bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of the hydraulic biotope concept to the classification of instream habitats
Authors: Wadeson R.A. , Rowntree K.M. 
Published: November 2008

Abstract
A simple matrix developed by a small group of ecologists, geomorphologists and an hydraulic engineer at a workshop in February 1995 was proposed as a standardised classification tool for the recognition of hydraulic biotopes, instream flow environments recognised on the basis of surface flow type and substrate class. Research was carried out in the Buffalo River, South Africa, to test the validity of this classification with respect to measurable hydraulic attributes. Hydraulic biotopes were classified at a number of sites representing a range of stream morphologies, channel scale and discharge. The hydraulic attributes at each sampling point were measured. Using simple measures of flow depth, velocity and bed roughness, hydraulic indices were calculated to describe both the near bed conditions (shear velocity and ‘roughness’ Reynolds number) and the mean flow in the water column (Froude number and Reynolds number). Results indicate that hydraulic biotope classes can be considered as significantly different in terms of flow hydraulics. Hydraulic characteristics appear to be consistent within classes across different spatial scales. An assessment of the influence of discharge showed that differences are recognised in the classes of the lower energy environments (pool and run) but despite considerable within class variability, no significant differences were observed across discharges in the higher energy environments. The hydraulic biotope classification and associated hydraulic biotope matrix shows good potential as a standardised method for classifying instream environments over a range of channel scales and discharges.
The relation between macroinvertebrate assemblages in the Rhine–Meuse delta (The Netherlands) and sediment quality
Authors: Reinhold-Dudok van Heel H.C. , den Besten P.J. 
Published: November 2008

AbstractData from ecological and ecotoxicological research were analysed together in order to gain more insight into the biological effects caused by sediment pollution in the delta of the rivers Rhine and Meuse. Information from the following three sources was integrated: surveys of the macroinvertebrate assemblages, chemical analyses in sediment and bioassays. On the basis of cluster analysis and multivariate analysis of a dataset consisting of macrofauna samples from 283 sampling points, it was concluded that the most important factors determining species composition are: presence of solid substrates, depth, current velocity, erosion caused by wind or shipping, and grain size distribution and organic matter content of the sediment. In order to evaluate the role of sediment toxicity in more detail, subsets of the dataset were formed that corresponded with more homogenous clusters of sampling points with regard to sediment characteristics. The degree of sediment toxicity was based on the effects observed in three bioassays with whole sediment or sediment pore water. Further multivariate statistical analysis was performed for four sediment types. Direct linear gradient analysis indicated that for the sediment types fine sand, sandy silt and silt, sediment toxicity can explain part of the variation in species composition. Sediment toxicity was positively correlated with the levels of heavy metals, mineral oil, hexachlorobenzene and/or endrin. It is concluded that the approach followed in this study can contribute to our understanding of the influence of chemical pollution on macroinvertebrate communities.
On the transformation from healthy to degraded aquatic ecosystems
Authors: Rapport David J. 
Published: November 2008

AbstractAquatic ecosystems that have become degraded under stress show similarities both in the signs of pathology and in the mechanisms that promote degradation. A review of the transformations in several aquatic systems, including the Laurentian Great Lakes (Canada/US), the Baltic Sea (Finland) and Lake Chapala (Mexico) reveals signs of ‘ecosystem distress’, including alterations in primary and secondary productivity, nutrient cycling, species diversity and biotic composition. A shift from a predominantly vertical to horizontal nutrient spiraling characterizes all three aquatic ecosystems, as does a reduction in the abundance of the larger (high-valued) fish stocks. Once the health of robust systems begins to decline, mechanisms are called into play that tend to perpetuate the ecosystem breakdown. The process may be difficult to reverse, even when sources of initial stress are removed.
Extending causality in the Great Lakes basin ecosystem
Authors: Vallentyne J.R. 
Published: November 2008

AbstractMichael Gilbertson (Gilbertson, M., 1997. Can. J. Fish. Aquat. Sci. 54, 483–495) has asserted that the adoption of an ecosystem approach to problem-solving in the Great Lakes Water Quality Agreement (GLWQA) of 1978 has undermined the ability of Canada and the United States to grapple effectively with transboundary water pollution. In opposition to this, arguments are presented to suggest that Gilbertson errs in: (1) identifying pollution as the main focus of the GLWQA of 1978; (2) failing to demonstrate that the rise of the ecosystem approach to management caused a reduction of progress in eliminating persistent toxic substances; (3) failing to realize through extended chains of causality that the ecosystem approach and forensic approach to transboundary problem-solving are complementary. The texts and discussions leading up to the signing of the GLWQAs of 1972 and 1978 make it clear that the ecosystem approach to transboundary problem-solving is essential to achieving the purpose of the Great Lakes Water Quality Agreement of 1978 both in regard to the “integrity” clause and the elimination of persistent toxic substances and other pollutants.
A novel signaling pathway impact analysis
Authors: Tarca Adi Laurentiu , Draghici Sorin , Khatri Purvesh , Hassan Sonia S. , Mittal Pooja , Kim Jung-sun , Kim Chong Jai , Kusanovic Juan Pedro , Romero Roberto 
Published: November 2008

Abstract
Motivation: Gene expression class comparison studies may identify hundreds or thousands of genes as differentially expressed (DE) between sample groups. Gaining biological insight from the result of such experiments can be approached, for instance, by identifying the signaling pathways impacted by the observed changes. Most of the existing pathway analysis methods focus on either the number of DE genes observed in a given pathway (enrichment analysis methods), or on the correlation between the pathway genes and the class of the samples (functional class scoring methods). Both approaches treat the pathways as simple sets of genes, disregarding the complex gene interactions that these pathways are built to describe.
Results: We describe a novel signaling pathway impact analysis (SPIA) that combines the evidence obtained from the classical enrichment analysis with a novel type of evidence, which measures the actual perturbation on a given pathway under a given condition. A bootstrap procedure is used to assess the significance of the observed total pathway perturbation. Using simulations we show that the evidence derived from perturbations is independent of the pathway enrichment evidence. This allows us to calculate a global pathway significance P-value, which combines the enrichment and perturbation P-values. We illustrate the capabilities of the novel method on four real datasets. The results obtained on these data show that SPIA has better specificity and more sensitivity than several widely used pathway analysis methods.
Availability: SPIA was implemented as an R package available at http://vortex.cs.wayne.edu/ontoexpress/
Contact: sorin@wayne.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Expression of interferon‐γ and tumour necrosis factor‐α messenger RNA does not correlate with protection in guinea pigs challenged with virulent Mycobacterium tuberculosis by the respiratory route
Authors: Jeevan Amminikutty , Bonilla Diana Lucia , McMurray David Neil 
Published: November 2008

SummaryCytokine messenger RNA (mRNA) expression was investigated in the spleen and lung digest cells of bacillus Calmette–Guérin (BCG)‐vaccinated and non‐vaccinated guinea pigs following low‐dose, pulmonary exposure to virulent Mycobacterium tuberculosis. After purified protein derivative (PPD) stimulation, the levels of lung cell interferon‐γ (IFN‐γ), tumour necrosis factor‐α (TNF‐α) and spleen cell interleukin‐12 (IL‐12) p40 mRNAs were significantly increased in the non‐vaccinated M. tuberculosis‐infected guinea pigs compared to the BCG‐vaccinated guinea pigs. In contrast, the expression of anti‐inflammatory transforming growth factor‐β and IL‐10 mRNAs was significantly enhanced in the spleens of BCG‐vaccinated animals. Despite the presence of protective cytokine mRNA expression, the non‐vaccinated guinea pigs had significantly higher lung and spleen bacterial burdens. In contrast, BCG‐vaccinated guinea pigs controlled the bacterial multiplication in their lungs and spleens, indicating that both protective as well as anti‐inflammatory cytokine responses are associated with a reduction in bacteria. In addition, lung digest cells from non‐vaccinated guinea pigs contained a significantly higher percentage of neutrophils, CD3+ and CD8+ T cells, while the percentage of macrophages was increased in the BCG‐vaccinated animals. Total and purified lung digest T cells co‐cultured with lung macrophages (LMøs) proliferated poorly after PPD stimulation in both non‐vaccinated and BCG‐vaccinated animals while robust proliferation to PPD was observed when T cells were co‐cultured with peritoneal macrophages (PMøs). Macrophages within the lung compartment appear to regulate the response of T cells irrespective of the vaccination status in guinea pigs. Taken together, our results suggest that type I cytokine mRNA expression is not associated with vaccine‐induced protection in the low‐dose guinea pig model of tuberculosis.
Hummocky cross‐stratification‐like structures in deep‐sea turbidites: Upper Cretaceous Basque basins (Western Pyrenees, France)
Authors: MULDER THIERRY , RAZIN PHILIPPE , FAUGERES JEAN‐CLAUDE 
Published: November 2008

AbstractHummocky cross‐stratification is a sedimentary structure which is widely interpreted as the sedimentary record of an oscillatory current generated by energetic storm waves remobilizing surface sediment on the continental shelf. Sedimentary structures named hummocky cross‐stratification‐like structures, similar to true hummocky cross‐stratification, have been observed in the Turonian–Senonian Basque Flysch Basin (south‐west France). The bathymetry (1000 to 1500 m) suggests that the observed sedimentary structures do not result from a hydrodynamic process similar to those acting on a continental shelf. The morphology of these three‐dimensional structures shares similarities with the morphology of hummocky cross‐stratification despite a smaller size. The lateral extent of these structures ranges from a few decimetres to many decimetres; they consist of convex‐up domes (hummock) and concave‐up swales with a non‐erosive base. Four types of hummocky cross‐stratification‐like geometries are described; they occur in association with structures such as climbing current ripple lamination and synsedimentary deformations. In the Basque Flysch, hummocky cross‐stratification‐like structures are only found in the Tc interval of the Bouma sequence. Hummocky cross‐stratification‐like structures are sporadic in the stratigraphic series and observed only in few turbidite beds or bed packages. This observation suggests that hummocky cross‐stratification‐like structures are linked genetically to the turbidity current but form under a very restricted range of parameters. These structures sometimes show an up‐current (upslope) migration trend (antidunes). In the described examples, they could result from standing waves forming at the upper flow interface because of Kelvin–Helmholtz instability.
Absidia parricida plays a dominant role in biotrophic fusion parasitism among mucoralean fungi (Zygomycetes): Lentamyces, a new genus for A. parricida and A. zychae
Authors: Hoffmann K. , Voigt K. 
Published: November 2008

AbstractWithin the order Mucorales (Zygomycetes), the facultative parasites Parasitella parasitica, Chaetocladium brefeldii, Chaetocladium jonesii and Absidia parricida are known to initiate biotrophic fusion parasitic interactions on a wide variety of other mucoralean hosts. Their phylogenetic relationship within the Mucorales and their ability to form parasitic structures with several known host species was examined. Together with interspecific reactions between the mycoparasites, this study found: (i) no evident differences in the spectrum of non‐parasitic hosts tested within the study; (ii) A. parricida parasitises all other fusion parasites; (iii) A. parricida is ancestral to all other parasites; (iv) A. parricida is reported for the first time as phylogenetically basal to all other mucoralean fungi except the Umbelopsidaceae and (v) based on phylogenetic analyses and physiological and morphological characteristics, the slow‐growing species A. parricida and Absidia zychae are removed from the genus Absidia and reclassified in the newly described genus Lentamyces.
Contrasting intra versus interspecies DNA sequence variation for representatives of the Batrachospermales (Rhodophyta): Insights from a DNA barcoding approach
Authors: Sherwood Alison R. , Vis Morgan L. , Entwisle Timothy J. , Necchi Jr Orlando , Presting Gernot G. 
Published: November 2008

SUMMARYSixty‐five accessions of the species‐rich freshwater red algal order Batrachospermales were characterized through DNA sequencing of two regions: the mitochondrial cox1 gene (664 bp), which is proposed as the DNA barcode for red algae, and the UPA (universal plastid amplicon) marker (370 bp), which has been recently identified as a universally amplifying region of the plastid genome. upgma phenograms of both markers were consistent in their species‐level relationships, although levels of sequence divergence were very different. Intraspecific variation of morphologically identified accessions for the cox1 gene ranged from 0 to 67 bp (divergences were highest for the two taxa with the greatest number of accessions; Batrachospermum helminthosum and Batrachospermum macrosporum); while in contrast, the more conserved universal plastid amplicon exhibited much lower intraspecific variation (generally 0–3 bp). Comparisons to previously published mitochondrial cox2–3 spacer sequences for B. helminthosum indicated that the cox1 gene and cox2–3 spacer were characterized by similar levels of sequence divergence, and phylogeographic patterns based on these two markers were consistent. The two taxa represented by the largest numbers of specimens (B. helminthosum and B. macrosporum) have cox1 intraspecific divergence values that are substantially higher than previously reported, but no morphological differences can be discerned at this time among the intraspecific groups revealed in the analyses. DNA barcode data, which are based on a short fragment of an organellar genome, need to be interpreted in conjunction with other taxonomic characters, and additional batrachospermalean taxa need to be analyzed in detail to be able to draw generalities regarding intraspecific variation in this order. Nevertheless, these analyses reveal a number of batrachospermalean taxa worthy of more detailed DNA barcode study, and it is predicted that such research will have a substantial effect on the taxonomy of species within the Batrachospermales in the future.
Three new records ofPadinain Japan based on morphological and molecular markers
Authors: Ni‐Ni‐Win  , Hanyuda Takeaki , Arai Shogo , Uchimura Masayuki , Abbott Isabella A. , Kawai Hiroshi 
Published: November 2008

SUMMARYThree species of the brown algal genusPadina(Dictyotales),Padina melemeleI.A. Abbott et Magruder,Padina moffittianaI.A. Abbott et Huisman, andPadina thivyaeDoty et Newhouse, which were originally described from Hawaii, are newly reported from some of the offshore islands of Southern Japan:P. melemelecollected from Okinawa (Ryukyu Islands) and Chichi‐jima (Ogasawara Islands),P. moffittianafrom Okinawa I. andP. thivyaefrom Tanega‐shima. Identifications are based on morphological comparisons with the original descriptions and herbarium specimens of these species identified by I. A. Abbott. Some minor differences included tetrasporangial sori that were formed only on one surface of the thallus in JapaneseP. melemeleandP. thivyae, whereas in the Hawaiian specimens they were sometimes formed on both surfaces. JapaneseP. moffittianahad entire margins, whereas the Hawaiian specimens generally had fimbriate margins. Molecular analyses usingrbcL and mitochondrialcox3 genes as molecular markers confirmed the identification ofP. melemeleandP. moffittiana. Unfortunately the record ofP. thivyaecould not be confirmed because we were unable to extract DNA from this species.
Randomized controlled trial of oral vs intravenous therapy for the clinically diagnosed acute uncomplicated diverticulitis
Authors: Ridgway P. F. , Latif A. , Shabbir J. , Ofriokuma F. , Hurley M. J. , Evoy D. , O’Mahony J. B. , Mealy K. 
Published: November 2008

AbstractObjective  Despite the high prevalence of hospitalization for left iliac fossa tenderness, there is a striking lack of randomized data available to guide therapy. The authors hypothesize that an oral antibiotic and fluids are not inferior to intravenous (IV) antibiotics and ‘bowel rest’ in clinically diagnosed acute uncomplicated diverticulitis.Method  A randomized controlled trial was constructed in two District General Hospitals. All clinically diagnosed patients presenting with acute uncomplicated diverticulitis were eligible for the study. Oral and IV regimens utilizing ciprofloxacin and metronidazole were compared. The primary outcomes studied were surrogates for resolution of symptoms (including tenderness on day 3 and length of stay) and failure of oral therapy. Secondary endpoints studied were serial constitutional and biomarker trends.Results  There were 41 patients in the oral arm and 38 in the IV arm (n = 79). No patient had to be converted to IV antibiotics from the oral group. There was a complete resolution of symptoms in both groups. Tenderness was equivalent in both groups on day 3. Among secondary endpoints, a serial decrease in C reactive protein was the best serological predictor of resolution for both groups.Conclusion  Oral antibiotics are not inferior to intravenous antibiotics in achieving resolution of clinically diagnosed diverticulitis.
Role of IL‐15 in spinal cord and sciatic nerve after chronic constriction injury: regulation of macrophage and T‐cell infiltration
Authors: Gómez‐Nicola D. , Valle‐Argos B. , Suardíaz M. , Taylor J. S. , Nieto‐Sampedro M. 
Published: November 2008

AbstractThe release of inflammatory mediators from immune and glial cells either in the peripheral or CNS may have an important role in the development of physiopathological processes such as neuropathic pain. Microglial, then astrocytic activation in the spinal cord, lead to chronic inflammation, alteration of neuronal physiology and neuropathic pain. Standard experimental models of neuropathic pain include an important peripheral inflammatory component, which involves prominent immune cell activation and infiltration. Among potential immunomodulators, the T‐cell cytokine interleukin‐15 (IL‐15) has a key role in regulating immune cell activation and glial reactivity after CNS injury. Here we show, using the model of chronic constriction of the sciatic nerve (CCI), that IL‐15 is essential for the development of the early inflammatory events in the spinal cord after a peripheral lesion that generates neuropathic pain. IL‐15 expression in the spinal cord was identified in both astroglial and microglial cells and was present during the initial gliotic and inflammatory (NFκB) response to injury. The expression of IL‐15 was also identified as a cue for macrophage and T‐cell activation and infiltration in the sciatic nerve, as shown by intraneural injection of the cytokine and activity blockage approaches. We conclude that the regulation of IL‐15 and hence the initial events following its expression after peripheral nerve injury could have a future therapeutic potential in the reduction of neuroinflammation.
Spatial and temporal statistical analysis of bycatch data: patterns of sea turtle bycatch in the North Atlantic
Authors: Gardner Beth , Sullivan Patrick J. , Morreale Stephen J. , Epperly Sheryan P. 
Published: November 2008

Loggerhead ( Caretta caretta ) and leatherback ( Dermochelys coriacea ) sea turtle distributions and movements in offshore waters of the western North Atlantic are not well understood despite continued efforts to monitor, survey, and observe them. Loggerhead and leatherback sea turtles are listed as endangered by the World Conservation Union, and thus anthropogenic mortality of these species, including fishing, is of elevated interest. This study quantifies spatial and temporal patterns of sea turtle bycatch distributions to identify potential processes influencing their locations. A Ripley’s K function analysis was employed on the NOAA Fisheries Atlantic Pelagic Longline Observer Program data to determine spatial, temporal, and spatio-temporal patterns of sea turtle bycatch distributions within the pattern of the pelagic fishery distribution. Results indicate that loggerhead and leatherback sea turtle catch distributions change seasonally, with patterns of spatial clustering appearing from July through October. The results from the space–time analysis indicate that sea turtle catch distributions are related on a relatively fine scale (30–200 km and 1–5 days). The use of spatial and temporal point pattern analysis, particularly K function analysis, is a novel way to examine bycatch data and can be used to inform fishing practices such that fishing could still occur while minimizing sea turtle bycatch.
Adsorption de colorant métallifère par les fibres de Posidonia oceanica
Authors: Ncibi Mohamed Chaker , Mahjoub Borhane , Seffen Mongi 
Published: November 2008

Les ægagropiles du végétal marin Posidonia oceanica (L.) ont été utilisées comme un adsorbant biologique renouvelable et bon marché pour l’élimination de colorant textile métallifère à partir de solutions aqueuses. Les expériences en batch ont été effectuées aussi bien pour les cinétiques que pour les isothermes d’adsorption. Les variables expérimentales étudiées étaient le pH, le temps de contact à différentes concentrations initiales et la quantité de fibres. La capacité d’adsorption s’est avérée maximale à un pH de 2. De plus, elle semble être optimisée par une augmentation de la concentration initiale de colorant et la quantité d’adsorbant jusqu’à 20 g/L. La modélisation des données expérimentales relatives aux cinétiques a montré que le modèle de pseudo-second ordre décrit d’une façon satisfaisante l’adsorption sur fibres brutes, suggérant ainsi une « chimiosorption ». De plus, les données à l'équilibre ont été modélisées en utilisant les équations de Langmuir, Freundlich, Temkin et Redlich-Peterson. L’analyse statistique des constantes relatives à chaque modèle par plusieurs méthodes de calcul de l’erreur a montré que les modèles de Langmuir et de Redlich-Peterson semblent être les plus appropriés pour décrire le présent phénomène d’adsorption avec une probable adsorption en monocouche sur des sites actifs d’affinités similaires.