bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis, Structure, and Magnetic Behavior of a 1‐D Coordination Polymer [Ni(NIT4py)2(ip)(H2O)]n
Authors: Wang Shu‐Ping , Gao Dong‐Zhao , Liao Dai‐Zheng , Jiang Zong‐Hui , Yan Shi‐Ping 
Published: January 2006

AbstractA new coordination polymer of the formula [Ni(NIT4py)2(ip)(H2O)]n(NIT4py = 2‐(4′‐pyridinyl)‐4,4,5,5‐tetramethylimidazoline‐1‐oxyl‐3‐oxide and ip = isophthalate dianion) has been synthesized and characterized by elemental analyses, IR spectrum, and single‐crystal X‐ray diffraction. The coordination about each Ni2+ ion is a distorted octahedra. Each isophthalate dianion binds two Ni2+ ions in monodentate‐bidentate mode, leading to a 1‐D chain. Among the chains, the coordinated water molecules and carboxylato oxygen atoms form hydrogen bonds, generating an infinite 1‐D ladder structure of a double‐chain. The magnetic study shows that the decrease of χMT value in the low temperature for the complex is mainly ascribed to the zero‐field splitting of the distorted octahedral Ni2+ ions.
Allosteric modulation, thermodynamics and binding to wild‐type and mutant (T277A) adenosine A1receptors of LUF5831, a novel nonadenosine‐like agonist
Authors: Heitman Laura H , Mulder‐Krieger Thea , Spanjersberg Ronald F , Von Frijtag Drabbe Künzel Jacobien K , Dalpiaz Alessandro , IJzerman Adriaan P 
Published: January 2006

The interaction of a new nonribose ligand (LUF5831) with the human adenosine A1receptor was investigated in the present study.Radioligand binding experiments were performed in the absence and presence of diverse allosteric modulators on both wild‐type (wt) and mutant (T277A) adenosine A1receptors. Thermodynamic data were obtained by performing these assays at different temperatures. In addition, cyclic adenosine monophosphate (cAMP) assays were performed.The presence of allosteric modulators had diverse effects on the affinity of LUF5831,N6‐cyclopentyladenosine (CPA), a full agonist, and 8‐cyclopentyl‐1,3‐dipropylxanthine (DPCPX), an inverse agonist/antagonist, for the adenosine A1receptor. PD81,723, for example, increased the affinity of CPA, while the affinity of LUF5831 was decreased. However, the affinity of DPCPX was decreased even more. In addition, LUF5831 was shown to have an affinity for the mutant (T277A) adenosine A1receptor (Ki=122±22 nM), whereas CPA's affinity was negligible. The results of temperature‐dependent binding assays showed that the binding of LUF5831 was entropy driven, in between the behaviour of CPA binding to the high‐ and low‐affinity states of the receptor, respectively.The inhibition of the forskolin‐induced production of cAMP through activation of the wt adenosine A1receptor showed that LUF5831 had a submaximal effect (37±1%) in comparison to CPA (66±5%). On the mutant receptor, however, neither CPA nor LUF5831 inhibited cAMP production.This study indicates that the nonribose ligand, LUF5831, is a partial agonist for the adenosine A1receptor.British Journal of Pharmacology(2006)147, 533–541. doi:10.1038/sj.bjp.0706655
Vanilloid VR1receptor is involved in rimonabant‐induced neuroprotection
Authors: Pegorini Simona , Zani Alessia , Braida Daniela , Guerini‐Rocco Chiara , Sala Mariaelvina 
Published: January 2006

Recently, a potential neuroprotective effect of rimonabant, independent of the CB1receptor interaction, has been proposed. In the present study, the role of transient receptor potential channel vanilloid subfamily member 1, named VR1, on neuroprotective effect of rimonabant, on global cerebral ischemia in gerbils, was investigated.Rimonabant (0.05–3 mg kg−1), given i.p. 5 min after recirculation, dose dependently antagonized the ischemia‐induced decrease in electroencephalographic (EEG) total spectral power and restored relative frequency band distribution 7 days after ischemia.Rimonabant (0.125–0.5 mg kg−1) fully prevented ischemia‐induced hyperlocomotion 1 day after ischemia and memory impairment evaluated in a passive avoidance task, 3 days after ischemia.At 7 days after ischemia, the survival of pyramidal cells, in the CA1subfield, was respectively 91 and 96%, in the animals given rimonabant 0.25 and 0.5 mg kg−1, compared to the vehicle group. Higher doses were not protective.The protection induced by rimonabant followed a bell‐shaped curve, the maximal active doses being 0.25 and 0.5 mg kg−1.Capsazepine (0.01 mg kg−1), a selective VR1vanilloid receptor antagonist, completely reversed rimonabant‐induced neuroprotective effects against EEG flattening, memory impairment and CA1hippocampal neuronal loss.These findings suggest that VR1vanilloid receptors are involved in rimonabant's neuroprotection even if other mechanisms can contribute to this effect.British Journal of Pharmacology(2006)147, 552–559. doi:10.1038/sj.bjp.0706656
Red wine alcohol promotes quercetin absorption and directs its metabolism towards isorhamnetin and tamarixetin in rat intestine in vitro
Authors: Dragoni Stefania , Gee Jennifer , Bennett Richard , Valoti Massimo , Sgaragli Giampietro 
Published: January 2006

Moderate consumption of red wine has been associated with beneficial effects on human health, and this has been attributed to the flavonoid content. Factors that influence the bioavailability of this group of polyphenolic compounds are therefore important.
Using the rat cannulated everted jejunal sac technique, we have investigated the effect of alcohol on the intestinal absorption of quercetin and its 3‐O‐glucoside from red wine. Tissue preparations were incubated in whole or dealcoholised red wine, diluted 1 : 1 with Krebs buffer for 20 min at 37°C, after which the mucosa was removed and processed for HPLC analysis. Tissues exposed to red wine had significantly higher amounts of both quercetin (× −3; P<0.001) and quercetin‐3‐O‐glucoside (× −1.5; P<0.01) associated with them, compared with sacs incubated in the dealcoholised equivalent. In addition, both tamarixetin (T) and isorhamnetin (I), in the mucosal tissue from sacs exposed to the whole wine, were significantly elevated approximately two fold (P<0.05; P<0.01, respectively).
Similar results were obtained when sacs were incubated in Krebs buffer containing a mixture of pure quercetin and quercetin‐3‐O‐glucoside with or without alcohol, and, although effects on the apparent absorption of Q and Q‐3‐G were not so marked, concentrations of the metabolites quercetin‐3‐O‐glucuronide and I were significantly increased by the presence of alcohol (P<0.01 and P<0.001, respectively).
It is therefore plausible that the moderate alcohol content of red wine contributes to its beneficial health effects in humans by both increasing the absorption of quercetin and quercetin‐3‐O‐glucoside and by channelling their metabolism towards O‐methylation to yield compounds (T and I), which have potential protective effects against cancer and cardiovascular diseases.

British Journal of Pharmacology (2006) 147, 765–771. doi:10.1038/sj.bjp.0706662
Capturing expert knowledge with argumentation: a case study in bioinformatics
Authors: Jefferys Benjamin R. , Kelley Lawrence A. , Sergot Marek J. , Fox John , Sternberg Michael J. E. 
Published: January 2006

Abstract
Motivation: The output of a bioinformatic tool such as BLAST must usually be interpreted by an expert before reliable conclusions can be drawn. This may be based upon the expert’s experience, additional data and statistical analysis. Often the process is laborious, goes unrecorded and may be biased. Argumentation is an established technique for reasoning about situations where absolute truth or precise probability is impossible to determine.
Results: We demonstrate the application of argumentation to 3D-PSSM, a protein structure prediction tool. The expert’s interpretation of results is represented as an argumentation framework. Given a 3D-PSSM result, an automated procedure constructs arguments for and against the conclusion that the result is a good predictor of protein structure. In addition to capturing the unique expertise of the author of 3D-PSSM for distribution to users, an improvement in recall of 5–10 percentage points is achieved. This technique can be applied to a wide range of bioinformatic tools.
Availability: Example public server and benchmarking data are available at . Source code available on request.
Contact: m.sternberg@imperial.ac.uk
AMiGA: the arthropodan mitochondrial genomes accessible database
Authors: Feijão Pedro Cipriano , Neiva Lissiene Silva , Azeredo-Espin Ana Maria Lima de , Lessinger Ana Cláudia 
Published: January 2006

Abstract
Summary: The Arthropodan Mitochondrial Genomes Accessible database (AMiGA) is a relational database developed to help in managing access to the increasing amount of data arising from developments in arthropodan mitochondrial genomics (136 mitochondrial genomes as of September 2005). The strengths of AMiGA include (1) a more accessible and up-to-date database containing a more comprehensive set of mitochondrial genomes for this phylum, (2) the provision of flexible search options for retrieving detailed information such as bibliographical data, genomic graphics, FASTA sequences and taxonomical status, (3) the possibility of enhanced comparative analyses by multiple alignment of single or concatenated sets of genes, (4) more accurate and updated information resulting from a specific curation process called AMiGA Notes and (5) the possibility of including unpublished sequences in a password-restricted area for comparative analysis with the other sequences stored in the database.
Availability:
Contact: lessinger@amiga.cbmeg.unicamp.br
Supplementary information: Detailed information, including an illustrated tutorial, is available from the above URL.
Field study on the interception efficiency of lightning protection systems and comparison with models
Authors: D'Alessandro F , Petrov N.I 
Published: January 2006

We present and analyse the collective statistical results of a long-term field study quantifying the number of lightning strikes to buildings equipped with lightning protection systems. The observations were made over the period 1990–2003 in a region with one of the highest lightning activities in the world. The data sample comprised 86 structures with a mean height and exposure time of 57 metres and 6.9 yr, respectively. These structures were subjected to 384 flashes over the total observation time of 592 yr. The positioning of the protective air terminals on these structures was carried out with an improved electrogeometric model of lightning attachment.
The collective observational data have been compared with the expected number of incident flashes using a variety of analytical relations and statistical tests. The expected strike frequency was determined with three different, contemporary models of lightning attachment to structures. The protection level or interception efficiency estimated from the models is compared with the actual value derived from the long-term field observations involving measurements of captured strikes and evidence of lightning by-pass events.
The results show that the observational data used in this study are well-described by a Poisson distribution. There is a highly significant positive correlation between the observational data and the number of strikes expected from the application of the theoretical models. Finally, the observed and expected values for the mean interception efficiency of the lightning protection systems in the study are shown to be in good agreement.
Clustered gases as a medium for efficient plasma waveguide generation
Authors: Milchberg H.M , Kim K.Y , Kumarappan V , Layer B.D , Sheng H 
Published: January 2006

Clustered gas jets are shown to be an efficient means for plasma waveguide generation, for both femtosecond and picosecond generation pulses. These waveguides enable significantly lower on-axis plasma density (less than 10
18
cm
−3
) than in conventional hydrodynamic plasma waveguides generated in unclustered gases. Using femtosecond pump pulses, self-guided propagation and strong absorption (more than 70%) are used to produce long centimetre scale channels in an argon cluster jet, and a subsequent intense pulse is coupled into the guide with 50% efficiency and guided at above 10
17
W cm
−2
intensity over 40 Rayleigh lengths. We also demonstrate efficient generation of waveguides using 100 ps axicon-generated Bessel-beam pump pulses. Despite the expected sub-picosecond cluster disassembly time, we observe long pulse absorption efficiencies up to a maximum of 35%. Simulations show that in the far leading edge of the long laser pulse, the volume of heated clusters evolves to a locally uniform and cool plasma already near ionization saturation, which is then efficiently heated by the remainder of the pulse.
Nuclear import and export of plant virus proteins and genomes
Authors: KRICHEVSKY ALEXANDER , KOZLOVSKY STANISLAV V. , GAFNI YEDIDYA , CITOVSKY VITALY 
Published: January 2006

SUMMARYNuclear import and export are crucial processes for any eukaryotic cell, as they govern substrate exchange between the nucleus and the cytoplasm. Proteins involved in the nuclear transport network are generally conserved among eukaryotes, from yeast and fungi to animals and plants. Various pathogens, including some plant viruses, need to enter the host nucleus to gain access to its replication machinery or to integrate their DNA into the host genome; the newly replicated viral genomes then need to exit the nucleus to spread between host cells. To gain the ability to enter and exit the nucleus, these pathogens encode proteins that recognize cellular nuclear transport receptors and utilize the host's nuclear import and export pathways. Here, we review and discuss our current knowledge about the molecular mechanisms by which plant viruses find their way into and out of the host cell nucleus.
Magnaporthe oryzae isolates causing gray leaf spot of perennial ryegrass possess a functional copy of the AVR1‐CO39 avirulence gene
Authors: PEYYALA REBECCA , FARMAN MARK L. 
Published: January 2006

SUMMARYGray leaf spot of perennial ryegrass (Lolium perenne) is a severe foliar disease caused by the ascomycete fungus Magnaporthe oryzae (formerly known as Magnaporthe grisea). Control of gray leaf spot is completely dependent on the use of fungicides because currently available perennial ryegrass cultivars lack genetic resistance to this disease. M. oryzae isolates from perennial ryegrass (prg) were unable to cause disease on rice cultivars CO39 and 51583, and instead triggered a hypersensitive response. Southern hybridization analysis of DNA from over 50 gray leaf spot isolates revealed that all of them contain sequences corresponding to AVR1‐CO39, a host specificity gene that confers avirulence to rice cultivar CO39, which carries the corresponding resistance gene Pi‐CO39(t). There was also an almost complete lack of restriction site polymorphism at the avirulence locus. Cloning and sequencing of the AVR1‐CO39 gene (AVR1‐CO39Lp) from 16 different gray leaf spot isolates revealed just two point mutations, both of which were located upstream of the predicted open reading frame. When an AVR1‐CO39Lp gene copy was transferred into ML33, a rice pathogenic isolate that is highly virulent to rice cultivar CO39, the transformants were unable to cause disease on CO39 but retained their virulence to 51583, a rice cultivar that lacks Pi‐CO39(t). These data demonstrate that the AVR1‐CO39 gene in the gray leaf spot pathogens is functional, and suggest that interaction of AVR1‐CO39Lp and Pi‐CO39(t) is responsible, at least in part, for the host specificity expressed on CO39. This indicates that it may be possible to use the Pi‐CO39(t) resistance gene as part of a transgenic strategy to complement the current deficiency of gray leaf spot resistance in prg. Furthermore, our data indicate that, if Pi‐CO39(t) can function in prg, the resistance provided should be broadly effective against a large proportion of the gray leaf spot pathogen population.
The UGA3‐GLT1 intergenic region constitutes a promoter whose bidirectional nature is determined by chromatin organization in Saccharomyces cerevisiae
Authors: Ishida Cecilia , Aranda Cristina , Valenzuela Lourdes , Riego Lina , DeLuna Alexander , Recillas‐Targa Félix , Filetici Patrizia , López‐Revilla Rubén , González Alicia 
Published: January 2006

SummaryTranscription of an important number of divergent genes of Saccharomyces cerevisiae is controlled by intergenic regions, which constitute factual bidirectional promoters. However, few of such promoters have been characterized in detail. The analysis of the UGA3‐GLT1 intergenic region has provided an interesting model to study the joint action of two global transcriptional activators that had been considered to act independently. Our results show that Gln3p and Gcn4p exert their effect upon cis‐acting elements, which are shared in a bidirectional promoter. Accordingly, when yeast is grown on a low‐quality nitrogen source, or under amino acid deprivation, the expression of both UGA3 and GLT1 is induced through the action of both these global transcriptional modulators that bind to a region of the bidirectional promoter. In addition, we demonstrate that chromatin organization plays a major role in the bidirectional properties of the UGA3‐GLT1 promoter, through the action of an upstream Abf1p‐binding consensus sequence and a polydAdTtract. Mutations in these cis‐elements differentially affect transcription of UGA3 and GLT1, and thus alter the overall relative expression. This is the first example of an intergenic region constituting a promoter whose bidirectional character is determined by chromatin organization.
The integration host factor (IHF) integrates stationary‐phase and virulence gene expression in Salmonella enterica serovar Typhimurium
Authors: Mangan Michael W. , Lucchini Sacha , Danino Vittoria , Cróinín Tadhg Ó , Hinton Jay C. D. , Dorman Charles J. 
Published: January 2006

SummaryThe integration host factor (IHF) is a DNA‐binding and ‐bending protein with roles in local DNA structural organization and transcriptional regulation in Gram‐negative bacteria. This heterodimeric protein is composed of the two highly homologous subunits IHFα and IHFβ. DNA microarray analysis was used to define the regulon of genes subject to IHF control in Salmonella enterica serovar Typhimurium (S. Typhimurium). The transcription profile of the wild type was compared with those of mutants deficient in IHFα, IHFβ, or both IHFα and IHFβ. Our data reveal a new connection between IHF and the expression of genes required by the bacterium to undergo the physiological changes associated with the transition from exponential growth to stationary phase. When a mutant lacking IHF entered stationary phase, it displayed downregulated expression of classic stationary‐phase genes in the absence of any concomitant change in expression of the RpoS sigma factor. Purified IHF was found to bind to the regulatory regions of stationary‐phase genes indicating an auxiliary and direct role for IHF in RpoS‐dependent gene activation. Loss of IHF also had a profound influence on expression of the major virulence genes and epithelial cell invasion, indicating a role in co‐ordinating regulation of the pathogenic traits with adaptation to stationary phase. Although the three mutants showed considerable overlaps in the genes affected by the ihf lesions, the observed patterns were not identical, showing that S. Typhimurium has not one but three overlapping IHF regulons.
Eosinophil interactions with Haemonchus contortus larvae in the ovine gastrointestinal tract
Authors: BALIC A. , CUNNINGHAM C. P. , MEEUSEN E. N. T. 
Published: January 2006

SUMMARY Sheep were immunized by weekly oral infections with Haemonchus contortus for 9 weeks followed by anthelmintic treatment. They were challenged either 9 or 22 weeks later with PBS (sham controls) or one million exsheathed L3 surgically injected in the abomasum, and killed 24 h or 48 h later. Sheep challenged 9 weeks after immunization displayed varying degrees of tissue eosinophilia that showed a significant inverse relationship with the number of intra‐epithelial mast cells (globule leucocytes). Close association of eosinophils with tissue larvae was observed mainly in the gastric pits (24 h) or on the mucosal surface (48 h). All L3‐challenged sheep in this group had detectable globule leucocytes and tissue IL‐4 mRNA, as measured by Southern blot RT‐PCR. In contrast, sheep challenged 22 weeks after immunization had no detectable globule leucocytes or IL‐4 mRNA and although they exhibited consistent tissue eosinophilia, eosinophils were not closely associated with tissue larvae. Scanning and transmission electron microscopy of sheep sensitized and rested for 9 weeks before challenge showed that L3 surrounded by eosinophils were at varying stages of damage and structural collapse. These studies strongly indicate that eosinophils can damage and probably kill gastrointestinal nematode larvae in vivo. In addition, they also suggest that effective killing by tissue eosinophils may depend on other microenvironmental factors such as intra‐epithelial mast cells and IL‐4.
Carbonates calibrated against oceanographic parameters along a latitudinal transect in the Gulf of California, Mexico
Authors: HALFAR J. , GODINEZ‐Orta L. , MUTTI M. , VALDEZ‐HOLGUIN J. E. , BORGES J. M. 
Published: January 2006

AbstractTrophic resources are an important control governing carbonate production. Though this importance has long been recognized, no calibration exists to quantitatively compare biogenic assemblages within trophic resource fields. This study presents a field calibration of carbonate producers in a range of settings against high‐resolution in situ measurements of nutrients, temperature and salinity. With its latitudinal extent from 30° to 23° N, the Gulf of California, Mexico, spans the warm‐temperate realm and encompasses nutrient regimes from oligo‐mesotrophic in the south to eutrophic in the north. Accordingly, from south to north carbonates are characterized by: (i) coral‐dominated shallow carbonate factories (5–20 m water depth) with average sea‐surface temperatures of 25 °C (min. 18 °C, max. 31 °C), average salinities of 35·06‰ and average chlorophyll a levels, which are a proxy for nutrients, of 0·25 mg Chl a m−3 (max. 0·48, min. 0·1). (ii) Red algal‐dominated subtidal to inner‐shelf carbonate formation (10–25 m) in the central Gulf of California exhibiting average temperatures of 23 °C (min. 18 °C, max. 30 °C), average salinities of 35·25‰, and average Chl a levels of 0·71 Chl a m−3 (max. 5·62, min. 0). (iii) Molluskan bryozoan‐rich inner to outer shelf factories in the northern Gulf of California (20–50 m) with average sea surface temperatures of only 20 °C (min. 13 °C, max 29 °C), average salinities of 35·01‰, and average contents of 2·2 mg Chl a m−3 (max. 8·38, min. 0). By calibrating sedimentological data with in situ measured oceanographic information in different environments, the response of carbonate producers to environmental parameters was established and extrapolated to carbonates on a global scale. The results demonstrate the importance of recognizing and quantifying trophic resources as a dominant control determining the biogenic composition and facies character of both modern and fossil carbonates.