bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of the river diversion, Mesopotamian Marsh drainage and restoration, and river damming on the marine environment of the northwestern Arabian Gulf
Authors: Al-Yamani F. Y. , Bishop J. M. , Al-Rifaie K. , Ismail W.
Published: September 2007

This paper summarizes the results of a study, which was conducted during the period of 1996-2005. It assesses the impact of river diversion (Third River), marsh drainage, and marsh restoration on Kuwait's marine environment. The results indicated lower salinity, higher nitrate concentration, higher chlorophyll-a, and higher sedimentation in the northern waters of Kuwait influenced by the discharge of the man-made Third River and marsh drainage. Five estuarine copepod species, which occur only in the northern waters of Kuwait due to their proximity to the mouth of the river, are reported here for the first time. Lower turbidity levels were observed in the northern waters of Kuwait during 2004 and 2005 possibly influenced by the marsh restoration process. The above results indicate the close interrelationship between the upstream river environment and the northern Arabian Gulf. River-related activities in the Tigris-Euphrates Basin have transboundary impacts downstream. Assumptions on the potential effects of the upstream damming of the Tigris and Euphrates Rivers on Kuwait's marine environment are included. It is expected that recent and planned river basin modifications in Turkey, Iran and Iraq will significantly reduce river discharge, permanently remove seasonal flooding, and impact the northern Gulf's marine environment, with serious implications for fisheries.
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.
Changes in the coastal zone of Abu Dhabi determined using satellite imagery (1972–2003)
Authors: Loughland R. A. , Saenger P. , Luker G. , Siddiqui K. , Saji B. , Belt M. , Crawford K.
Published: September 2007

The coastal and marine resources of Abu Dhabi have sustained the local inhabitants for thousands of years. However, rapid development following the discovery and exploitation of mineral oil reserves in the second half of the 20th Century changed the intensity and use of the natural resources. Changes in coastal geomorphology, landuse and vegetation were documented using remote sensed images covering the period from 1972 to 2003. The study indicated that there have been major geomorphologic and landuse changes within the coastal zone of Abu Dhabi as a result of urban and industrial development. Vegetation, both cultivated and intertidal, has increased within the study period. The data collected emphasises the urgency for developing sustainable coastal management strategies in Abu Dhabi and the region.
Petroleum hydrocarbons in water and sediments of northwest Arabian Gulf 1980–2005
Authors: Al-Imarah Faris J. M. , Hantoosh Abass A. , Nasir Ali M.
Published: September 2007

A survey has been conducted to evaluate pollution by petroleum hydrocarbons (PHC's) in water, sediments and living organisms of southern Iraqi sectors represented by Shatt Al-Arab River, Khor Al-Zubair, Umm Qasser, Khor Abdullah and the northwest Arabian Gulf. Petroleum hydrocarbons in water as dissolved and particulate, in sediments as exchangeable and residual and in the organs of living organisms were reported for the period 1980–2002. During 1980, levels of PHC's reported in Shatt Al-Arab river ranged from a lower value of 2.6 μ g l−1 in Qurnah and a higher value of 44 μ g l−1 in Basrah, while the range was little bit higher in the estuary of Shatt Al-Arab reaching 16–56 μ g l−1 during the same period. Then this range was lowered afterwards to reach 4–14 μ g l−1 in Shatt Al-Arab and 6–7 μ g l−1 in it's estuary during the year 1993, then it jumped afterwards to reach 2.5–47 μ g l−1 and 31–80 μg l−1 in Shatt Al-Arab river and it's estuary respectively during the year 2000. The same trend was found for the northwest Arabian Gulf. For sediments it seems that total petroleum hydrocarbons declined from Shatt Al-Arab River towards its estuary, Khor Al-Zubair, Khor Abdullah and the northwest Arabian Gulf.
The development of a marine and coastal natural resource atlas: Abu Dhabi Emirate, United Arab Emirates
Authors: Loughland R. A. , Darwish A. M. , Saddiqui K. , Fadel S. S. , Al-Ali A. A. , Crawford K.
Published: September 2007

The goal of the study was to collect, analyze and document environmental data for the sustainable use of Abu Dhabi's marine and coastal resources. Prior to the study there was no detailed ecological data relating to the marine environment; and with increasing development demands, and no data to assist in planning, the coastal and marine resources were under serious threat of degradation. From 1999 to 2001 extensive field research was undertaken to collect ecological data throughout the coastal and marine areas of Abu Dhabi Emirate. The program incorporated the training of UAE postgraduate students. The atlas program successfully documented data on the location and extent of coastal habitats, the distribution of marine wildlife and areas of international conservation importance throughout the Emirate of Abu Dhabi. All data was geographically corrected and checked for accuracy and completeness, and Arabic and English place names were assigned to all localities in the Emirate. The atlas program provided an opportunity for detailed scientific survey to be undertaken in an area where data generally had not been previously collected. It is envisaged that the atlas will contribute towards the protection of the marine environment, and facilitate sustainable coastal development throughout Abu Dhabi Emirate.
Halophytes and associated properties of natural soils in the Doha area, Qatar
Authors: Yasseen B. T. , Al-Thani R. F.
Published: September 2007

Plant life and the life they support are being eliminated and cannot cope with the construction activities in Doha City. One of the most important reasons behind this study is the fast rate at which many habitats are disappearing due to the higher activities in the construction sites throughout Doha City. These activities are not accompanied by any assessments of the impact on natural habitats nor by any plans for future restoration. This study focuses on the eco-physiology of the dominant wild plant species. Locations 1 and 2 are inhabited with Avicennia marina, Halopeplis perfoliata, Halocnemum strobilaceum, Arthrocnemum macrostachyum, Limonium axillare, Seidlitzia rosmarinus, Suaeda vermiculata and Zygophyllum qatarense, while the remaining species, including some xerophytes, were found in the other locations. Analysis of soil samples revealed a considerable variation in all studied parameters including the ECe, water content and pH. The most abundant ions in the soil as expected were Cl− and Na+. The plants studied showed different abilities to accumulate proline in nearly all studied plants. Most plants accumulated higher concentrations of Na+, Cl−, and Ca2+, and lower concentrations of K+ and Mg2 +. Finally, it would be very useful for local authorities to consult research centers before any future construction plans and to support modern research in molecular biology taking advantage of having gene banks from halophytes.
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.
Evolution and the Explanation of Meaning
Authors: Huttegger Simon M.
Published: September 2007

Signaling games provide basic insights into some fundamental questions concerning the explanation of meaning. They can be analyzed in terms of rational choice theory and in terms of evolutionary game theory. It is argued that an evolutionary approach provides better explanations for the emergence of simple communication systems. To substantiate these arguments, I will look at models similar to those of Skyrms (2000) and Komarova and Niyogi (2004) and study their dynamical properties. My results will lend partial support to the thesis that evolution leads to communication. In general, states of partial communication may evolve with positive probability under standard evolutionary dynamics. However, unlike states of perfect communication, they are unstable relative to neutral drift.
Reconstructing Scientific Realism to Rebut the Pessimistic Meta-induction
Authors: Doppelt Gerald
Published: September 2007

This paper develops a stronger version of ‘inference-to-the-best explanation’ scientific realism. I argue against three standard assumptions of current realists: (1) realism is confirmed if it provides the best explanation of theories’ predictive success; (2) the realist claim that successful theories are always approximately true provides the best explanation of their success; and (3) realists are committed to giving the same sort of truth-based explanation of superseded theories’ success that they give to explain our best current theories’ success. On the positive side, I argue that (1) the confirmation of realism requires explaining theories’ explanatory success, not just their predictive success; (2) in turn this task requires a richer realist model of explanation that brings into the explanans both (a) successful theories’ epistemic virtues (e.g., unification and simplicity) and (b) the standards governing these virtues, as well as truth; (3) this richer realist model is further confirmed because it can better explain the success of theories in gaining wide acceptance among scientists; and (4) the model is further supported because it is superior to ‘preservative realism’ in providing a plausible rebuttal of the pessimistic meta-induction from the many past successful-but-false theories to the likelihood that our best current theories are likewise false.
Coherence, Truth, and the Development of Scientific Knowledge
Authors: Thagard Paul
Published: September 2007

What is the relation between coherence and truth? This paper rejects numerous answers to this question, including the following: truth is coherence; coherence is irrelevant to truth; coherence always leads to truth; coherence leads to probability, which leads to truth. I will argue that coherence of the right kind leads to at least approximate truth. The right kind is explanatory coherence, where explanation consists in describing mechanisms. We can judge that a scientific theory is progressively approximating the truth if it is increasing its explanatory coherence in two key respects: broadening by explaining more phenomena and deepening by investigating layers of mechanisms. I sketch an explanation of why deepening is a good epistemic strategy and discuss the prospect of deepening knowledge in the social sciences and everyday life.
Interaction of Ezrin with the Novel Guanine Nucleotide Exchange Factor PLEKHG6 Promotes RhoG-dependent Apical Cytoskeleton Rearrangements in Epithelial Cells
Authors: D'Angelo Romina , Aresta Sandra , Blangy Anne , Del Maestro Laurence , Louvard Daniel , Arpin Monique
Published: September 2007

The mechanisms underlying functional interactions between ERM (ezrin, radixin, moesin) proteins and Rho GTPases are not well understood. Here we characterized the interaction between ezrin and a novel Rho guanine nucleotide exchange factor, PLEKHG6. We show that ezrin recruits PLEKHG6 to the apical pole of epithelial cells where PLEKHG6 induces the formation of microvilli and membrane ruffles. These morphological changes are inhibited by dominant negative forms of RhoG. Indeed, we found that PLEKHG6 activates RhoG and to a much lesser extent Rac1. In addition we show that ezrin forms a complex with PLEKHG6 and RhoG. Furthermore, we detected a ternary complex between ezrin, PLEKHG6, and the RhoG effector ELMO. We demonstrate that PLEKHG6 and ezrin are both required in macropinocytosis. After down-regulation of either PLEKHG6 or ezrin expression, we observed an inhibition of dextran uptake in EGF-stimulated A431 cells. Altogether, our data indicate that ezrin allows the local activation of RhoG at the apical pole of epithelial cells by recruiting upstream and downstream regulators of RhoG and that both PLEKHG6 and ezrin are required for efficient macropinocytosis.
Dystroglycan and ProteinO-Mannosyltransferases 1 and 2 Are Required to Maintain Integrity ofDrosophilaLarval Muscles
Authors: Haines Nicola , Seabrooke Sara , Stewart Bryan A.
Published: September 2007

In vertebrates, mutations in Protein O-mannosyltransferase1 (POMT1) or POMT2 are associated with muscular dystrophy due to a requirement for O-linked mannose glycans on the Dystroglycan (Dg) protein. In this study we examine larval body wall muscles of Drosophila mutant for Dg, or RNA interference knockdown for Dg and find defects in muscle attachment, altered muscle contraction, and a change in muscle membrane resistance. To determine if POMTs are required for Dg function in Drosophila, we examine larvae mutant for genes encoding POMT1 or POMT2. Larvae mutant for either POMT, or doubly mutant for both, show muscle attachment and muscle contraction phenotypes identical to those associated with reduced Dg function, consistent with a requirement for O-linked mannose on Drosophila Dg. Together these data establish a central role for Dg in maintaining integrity in Drosophila larval muscles and demonstrate the importance of glycosylation to Dg function in Drosophila. This study opens the possibility of using Drosophila to investigate muscular dystrophy.
Cyclin D1 Is Transcriptionally Down-Regulated by ZO-2 via an E Box and the Transcription Factor c-Myc
Authors: Huerta Miriam , Muñoz Rodrigo , Tapia Rocío , Soto-Reyes Ernesto , Ramírez Leticia , Recillas-Targa Félix , González-Mariscal Lorenza , López-Bayghen Esther
Published: September 2007

Recent reports have indicated the participation of tight junction (TJ) proteins in the regulation of gene expression and cell proliferation. Here, we have studied the role of zona occludens (ZO)-2, a TJ peripheral protein, in the regulation of cyclin D1 transcription. We found that ZO-2 down-regulates cyclin D1 transcription in a dose-dependent manner. To understand how ZO-2 represses cyclin D1 promoter activity, we used deletion analyses and found that ZO-2 negatively regulates cyclin D1 transcription via an E box and that it diminishes cell proliferation. Because ZO-2 does not associate directly with DNA, electrophoretic mobility shift assay and chromatin immunoprecipitation (ChIP) assay were used to identify the transcription factors mediating the ZO-2–repressive effect. c-Myc was found to bind the E box present in the cyclin D1 promoter, and the overexpression of c-Myc augmented the inhibition generated by ZO-2 transfection. The presence of ZO-2 and c-Myc in the same complex was further demonstrated by immunoprecipitation. ChIP and reporter gene assays using histone deacetylases (HDACs) inhibitors demonstrated that HDACs are necessary for ZO-2 repression and that HDAC1 is recruited to the E box. We conclude that ZO-2 down-regulates cyclin D1 transcription by interacting with the c-Myc/E box element and by recruiting HDAC1.
Atf1 Is a Target of the Mitogen-activated Protein Kinase Pmk1 and Regulates Cell Integrity in Fission Yeast
Authors: Takada Hirofumi , Nishimura Masayuki , Asayama Yuta , Mannse Yoshiaki , Ishiwata Shunji , Kita Ayako , Doi Akira , Nishida Aiko , Kai Naoyuki , Moriuchi Sayako , Tohda Hideki , Giga-Hama Yuko , Kuno Takayoshi , Sugiura Reiko
Published: September 2007

In fission yeast, knockout of the calcineurin gene resulted in hypersensitivity to Cl−, and the overexpression of pmp1+encoding a dual-specificity phosphatase for Pmk1 mitogen-activated protein kinase (MAPK) or the knockout of the components of the Pmk1 pathway complemented the Cl−hypersensitivity of calcineurin deletion. Here, we showed that the overexpression of ptc1+and ptc3+, both encoding type 2C protein phosphatase (PP2C), previously known to inactivate the Wis1–Spc1–Atf1 stress-activated MAPK signaling pathway, suppressed the Cl−hypersensitivity of calcineurin deletion. We also demonstrated that the mRNA levels of these two PP2Cs and pyp2+, another negative regulator of Spc1, are dependent on Pmk1. Notably, the deletion of Atf1, but not that of Spc1, displayed hypersensitivity to the cell wall-damaging agents and also suppressed the Cl−hypersensitivity of calcineurin deletion, both of which are characteristic phenotypes shared by the mutation of the components of the Pmk1 MAPK pathway. Moreover, micafungin treatment induced Pmk1 hyperactivation that resulted in Atf1 hyperphosphorylation. Together, our results suggest that PP2C is involved in a negative feedback loop of the Pmk1 signaling, and results also demonstrate that Atf1 is a key component of the cell integrity signaling downstream of Pmk1 MAPK.
Copper and Manganese Induce Yeast Apoptosis via Different Pathways
Authors: Liang Qiuli , Zhou Bing
Published: September 2007

Metal ions are essential as well as toxic to the cell. The mechanism of metal-induced toxicity is not well established. Here, for the first time we studied two essential nutritional elements, copper and manganese, for their apoptotic effects in yeast Saccharomyces cerevisiae. Although beneficial at subtoxic levels, we demonstrated that at moderately toxic levels, both metals induce extensive apoptosis in yeast cells. At even higher concentrations, necrosis takes over. Furthermore, we investigated the molecular pathways mediating Cu- and Mn-mediated apoptotic action. Mitochondria-defective yeast exhibit a much reduced apoptotic marker expression and better survival under Cu and Mn stress, indicating mitochondria are involved in both Cu- and Mn-induced apoptosis. Reactive oxygen species (ROS) are generated in high amounts in Cu- but not in Mn-induced cell death, and Cu toxicity can be alleviated by overexpression of superoxide dismutase 2, suggesting ROS mediate Cu but not Mn toxicity. Yeast metacaspase Yca1p is not involved in Cu-induced apoptosis, although it plays an important role in the Mn-induced process. A genetic screen identified Cpr3p, a yeast cyclophilin D homologue, as mediating the Cu-induced apoptotic program. Cpr3p mutant seems to eliminate Cu-induced apoptosis without affecting ROS production, while leaving necrosis intact. These results may provide important insight into a detailed understanding at the molecular and cellular level of metal toxicity and metal accumulation diseases.
Kalirin/Trio Rho Guanine Nucleotide Exchange Factors Regulate a Novel Step in Secretory Granule Maturation
Authors: Ferraro Francesco , Ma Xin-Ming , Sobota Jacqueline A. , Eipper Betty A. , Mains Richard E.
Published: September 2007

The molecular mechanisms involved in the maturation of secretory granules, organelles that store hormones and neuropeptides, are poorly understood. As granule content proteins are processed, the composition of granule membranes changes, yielding constitutive-like secretion of immature content proteins and producing secretagogue-responsive mature granules. Constitutive-like secretion was not previously recognized as a process subject to regulation. We show that Kalirin and Trio, homologous Rho guanine nucleotide exchange factors (GEFs), which interact with a secretory granule resident protein, modulate cargo secretion from immature granules. Some of the Kalirin and Trio isoforms expressed in neuroendocrine cells colocalize with immature granules. Overexpression of their N-terminal GEF domain (GEF1) enhances secretion from immature granules, depleting cells of secretory cargo in the absence of secretagogue. This response requires GEF1 activity and is mimicked by Kalirin/Trio substrates Rac1 and RhoG. Accordingly, selective pharmacological inhibition of endogenous GEF1 activity decreases secretagogue-independent release of hormone precursors, accumulating product peptide in mature secretory granules. Kalirin/Trio modulation of cargo secretion from immature granules provides secretory cells with an extra layer of control over the sets of peptides released. Control of this step enhances the range of physiological responses that can be elicited, whereas lack of control could have pathological consequences.
Membrane-active Compounds Activate the Transcription Factors Pdr1 and Pdr3 Connecting Pleiotropic Drug Resistance and Membrane Lipid Homeostasis inSaccharomyces cerevisiae
Authors: Schüller Christoph , Mamnun Yasmine M. , Wolfger Hubert , Rockwell Nathan , Thorner Jeremy , Kuchler Karl
Published: September 2007

The Saccharomyces cerevisiae zinc cluster transcription factors Pdr1 and Pdr3 mediate general drug resistance to many cytotoxic substances also known as pleiotropic drug resistance (PDR). The regulatory mechanisms that activate Pdr1 and Pdr3 in response to the various xenobiotics are poorly understood. In this study, we report that exposure of yeast cells to 2,4-dichlorophenol (DCP), benzyl alcohol, nonionic detergents, and lysophospholipids causes rapid activation of Pdr1 and Pdr3. Furthermore, Pdr1/Pdr3 target genes encoding the ATP-binding cassette proteins Pdr5 and Pdr15 confer resistance against these compounds. Genome-wide transcript analysis of wild-type and pdr1Δ pdr3Δ cells treated with DCP reveals most prominently the activation of the PDR response but also other stress response pathways. Polyoxyethylene-9-laurylether treatment produced a similar profile with regard to activation of Pdr1 and Pdr3, suggesting activation of these by detergents. The Pdr1/Pdr3 response element is sufficient to confer regulation to a reporter gene by these substances in a Pdr1/Pdr3-dependent manner. Our data indicate that compounds with potential membrane-damaging or -perturbing effects might function as an activating signal for Pdr1 and Pdr3, and they suggest a role for their target genes in membrane lipid organization or remodeling.
Moderated statistical tests for assessing differences in tag abundance
Authors: Robinson Mark D. , Smyth Gordon K.
Published: September 2007

Motivation: 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.au

Supplementary 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

Motivation: 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.html

Contact:  breit@science.uva.nl

Supplementary 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

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

We 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.
Safety and efficacy of a plasma‐derived monoclonal purified factor VIII concentrate during 10 years of follow‐up
Authors: MAUSER‐BUNSCHOTEN E. P. , POSTHOUWER D. , FISCHER K. , VAN DEN BERG H. M.
Published: September 2007

Summary.  In 1995, AAFACT®, a new monoclonal purified factor VIII concentrate (FVIII), derived from human plasma, was introduced in the Netherlands. The monoclonal purification based production process includes a viral inactivation step by solvent/detergent treatment. Products manufactured according to this procedure, for example Hemofil M® are used worldwide. The aim of the present study was to assess inhibitor development in a large cohort of previously treated patients (PTPs) who were followed up for 10 years. In addition, efficacy, HIV and hepatitis C virus (HCV) transmission, and allergic reactions were monitored. All 165 patients with severe haemophilia A (FVIII < 1%) known at the van Creveldkliniek who ever used AAFACT® during the period from October 1995 to September 2005 were included. Two of them were previously untreated patients (PUPs) and two others had <50 exposure days. Data on FVIII consumption, number of exposures, bleedings and hospitalization days were collected from start of AAFACT® until last clinical and laboratory evaluation while on this product. At the end of follow‐up, 91 patients were still using this plasma‐derived FVIII. Median age at start of follow‐up was 26 years (range 1–52). None of the patients reported lack of efficacy. Median FVIII consumption per patient during follow‐up was 2058 IU kg−1 bodyweight per year, and median number of exposures was 148 per year. During 1029 patient‐years of follow‐up, one inhibitor was diagnosed in a previously treated patient PTP. This patient developed high titre inhibitor following surgery for which he, during 1 week, had been treated with continuous infusion with recombinant FVIII. No inhibitor occurred during 68 cases of surgery using continuous infusion with AAFACT®. No viral transmissions or other adverse events occurred during 10 years of follow‐up; AAFACT® appeared to be an effective and safe FVIII product.
The genetics of pathogen avoidance inCaenorhabditis elegans
Authors: Schulenburg Hinrich , Ewbank Jonathan J.
Published: September 2007

Much 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

This 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

Two 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

Contents

This 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.
A case of spontaneous rupture perforation of leiomyosarcoma in the urachus of a young boy
Authors: Kim Sun‐Ouck , Kwon Dongdeuk , Choi Chan , Baek Hee Jo , Park Kwangsung , Ryu Soo Bang
Published: September 2007

Abstract:  A case of spontaneous rupture of the urachal leiomyosarcoma in a 12‐year‐old boy is presented. This is of interest because massive hemoperitoneum due to spontaneous rupture of the urachal leiomyosarcoma is remarkably rare. We diagnosed based on histopathological features. Partial cystectomy and adjuvant chemo‐radiation therapy was done with no sign of local recurrence or metastasis until 6 months after the operation.
Primary vesical actinomycosis: A case report and literature review
Authors: Al‐Kadhi Sabah , Venkiteswaran Krishna Prasad , Al‐Ansari Abdulla , Shamsudini Ahmed , Al‐Bozom Issam , Kiliyanni Abdul Salim
Published: September 2007

Abstract:  Pelvic actinomycosis is a chronic granulomatous infection caused by the gram‐positive anaerobic bacteria, Actinomyces Israelli. Vesical lesions, particularly without any obvious source of infection, are rare. We report a case of primary vesical actinomycosis which presented as a bladder mass, giving suspicion of malignancy. Repeated trans‐urethral deep resections and histo‐pathological examinations revealed the true nature of the mass, which was treated by medical means. A high index of suspicion of potentially benign bladder lesions, particularly in a younger age group of patients, is advocated, to prevent unnecessary major surgical procedures.
Laparoscopic partial cystectomy with en bloc resection of the urachus for urachal adenocarcinoma
Authors: Hong Sung‐Hoo , Kim Joon Chul , Hwang Tae‐Kon
Published: September 2007

Abstract:  Urachal carcinoma accounts for less than 1% of bladder cancers. The preferred treatment is wide local excision with partial or radical cystectomy. Two patients who presented with urachal carcinoma underwent laparoscopic partial cystectomy with en bloc resection of the urachus and bilateral pelvic lymphadenectomy as a less morbid, minimally invasive surgical alternative. Laparoscopic excision was successfully carried out in two cases with an uneventful convalescence.
Squamous cell carcinoma of the urachus
Authors: Fujiyama Chisato , Nakashima Nobuyo , Tokuda Yuji , Uozumi Jiro
Published: September 2007

Abstract:  A 64‐year‐old man was admitted with complaints of abdominal pain and pollakisuria. A soft mass was palpable under his navel. Magnetic resonance imaging (MRI) revealed a 9 × 6 cm tumor, which was composed of a cystic lesion arising from the urachus and a solid mass component at the urinary bladder dome. Urine cytology specimens showed squamous cell carcinoma (SCC). Serum SCC level was increased and the tumor was removed surgically. Histological examination detected well‐differentiated SCC, which had invaded the urinary bladder and the peritoneum. The patient has been followed up without recurrence for 6 months.
Continuous urinary incontinence presenting as the initial symptoms demonstrating acontractile detrusor and intrinsic sphincter deficiency in multiple system atrophy
Authors: Mashidori Tomoko , Yamanishi Tomonori , Yoshida Ken‐Ichiro , Sakakibara Ryuji , Sakurai Kunihiko , Hirata Koichi
Published: September 2007

Abstract:  Severe stress incontinence due to intrinsic sphincter deficiency may be common in aged women. However stress urinary incontinence could be the initial symptom of severe neurogenic bladder even if no neurological signs have previously been recognized. Urodynamic study is necessary in such a case. Tension‐free vaginal tape surgery and intermittent self‐catheterization may be one option, but self catheterization might become difficult when the neurological disorders develop. In this case report, we highlight the need for caution in identifying the presence of an occult neurogenic bladder when intending to carry out surgery for patients with severe stress incontinence.
A case of polymyositis associated with adrenal carcinoma
Authors: Hirai Toshiaki , Tsujihata Masao , Ueda Tomohiro , Nonomura Norio , Okuyama Akihiko
Published: September 2007

Abstract:  The association between idiopathic inflammatory myositis and cancer is well recognized. Most descriptions have been of dermatomyositis‐associated cancer, however, a few have been of polymyositis‐associated adrenal cancer. Here, we report a 69‐year‐old man in whom polymyositis‐associated adrenal cancer was diagnosed. The patient complained of difficulty with walking and with standing unassisted. Physical examination and electrophysiological studies revealed an abnormality of the proximal muscles. Serum levels of creatine kinase and lactic dehydrogenase were increased. Imaging studies showed a solid tumor measuring 14 × 9 cm in the retroperitoneum. After surgical excision of the tumor, including the left kidney, the serum levels of creatine kinase and lactic dehydrogenase normalized, and symptoms of myositis disappeared.