bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sciatic nerve cuffing in mice: A model of sustained neuropathic pain
Authors: Benbouzid Malika , Pallage Viviane , Rajalu Mathieu , Waltisperger Elisabeth , Doridot Stéphane , Poisbeau Pierrick , Freund‐Mercier Marie José , Barrot Michel 
Published: November 2007

AbstractBecause of its severity, chronicity, resistance to usual therapy and its consequences on quality of life, neuropathic pain represents a real clinical challenge. Fundamental research on this pathology uses metabolic, pharmacological or traumatic models in rodents that reproduce the characteristic human pain symptoms. In 1996, Mosconi and Kruger morphologically described a model of peripheral neuropathy in which a cuff of polyethylene tubing was placed around the sciatic nerve in rats. In the present study, we evaluated the behavioral consequences of this neuropathic pain model in C57Bl/6J mice which is the main genetic background used for studies in transgenic mice. A short cuff of polyethylene tubing was unilaterally placed around the main branch of the sciatic nerve. It induced an ipsilateral heat thermal hyperalgesia lasting around 3 weeks, and a sustained ipsilateral mechanical allodynia lasting at least 2 months. We showed that this neuropathic pain model is insensitive to ketoprofen, a non‐steroidal anti‐inflammatory drug. Morphine treatment acutely suppressed the mechanical allodynia, but tolerance to this effect rapidly developed. The analysis of video recordings revealed that most aspects of spontaneous behavior remained unaffected on the long term, excepted for a decrease in the time spent at social interaction for the neuropathic mice. Using the elevated plus‐maze and the marble‐burying test, we also showed that neuropathic mice develop an anxiety phenotype. Our data indicate that sciatic nerve cuffing in mice is a pertinent model for the study of nociceptive and emotional consequences of sustained neuropathic pain.
Overexpression of thioredoxin reductase 1 inhibits migration of HEK‐293 cells
Authors: Sroka Jolanta , Antosik Agata , Czyż Jarosław , Nalvarte Ivan , Olsson Jerker M. , Spyrou Giannis , Madeja Zbigniew 
Published: November 2007

Background information. TrxR (thioredoxin reductase), in addition to protecting against oxidative stress, plays a role in the redox regulation of intracellular signalling pathways controlling, among others, cell proliferation and apoptosis. The aim of the present study was to determine whether TrxR1 is involved in the regulation of cell migration.Results. Stably transfected HEK‐293 (human embryonic kidney) cells which overexpress cytosolic TrxR1 (HEK‐TrxR15 and HEK‐TrxR11 cells) were used in the present study. We found that the stimulation of cell motility induced by PKC (protein kinase C) activators, PMA and DPhT (diphenyltin), was inhibited significantly in the HEK‐TrxR15 and HEK‐TrxR11 cells compared with control cells. The overexpression of TrxR1 also inhibited characteristic morphological changes and reorganization of the F‐actin cytoskeleton induced by PMA and DPhT. In addition, the selective activation of PKCδ by DPhT was inhibited in cells that overexpressed cytosolic TrxR1. Furthermore, rottlerin, a selective inhibitor of PKCδ, and PKCδ siRNA (small interfering RNA), suppressed the morphological changes induced by DPhT in the control cells.Conclusions. The overexpression of TrxR1 inhibits migration of HEK‐293 cells stimulated with PMA and DPhT. Moreover, our observations suggest that this effect is mediated by the inhibition of PKCδ activation.
The SBML discrete stochastic models test suite
Authors: Evans Thomas W. , Gillespie Colin S. , Wilkinson Darren J. 
Published: November 2007

Abstract
Motivation: Stochastic simulation is a very important tool for mathematical modelling. However, it is difficult to check the correctness of a stochastic simulator, since any two realizations from a single model will typically be different.
Results: We have developed a test suite of stochastic models that have been solved either analytically or using numerical methods. This allows the accuracy of stochastic simulators to be tested against known results. The test suite is already being used by a number of stochastic simulator developers.
Availability: The latest version of the test suite can be obtained from http://www.calibayes.ncl.ac.uk/Resources/dsmts/ and is licensed under GNU Lesser General Public License.
Contact: D.J.Wilkinson@ncl.ac.uk
Spatial considerations for the Dakhla stock of Octopus vulgaris: indicators, patterns, and fisheries interactions
Authors: Faraj Abdelmalek , Bez Nicolas 
Published: November 2007

Abstract
Faraj, A., and Bez, N. 2007. Spatial considerations for the Dakhla stock of Octopus vulgaris: indicators, patterns, and fisheries interactions. – ICES Journal of Marine Science, 64: 1820–1828. The common octopus (Octopus vulgaris) is the target species of the cephalopod fishery that exploits two stocks, Dakhla and Cap Blanc, off southern Morocco (26°N 21°N), an area commonly referred to as the Saharan Bank. Octopusvulgaris is also one of the most abundant demersal species in this highly productive area, and plays a key role in the upwelling ecosystem. Spatial patterns of the main phases of the Octopus vulgaris life cycle of the Dakhla stock are described, using trawl surveys carried out twice a year from 1998 to 2003. Using geostatistics and spatial indicators, mature females and juveniles are analysed and mapped to characterize the main features of the spawning and recruitment phases. There are clear distinctions between the spatial patterns of the spawning and recruitment phases: juveniles are more coastal, less spatially dispersed, more anisotropically distributed, and more patchy. Our results suggest that the spatial pattern of the Octopus vulgaris Dakhla stock is different from that of the same species in other ecosystems such as the Mediterranean. GIS reveals that the spawning–stock biomass is globally more accessible to the industrial fleet than to the artisanal one, a finding contrary to contemporary thinking and with important resource management implications.
Improving the quantitative estimation of trawling impacts from sidescan-sonar and underwater-video imagery
Authors: Smith C. J. , Banks A. C. , Papadopoulou K-N. 
Published: November 2007

Abstract
Smith, C. J., Banks, A. C., and Papadopoulou, K.-N. 2007. Improving the quantitative estimation of trawling impacts from sidescan-sonar and underwater-video imagery. – ICES Journal of Marine Science, 64: 1692–1701. The techniques of sidescan sonar and towed, underwater-video sled were assessed as rapid-assessment methodologies for investigating trawl impacts on the substratum. Sidescan sonar is able to image a swathe of ∼200 m with a resolution of ∼20 cm at a speed of 2–3 knots, and marks of trawl doors could be observed. The towed video system imaged a swathe of 1–2 m with a resolution of 1–2 cm at a speed of ∼1 knot, and trawl-door marks, scrape marks, local bioturbation features, and fauna could be observed. Multiple tows using both methodologies were carried out in two areas in Heraklion Bay, Crete. One area, experimentally trawled, was 80–90 m deep and characterized by mixed, maerly sediments; the other was a commercial trawl lane ∼200 m deep characterized by silty-clay sediment. Descriptions of the types of trawling feature and impacts caused by trawling were made for both areas. Images were analysed from the commercial deeper trawling ground for area assessment. For sidescan-sonar records, direction of trawling and trawl-mark density by category were estimated at periodic intervals along the track. For video, categories for trawl-mark density and level of bioturbation were estimated, along with the density of the crinoid Leptometra phalangium. Using geo-referenced positioning for each data point, area maps were constructed for each of the parameters, and correlations were tested between the different datasets. The use of the assessment techniques (characteristics, data usage, mapping, complementarity) in relation to trawling-impact studies is discussed, as well as possibilities for the use of the resulting data for management.
A de novo designed protein–protein interface
Authors: Huang Po‐Ssu , Love John J. , Mayo Stephen L. 
Published: November 2007

AbstractAs an approach to both explore the physical/chemical parameters that drive molecular self‐assembly and to generate novel protein oligomers, we have developed a procedure to generate protein dimers from monomeric proteins using computational protein docking and amino acid sequence design. A fast Fourier transform‐based docking algorithm was used to generate a model for a dimeric version of the 56‐amino‐acid β1 domain of streptococcal protein G. Computational amino acid sequence design of 24 residues at the dimer interface resulted in a heterodimer comprised of 12‐fold and eightfold variants of the wild‐type protein. The designed proteins were expressed, purified, and characterized using analytical ultracentrifugation and heteronuclear NMR techniques. Although the measured dissociation constant was modest (∼300 μM), 2D‐[1H,15N]‐HSQC NMR spectra of one of the designed proteins in the absence and presence of its binding partner showed clear evidence of specific dimer formation.
Requirements for peptidyl‐prolyl isomerization activity: A comprehensive mutational analysis of the substrate‐binding cavity of FK506‐binding protein 12
Authors: Ikura Teikichi , Ito Nobutoshi 
Published: November 2007

AbstractPeptidyl‐prolyl isomerase (PPIase) activity is exhibited by many proteins belonging to the PPIase family. However, the catalytic mechanism of this activity remains to be completely elucidated. Here, we selected human FK506‐binding protein 12 (FKBP12) as the model PPIase and investigated the nature of amino acid residues essential for the activity. The crystal structures of several complexes of PPIase with short peptides revealed that the residues Asp37, Arg42, Phe46, Val55, Trp59, and Tyr82 in the substrate‐binding cavity of FKBP12 appear to play key roles in the PPIase activity. Each of these six residues was substituted by 20 common amino acid residues. The activity of each mutant protein was measured using a peptide analog by the chymotrypsin digestion assay and then compared with wild‐type FKBP12. It was found that site‐specific interactions by the side chains of amino acid residues constituting the substrate‐binding cavity were not essential for the PPIase activity, although the 37th, 55th, and 82nd amino acid residues significantly contributed to the activity. This suggests that the PPIase activity requires only the hydrophobic cavity that captures the Pro‐containing peptide.
Tuberculin reactivity and allergic disorders in schoolchildren, Okinawa, Japan
Authors: Miyake Y. , Arakawa M. , Tanaka K. , Sasaki S. , Ohya Y. 
Published: November 2007

SummaryBackground
Bacillus Calmette‐Guérin (BCG) vaccination triggers a T‐helper type 1 response. Whether BCG vaccination and positive tuberculin reactivity are preventive against allergic disorders remains controversial.Objective
The current cross‐sectional study investigated the relationship of BCG vaccination and tuberculin reactivity with the prevalence of allergic disorders using data from the Ryukyus Child Health Study (RYUCHS).Methods
Subjects were 5717 schoolchildren aged 8–11 years in Okinawa, Japan. The RYUCHS collected information on symptoms of allergic disorders and potential confounding factors. The outcomes were based on diagnostic criteria from the International Study of Asthma and Allergies in Childhood. Data on BCG vaccination and tuberculin tests were obtained from school records. Allowance was made for grade, sex, sibship size, smoking in the household, paternal and maternal history of asthma, atopic eczema, and allergic rhinitis, and paternal and maternal educational level.Results
No measurable relationship was found between BCG vaccination in infants and the prevalence of allergic disorders. Among 5567 BCG‐vaccinated children, positive tuberculin reactivity (induration 10 mm) in the first grade was independently associated with a decreased prevalence of wheeze, asthma, and atopic eczema: the multivariate odds ratios for wheeze, asthma, and atopic eczema were 0.80 (95% confidence interval [CI], 0.67–0.94), 0.78 (95% CI, 0.64–0.95), and 0.77 (95% CI, 0.62–0.95), respectively. The inverse associations were more pronounced in children with a negative parental allergic history than in those with a positive parental allergic history. There was no significant relationship between tuberculin reactivity and allergic rhinoconjunctivitis.Conclusions
The findings suggest that positive tuberculin reactivity may be inversely associated with the prevalence of wheeze, asthma, and atopic eczema, but not allergic rhinoconjunctivitis, especially among Japanese children without a parental allergic history.
Peroxisome proliferator activated receptor γ is not necessary for the development of LPS‐induced tolerance in macrophages
Authors: Zingarelli Basilia , Fan Hongkuan , Ashton Sarah , Piraino Giovanna , Mangeshkar Prajakta , Cook James A. 
Published: November 2007

SummaryPeroxisome proliferator activated receptor‐γ (PPARγ) has been reported to exert anti‐inflammatory properties in endotoxic shock and sepsis. One phenomenon that alters the inflammatory response to endotoxin [lipopolysaccharide (LPS)] is endotoxin tolerance, which is caused by previous exposure to endotoxin. Here, we investigate whether changes in endogenous PPARγ function regulate this phenomenon using three different models of LPS‐induced tolerance in macrophages. In a first in vitro model, previous LPS exposure of murine J774.2 macrophages suppressed tumour necrosis factor‐α (TNF‐α) release in response to subsequent LPS challenge. Treatment of J774.2 cells with the PPARγ inhibitor GW9662 did not alter tolerance induction because these cells were still hyporesponsive to the secondary LPS challenge. In a second ex vivo model, primary rat peritoneal macrophages from LPS‐primed rats exhibited suppression of thromboxane B2 and TNF‐α production, while maintaining nitrite production in response to in vitro LPS challenge. Pretreatment of rats with the PPARγ inhibitor GW9662 in vivo failed to alter the tolerant phenotype of these primary macrophages. In a third ex vivo model, primary peritoneal macrophages with conditional deletion of PPARγ were harvested from LPS‐primed Cre‐lox mice (Cre+/+ PPARγ−/−) and exhibited significant suppression of TNF‐α production in response to in vitro LPS challenge. Furthermore, both LPS‐primed PPARγ‐deficient Cre+/+ PPARγ−/− mice and wild‐type Cre−/− PPARγ+/+ mice exhibited reduced plasma TNF‐α levels in response to a high dose of LPS in vivo. These data demonstrate that PPARγ does not play a role in the LPS‐induced tolerant phenotype in macrophages.
Is it the injection device or the anxiety experienced that causes pain during dental local anaesthesia?
Authors: KUSCU OZGUR ONDER , AKYUZ SERAP 
Published: November 2007

Aim.  The aim of this study was to investigate the influence of anxiety and type of dental injection, a plastic syringe or an electronic computerized device, on the pain perceived by children.Design.  Two dental injectors, a computerized device (Wand®, Milestone Scientific, Livingston, NJ, USA) and a traditional plastic syringe, were compared. Forty‐one children, aged 9–13 years, who had registered for treatment in Marmara University, Istanbul, Turkey, were included in the study. Both anxious and non‐anxious children were included in the study group. The Children's Fear Survey Schedule–Dental Subscale, Facial Image Scale, Spielberger's State Anxiety Index for Children, and heart rates were used to determine the anxiety levels. Participants were assigned to interventions by using random allocation. The first appointment was designed as an introductive familiarization session and injections were administered in the second and third sessions, with one or the other injector. The visual analogue scale was used for pain measurement after injections.Results.  No significant differences in injection pain scores were observed between the Wand and traditional plastic injector. Higher levels of pre‐injection anxiety were found to be related to more severe pain reports by the children.Conclusions.  Anxiety plays an important role in the pain reaction of children, and was found to be more determinative in pain perception than the injection devices preferred.
5′ flanking region of var genes nucleate histone modification patterns linked to phenotypic inheritance of virulence traits in malaria parasites
Authors: Lopez‐Rubio Jose Juan , Gontijo Alisson M. , Nunes Marta C. , Issar Neha , Hernandez Rivas Rosaura , Scherf Artur 
Published: November 2007

SummaryIn the human malaria parasite Plasmodium falciparum antigenic variation facilitates long‐term chronic infection of the host. This is achieved by sequential expression of a single member of the 60‐member var family. Here we show that the 5′ flanking region nucleates epigenetic events strongly linked to the maintenance of mono‐allelic var gene expression pattern during parasite proliferation. Tri‐ and dimethylation of histone H3 lysine 4 peak in the 5′ upstream region of transcribed var and during the poised state (non‐transcribed phase of var genes during the 48 h asexual life cycle), ‘bookmarking’ this member for re‐activation at the onset of the next cycle. Histone H3 lysine 9 trimethylation acts as an antagonist to lysine 4 methylation to establish stably silent var gene states along the 5′ flanking and coding region. Furthermore, we show that competition exists between H3K9 methylation and H3K9 acetylation in the 5′ flanking region and that these marks contribute epigenetically to repressing or activating var gene expression. Our work points to a pivotal role of the histone methyl mark writing and reading machinery in the phenotypic inheritance of virulence traits in the malaria parasite.
Use of the air pouch model to investigate immune responses to a hookworm vaccine containing the Na‐ASP‐2 protein in rats
Authors: MENDEZ S. , D’ SAMUEL A. , ANTOINE A. D. , AHN S. , HOTEZ P. 
Published: November 2007

SUMMARY Hookworms are gastrointestinal nematodes that affect approximately 600 million people in developing countries. Using the air pouch model, we have examined the effects of vaccination with the recombinant hookworm larval antigen Na‐ASP‐2 and the adjuvant Alhydrogel® on the skin immune response to hookworms in Sprague Dawley rats. Following vaccination, rats were inoculated 100 Necator americanus L3 into the air pouch, and the exudates and cell infiltrates were collected from the pouch 24 h later. Larval inoculation induced leucocyte recruitment into the pouch. Exudates of rats vaccinated with Na‐ASP‐2 showed an increase of cytokines such as IL‐4, IL‐10, IFN‐γ and especially, IL‐5, as well as IgG1 and IgG2 antibodies. The increased amount of antigen‐presenting cells and cytokines in the pouch of vaccinated animals suggests that vaccination could potentially restrain this parasite to the inoculation site, avoiding its migration and establishment in the host. Moreover, the air pouch model could constitute an alternative to screen immune responses to L3 antigens.
Sedimentary facies of a glacially influenced continental succession in the Pennsylvanian Jericho Formation, Galilee Basin, Australia
Authors: JONES ANDREW T. , FIELDING CHRISTOPHER R. 
Published: November 2007

AbstractRecent work on the Late Palaeozoic Ice Age in eastern Australia has shown the Joe Joe Group in the eastern Galilee Basin, Queensland, to be of critical importance as it is one of few records of Pennsylvanian glacial activity outside South America. This paper presents detailed sedimentological data, from which the Late Palaeozoic environment of the region is reconstructed and which, consequently, allows for robust comment on the broader Gondwanan glaciation. The Jericho Formation, in the lower Joe Joe Group, was deposited in an active extensional basin in lacustrine to fluvial environments, during the mid‐Namurian to early Stephanian. The region experienced a cool climate during this time, and polythermal mountain or valley‐type glaciers periodically advanced into the area from highlands to the north‐east. The Jericho Formation preserves a suite of proglacial to terminal glacial facies that is characterized by massive and stratified diamictites deposited from debris flows, massive and horizontally laminated conglomerates and sandstones deposited from hyperconcentrated density flows, laminated siltstones with outsized clasts and interlaminated siltstone/conglomerate deposited through ice‐rafting into lakes, and sedimentary dykes and breccias deposited through overpressurization of groundwater beneath permafrost. Non‐glacial facies are dominated by fluvial sandstones and lacustrine/overbank siltstones. The glacigenic rocks of the Jericho Formation are confined to discrete packages, recording three separate glacial advances during the latest Namurian to late Westphalian. This arrangement is consistent with the temporal distribution of glacigenic rocks from around the remainder of Australia and Gondwana, which supports the theory that glacial deposits occurred in discrete intervals. The Joe Joe Group is a key succession in the world in this context as, at this time, eastern Australia provides the only unequivocal evidence of a Namurian/Westphalian glaciation outside South America. The continuous record of sedimentation through the Pennsylvanian and Early Permian is indicative of significant warming between glacial intervals, which is difficult to reconcile with the development of long‐lived, cold‐based ice sheets across the supercontinent.
Sediment trend models fail to reproduce small‐scale sediment transport patterns on an intertidal beach
Authors: MASSELINK GERHARD , BUSCOMBE DANIEL , AUSTIN MARTIN , O'HARE TIM , RUSSELL PAUL 
Published: November 2007

AbstractA rigorous test is presented of the application of sediment trend models to an intertidal beach environment characterized by bar morphology. Sediment samples were collected during low tide from a regular grid and their sediment fall velocity distributions, obtained using a settling tube, were analysed using moment analysis. The net sediment transport direction determined from beach surveys, hydrodynamic measurements, wave ripple observations and sediment transport modelling was compared with predictions by sediment trend models based on the spatial distribution of sediment parameters. It was found that the sediment transport pathways and patterns of sedimentation predicted using sediment trend models were at odds with field observations, and varied significantly depending on whether surface or sub‐surface sediment samples were used. The sediment trend models are thought to fail because, in energetic and morphologically variable beach environments, spatial patterns in sediment characteristics are mainly attributed to the presence of different hydrodynamic regions and associated morphology, rather than sediment pathways. The use of sediment trend models cannot replace the collection of morphological, hydrodynamic and sediment transport data in the field to define relationships between flows, forms and sedimentation patterns on a dynamic intertidal beach.