bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Cytokine 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

Hummocky 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

Within 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

Sixty‐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

Three 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

Objective  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.
TOWARD A MODULAR THEORY OF AUXILIARY SELECTION
Authors: Kayne Richard S.
Published: November 2008

Abstract. There is no auxiliary selection rule. ‘Have’ is identical to ‘be’ but for the incorporation of an abstract preposition (cf. Freeze (1992). The alternation is to be understood largely in terms of properties of the participial clause complement‐whether it is full or reduced, whether AGR‐S raises or not, whether Spec, AGR‐O is moved through or not, how many arguments the V has that need to be Case‐licensed. Primarily Romance languages are considered, including a number not traditionally taken into consideration.
THE REPRESENTATION OF OPERATOR‐VARIABLE DEPENDENCIES IN SENTENTIAL NEGATION*
Authors: Acquaviva Paolo
Published: November 2008

Abstract.Despite the desirability of an analysis of sentential negation based on the Negative Criterion and the NegP hypothesis, current approaches are unsatisfactory both on the theoretical and on the empirical level. I argue that the ultimate source of such inadequacies is the idea that negative expressions are quantifiers and must accordingly reach a scope position. The alternative view that negatives are negated indefinites affords a general analysis of sentential negation as unselective binding of the event variable and possibly of variables associated with indefinites, including negative indefinites. This approach solves the noted problems without rejecting the starting assumptions, and provides a unified syntactic analysis for negative sentences grounded on their semantics.
GENERALIZED TRANSFORMATIONS AND THE THEORY OF GRAMMAR*
Authors: Frank Robert , Kroch Anthony
Published: November 2008

Abstract.The compositional approach to phrase structure proposed in Chomsky's ‘Minimalist Program’ paper (1992) can be implemented in various ways. This paper explores the use of Tree Adjoining Grammar (Kroch & Joshi 1985, 1986; Frank 1992,inter alia) as a formal mechanism for syntactic composition and compares it to the operations proposed in Chomsky (1992). The TAG approach avoids the need for distinguishing two modes of phrase structure composition, ‘GT’ and ‘adjunction’, and allows the elimination of the requirement ‘extension requirement’. Further, it permits a purely local interpretation of transformational movement and a simplification of the conception of derivational economy. It also has important consequences for the proper treatment of the binding and scope effects of successive cyclic movement.
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

The 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.
The role of metastasis suppressor genes in metastatic dormancy
Authors: HORAK CHRISTINE E. , LEE JONG HEUN , MARSHALL JEAN‐CLAUDE , SHREEVE S. MARTIN , STEEG PATRICIA S.
Published: November 2008

Metastasis suppressor genes (MSGs) are defined by their ability to inhibit overt metastasis in a secondary organ without affecting tumor growth at the primary site. Over 20 MSGs have been confirmed in vivo. This class of genes is only unified by their capacity to suppress metastasis, as they encode for proteins with a wide range of biochemical activities that are components of a variety of signaling pathways. In addition, metastasis suppressors impinge upon different stages of the metastatic cascade to manifest their suppressive effects. The MSGs KISS1, KAI1, MKK4/7 and Nm23‐H1 promote tumor dormancy at the metastatic site, since tumor cells with induced expression of these MSGs disseminate, but do not form overt metastases in the secondary organ throughout the duration of a metastasis assay. Evidence suggests that KISS1 triggers dormancy in solitary, metastatic tumor cells by causing growth arrest of solitary cells at the secondary site. KAI1 induces growth arrest prior to extravasation by binding a vascular endothelial cell surface marker. MKK4, MKK7 and Nm23‐H1 appear to promote dormancy of micrometastatic colonies, after disseminated tumor cells have undergone several rounds of proliferation. Other MSGs may also function in tumor dormancy, but so far their role has not been fully elucidated. Therapeutic approaches that either mimic the effects of MSGs or re‐establish MSG expression in metastatic lesions may hold promise for the establishment or maintenance of dormancy.
New clinical and experimental approaches for studying tumor dormancy: does tumor dormancy offer a therapeutic target?
Authors: GOSS PAUL , ALLAN ALISON L. , RODENHISER DAVID I. , FOSTER PAULA J. , CHAMBERS ANN F.
Published: November 2008

Tumor dormancy is a significant clinical problem. Primary treatment of a cancer may be apparently successful, and yet the tumor may recur either locally or as distant metastases years or even decades later. The ability to predict which patients are likely to develop recurrences is imprecise, relying on probabilities of recurrence based on features of the primary cancer. This uncertainty presents clinical challenges regarding who to treat and how, in order to prevent recurrence after periods of dormancy. Recent clinical trials in breast cancer support the idea that some patients may harbor tumor cells that are capable of forming late‐developing metastases years after removal of the primary tumor, and that these dormant cancer cells may in some cases be effectively treated with long‐term therapy. Advances in experimental studies of tumor dormancy are shedding light on the nature of dormancy, and are providing both new technologies and conceptual approaches for studying tumor dormancy. A better understanding of mechanisms responsible for tumor dormancy and recurrence will be important for improving care of patients at risk for late‐developing metastases.
Photoexcited CRY2 Interacts with CIB1 to Regulate Transcription and Floral Initiation in
Arabidopsis
Authors: Liu Hongtao , Yu Xuhong , Li Kunwu , Klejnot John , Yang Hongyun , Lisiero Dominique , Lin Chentao
Published: November 2008

Cryptochromes (CRY) are photolyase-like blue-light receptors that mediate light responses in plants and animals. How plant cryptochromes act in response to blue light is not well understood. We report here the identification and characterization of the
Arabidopsis
CIB1 (cryptochrome-interacting basic-helix-loop-helix) protein. CIB1 interacts with CRY2 (cryptochrome 2) in a blue light–specific manner in yeast and
Arabidopsis
cells, and it acts together with additional CIB1-related proteins to promote CRY2-dependent floral initiation. CIB1 binds to G box (CACGTG) in vitro with a higher affinity than its interaction with other E-box elements (CANNTG). However, CIB1 stimulates
FT
messenger RNA expression, and it interacts with chromatin DNA of the
FT
gene that possesses various E-box elements except G box. We propose that the blue light–dependent interaction of cryptochrome(s) with CIB1 and CIB1-related proteins represents an early photoreceptor signaling mechanism in plants.
Host–parasite relations in a mycoparasite. VI. Leakage of electrolytes, amino acids, and sugars after infection with Piptocephalis virginiana
Authors: Manocha M. S. , Maharaj R.
Published: November 2008

The leakage of electrolytes, amino acids, and sugars from Choanephora cucurbitarum infected by a biotrophic haustorial mycoparasite, Piptocephalis virginiana was investigated and compared with published reports of leakage from plant hosts infected by biotrophic pathogens. During early stages of infection (24 h after inoculation), the mycoparasitic system showed a significant increase in the leakage of electrolytes, amino acids, and sugars contrary to plant host–pathogen systems which exhibit pronounced leakage during later stages of disease development. Among the 26 amino acids and amino compounds, aspartic acid, glutamic acid, and alanine exuded in higher amounts. No new species of amino acid or amino compound was detected in the leachate of the infected host. Sugar analysis of leachate showed the presence of eight different sugars among which glucose was found in significant amounts (50–53%). Comparison between leachate sugars and internal pool sugars of the infected and control hosts suggested that the leakage of sugars was selective. The nutritional implication of this preferential leakage is discussed.
Effect of ambient water volume on root growth, cell cycle duration, and mitotic synchrony during germination and seedling growth of Vicia faba
Authors: Thomas J. E. , Davidson D.
Published: November 2008

The relationship between root length, time of onset of mitotic activity, and the degree of synchrony of cells initiating mitosis was studied in germinating seed and seedlings of Vicia faba. These three parameters are related, but their relationship changes (1) with time during germination and seedling growth, and (2) in response to alterations in the volume of ambient water. Beans sown in 5 mm of water for 0–24 h gave better root growth and higher mitotic indices, at 68 h, than beans sown in 10 or 20 mm of water: conditions during the first 24 h after sowing influence growth at later times. Beans were also grown, from 24 to 70 h, in moistened sand or vermiculite–perlite (20 to 50 mL of water/100 mL of substrate). A well-defined optimum volume of water was identified; it gave the highest mean mitotic index (MI) and the greatest mean root length. Supra-optimal volumes of water resulted in an inhibition of root growth and a reduction in MI. Variation in the ambient water volume affects (i) root growth; (ii) the time taken to complete the first cell cycle and; (iii) the degree of synchrony of entry into mitosis. As the time taken to complete the first interphase increases, the degree of mitotic synchrony decreases.
Marine fungi from Martinique
Authors: Kohlmeyer Jan
Published: November 2008

Collections of filamentous higher marine fungi in Martinique (French Antilles) resulted in a list of 20 species, 18 of which are new records for this island. New species are Ceriosporopsis capillacea Kohlm., sp.nov. (Martinique) and Remispora crispa Kohlm., sp.nov. (Hawaii, Liberia, Martinique). Substrates include leaves and rhizomes of Thalassia testudinum, pneumatophores of Avicennia germinans, prop roots of Rhizophora mangle, roots of Hibiscus tiliaceus, and intertidal and subtidal wood of unidentified hosts. A distinctive mycota appears to exist in subtidal habitats. The separation of marine fungi into the following groups is discussed: obligate intertidal species, facultative inter- or subtidal species, obligate subtidal species, and deep-sea species.
Vegetation and habitat conditions in Western Head Bog, a southern Nova Scotian plateau bog
Authors: Damman Antoni W. H. , Dowhan Joseph J.
Published: November 2008

The southernmost plateau bogs in eastern North America are found in southern Nova Scotia. They are characterized by an extremely wet plateau with high conical hummocks, a partly forested bog slope, and several disjunct species of the Coastal Plain flora.Prevailing water levels on the plateau are high and fluctuate little. They do not start to drop until very close to the plateau margin, and are lowest on the forested parts of the slope. The lagg is wet and has the most strongly fluctuating water levels.Water table location, and thus microtopography of the surface, controls the vegetation pattern of the plateau. A Gaylussacia baccata dwarf shrub heath occupies hummocks 25 cm or more above the 50% summer water table. Utricularia mud bottoms are regularly flooded in summer and the water table never drops more than 5 cm below the surface. The two Scirpus lawn communities occupy an intermediate position.A complex gradient, involving both water level and nutrient regime, controls vegetation changes from the center to the bog border. The bog slope, especially under the forest, is enriched by the detritus cycle. Floristic changes in the vegetation indicate an enrichment of the plateau margin, and possibly also the slope, by drainage water seeping from the plateau. Peat analyses failed to confirm this. Within the lagg, differences in minerotrophy separate the two fen communities, but floristic changes on the hummocks are caused by differences in water table location, nutrient supply, and shading.These plateau bogs are distinguished clearly from those along the west side of the Bay of Fundy by the dominance of mud bottoms rather than lawn communities on the plateau, by the occurrence of many nutrient-demanding species in the ombrotrophic vegetation, and by the presence of Coastal Plain disjuncts, such as Ilex glabra.
Models and model selection uncertainty in estimating growth rates of endangered freshwater mussel populations
Authors: Jiao Yan , Neves Richard , Jones Jess
Published: November 2008

Appropriate inference of population status for endangered species is extremely important. Using a single model for estimating population growth rates is typically inadequate for assessing endangered species because inferences based on only one “best” model ignore model uncertainty. In this study, the endangered dromedary pearlymussel ( Dromus dromas ) in the Clinch and Powell rivers of eastern Tennessee, USA, was used as an example to demonstrate the importance of multiple models, with consideration of environmental noises for evaluating population growth. Our results showed that more than one model deserves consideration in making inferences of population growth rate. A Bayesian model averaging approach was used to make inferences by weighting each model using the deviance information criterion. To test the uncertainty resulting from model selection and the efficiency of the Bayesian averaging approach, a simulation study was conducted on the dromedary pearlymussel populations, which showed that model selection uncertainty is very high. The results of these tests lead us to recommend using Bayesian model averaging to assess population growth status for endangered species, by balancing goodness-of-fit and selection uncertainty among alternate models.
Estimating population age structure using otolith morphometrics: a test with known-age Atlantic cod (Gadus morhua) individuals
Authors: Doering-Arjes P. , Cardinale M. , Mosegaard H.
Published: November 2008

Traditional age reading is a rather subjective method that lacks true reproducibility, producing ageing error that propagates up to stock assessment. One alternative is represented by the use of otolith morphometrics as a predictor of age. An important issue with such a method is that it requires known-age fish individuals. Here we used known-age Atlantic cod ( Gadus morhua ) from the Faroe Bank and Faroe Plateau stocks. Cod populations usually show quite large variation in growth rates and otolith shape. We showed that including otolith morphometrics into ageing processes has the potential to make ageing objective, accurate, and fast. Calibration analysis indicated that a known-age sample from the same population and environment is needed to obtain robust calibration; using a sample from a different stock more than doubles the error rate, even in the case of genetically highly related populations. The intercalibration method was successful but generalization from one stock to another remains problematic. The development of an otolith growth model is needed for generalization if an operational method for different populations is required in the future.
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.
Assessment of two a posteriori error estimators for elasticity problems
Authors: ElSheikh A. H. , Chidiac S. E. , Smith S.
Published: November 2008

The main focus of this paper is on the evaluation of local a posteriori error estimation techniques for the finite element method (FEM). The standard error estimation techniques are presented for the coupled displacement fields appearing in elasticity problems. The two error estimators, the element residual method (ERM) and Zienkiewicz–Zhu (ZZ) patch recovery technique, are evaluated numerically and then used as drivers for a mesh adaptation process. The results demonstrate the advantages of employing a posteriori error estimators for obtaining finite element solutions with a pre-specified error tolerance. Of the two methods, the ERM is shown to produce adapted meshes that are similar to those adapted by the exact error. Furthermore, the ERM provides higher quality estimates of the error in the global energy norm when compared to the ZZ estimator.
Applicability of flash laser distance and ranging to three-dimensional spatial information acquisition and modeling on a construction site
Authors: Kim Changwan , Son Hyojoo , Kim Hyoungkwan , Han Seung Heon
Published: November 2008

In recent decades, the need for effective automation of data acquisition and three-dimensional (3D) modeling in the construction industry has been increasing. Most of the 3D modeling methods developed thus far are generally inadequate for construction automation on account of the long processing times involved and the high cost of the devices used for that purpose; moreover, they tend to include a significant level of manual operation. Flash laser distance and ranging (LADAR), which has been developed recently, entails illumination of an entire scene with diffuse laser light. This characteristic enables it to rapidly model actual construction sites in a comparatively fast and cost-effective manner. In this study, flash LADAR technology was tested for its ability to handle the dynamic nature of a construction site in an effective way. Indoor experiments were carried out to characterize the performance of the flash LADAR system, and outdoor experiments were performed on actual construction sites to demonstrate the applicability of the system to 3D modeling of such environments. The results indicate that 3D modeling via flash LADAR has the potential of being quite beneficial for construction automation.
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.
An earthflow in sensitive Champlain Sea sediments at Lemieux, Ontario, June 20, 1993, and its impact on the South Nation River
Authors: Evans S.G. , Brooks G.R.
Published: November 2008

A large (est. volume 2.8 × 106 m3) landslide occurred in sensitive Leda clay on the east bank of the South Nation River at Lemieux, Ontario (45.4°N, 75.06°W), on June 20, 1993. The earthflow involved an area of about 17 ha and retrogressed a total of 680 m, 555 m into the flat plain above the river. No lives were lost but a motorist was injured when he drove into the landslide crater. The 1993 landslide occurred 4.5 km downstream of the well-known 1971 South Nation River landslide along a stretch of river that had experienced other historical landslides in 1895 and 1910. A band of earlier, undated, retrogressive sliding, between 100–130 m in width, was present at the base of the slope that failed in 1993, and the earthflow was probably triggered by a reactivation of these failures. Borehole information obtained in 1986 and 1987 in the vicinity of the landslide indicates that a zone of soft, sensitive marine clay existed beneath the flat farmland, which was overlain by a stiffer cap consisting of laminated marine-estuarine sands and deltaic silts and sands. The morphology of the debris suggests a mechanism that involves the fluidization of much of the landslide mass and subsidence, translation, and rotation of cap blocks. The stability number for the site was approximately 9.6, suggesting that the flow could have occurred as a result of extrusion of the soft sensitive clay layer due to undrained cap loading. Landslide debris temporarily blocked the South Nation River, causing flooding upstream and adversely affecting water quality downstream. Key words : landslide, earthflow, sensitive clay, debris hazards, water quality.
An estimation of ground settlement due to shield tunnelling by the Peck–Fujita method
Authors: Fang Y.S. , Lin J.S. , Su C.S.
Published: November 2008

In this paper, an empirical method based on Peck and Fujita's study is proposed to estimate the magnitude and extent of surface settlement associated with shield tunnelling. It is found that the ground-settlement curves calculated with the proposed method for various types of shields, ground conditions, tunnel diameters, and depths are in reasonably good agreement with field measurements. For open shields tunnelled through clayey soils, the stability ratio has a significant influence on the surface settlement induced. Field measurement data suggest that the Peck–Fujita method may be used to estimate the ground subsidence associated with the construction of parallel tunnels. Key words : empirical method, field measurement, settlement, soft ground, tunnelling.
Structural characterization of Haemophilus parainfluenzae lipooligosaccharide and elucidation of its role in adherence using an outer core mutant
Authors: Pollard Angela , St. Michael Frank , Connor Lynn , Nichols Wade , Cox Andrew
Published: November 2008

The opportunistic pathogen Haemophilus parainfluenzae is a gram-negative bacterium found in the oropharynx of humans. Haemophilus parainfluenzae is a member of the Pasteurellaceae family in which it is most closely related to Haemophilus sengis and Actinobacillus . Characterization of surface displayed lipooligosaccharide has identified components that are crucial in adherence. We examined the oligosaccharide structure of lipooligosaccharide from 2 clinical isolates of H. parainfluenzae. Core oligosaccharide was isolated by standard methods from purified lipooligosaccharide. Structural information was established by a combination of monosaccharide and methylation analyses, nuclear magnetic resonance spectroscopy, and mass spectrometry revealing the following structures: R-(1-6)-β-Glc-(1-4)-d,d-α-Hep-(1-6)-β-Glc-(1-4)- substituting a tri-heptose-Kdo inner core of L,d-α-Hep-(1-2)-l,d-α-Hep-(1-3)-l,d-α-Hep-(1-5)-α-Kdo at the 4-position of the proximal l,d-α-Hep residue to Kdo, and with a PEtn residue at the 6-position of the central l,d-α-Hep residue. In strain 4282, the R substituent is β-galactose and in strain 4201 there is no substituent at the distal glucose. These analyses have revealed that multiple structural aspects of H. parainfluenzae lipooligosaccharide are comparable with nontypeable Haemophilus influenzae lipooligosaccharide. This study also identified a galactan in strain 4201 and a glucan in strain 4282. Haemophilus parainfluenzae was shown to adhere to a bronchial epithelial cell line to the same degree as nontypeable H. influenzae. However, an H. parainfluenzae mutant lacking the outer core of the lipooligosaccharide showed diminished adherence to the epithelial cells, suggesting that H. parainfluenzae lipooligosaccharide plays a role in tissue colonization.
THE NEW APPROACH FOR REGRESSION MODELS ANALYSIS
Authors: BASKIN E. M.
Published: November 2008

A new approach to the regression models analysis has been presented. It is based on the use of the Generalized Law of Reliability and a method allowing one to transform initial lifetime data to fit a model of accelerated tests. A model of the accelerated tests and regression models of both lung cancer and leukemia trails have been considered.
Gut peristalsis is governed by a multitude of cooperating mechanisms
Authors: Huizinga Jan D. , Lammers Wim J. E. P.
Published: November 2008

Peristaltic motor activity of the gut is an essential activity to sustain life. In each gut organ, a multitude of overlapping mechanisms has developed to acquire the ability of coordinated contractile activity under a variety of circumstances and in response to a variety of stimuli. The presence of several simultaneously operating control systems is a challenge for investigators who focus on the role of one particular control activity since it is often not possible to decipher which control systems are operating or dominant in a particular situation. A crucial advantage of multiple control systems is that gut motility control can withstand injury to one or more of its components. Our efforts to increase understanding of control mechanism are not helped by recent attempts to eliminate proven control systems such as interstitial cells of Cajal (ICC) as pacemaker cells, or intrinsic sensory neurons, nor does it help to view peristalsis as a simple reflex. This review focuses on the role of ICC as slow-wave pacemaker cells and places ICC into the context of other control mechanisms, including control systems intrinsic to smooth muscle cells. It also addresses some areas of controversy related to the origin and propagation of pacemaker activity. The urge to simplify may have its roots in the wish to see the gut as a consequence of a single perfect design experiment whereas in reality the control mechanisms of the gut are the messy result of adaptive changes over millions of years that have created complementary and overlapping control systems. All these systems together reliably perform the task of moving and mixing gut content to provide us with essential nutrients.
Fluid shear stress induces arterial differentiation of endothelial progenitor cells
Authors: Obi Syotaro , Yamamoto Kimiko , Shimizu Nobutaka , Kumagaya Shinichiro , Masumura Tomomi , Sokabe Takaaki , Asahara Takayuki , Ando Joji
Published: November 2008

Endothelial progenitor cells (EPCs) are mobilized from bone marrow to peripheral blood and contribute to angiogenesis in tissues. In the process, EPCs are exposed to the shear stress generated by blood flow and tissue fluid flow. Our previous study showed that shear stress promotes differentiation of EPCs into mature endothelial cells. In this study, we investigated whether EPCs differentiate into arterial or venous endothelial cells in response to shear stress. When cultured EPCs derived from human peripheral blood were exposed to controlled levels of shear stress in a flow-loading device, the mRNA levels of the arterial endothelial cell markers ephrinB2, Notch1/3, Hey1/2, and activin receptor-like kinase 1 increased, but the mRNA levels of the venous endothelial cell markers EphB4 and neuropilin-2 decreased. Both the ephrinB2 increase and the EphB4 decrease were shear stress dependent rather than shear rate dependent. EphrinB2 protein was increased in shear-stressed EPCs, and the increase in ephrinB2 expression was due to activated transcription and not mRNA stabilization. Deletion analysis of the ephrinB2 promoter indicated that the cis-element (shear stress response element) is present within 106 bp 5′ upstream from the transcription initiation site. This region contains the Sp1 consensus sequence, and a mutation in its sequence decreased the basal level of transcription and abolished shear stress-induced ephrinB2 transcription. Electrophoretic mobility shift assays and chromatin immunoprecipitation assays showed that shear stress markedly increased binding of Sp1 to its consensus sequence. These results indicate that shear stress induces differentiation of EPCs into arterial endothelial cells by increasing ephrinB2 expression in EPCs through Sp1 activation.
Spaceflight effects on T lymphocyte distribution, function and gene expression
Authors: Gridley Daila S. , Slater James M. , Luo-Owen Xian , Rizvi Asma , Chapes Stephen K. , Stodieck Louis S. , Ferguson Virginia L. , Pecaut Michael J.
Published: November 2008

The immune system is highly sensitive to stressors present during spaceflight. The major emphasis of this study was on the T lymphocytes in C57BL/6NTac mice after return from a 13-day space shuttle mission (STS-118). Spleens and thymuses from flight animals (FLT) and ground controls similarly housed in animal enclosure modules (AEM) were evaluated within 3–6 h after landing. Phytohemagglutinin-induced splenocyte DNA synthesis was significantly reduced in FLT mice when based on both counts per minute and stimulation indexes ( P < 0.05). Flow cytometry showed that CD3+T and CD19+B cell counts were low in spleens from the FLT group, whereas the number of NK1.1+natural killer (NK) cells was increased ( P < 0.01 for all three populations vs. AEM). The numerical changes resulted in a low percentage of T cells and high percentage of NK cells in FLT animals ( P < 0.05). After activation of spleen cells with anti-CD3 monoclonal antibody, interleukin-2 (IL-2) was decreased, but IL-10, interferon-γ, and macrophage inflammatory protein-1α were increased in FLT mice ( P < 0.05). Analysis of cancer-related genes in the thymus showed that the expression of 30 of 84 genes was significantly affected by flight ( P < 0.05). Genes that differed from AEM controls by at least 1.5-fold were Birc5, Figf, Grb2, and Tert (upregulated) and Fos, Ifnb1, Itgb3, Mmp9, Myc, Pdgfb, S100a4, Thbs, and Tnf (downregulated). Collectively, the data show that T cell distribution, function, and gene expression are significantly modified shortly after return from the spaceflight environment.
Ectopic Varices and Collaterals Development after Band Ligation Treatment in a Patient with Portal Hypertension
Authors: Frossard Jean Louis , Seirafi Mariam , Spahr Laurent
Published: November 2008

Esophageal and gastric varices may complicate the course of cirrhosis as a direct consequence of portal hypertension. Variceal hemorrhage has been reported to occur in 25–40% of patients with cirrhosis [Gastroenterol Clin North Am 1992;21:149–161]. Occasionally, varices develop at sites other than the esophagus and are detected either when they bleed or incidentally during upper or lower endoscopy [Eur J Gastroenterol Hepatol 2006;18:1155–1160; Digestion 2000;61:149–150]. Endoscopic treatment is often unsuccessful in these cases, and traditional treatment is usually surgical, while it has been suggested that bleeding can also be controlled by a transjugular intrahepatic portosystemic shunt (TIPS) [Endoscopy 1995;27:626–627]. Moreover, esophageal band ligation may interfere with the collateral web. We here report a case of an ectopic duodenal varix and the development of a large collaterals web that appeared after band ligation.
Expression of the Epidermal Growth Factor System in Eutopic Endometrium from Women with Endometriosis Differs from That in Endometrium from Healthy Women
Authors: Ejskjær Kirsten , Sorensen Boe Sandahl , Poulsen Steen Seier , Mogensen Ole , Forman Axel , Nexo Ebba
Published: November 2008

Background: The epidermal growth factor (EGF) system comprises four receptors, HER1–4, and several ligands, and is cyclically expressed in endometrium from healthy fertile women. Our aim is to identify differences in expression of the EGF system between endometriotic and normal endometrium. Methods: We previously examined the EGF system in endometrial samples from healthy women (n = 14). Here we examine samples from endometrium (n = 23), endometriomas (n = 10) and peritoneal endometriosis (n = 9) from women with endometriosis (n = 23). mRNA expression of receptors and ligands from the EGF system was analyzed by real-time PCR, and proteins were localized by immunohistochemistry. Results: Endometrial mRNA for HER1–3 was high compared with our previous findings in healthy endometrium, whereas HER4 and the ligands were unchanged. Endometriomas show lower expression of HER1–3 and no HER4 expression. Significant differences were demonstrated in late secretory phase for HER1 and HER2 and in the proliferative phase for HER3 compared to healthy women. Immunohistochemically, HER2 was identified in all samples, predominately in glands and surface epithelium. In a few glands, HER2 was in both cytoplasm and cell membrane. Conclusion: We report quantitative and qualitative differences in the EGF system in endometriotic eutopic endometrium compared to endometrium from healthy individuals.
The Brain and the Kidney – Organ Cross Talk and Interactions
Authors: Davenport Andrew
Published: November 2008

The kidney and the brain play a major role in maintaining normal homeostasis of the extracellular fluid, and as such regulate intracellular volume, by controlling sodium and water balance. However, both hyponatraemic and hypernatraemic states commonly account for acute medical admissions, and also frequently occur during hospital in-patient stays. Both acute and chronic kidney damage can not only affect sodium and water homeostasis, but also the accumulation of uremic toxins; impairs cerebral higher functions and the ability of the brain to adapt to extracellular changes. Acute brain injury, leading to brain stem death, leads to a cytokine storm, inducing inflammation in cadaveric organs used for transplantation, with increased risk of delayed graft function and acute rejection.