôme , Mourocq Emeline , Schoen Valérie , Ridoux Vincent
Published: March 2010

Spitz, J., Mourocq, E., Schoen, V., and Ridoux, V. 2010. Proximate composition and energy content of forage species from the Bay of Biscay: high- or low-quality food? – ICES Journal of Marine Science, 67: 909–915. Collapses of high-energy dense concentrations of prey species induce negative effects on populations of top predators. Knowledge of prey quality appears to be crucial in ecosystem modelling and management. The aim here was to provide baseline data of forage species quality in the Bay of Biscay. Proximate composition (water, ash, protein, and lipid) and energy content have been determined to assess the quality of 78 species, including jellyfish, crustaceans, cephalopods, cartilaginous fish, and bony fish. Results show broad variations between species, with energy densities ranging from 2 to 10 kJ g−1. Lipids are the most structuring component and largely determined prey quality, and prey species are not necessarily interchangeable for the fulfilment of a predator's energy and food requirements. In ecosystem models, therefore, multispecies compartments of forage organisms would ideally be constituted using prey species of equivalent quality and hence of equivalent benefit to top predators.
Insonification orientation and its relevance for image-based classification of multibeam backscatter
Authors: McGonigle Christopher , Brown Craig J. , Quinn Rory
Published: March 2010

McGonigle, C., Brown, C. J., and Quinn, R. 2010. Insonification orientation and its relevance for image-based classification of multibeam backscatter. – ICES Journal of Marine Science, 67: 1010–1023. The use of multibeam echosounders (MBES) for mapping benthic habitat has gained widespread acceptability. Multibeam backscatter imagery provides an objective tool for scientists and managers to chronicle the extent and condition of the benthic resource. However, there are no standardized methods describing how best to process backscatter data to derive meaningful segmentations, although several acquisition parameters have been identified as having the capacity to affect the classification result. This research attempts to determine how the orientation at which a feature is insonified can affect classification outcome using commercially available software (QTC-Multiview), and to evaluate this significance related to vessel speed as a proxy for data density. A complex 2-km2 area of Stanton Banks, UK, was selected as the test site for the study. The area was insonified using a Kongsberg Simrad EM1002 MBES at perpendicularly opposing orientations, at two different vessel speeds within the same 24-h period. The classifications displayed 53% (k = 0.396) similarity at 4 m s−1 and 49% (k = 0.342) at 2 m s−1 from opposing orientations. Common orientations at different speeds were 68% (k = 0.583) similar (east–west) and 53% (k = 0.384; north–south). Most of the variation was in topographically complex areas, which coincided with shallow depths (<60 m). Meteorological and oceanographic conditions at the time the data were collected were evaluated as having had the potential to influence the outcome of the classifications. Interpretation of the results suggests that the orientation at which insonification occurs has a greater ability to influence the classification result than vessel speed using an image-based technique.
Stochastic bioeconomic modelling of alternative management measures for anchovy in the Mediterranean Sea
Authors: Maravelias Christos D. , Hillary Richard , Haralabous John , Tsitsika Efthymia V.
Published: March 2010

Maravelias, C. D., Hillary, R., Haralabous, J., and Tsitsika, E. V. 2010. Stochastic bioeconomic modelling of alternative management measures for anchovy in the Mediterranean Sea. – ICES Journal of Marine Science, 67: 1291–1300. The purse-seine fishery for anchovy in the Aegean Sea consists of two main fleet segments (12–24 and 24–40 m vessels); this paper investigates economically and biologically preferable effort and capacity scenarios for the fishery. Attention is paid to a bioeconomic analysis of fleets composed of segments with varying levels of efficiency (in terms of catch rate) and costs (fixed and variable) and the role this might play in optimal effort allocation at a fleet level. An age-structured stochastic bioeconomic operating model for Aegean anchovy (Engraulis encrasicolus) is constructed. It attempts to account robustly for the multiple uncertainties in the system, including (i) the effort–fishing mortality relationship, (ii) the selectivity, and (iii) the stock–recruit dynamics of the population. A method is proposed for determining the economically optimal level of long-term effort in a fishery such as this, with similar characteristics in terms of stock dynamics, fishery, and markets. Lower values of effort and capacity are predicted to yield greater future profit when viewing the fleet in its entirety, but even lower values may be advisable to maintain the long-term biological integrity of the stock. The results may prove useful in balancing the productivity of the stock with the harvesting capacity of the fleet, while managing to ensure the long-term profitability of the fleet along with the sustainability of the resource.
Bayesian Model Averaging: Theoretical Developments and Practical Applications
Authors: Montgomery Jacob M. , Nyhan Brendan
Published: March 2010

Political science researchers typically conduct an idiosyncratic search of possible model configurations and then present a single specification to readers. This approach systematically understates the uncertainty of our results, generates fragile model specifications, and leads to the estimation of bloated models with too many control variables. Bayesian model averaging (BMA) offers a systematic method for analyzing specification uncertainty and checking the robustness of one's results to alternative model specifications, but it has not come into wide usage within the discipline. In this paper, we introduce important recent developments in BMA and show how they enable a different approach to using the technique in applied social science research. We illustrate the methodology by reanalyzing data from three recent studies using BMA software we have modified to respect statistical conventions within political science.
First Report of Twig Canker of Blueberry Caused by Sporocadus lichenicola (Corda) in Oregon
Authors: Serdani Maryna , Curtis Marc , Putnam Melodie L.
Published: March 2010

To our knowledge, this is the first report of S. lichenicola causing stem cankers of blueberry in the western United States.

Accepted for publication 15 December 2009. Published 15 March 2010.
First Report of Powdery Mildew of Tecoma capensis Caused by Erysiphe peruviana in North America
Authors: Glawe Dean A. , Barlow Tess , Matheron Michael E.
Published: March 2010

Tecoma capensis (Thunb.) Lindl. (Bignoniaceae, common name: Cape honeysuckle), native to southern Africa, is grown as an ornamental plant in warm regions of the USA. The powdery mildew reported previously from T. capensis in North America was an undetermined Oidium species in Florida. The present report documents the occurrence of the powdery mildew fungus Erysiphe peruviana (Syd.) U. Braun & S. Takam. on T. capensis in Arizona.

Accepted for publication 4 January 2010. Published 15 March 2010.
Photobacterium swingsii sp. nov., isolated from marine organisms
Authors: Gomez-Gil Bruno , Roque Ana , Rotllant Guiomar , Peinado Lauro , Romalde Jesus L. , Doce Alejandra , Cabanillas-Beltrán Hector , Chimetto Luciane A. , Thompson Fabiano L.
Published: March 2010

Six Gram-negative coccobacilli were isolated from Pacific oysters (Crassostrea gigas) from Mexico and haemolymph of spider crabs (Maja brachydactyla) from Spain. All of the isolates grew as small green colonies on thiosulphate-citrate-bile salts-sucrose (TCBS) agar and were facultatively anaerobic, oxidase-positive and sensitive to the vibriostatic agent O/129. Repetitive palindromic PCR analysis revealed a high degree of genomic homogeneity among the isolates. Several phenotypic traits differentiated the isolates from the type strains of species of the genus Photobacterium. DNA–DNA relatedness between two representative isolates and their closest phylogenetic neighbours by 16S rRNA gene sequence similarity, Photobacterium aplysiae CAIM 14T and Photobacterium frigidiphilum CAIM 20T, was 44.01–53.85 %. We propose a novel species of the genus Photobacterium to accommodate the six isolates, with the name Photobacterium swingsii sp. nov. The type strain is CAIM 1393T (=CECT 7576T).
Genetic characterization of root-nodule bacteria associated with Acacia salicina and A. stenophylla (Mimosaceae) across south-eastern Australia
Authors: Hoque Mohammad S. , Broadhurst Linda M. , Thrall Peter H.
Published: March 2010

Symbiotic relationships between legumes and nitrogen-fixing soil micro-organisms are of ecological importance in plant communities worldwide. For example, nutrient-poor Australian soils are often dominated by shrubby legumes (e.g. species ofAcacia). However, relatively few studies have quantified patterns of diversity, host-specificity and effectiveness of these ecologically important plant–microbe interactions. In this study, 16S rRNA gene sequence and PCR-RFLP analyses were used to examine bacterial strains isolated from the root nodules of two widespread south-eastern Australian legumes,Acacia salicinaandAcacia stenophylla, across nearly 60 sites. The results showed that there was extensive genetic diversity in microbial populations, including a broad range of novel genomic species. While previous studies have suggested that most native Australian legumes nodulate primarily with species of the genusBradyrhizobium, our results indicate significant associations with members of other root-nodule-forming bacterial genera, includingRhizobium,Ensifer,Mesorhizobium,Burkholderia,PhyllobacteriumandDevosia. Genetic analyses also revealed a diverse suite of non-nodulating bacterial endophytes, only a subset of which have been previously recorded. Although the ecological roles of these endosymbionts are not well understood, they may play both direct and indirect roles in promoting plant growth, nodulation and disease suppression.
Kocuria salsicia sp. nov., isolated from salt-fermented seafood
Authors: Yun Ji-Hyun , Roh Seong Woon , Jung Mi-Ja , Kim Min-Soo , Park Eun-Jin , Shin Kee-Sun , Nam Young-Do , Bae Jin-Woo
Published: March 2010

Strain 104T was isolated from a traditional salt-fermented seafood in Korea. It was a Gram-positive, non-motile, coccus-shaped bacterium. It formed lemon–yellow, opaque colonies that were circular with entire margins. Optimal growth occurred at 30–37 °C, pH 7–8 and in the presence of 0–2 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences from strain 104T and reference species of the genus Kocuria indicated that strain 104T formed an independent line. The G+C content of the chromosomal DNA was 60.6 mol%. MK-7 was the major menaquinone and the predominant fatty acids were anteiso-C15 : 0 (76.7 %), anteiso-C17 : 0 (10.9 %) and iso-C16 : 0 (4.5 %). Strain 104T was most closely related to Kocuria rhizophila TA68T (98.9 % 16S rRNA gene sequence similarity). The DNA–DNA hybridization value between strain 104T and K. rhizophila TA68T was 14.1±3.4 %. On the basis of this polyphasic taxonomic analysis, strain 104T appears to represent a novel species in the genus Kocuria. The name Kocuria salsicia sp. nov. is proposed. The type strain is 104T (=KACC 21128T=JCM 16361T).
Gangjinia marincola gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae
Authors: Lee Dong-Heon , Moon Sung-Ran , Park Young-Hyun , Lee Young Sun , Jung Jae Sung , Kim Jung Ho , Kim Hoon , Kahng Hyung-Yeel
Published: March 2010

A novel strictly aerobic, orange-pigmented, Gram-stain-negative bacterium, designated strain GJ16T, was isolated from coastal seawater of Gangjin Bay, the southernmost part of the Korean peninsula, and subjected to a polyphasic taxonomic study. It grew optimally at 25–30 °C, at pH 7.0–8.0 and in the presence of 3 % NaCl. Comparative 16S rRNA gene sequence analysis revealed that strain GJ16T formed a distinct lineage within the family Flavobacteriaceae and shared less than 91.2 % 16S rRNA gene sequence similarity with members of the genera Leptobacterium, Zhouia, Winogradskyella, Dokdonia and Krokinobacter. The predominant cellular fatty acids were iso-C15 : 0 (40.2 %), iso-C15 : 1 G (12.8 %), iso-C17 : 0 3-OH (11.2 %) and C15 : 0 (6.6 %). The G+C content of the genomic DNA was 39.4 mol% and the major respiratory isoprenoid quinone was MK-6. On the basis of phenotypic and genotypic data, strain GJ16T represents a novel species in a new genus in the family Flavobacteriaceae, for which the name Gangjinia marincola gen. nov., sp. nov. is proposed; the type strain is GJ16T (=KCTC 22649T =JCM 16082T).
Paenibacillus chungangensis sp. nov., isolated from a tidal-flat sediment
Authors: Park Mi-Hak , Traiwan Jitsopin , Jung Min Young , Nam Yun Sung , Jeong Ji Hoon , Kim Wonyong
Published: March 2010

A Gram-stain-positive, rod-shaped, endospore-forming bacterium, strain CAU 9038T, was isolated from a tidal-flat sediment of DaeYiJac Island, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, the major isoprenoid quinone was MK-7 and the dominant cellular fatty acid was anteiso-C15 : 0. The DNA G+C content was 51.6 mol%. 16S rRNA gene sequence analysis showed that the strain belonged to the genus Paenibacillus, with <96.1 % sequence similarity to type strains of Paenibacillus species with validly published names. The most closely related type strains to CAU 9038T were Paenibacillus thailandensis S3-4AT (96.1 % similarity) and Paenibacillus agaridevorans DSM 1355T (95.3 %). The phenotypic, chemotaxonomic and genotypic data clearly indicated that strain CAU 9038T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus chungangensis sp. nov. is proposed. The type strain is CAU 9038T (=KCTC 13717T =CCUG 59129T).
Parvibaculum indicum sp. nov., isolated from deep-sea water
Authors: Lai Qiliang , Wang Liping , Liu Yuhui , Yuan Jun , Sun Fengqin , Shao Zongze
Published: March 2010

A taxonomic study was carried out on strain P31T, which was isolated from a polycyclic aromatic hydrocarbon (PAH)-degrading consortium enriched with deep-sea water of the Indian Ocean. The isolate was Gram-reaction-negative, rod-shaped, motile by means of a polar flagellum and incapable of reducing nitrate to nitrite. Growth was observed at 0.5–8 % NaCl and at 10–41 °C. Strain P31T was unable to degrade Tween 80 or gelatin. The major respiratory quinone was ubiquinone 11 (Q-11). The dominant fatty acids were C18 : 1
ω7c (39.79 %), 11-methyl C18 : 1
ω7c (17.84 %), C19 : 0 cyclo ω8c (12.05 %) and C18 : 0 (6.09 %). The G+C content of the chromosomal DNA was 62.1 mol%. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain P31T and Parvibaculum lavamentivorans DS-1T formed a distinct lineage in the family Phyllobacteriaceae; these two strains showed 95.7 % sequence similarity, while similarities between P31T and other members of the genus Parvibaculum were below 93 %. Based on the genotypic and phenotypic data, strain P31T represents a novel species of the genus Parvibaculum, for which the name Parvibaculum indicum sp. nov. is proposed. The type strain is P31T (=CCTCC AB 208230T =LMG 24712T =MCCC 1A01132T).
Flavobacterium dongtanense sp. nov., isolated from the rhizosphere of a wetland reed
Authors: Xiao Yi-Ping , Hui Wei , Lee Jung-Sook , Lee Keun Chul , Quan Zhe-Xue
Published: March 2010

Two strains of Gram-reaction-negative, rod-shaped, non-spore-forming, non-motile, aerobic bacteria, designated LW30T and LW29, were isolated from the rhizosphere of a wetland reed in Dongtan, Chongming Island, China. The strains formed pale-yellow colonies on R2A plates. Growth occurred at 4–37 °C (optimum 30 °C), at pH 6–9 (optimum pH 7–8) and in the presence of 0–3 % (w/v) NaCl (optimum 0–1 %). Oxidase and catalase activities and flexirubin-type pigments were absent. MK-6 was the major respiratory quinone. The major fatty acids were iso-C15 : 0, C15 : 0, iso-C15 : 1 G and iso-C17 : 1
ω9c. Strains LW30T and LW29 could be differentiated from related species by several phenotypic characteristics. Phylogenetic analyses based on 16S rRNA gene sequences placed strains LW30T and LW29 in the genus Flavobacterium with high sequence similarity to Flavobacterium cheniae NJ-26T (94.0 %) and Flavobacterium indicium GPTSA 100-9T (93.9 %). Together with F. indicium GPTSA 100-9T, strains LW30T and LW29 formed a distinct group in the phylogenetic tree. The DNA G+C content was 30 mol%. On the basis of the phylogenetic and phenotypic evidence, strains LW30T and LW29 represent a novel species of the genus Flavobacterium, for which the name Flavobacterium dongtanense sp. nov. is proposed. The type strain is LW30T (=KCTC 22671T =CCTCC AB 209201T).
Nitratireductor indicus sp. nov., isolated from deep-sea water
Authors: Lai Qiliang , Yu Zhiwei , Yuan Jun , Sun Fengqin , Shao Zongze
Published: March 2010

A taxonomic study was carried out on a novel bacterial strain, designated C115T, isolated from a crude-oil-degrading consortium, enriched from deep-sea water of the Indian Ocean. Cells were Gram-negative short rods, mobile by means of a monopolar flagellum. Growth was observed at salinities of 0–7 % and at 10–43 °C. It was unable to degrade Tween 80 or gelatin. 16S rRNA gene sequence analysis showed that strain C115T was related most closely to Nitratireductor aquibiodomus NL21T (96.5 % similarity), Nitratireductor kimnyeongensis KY 101T (96.4 %) and Nitratireductor basaltis J3T (96.2 %). The predominant fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c, 81.8 %) and C18 : 0 (7.0 %). The G+C content of the chromosomal DNA of strain C115T was 59 mol%. Based on its morphology, physiology and fatty acid composition together with 16S rRNA gene sequence comparisons, the novel strain most appropriately belongs to the genus Nitratireductor, but can be distinguished readily from recognized species of the genus. Strain C115T is therefore considered to represent a novel species of the genus Nitratireductor, for which the name Nitratireductor indicus sp. nov. is proposed. The type strain is C115T (=RC92-7T =CCTCC AB 209298T =LMG 25540T =MCCC 1A01260T).
Study of Plastid Genome Stability in Tobacco Reveals That the Loss of Marker Genes Is More Likely by Gene Conversion Than by Recombination between 34-bp loxP Repeats
Authors: Tungsuchat-Huang Tarinee , Sinagawa-García Sugey Ramona , Paredes-López Octavio , Maliga Pal
Published: March 2010

In transformed tobacco (Nicotiana tabacum) plastids, we flank the marker genes with recombinase target sites to facilitate their posttransformation excision. The P1 phage loxP sites are identical 34-bp direct repeats, whereas the phiC31 phage attB/attP sites are 54- and 215-bp sequences with partial homology within the 54-bp region. Deletions in the plastid genome are known to occur by recombination between directly repeated sequences. Our objective was to test whether or not the marker genes may be lost by homologous recombination via the directly repeated target sites in the absence of site-specific recombinases. The sequence between the target sites was the barau gene that causes a golden-yellow (aurea) leaf color, so that the loss of the barau gene can be readily detected by the appearance of green sectors. We report here that transplastomes carrying the barau gene marker between recombinase target sites are relatively stable because no green sectors were detected in approximately 36,000 seedlings (Nt-pSS33 lines) carrying attB/attP-flanked barau gene and in approximately 38,000 seedlings (Nt-pSS42 lines) carrying loxP-flanked barau gene. Exceptions were six uniformly green plants in the Nt-pSS42-7A progeny. Sequencing the region of plastid DNA that may derive from the vector indicated that the barau gene in the six green plants was lost by gene conversion using wild-type plastid DNA as template rather than by deletion via directly repeated loxP sites. Thus, the recombinase target sites incorporated in the plastid genome for marker gene excisions are too short to mediate the loss of marker genes by homologous recombination at a measurable frequency.