bluuebunny/crossref_metadata_2025_split huggingface dataset:
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments
Authors: Suyama Mikita , Torrents David , Bork Peer 
Published: March 2004

Abstract
Summary: BLAST2GENE is a program that allows a detailed analysis of genomic regions containing completely or partially duplicated genes. From a BLAST (or BL2SEQ) comparison of a protein or nucleotide query sequence with any genomic region of interest, BLAST2GENE processes all high scoring pairwise alignments (HSPs) and provides the disposition of all independent copies along the genomic fragment. The results are provided in text and PostScript formats to allow an automatic and visual evaluation of the respective region.
Availability: The program is available upon request from the authors. A web server of BLAST2GENE is maintained at http://www.bork.embl.de/blast2gene
Time-dependent Inhibition of G Protein–coupled Receptor Signaling by Local Anesthetics
Authors: Hollmann Markus W. , Herroeder Susanne , Kurz Katrin S. , Hoenemann Christian W. , Struemper Danja , Hahnenkamp Klaus , Durieux Marcel E. 
Published: March 2004

Background
Several beneficial effects of local anesthetics (LAs) were shown to be due to inhibition of G protein-coupled receptor signaling. Differences in exposure time might explain discrepancies in concentrations of LAs required to achieve these protective effects in vivo and in vitro (approximately 100-fold higher). Using Xenopus oocytes and human neutrophils, the authors studied time-dependent effects of LAs on G protein-coupled receptor signaling and characterized possible mechanisms and sites of action.

Methods
Measurement of agonist-induced Ca2+-activated Cl currents, using a two-electrode voltage clamp technique, and determination of superoxide anion production by cytochrome c assay were used to assess the effects of LAs on G protein-coupled receptor signaling in oocytes and primed and activated human neutrophils, respectively. Antisense knockdown of G alpha q protein and inhibition of various proteins within the signaling pathway served for defining mechanisms and sites of action more specifically.

Results
LAs attenuated G protein-coupled receptor signaling in both models in a time-dependent and reversible manner (lidocaine reduced lysophosphatidic acid signaling to 19 +/- 3% after 48 h and 25 +/- 2% after 6 h of control response in oocytes and human neutrophils, respectively). Whereas no effect was observed after extracellularly applied or intracellularly injected QX314, a lidocaine analog, using G alpha q-depleted oocytes, time-dependent inhibition also occurred after intracellular injection of QX314 into undepleted oocytes. Inhibition of phosphatases or protein kinases and agonist-independent G-protein stimulation, using guanosine 5'-O-3-thiotriphosphate or aluminum fluoride, did not affect time-dependent inhibition by LAs.

Conclusion
Inhibition of G protein-coupled receptor signaling by LAs was found to be time dependent and reversible. Critically requiring G alpha q-protein function, this effect is located downstream of guanosine diphosphate-guanosine triphosphate exchange and is not dependent on increased guanosine triphosphatase activity, phosphatases, or protein kinases.
Sevoflurane Inhibits Angiotensin II–induced, Protein Kinase C–mediated but Not Ca2+-elicited Contraction of Rat Aortic Smooth Muscle
Authors: Yu Jingui , Tokinaga Yasuyuki , Ogawa Koji , Iwahashi Shizue , Hatano Yoshio 
Published: March 2004

Background
Whether volatile anesthetics attenuate angiotensin II-mediated vascular tone has not been determined. The current study was designed to investigate the effects of sevoflurane on the angiotensin II-stimulated, Ca2+- and protein kinase C (PKC)-mediated contraction of rat aortic smooth muscle.

Methods
The dose-dependent effects of sevoflurane on angiotensin II (10 m)-induced contraction, the increase in intracellular Ca2+ concentration, and PKC phosphorylation of rat aortic smooth muscle were measured using an isometric force transducer, a fluorometer, and Western blotting, respectively.

Results
Angiotensin II induced a transient increase in intracellular Ca2+ concentration, phosphorylation of Ca2+-dependent PKC (cPKC)-alpha, and consequently, a transient contraction of rat aortic smooth muscle. Phosphorylation of the Ca2+-independent PKC-epsilon was not detected. The angiotensin II-induced contraction was almost completely abolished by removing extracellular Ca2+ and was significantly inhibited by the selective cPKC inhibitor Gö 6976 (10 M) but was not inhibited by the nonselective PKC inhibitor Ro 31-8425 (10 M). Sevoflurane dose-dependently inhibited the angiotensin II-induced contraction, with reductions of 14.2 +/- 5.2% (P > 0.05), 26.7 +/- 8.9% (P < 0.05), and 38.5 +/- 12.8% (P < 0.01) (n = 10) in response to 1.7, 3.4, and 5.1% sevoflurane, respectively. The angiotensin II-elicited increase in intracellular Ca2+ concentration was not significantly influenced by 3.4, 5.1, or 8.5% sevoflurane. However, cPKC-alpha phosphorylation induced by angiotensin II was inhibited dose dependently by 1.7, 3.4, and 5.1% sevoflurane, with depressions of 20.5 +/- 14.2% (P > 0.05), 37.0 +/- 17.8% (P < 0.05), and 62.5 +/- 12.2% (P < 0.01) (n = 4), respectively.

Conclusion
The current study indicates that Ca2+ and cPKC-alpha are involved in angiotensin II-induced vascular contraction. Sevoflurane dose-dependently inhibited the angiotensin II-stimulated, cPKC-mediated but not Ca2+-elicited contraction of rat aortic smooth muscle.
Antiallodynic Effects of Systemic and Intrathecal Morphine in the Spared Nerve Injury Model of Neuropathic Pain in Rats
Authors: Zhao Chengshui , Tall Jill M. , Meyer Richard A. , Raja Srinivasa N. 
Published: March 2004

Background
The efficacy of opioids for neuropathic pain remains controversial. The effects of morphine on pain behavior were investigated in two animal models of neuropathic pain: the spared nerve injury (SNI) model and the spinal nerve ligation (SNL) model.

Methods
Nerve injuries were created in rats either by tight ligation and section of the left tibial and common peroneal nerves (SNI) or by unilateral ligation of L5 and L6 spinal nerves (SNL). Paw withdrawal threshold to mechanical stimuli was measured using the up-down method in the hairy and glabrous skin territories of the sural nerve for SNI rats or in the mid-plantar paw of SNL rats.

Results
Before SNI, the median paw withdrawal thresholds in hairy and glabrous skin were similar (26 g [25%, 75% quartiles: 26, 26 g]). The paw withdrawal threshold decreased after SNI in both hairy and glabrous skin (P < 0.001). Thirty days after the SNI, the threshold in hairy skin (0.3 g) was significantly lower than in glabrous skin (1.9 g; P < 0.001). In blinded experiments, both subcutaneous and intrathecal morphine (0.1-10 microg) dose-dependently attenuated mechanical allodynia induced by SNI measured in the hairy skin, an effect that was naloxone reversible. The ED50 for the intrathecal morphine was 0.52 microg (95% confidence interval, 0.31-0.90 microg). Morphine (1 microg intrathecal) attenuated SNI-induced mechanical allodynia in glabrous skin with potency similar to that in hairy skin. In SNL rats, morphine (30 microg intrathecal) almost completely reversed the SNL-induced mechanical allodynia.

Conclusions
(1) SNI-induced mechanical allodynia is characterized by a lower paw withdrawal threshold in hairy versus glabrous skin; (2) systemic and intrathecal morphine reverse SNI-induced mechanical allodynia in a dose-dependent fashion; and (3) intrathecal morphine also reverses SNL-induced mechanical allodynia. These results suggest that intrathecal opioids are likely to be effective in the treatment of neuropathic pain.
Dissociable Brain Activation Responses to 5-Hz Electrical Pain Stimulation
Authors: Alkire Michael T. , White Nathan S. , Hsieh Raymond , Haier Richard J. 
Published: March 2004

Background
To elucidate neural correlates associated with processing of tonic aching pain, the authors used high-field (3-T) functional magnetic resonance imaging with a blocked parametric study design and characterized regional brain responses to electrical stimulation according to stimulus intensity-response functions.

Methods
Pain was induced in six male volunteers using a 5-Hz electrical stimulus applied to the right index finger. Scanning sequences involved different levels of stimulation corresponding to tingling sensation (P1), mild pain (P2), or high pain (P3). Common effects across subjects were sought using a conjunction analyses approach, as implemented in statistical parametric mapping (SPM-99).

Results
The contralateral posterior/mid insula and contralateral primary somatosensory cortex were most associated with encoding stimulus intensity because they showed a positive linear relation between blood oxygenation level-dependent signal responses and increasing stimulation intensity (P1 < P2 < P3). The contralateral secondary somatosensory cortex demonstrated a response function most consistent with a role in pain intensity encoding because it had no significant response during the innocuous condition (P1) but proportionally increased activity with increasingly painful stimulus intensities (0 < P2 < P3). Finally, a portion of the anterior cingulate cortex (area 24) and supplementary motor area 6 demonstrated a high pain-specific response (P3).

Conclusions
The use of response function modeling, conjunction analysis, and high-field imaging reveals dissociable regional responses to a tonic aching electrical pain. Most specifically, the primary somatosensory cortex and insula seem to encode stimulus intensity information, whereas the secondary somatosensory cortex encodes pain intensity information. The cingulate findings are consistent with its proposed role in processing affective-motivational aspects of pain.
Comparative analysis of isolated cellular organelles by means of soft X‐ray contact microscopy with laser‐plasma source and transmission electron microscopy
Authors: Limongi T. , Palladino L. , Tomassetti G. , Reale L. , Cesare P. , Flora F. , Aimola P. , Ragnelli A. M. 
Published: March 2004

SummarySoft X‐ray contact microscopy (SXCM) is, at present, a useful tool for the examination at submicrometre resolution of biological systems maintained in their natural hydrated conditions. Among current X‐ray‐generating devices, laser‐plasma sources are now easily available and, owing to their pulse nature, offer the opportunity to observe living biological samples before radiation damage occurs, even if the resolution achievable is not as high as with synchrotron‐produced X‐rays. To assess the potential of laser‐plasma source SXCM in the study of cellular organelles, we applied it for the analysis of chloroplasts extracted from spinach leaves and mitochondria isolated from bovine heart and liver. X‐ray radiation was generated by a nanosecond laser‐plasma source, produced by a single shot excimer XeCl laser focused onto an yttrium target. The images obtained with SXCM were then compared with those produced by transmission electron microscopy observation of the same samples prepared with negative staining, a technique requiring no chemical fixation, in order to facilitate their interpretation and test the applicability of SXCM imaging.
Use of truncated pyramid representation methodology in three‐dimensional reconstruction: an example
Authors: Papadimitriou C. , Yapijakis C. , Davaki P. 
Published: March 2004

SummaryThis paper describes a new methodology for three‐dimensional (3D) representation of biological structures contained in a series of sections, using an illustrative example. Spatial reconstruction of a specific area of an astrocytoma biopsy was carried out with alignment of the serial sections at an accuracy of 0.01% (or 1 µm cm−1), using the truncated pyramid representation (TPR) methodology. TPR includes: (a) serial tissue sectioning in a ribbon form; (b) alignment of the serial sections based on the properties of a ‘truncated pyramid’; (c) identification and localization of structures in every section using a field frame, and representation of the contours of the structures in every section as topographic contours (charting); (d) artificial reconstruction of the missing space between serial sections, by drawing intermediate contours based on the prototype contours of successive sections in order to provide smoother and more elegant representation of the volumes (complementation); and (e) 3D reconstruction. Application of TPR in a selected area of the astrocytoma enabled us to observe the morphology and spatial distribution of neoplastic astrocytic nuclei, which encircled an adjacent blood vessel.
Magnetic characterization of microscopic particles by MO‐SNOM
Authors: Schoenmaker J. , Lancarotte M. S. , Seabra A. C. , Souche Y. , Santos A. D. 
Published: March 2004

SummaryThis paper reports on the development of a magneto‐optical scanning near‐field optical microscope and the experimental near‐field study of the domain structure for a model magnetic particle of 16 × 16 µm2 of a Co70.4Fe4.6Si15B10 amorphous thin film, deposited on a silicon substrate. We present the topographic, optical and magneto‐optical differential susceptibility (MODS) images of the particle. Imaging by using the local MODS reveals the domain structure. These images are also used for positioning the tip in order to acquire local hysteresis loops, with submicrometre spatial resolution.
Interaction of mannan‐binding lectin with Trichinella spiralis glycoproteins, a possible innate immune mechanism
Authors: Gruden‐Movsesijan Alisa , Petrovic Miomir , Sofronic‐Milosavljevic Ljiljana 
Published: March 2004

SUMMARY Complex and variable glycoconjugates presented by parasitic nematodes during infection are very important in the host–parasite interplay. Predominantly carbohydrate‐rich antigens are involved in the stimulation and modulation of the stage‐specific immune response of the host. The non‐specific innate immune system, however, acts as the first line of host defence against pathogens, before the appearance of antigen‐specific responses. The functional entities of the innate system are lectins that recognize the surface ligands of pathogens: mannan‐binding lectin (MBL) is a key recognition element involved in binding oligosaccharide structures exposed on microorganisms. In the present study we investigated whether MBL binds to the parasitic nematode Trichinella spiralis (T. spiralis). Since the parasite is coated with mannose‐containing glycans, these structures could represent potential ligands for MBL and contribute to activation of the innate immune response of the host. Histochemical staining revealed MBL on the surface and internal organs of T. spiralis muscle larvae. MBL bound in a mannose‐inhibitable manner to both crude extracts of T. spiralis muscle larvae and larvae excretory/secretory products. Western blot analyses showed that MBL recognized glycoproteins from all stages of T. spiralis. In vitro complement activation assays suggested that MBL is capable of fixing complement components on T. spiralis crude extract coated plates and activating the complement cascade through the ‘lectin pathway’.
Aspartyl proteases from the intestinal brush border of Haemonchus contortus as protective antigens for sheep
Authors: Smith W. D. , Skuce P. J. , Newlands G. F. J. , Smith S. K. , Pettit D. 
Published: March 2004

SUMMARY A novel pepsin‐like aspartyl protease was identified as a component of Haemonchus galactose‐containing glycoprotein (H‐gal‐GP), which is an integral membrane glycoprotein complex located on the intestinal cells of Haemonchus contortus, and a highly protective antigen for sheep. This molecule, designated HcPEP2, showed 50% sequence identity with a previously described aspartyl protease from H‐gal‐GP known as HcPEP1. Fractions of H‐gal‐GP, either containing both HcPEP1 and 2 or other lower molecular weight components of the complex, were evaluated as protective antigens in immunization – challenge trials in sheep. When separated from the rest of the complex by gel filtration in 8 m urea, the HcPEP1 and 2 fraction significantly reduced H. contortus egg counts by 48% and worm numbers by 36%, but the lower molecular weight components were not significantly protective. However, the HcPEP1 and 2 fraction did not protect if electro‐eluted from SDS‐dissociated H‐gal‐GP, nor did bacterially expressed recombinant HcPEP1, suggesting that conformational epitopes are important for inducing immunity.
North American Natural Gas Demand — Outlook 2020
Authors: Ghouri Salman Saif 
Published: March 2004

AbstractThis paper analyses natural gas demand in the United States of America, Canada and Mexico for the period 1980–2001. Visual inspections of the historical trends for natural gas demand, GDP and natural gas prices provide an initial assessment of the relationship between these variables.The paper then estimates various regressions, using the Almon polynomial distributed lag model. Several regressions, utilizing different combinations of explanatory variables, were run with or without an autoregressive scheme of various orders. The best‐fitting model in each country was selected, and this was later used to generate natural gas demand forecasts for the respective countries to 2020.The results show that the income elasticity for Canada is more than unity (1.4), compared with less then unity for the USA (0.8) and Mexico (0.65). Changes in natural gas consumption generally lag by a few years, before the full impact of the changes in gas prices is realised. The length of lags varies between countries, but generally the effect of a price change on natural gas consumption dissipates after three‐to‐four years. Population is one of the important explanatory variables for Mexico, while it is not significant for the USA and Canada.The model predicts that natural gas demand in the USA (base case) will increase at an annualised growth rate of 1.9 per cent and, by 2020, should reach 919 billion cubic metres. This is not very different to the forecast of the US Department of Energy's Energy Information Administration (EIA) (900 bcm). Similarly, the base case forecast for Canada to 2020 is 128 bcm, compared with that of the EIA at 125 bcm. The forecast for Mexico (92 bcm) is significantly different to that of the EIA (120), perhaps due to different economic growth assumptions.The paper concludes that there is an urgent need to enhance exploration efforts and investment in liquefied natural gas (LNG) terminals, to be able to receive LNG from multiple sources, particularly in the USA and Mexico.
Beautiful and not So Beautiful Minds: An Introductory Essay on Economic Theory and the Supply of Oil
Authors: Banks Ferdinand E. 
Published: March 2004

AbstractBoth the teaching and the studying of energy economics have been severely disadvantaged by the emphasis placed on the Hotelling theory of resource exhaustion. For example, in the study of oil and gas economics, this unrealistic construction is fundamentally irrelevant, because it does not consider fixed investment, nor the (real) options associated with such things as starting or interrupting production. In addition, both economics students and teachers have failed to recognize the crucial importance of the reserves‐to production ratio, as well as the research of M. King Hubbert. Among other things, this oversight has led to an irrational optimism, where expectations of the future availability of oil are concerned. To be more specific, the probability that the oil pessimists are correct is large enough to justify the attachment of a sizable discount factor to any claim of future oil abundance.
Randomized, double‐blind, placebo‐controlled trial of oral aloe vera gel for active ulcerative colitis
Authors: Langmead L. , Feakins R. M. , Goldthorpe S. , Holt H. , Tsironi E. , De Silva A. , Jewell D. P. , Rampton D. S. 
Published: March 2004

SummaryBackground : The herbal preparation, aloe vera, has been claimed to have anti‐inflammatory effects and, despite a lack of evidence of its therapeutic efficacy, is widely used by patients with inflammatory bowel disease.Aim : To perform a double‐blind, randomized, placebo‐controlled trial of the efficacy and safety of aloe vera gel for the treatment of mildly to moderately active ulcerative colitis.Methods : Forty‐four evaluable hospital out‐patients were randomly given oral aloe vera gel or placebo, 100 mL twice daily for 4 weeks, in a 2 : 1 ratio. The primary outcome measures were clinical remission (Simple Clinical Colitis Activity Index ≤ 2), sigmoidoscopic remission (Baron score ≤ 1) and histological remission (Saverymuttu score ≤ 1). Secondary outcome measures included changes in the Simple Clinical Colitis Activity Index (improvement was defined as a decrease of ≥ 3 points; response was defined as remission or improvement), Baron score, histology score, haemoglobin, platelet count, erythrocyte sedimentation rate, C‐reactive protein and albumin.Results : Clinical remission, improvement and response occurred in nine (30%), 11 (37%) and 14 (47%), respectively, of 30 patients given aloe vera, compared with one (7%) [P = 0.09; odds ratio, 5.6 (0.6–49)], one (7%) [P = 0.06; odds ratio, 7.5 (0.9–66)] and two (14%) [P < 0.05; odds ratio, 5.3 (1.0–27)], respectively, of 14 patients taking placebo. The Simple Clinical Colitis Activity Index and histological scores decreased significantly during treatment with aloe vera (P = 0.01 and P = 0.03, respectively), but not with placebo. Sigmoidoscopic scores and laboratory variables showed no significant differences between aloe vera and placebo. Adverse events were minor and similar in both groups of patients.Conclusion : Oral aloe vera taken for 4 weeks produced a clinical response more often than placebo; it also reduced the histological disease activity and appeared to be safe. Further evaluation of the therapeutic potential of aloe vera gel in inflammatory bowel disease is needed.
High efficacy of 1‐week doxycycline‐ and amoxicillin‐based quadruple regimen in a culture‐guided, third‐line treatment approach for Helicobacter pylori infection
Authors: Cammarota G. , Martino A. , Pirozzi G. , Cianci R. , Branca G. , Nista E. C. , Cazzato A. , Cannizzaro O. , Miele L. , Grieco A. , Gasbarrini A. , Gasbarrini G. 
Published: March 2004

SummaryBackground : Helicobacter pylori infection may persist after both first‐ and second‐line current treatments.Aim : To assess the efficacy of a third‐line, culture‐guided treatment approach for the eradication of H. pylori.Methods : Patterns of resistance were analysed in H. pylori isolates from 94 consecutive patients in whom H. pylori infection had persisted after two eradication attempts. Using the epsilometer test, susceptibility analysis was performed for amoxicillin, clarithromycin, metronidazole, tetracycline and levofloxacin. Patients were then treated with a culture‐guided, third‐line regimen: 89 patients with a 1‐week quadruple regimen including omeprazole, bismuth, doxycycline and amoxicillin, and five patients with a 1‐week triple regimen containing omeprazole, amoxicillin and levofloxacin or clarithromycin.Results : Ninety‐four subjects (100%) were resistant to metronidazole, 89 (95%) to clarithromycin, 29 (31%) to levofloxacin and five (5%) to tetracycline. No resistance to amoxicillin was found in any patient. Overall, H. pylori eradication was obtained in 90% of subjects. The quadruple regimen was effective in 81 patients (92% by per protocol and 91% by intention‐to‐treat analysis). Four patients (80%, both per protocol and intention‐to‐treat analysis) were H. pylori‐negative after the triple regimen.Conclusions : A culture‐guided, third‐line therapeutic approach is effective for the eradication of H. pylori. Furthermore, the 1‐week doxycycline‐ and amoxicillin‐based quadruple regimen is a good third‐line ‘rescue’ treatment option.