bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gulf desert developments encompassing a marine environment, a compensatory solution to the loss of coastal habitats by infill and reclamation: The case of the Pearl City Al-Khiran, Kuwait
Authors: Jones D. A. , Ealey T. , Baca B. , Livesey S. , Al-Jamali F. 
Published: September 2007

Despite recent scientific evidence demonstrating the ecological value of intertidal and shallow subtidal ecosystems, these systems are disappearing rapidly in the Gulf. Infill and dredging for waterfront developments and artificial islands has impacted the natural shores of most western Gulf countries and fisheries are declining due to the loss of nursery and feeding grounds.
In contrast, developments such as West Bay lagoon, Qatar and the Al-Khiran Pearl City, Kuwait have created new habitats by constructing marine waterways in saline sabkha and hypersaline khors of low ecological value. Studies in West Bay Lagoon, open to the sea since 1996, demonstrate that typical intertidal and subtidal ecosystems are re-established and that recent introduction of sea grass is successful.
At Al-Khiran over 170 km of new waterways and intertidal habitats are planned. Phase A1 with 127 ha of 2–3 m deep waterways, 16 ha of sand beach and 9 ha of planted mangrove/salt marsh was opened to the sea in 2004. A marine ecological survey of these waterways in September 2005 collected quantitative samples of macrobiota from 3 sites, both intertidally and subtidally, and epibiota was sampled using a benthic sledge. Semi-quantitative fishing was conducted using gargoors and a seine net and diving employed to photograph marine life.
Physio-chemical water column measurements and plankton samples demonstrate that the sea water is of high quality. Biological samples reveal that over 215 macrobiota and 37 fish species already exist within the waterways. Diversity now far exceeds that recorded for the khors before construction. The supralittoral of the new beaches and salt marsh remains impoverished, but lower shore and subtidal diversity and abundance are similar to open sea habitats. Catches of market size grouper and mullet, and planktonic shrimp and fish larvae, indicate these waterways enhance existing marine productivity and act as a nursery for commercial species.
Multiple stressors and ecosystem-based management in the Gulf
Authors: Khan Nuzrat Yar 
Published: September 2007

Rapid and largely unchecked coastal development in the Gulf countries as a result of the oil boom has caused considerable ecological stress in the Gulf ecosystem. Coastal habitats have begun to show symptoms of ecological imbalance generally associated with multiple stressors caused by pollution and habitat destruction: harmful algal blooms and fish kills are of common occurrence in coastal areas, fish stocks are declining, and coastal sediments are contaminated by a variety of toxic chemicals. The present state of the Gulf ecosystem reflects the constraints inherently associated with fragmented jurisdictions in the management of coastal areas at both national and regional levels. Its management is largely driven by management frameworks representing arbitrary jurisdictions of political units rather than a shared vision of the health and sustainability of the entire Gulf ecosystem. In view of the complex, dynamic, and semi-enclosed nature of the Gulf ecosystem, a paradigm shift from resource management characterized by short-term perspectives on small spatial scales to resource management that is ecosystem-based with long-term perspectives, is urgently needed.
Since an ecosystem-based management of the Gulf is implicit in the provisions of Kuwait Convention and Kuwait Action Plan, we recommend that ROPME (Regional Organization for the Protection of the Marine Environment), which provides the focal point for regional cooperation under these regional agreements, be provided with a renewed mandate to coordinate an ecosystem-based management of the Gulf.
Moderated statistical tests for assessing differences in tag abundance
Authors: Robinson Mark D. , Smyth Gordon K. 
Published: September 2007

AbstractMotivation: Digital gene expression (DGE) technologies measure gene expression by counting sequence tags. They are sensitive technologies for measuring gene expression on a genomic scale, without the need for prior knowledge of the genome sequence. As the cost of sequencing DNA decreases, the number of DGE datasets is expected to grow dramatically.Various tests of differential expression have been proposed for replicated DGE data using binomial, Poisson, negative binomial or pseudo-likelihood (PL) models for the counts, but none of the these are usable when the number of replicates is very small.Results: We develop tests using the negative binomial distribution to model overdispersion relative to the Poisson, and use conditional weighted likelihood to moderate the level of overdispersion across genes. Not only is our strategy applicable even with the smallest number of libraries, but it also proves to be more powerful than previous strategies when more libraries are available. The methodology is equally applicable to other counting technologies, such as proteomic spectral counts.Availability: An R package can be accessed from http://bioinf.wehi.edu.au/resources/Contact: smyth@wehi.edu.auSupplementary information: http://bioinf.wehi.edu.au/resources/
A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data
Authors: Post Lennart J. G. , Roos Marco , Marshall M. Scott , van Driel Roel , Breit Timo M. 
Published: September 2007

AbstractMotivation: The numerous public data resources make integrative bioinformatics experimentation increasingly important in life sciences research. However, it is severely hampered by the way the data and information are made available. The semantic web approach enhances data exchange and integration by providing standardized formats such as RDF, RDF Schema (RDFS) and OWL, to achieve a formalized computational environment. Our semantic web-enabled data integration (SWEDI) approach aims to formalize biological domains by capturing the knowledge in semantic models using ontologies as controlled vocabularies. The strategy is to build a collection of relatively small but specific knowledge and data models, which together form a ‘personal semantic framework’. This can be linked to external large, general knowledge and data models. In this way, the involved scientists are familiar with the concepts and associated relationships in their models and can create semantic queries using their own terms. We studied the applicability of our SWEDI approach in the context of a biological use case by integrating genomics data sets for histone modification and transcription factor binding sites.Results: We constructed four OWL knowledge models, two RDFS data models, transformed and mapped relevant data to the data models, linked the data models to knowledge models using linkage statements, and ran semantic queries. Our biological use case demonstrates the relevance of these kinds of integrative bioinformatics experiments. Our findings show high startup costs for the SWEDI approach, but straightforward extension with similar data.Availability: Software, models and data sets, http://www.integrativebioinformatics.nl/swedi/index.htmlContact: breit@science.uva.nlSupplementary information: Supplementary data are available at Bioinformatics online.
The rise and fall of electrical beam trawling for shrimp in the East China Sea: technology, fishery, and conservation implications
Authors: Yu Congda , Chen Zhihai , Chen Lianyuan , He Pingguo 
Published: September 2007

Abstract
Yu, C., Chen, Z., Chen, L., and He, P. 2007. The rise and fall of electrical shrimp beam trawling in the East China Sea: technology, fishery, and conservation implications. – ICES Journal of Marine Science, 64: 1592–1597. Since the 1980s, shrimp beam trawling has flourished in inshore waters of the East China Sea (ECS) off Zhejiang Province. By 2000, there were more than 10 000 beam trawlers operating in the area. The fishery targets several species of shrimp, including Parapenaeopsis hardwickii, Solenocera crassicornis, Parapenaeus fissuroides, and Trachypenaeus curvirostris. In the early 1990s, electrical beam trawls using pulse generators, powered either from the vessel or from underwater battery packs, became popular in the fishery. As a result of this new technology, the catch rates of shrimp, especially the burrowing shrimp species, increased. At its peak usage, there were more than 3000 vessels using electrical beam trawls in Zhejiang Province and another 500 or more in the adjacent provinces of Jiangsu and Fujian. This technology was also widespread along the Chinese coast, but a lack of regulation resulted in the misuse of electrical pulse parameters that caused damage to juvenile shrimps and other benthic species. In 2001, this fishing method was banned from the waters off Zhejiang Province, and subsequently in other parts of the ECS. This paper reviews the research on electrical beam trawls, the fishery, and fishery-management issues associated with this new technology.
Acidic episodes retard the biological recovery of upland British streams from chronic acidification
Authors: KOWALIK RENATA A. , COOPER D. M. , EVANS C. D. , ORMEROD S. J. 
Published: September 2007

AbstractWe tested two predictions required to support the hypothesis that anthropogenic acidic episodes might explain the poor biological response of upland British streams otherwise recovering from acidification: (i) that invertebrate assemblages should differ between episodic and well‐buffered streams and (ii) these effects should differentiate between sites with episodes caused by anthropogenic acidification as opposed to base‐cation dilution or sea‐salt deposition. Chronic and episodically acidic streams were widespread, and episodes reflected acid titration more than dilution. Nonmarine sulphate (16–18% vs. 5–9%), and nitrate (4–6% vs. 1–2%) contributed more to anion loading during episodes in Wales than Scotland, and Welsh streams also had a larger proportion of total stream sulphate from nonmarine sources (64–66% vs. 35–46%). Sea‐salts were rarely a major cause of episodic ANC or pH reduction during the events sampled. By contrast, streams with episodes driven by strong anthropogenic acids had lower pH (5.0±0.6) and more dissolved aluminium (288±271 μg L−1) during events than where episodes were caused by dilution (pH 5.4±0.6; 116±110 μg Al L−1) or where streams remained circumneutral (pH 6.7±1.0; 50±45 μg Al L−1). Both biological predictions were supported: invertebrate assemblages differed among sites with different episode chemistry while several acid‐sensitive species were absent only where episodes reflected anthropogenic acidification. We conclude that strong acid anions – dominantly nonmarine sulphate – still cause significant episodic acidification in acid‐sensitive areas of Britain and may be a sufficient explanation for slow biological recovery in many locations.
The genetics of pathogen avoidance inCaenorhabditis elegans
Authors: Schulenburg Hinrich , Ewbank Jonathan J. 
Published: September 2007

SummaryMuch attention is rightly focused on how microbes cause disease, but they can also affect other aspects of host physiology, including behaviour. Indeed, pathogen avoidance behaviours are seen across animal taxa and are probably of major importance in nature. Here, we review what is known about the molecular genetics underlying pathogen avoidance in the nematodeCaenorhabditis elegans. In its natural environment, the soil, this animal feeds on microbes and is continuously exposed to a diverse mix of microorganisms. Nematodes that develop efficient behavioural responses that enhance their attraction to sources of food and avoidance of pathogens will have an evolutionary advantage.C. eleganscan specifically detect natural products of bacteria, including surfactants (such as serrawettin) and acylated homoserine lactone autoinducers, and it can learn to avoid pathogenic species. To date, several distinct mechanisms have been shown to be involved in pathogen avoidance. They are based on G protein‐like, insulin‐like and neuronal serotonin signalling. We discuss recent findings on the mechanisms of pathogen recognition inC. elegans, the relationship between alternative behavioural defences and also between these and other life‐history traits. We propose that the selective pressure associated with avoidance behaviours influence both pathogen and host evolution.
Relationship of Carbon Isotope Discrimination to Water Use Efficiency and Productivity of Barley Under Field and Greenhouse Conditions
Authors: Anyia A. O. , Slaski J. J , Nyachiro J. M. , Archambault D. J. , Juskiw P. 
Published: September 2007

AbstractThis study was conducted to evaluate the application of carbon isotope discrimination (CID) as a selection criterion for improving water use efficiency (WUE) and productivity of barley (Hordeum vulgare L.) under field and drought‐stress conditions in a greenhouse. A total of 54 genotypes were screened for variability in CID under field conditions, while 23 genotypes were evaluated under water‐deficit conditions in the greenhouse. A survey of leaf CID of 54 genotypes at two field locations showed more than 2.14‰ difference between extreme genotypes. Significant (P ≤ 0.05) genotypic variation was found in WUE and CID that had a negative strong correlation. There was a negative correlation between leaf CID and aerial biomass in the greenhouse and among six‐row genotypes in the field. Correlations between leaf CID across field locations and across irrigation regimes in the greenhouse were significant (experiment 1, r = 0.79 and 0.94 for six‐ and two‐row genotypes), suggesting stability of the CID trait across different environments. Overall, these results indicate the potential of leaf CID as a reliable method for selecting for high WUE and productivity in barley breeding programmes in the Canadian prairies. Further work is currently underway to determine heritability/genetics of leaf CID and application of molecular marker‐assisted selection for the traits in barley breeding programmes.
Physiological Effects of Waterlogging on Two Lucerne Varieties Grown Under Glasshouse Conditions
Authors: Irving L. J. , Sheng Y.‐B. , Woolley D. , Matthew C. 
Published: September 2007

AbstractTwo lucerne (Medicago sativa) varieties, an anecdotally waterlogging‐intolerant old New Zealand variety, Grasslands Wairau, and a reputedly waterlogging‐tolerant new variety, Pioneer 54Q53, were subjected to waterlogging stress and a range of physiological and agronomic measurements performed. Waterlogging stress was characterized by measurement of soil oxygen depletion and soil carbon dioxide accumulation. Both varieties exhibited strong responses to waterlogging stress, including reduction in leaf soluble protein concentration, photosynthetic rate and tap root weight, but also exhibited differences in response, notably a decrease in carboxylation efficiency and in the steady‐state quantum yield of electron flow through PSII (ΦPSII) in Wairau, but not in Pioneer. Implications for understanding of waterlogging effects on photosynthesis, and for field management of lucerne on wet soils are discussed.
Factors Influencing Pregnancy Rate and Late Embryonic Loss in Dairy Cattle
Authors: Gábor G , Tóth F , Ózsvári L , Abonyi‐Tóth Zs , Sasser RG 
Published: September 2007

ContentsThis trial was conducted on three Hungarian dairy farms between March 2003 and April 2004. The aims of this study were to examine the effect of milk production and milk contents, the day after calving (DAC) and the sire for the pregnancy rate (PR) and late embryonic loss (LEL) in dairies. Five thousand three hundred and eighty insemination was carried out in this period. Pregnancies (n = 1969) were detected by BioPrynTM test from 3919 blood samples between 30–36 days post insemination (PI). Retention of pregnancy was determined by rectal palpation on Day 60. LEL has been determined by the optical density (OD) of blood samples/cutoff ratio and the serum progesterone (P4) concentration 30–36 days PI. According to serum progesterone concentration the authors predicted a presumed or possible embryonic loss or maintenance of the pregnancy. The efficiency of the artificial inseminations (AI) was significantly lower 60 days within post‐partum. Significant positive correlation was found between the result of early and late PR and DAC and the milk protein/fat ratio. Significant negative correlation was detected between the early and late PR the milk protein and fat content. A later stage (60 days PI) of pregnancy the milk production has a negative effect for retaining of pregnancy. More data would be necessary to state that sires can influence the reproduction ability of their progenies. This is a really important issue, because the AI bulls have a great impact on the herds and the one‐way selection may cause decreased fertility on breed level as well.
Psychological distress in Japanese men with localized prostate cancer
Authors: Namiki Shunichi , Saito Seiichi , Tochigi Tatsuo , Numata Isao , Ioritani Naomasa , Arai Yoichi 
Published: September 2007

Objective:  To investigate: (i) the level of psychological distress; and (ii) the relationships between the level of psychological distress and general or disease‐specific HRQOL of Japanese men with localized prostate cancer following surgery or radiotherapy.Patients and methods:  The study was a retrospective cross‐sectional survey of 253 men with localized prostate cancer treated with radical prostatectomy and 87 with external beam radiotherapy were collected. The measures used four questionnaires including: (i) the Medical Outcomes Study 36‐Item Health Survey; (ii) The University of California, Los Angeles Prostate Cancer Index; (iii) International Prostate Symptom Score; and (iv) Hospital Anxiety and Depression Scale (HADS).Results:  Mean anxiety and depression scores were 4.0 and 4.7, respectively (standard deviation, 3.3 and 3.7). On the anxiety section of HADS, 291 patients (85%) scored 7 points or less; and on the depression scale, 183 (54%) patients scored 4 points or less. Those ‘cases’ (HADS total, >10) with psychological distress scored lower in all domains of the general and disease related health‐related quality of life (HRQOL) than the ‘non‐cases’ (HADS total, ≤10) except for sexual domains. Logistic regression modeling suggested that the men who tended to experience moderate to high distress suffered from worse urinary and bowel symptoms.Conclusion:  Most patients who underwent radical prostatectomy or external beam radiotherapy for localized prostate cancer experienced low levels of psychological distress after treatment. However, men who were experiencing urinary and bowel symptoms tended to suffer from moderate to higher distress compared with men reporting no or fewer such symptoms.
Non-Governmental Organizations as Motors of Change
Authors: Beyer Cornelia 
Published: September 2007

AbstractOn one hand, NGOs are seen as experts because of their proximity to the problems they address. They provide knowledge relevant to the solution of these problems and can bring this into the political process. They are able to increase the efficiency of global governance by participating in the policy-formation processes of international organizations. In this paper I will explain the role and functions of NGOs as described in the debate about their legitimacy and theorize – while applying Ernst Haas's theory of organizational learning – on the mechanisms likely to lead to their increasing integration into international institutions as well as the implications of this integration.
Electoral System Reform in Democracy's Grey Zone: Lessons from Putin's Russia
Authors: Moraski Bryon 
Published: September 2007

AbstractBesides seat maximization, what factors motivate an incumbent regime in the grey zone between democracy and dictatorship to alter a relatively institutionalized parliamentary electoral system? To answer this question, this article seeks to uncover the rationale guiding the 2005 changes to Russia's electoral system. It presents evidence to suggest that the same strategies that allowed Russia's current party of power to use the existing electoral system to its advantage in the 2003 Duma election, threatened to spoil the fruits of that advantage in the years to come. Yet it also points out that moving from a mixed electoral system to a purely proportional system could be good for Russian democracy in the future. As a result, the work contends that seemingly authoritarian incumbents will promote reforms that aid the future cause of democracy when these same reforms serve their more immediate interests.
Being American (Politics of Identity – XI)
Authors: King Preston 
Published: September 2007

Abstract‘Being American’ is a two-sided identity called ‘citizenship’. This involves a set (the state) and its members (citizens). The citizen (say Whitman) may be ‘fully’ American, just as some particular nation (say Native American, African, British, Jewish) may be so. But no one citizen (the patriot), or subset of citizens (perhaps the ethnic group), nor even the set of all citizens (past and present) reflects or symbolizes the whole of what ‘being American’ might mean. Nor can we reduce America's multitudes, and multitudinous practices, to one thickset/hotfoot Creed producing the sexy ‘American’/‘Un-American’ binary. Being American hangs upon a paramount constitutionalism that coolly reconciles, without melting, underlying identities. ‘Constitutionalism’ is informed by some abstract notion of justice, is grounded in mutual regard and equal liberty, and mere possession of ‘a constitution’ does not suffice to deliver it.
Somatic embryogenesis and multiple‐shoot formation from seed‐derived shoot apical meristems of rhodesgrass (Chloris gayana Kunth)
Authors: Gondo Takahiro , Matsumoto Jun , Yamakawa Kazutomi , Tsuruta Shin‐ichi , Ebina Masumi , Akashi Ryo 
Published: September 2007

AbstractHigh‐frequencies of somatic embryogenesis and multiple‐shoot formation were achieved with seed‐derived shoot apical meristems of rhodesgrass (Chloris gayana Kunth). Shoot apices as initial explants were isolated from aseptically germinated seedlings, and cultured in vitro. Embryogenic calli and the multiple shoots were induced and maintained on MS basal medium with various combinations of 2,4‐dichlorophnoxyacetic acid (2,4‐D) and 6‐benzylaminopurine (BAP), the two most effective treatments being 2.0 mg L−1 2,4‐D and 0.1 mg L−1 2,4‐D + 2.0 mg L−1 BAP. These embryogenic calli and multiple‐shoot formations could be used as alternative regenerable target tissues for genetic transformation using particle bombardment of rhodesgrass.
Phytosociological study of steppe vegetation in east Kazakhstan
Authors: Cheng Yunxiang , Nakamura Toru 
Published: September 2007

AbstractFollowing phytosociological methods, vegetation data were collected from 74 stands in the steppe area of east Kazakhstan, including Almaty, Pavlodar and Semipalatinsk Provinces. Detrended correspondence analysis (DCA) was used to extract the main compositional gradients of each of the 74 stands. In east Kazakhstan, four steppe vegetation communities were identified based on their species composition. The first ordination axis produced by DCA of species composition was associated with a decreasing Kira's warmth index (r = 0.84, P < 0.01) and an increasing Köppen P/E ratio (r = 0.70, P < 0.01). The second axis was associated with succession trends within the community as a result of different human activities. We identified a strong correlation with climatic factors, indicating that temperature and precipitation may influence the species composition of the east Kazakhstan steppe irrespective of human activities. Species composition, however, is affected by human disturbance, especially in such a severe environment where mean annual precipitation is below 300 mm in Pavlodar Province.