bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survival of reared and wild Atlantic salmon smolts: size matters more in bad years
Authors: Saloniemi I. , Jokikokko E. , Kallio-Nyberg I. , Jutila E. , Pasanen P. 
Published: July 2004

Abstract
We compared the marine survival of Carlin-tagged wild and hatchery-reared Atlantic salmon smolts of the Simojoki river, northern Baltic Sea. All the reared and released smolts were the offspring of native spawners returning to the river. Reared smolts were adipose-fin-clipped and released from the hatchery several weeks before tagging. The wild and reared smolts were simultaneously caught and tagged at a smolt trap located at the Simojoki river mouth. The study was conducted in two years, 1991 and 1993, when post-smolt survival in the Baltic Sea was different. Tags were returned by fishermen and return rates were used to estimate the survival of the smolt groups. We applied generalized linear models with survival as response variable and the year, origin, and smolt size as explanatory variables. On average, wild smolts had a 4.5 times higher survival rate than reared fish of the same smolt size. The difference in observed tag recovery rates as such was only about twofold or less, as the larger size of the reared smolts compared with the wild ones compensated for their lower survival rate. The better survival of wild than reared smolts was more pronounced in the low-survival year (1993 smolt year class) than in the high-survival year (1991 smolt year class).
Fear conditioning is impaired in adult rats by ethanol doses that do not affect periadolescents
Authors: Land Cantey , Spear Norman E. 
Published: July 2004

AbstractAdolescent rats and humans exhibit physiological, behavioral, and cognitive differences compared to their adult counterparts. These differences are apparent also in reactions to psychoactive drugs, such as ethanol. Recent studies have shown that though less sensitive to several behavioral indices of intoxication by ethanol, adolescent rats are more sensitive to the cognition‐impairing effects of ethanol. Ethanol's effects, in the present experiment, were assessed in terms of a fear conditioning test not previously used in comparison of adult and adolescent Sprague–Dawley albino rats. Separate groups of both ages were given intraperitoneal (i.p.) ethanol before or after tone–shock conditioning. This task features a hippocampus‐independent component, learned freezing to a tone, and a hippocampus‐dependent component, learned freezing to context. Post‐training ethanol had no effect on retention in either age, but pre‐acquisition ethanol impaired adult learning more than adolescent learning, as indexed by the expression of fear at the test. Blood alcohol was equivalent in adolescents and adults at a dose that produced cognitive discrepancies. Unlike other reports, these experiments demonstrate that adolescents may not be more sensitive to ethanol's effects in all cases of learning.
Irbesartan inhibits human T‐lymphocyte activation through downregulation of activator protein‐1
Authors: Cheng Shu‐Meng , Yang Shih‐Ping , Ho Ling‐Jun , Tsao Tien‐Ping , Chang Deh‐Ming , Lai Jenn‐Haung 
Published: July 2004

Irbesartan is a promising antihypertensive drug with beneficial effects on atherosclerotic processes. In the progression of atherosclerosis, human T‐lymphocytes play an important role, but it is not yet known how irbesartan modulates human T‐lymphocytes activation. To gain insight into the mechanisms by which irbesartan acts, we investigated its effects on human T‐lymphocytes.
Primary human T‐lymphocytes were isolated from whole blood. Cytokines were determined by ELISA. Activator protein‐1 (AP‐1) and related protein activities were determined by electrophoretic mobility shift assays, kinase assays, Western blotting and transfection assays.
Irbesartan inhibited the production of both tumor necrosis factor‐alpha and interferon‐gamma by activated T‐cells, especially at therapeutic concentrations. Further investigation at the molecular level indicated that the inhibition of activated human T‐lymphocytes specifically correlated with the downregulation of AP‐1 DNA‐binding activity. In the Jurkat T‐cell line, irbesartan also inhibited AP‐1 transcriptional activity. Finally, we revealed that irbesartan is unique in its ability to inhibit the activation of both c‐Jun NH2‐terminal protein kinase and p38 MAPK.
Our studies show that irbesartan may modulate inflammation‐based atherosclerotic diseases through a cell‐mediated mechanism involving suppression of human T‐lymphocytes activation via downregulation of AP‐1 activity.

British Journal of Pharmacology (2004) 142, 933–942. doi:10.1038/sj.bjp.0705785
Methylene ATP analogs as modulators of extracellular ATP metabolism and accumulation
Authors: Joseph Sheldon M , Pifer Matthew A , Przybylski Ronald J , Dubyak George R 
Published: July 2004

Transient accumulation of extracellular ATP reflects both release of ATP from intracellular stores and altered rates of ATP metabolism by ecto‐enzymes. Ecto‐nucleoside triphosphate diphosphohydrolases (eNTPDases) and ecto‐nucleotide pyrophosphatases (eNPPs) degrade ATP, while ecto‐nucleotide diphosphokinases (eNDPKs) synthesize ATP from ambient ADP.
Although the methylene ATP analogs βγ‐meATP and αβ‐meATP are widely used as metabolically stable tools for the analysis of purinergic signaling, their specific effects on eNTPDase, eNPP, and eNDPK activities have not been defined. This study compared the actions of these analogs on extracellular ATP metabolism by human 1321N1 astrocytes, rat PC12 pheochomocytoma cells, and rat C6 glioma cells.
Both analogs significantly reduced clearance of extracellular ATP by 1321N1 cells that express both eNTPDases and eNPPs, as well as by C6 cells that exclusively express eNPPs. In contrast, both analogs were much less efficacious in inhibiting ATP clearance by PC12 cells that predominantly express eNTPDases. βγ‐meATP, but not αβ‐meATP, was effectively hydrolyzed by the 1321N1 and C6 cells; PC12 cells did not significantly degrade this analog.
αβ‐meATP, but not βγ‐meATP, acted as a substrate for purified yeast NDPK to generate ATP via trans‐phosphorylation of ADP. αβ‐meATP also acted as substrate for the eNDPK activities expressed by 1321N1, PC12, and C6 cells and thereby induced extracellular ATP accumulation in the presence of ambient or exogenously added ADP.
These results indicate that methylene ATP analogs exert complex and cell‐specific effects on extracellular ATP metabolism that can significantly modify interpretation of studies that use these reagents as probes of purinergic signal transduction in intact tissues.

British Journal of Pharmacology (2004) 142, 1002–1014. doi:10.1038/sj.bjp.0705865
Chelerythrine and other benzophenanthridine alkaloids block the human P2X7 receptor
Authors: Shemon Anne N , Sluyter Ronald , Conigrave Arthur D , Wiley James S 
Published: July 2004

Extracellular ATP can activate a cation‐selective channel/pore on human B‐lymphocytes, known as the P2X7 receptor. Activation of this receptor is linked to PLD stimulation. We have used ATP‐induced 86Rb+ (K+) efflux to examine the effect of benzophenanthridine alkaloids on P2X7 channel/pore function in human B‐lymphocytes.
Both ATP and the nucleotide analogue 2′‐3′‐O‐(4‐benzoylbenzoyl)‐ATP (BzATP) induced an 86Rb+ efflux, which was completely inhibited by the isoquinoline derivative 1‐(N,O‐bis[5‐isoquinolinesulphonyl]‐N‐methyl‐L‐tyrosyl)‐4‐phenylpiperazine (KN‐62), a potent P2X7 receptor antagonist.
The benzophenanthridine alkaloid chelerythrine, a potent PKC inhibitor, inhibited the ATP‐induced 86Rb+ efflux by 73.4±3.5% and with an IC50 of 5.6±2.3 μM. Similarly, other members of this family of compounds, sanguinarine and berberine, blocked the ATP‐induced 86Rb+ efflux by 58.8±4.8 and 61.1±8.0%, respectively.
Concentration–effect curves to ATP estimated an EC50 value of 78 μM and in the presence of 5 and 10 μM chelerythrine this increased slightly to 110 and 150 μM, respectively, which fits a noncompetitive inhibitor profile for chelerythrine.
Chelerythrine at 10 μM was effective at inhibiting the ATP‐induced PLD stimulation in B‐lymphocytes by 94.2±21.9% and the phorbol 12‐myristate 13‐acetate‐induced PLD stimulation by 68.2±7.4%.
This study demonstrates that chelerythrine in addition to PKC inhibition has a noncompetitive inhibitory action on the P2X7 receptor itself.

British Journal of Pharmacology (2004) 142, 1015–1019. doi:10.1038/sj.bjp.0705868
Junctional and nonjunctional effects of heptanol and glycyrrhetinic acid derivates in rat mesenteric small arteries
Authors: Matchkov Vladimir V , Rahman Awahan , Peng Hongli , Nilsson Holger , Aalkjær Christian 
Published: July 2004

Heptanol, 18α‐glycyrrhetinic acid (18αGA) and 18β‐glycyrrhetinic acid (18βGA) are known blockers of gap junctions, and are often used in vascular studies. However, actions unrelated to gap junction block have been repeatedly suggested in the literature for these compounds. We report here the findings from a comprehensive study of these compounds in the arterial wall.
Rat isolated mesenteric small arteries were studied with respect to isometric tension (myography), [Ca2+]i (Ca2+‐sensitive dyes), membrane potential and – as a measure of intercellular coupling – input resistance (sharp intracellular glass electrodes). Also, membrane currents (patch‐clamp) were measured in isolated smooth muscle cells (SMCs). Confocal imaging was used for visualisation of [Ca2+]i events in single SMCs in the arterial wall.
Heptanol (150 μM) activated potassium currents, hyperpolarised the membrane, inhibited the Ca2+ current, and reduced [Ca2+]i and tension, but had little effect on input resistance. Only at concentrations above 200 μM did heptanol elevate input resistance, desynchronise SMCs and abolish vasomotion.
18βGA (30 μM) not only increased input resistance and desynchronised SMCs but also had nonjunctional effects on membrane currents. 18αGA (100 μM) had no significant effects on tension, [Ca2+]i, total membrane current and synchronisation in vascular smooth muscle.
We conclude that in mesenteric small arteries, heptanol and 18βGA have important nonjunctional effects at concentrations where they have little or no effect on intercellular communication. Thus, the effects of heptanol and 18βGA on vascular function cannot be interpreted as being caused only by effects on gap junctions. 18αGA apparently does not block communication between SMCs in these arteries, although an effect on myoendothelial gap junctions cannot be excluded.

British Journal of Pharmacology (2004) 142, 961–972. doi:10.1038/sj.bjp.0705870
Hepatocytes from α1B‐adrenoceptor knockout mice reveal compensatory adrenoceptor subtype substitution
Authors: Deighan Clare , Woollhead Alison M , Colston Janet F , McGrath John C 
Published: July 2004

α1‐Adrenoceptors (ARs) play an important functional role in the liver; yet little is known about their cellular location. We identified the subtypes present in wild‐type (WT) and α1B‐AR knockout (KO) mice livers at 3 and 4 months of age, and investigated their distribution in hepatocytes.
The fluorescent α1‐AR antagonist quinazolinyl piperazine borate‐dipyrromethene (QAPB) was used to visualise hepatic α1‐ARs and radioligand binding with [3H]‐prazosin was used to quantify the α1‐AR population.
QAPB and [3H]‐prazosin bound specifically to hepatic α1‐ARs with nanomolar affinity. The cellular distribution of α1‐ARs was similar in WT and α1B‐AR KO hepatocytes; QAPB binding was distributed diffusely throughout the cell with no binding evident on the plasma membrane. Radioligand binding produced Bmax values as follows: 3‐month WT – 76±3.3 fmol mg−1; 4‐month WT – 50±3.1 fmol mg−1; 3‐month α1B‐AR KO – 7.4±0.73 fmol mg−1; 4‐month α1B‐AR KO – 30±2.0 fmol mg−1.
In 3‐ and 4‐month WT liver, all antagonists acted competitively. RS100329 (α1A‐selective) and BMY7378 (α1D‐selective) bound with low affinities, indicating the presence of α1B‐ARs. In 4‐month α1B‐AR KO liver prazosin produced a biphasic curve, whereas RS100329 and BMY7378 produced monophasic curves of high and low affinity, respectively, indicating the presence of α1A‐ARs.
In conclusion, we have made the novel observation that α1‐ARs can compensate for one another in the absence of the endogenously expressed receptor; yet there appears to be no subtype‐specific subcellular location of α1‐ARs; the WT livers express α1B‐ARs, while α1B‐AR KO livers express α1A‐ARs. This study provides new insights into both hepatocyte and α1‐AR biology.

British Journal of Pharmacology (2004) 142, 1031–1037. doi:10.1038/sj.bjp.0705872
Dermatofibrosarcoma protuberans – An Update
Authors: Breuninger Helmut , Sebastian Günther , Garbe Claus 
Published: July 2004

SummaryDermatofibrosarcoma protuberans (DFSP) is a rare fibroblastic skin tumor of intermediate malignancy. Its pathogenesis has not yet been fully clarified. Recent basic genetic research has shown chromosomal translocations, generally termed “ring chromosomes”, in DFSP. These arise from a fusion of chromosome regions 17q22 and 22q13, the gene loci which code the alpha chain of type I collagen.The diagnosis is made histologically. Differentiation from atypical dermatofibroma and dermatomyofibroma, as well as from malignant fibrous histiocytoma, whose prognosis is usually much less favorable, can be improved by immunostaining for CD 34 and Factor XIIIa. The extent of the tumors can be estimated by CT and more precisely with MRI. All these techniques fail to detect the fine tumor fascicles extending into the adjacent connective tissue and fat.Surgery is the therapy of choice for DFSP. The locally infiltrative growth pattern features clinically inapparent extensions which often extend for long distances in a horizontal direction. These tumor extensions are best detected by uninterrupted histological check of all margins, including the base (3‐D‐histology), with paraffin sections. Re‐excision of tumor‐positive areas until tumor‐free margins are obtained (“histographic surgery”) insures a high cure rate (97 %) while preserving normal tissue.
Interactive gene-order comparison for multiple small genomes
Authors: Kaluszka Aaron , Gibas Cynthia 
Published: July 2004

Abstract
Summary: The Genome Organization Analysis Tool (GOAT) is a program that performs comparative sequence analysis on ordered gene lists from annotated genomes, provides visual and tabular output, and provides means of accessing and analyzing related gene sequence data, for the purpose of comparing genome organization at the gene-order level. GOAT can be used to compare any two or more genomes or chromosomes on demand, or configured to provide access to precomputed comparisons of a specific group of genome sequences.
Availability: Demonstration web server and software download, subject to the Virginia Tech Noncommercial License are available at http://gaia.biotech.vt.edu/goat/
Supplementary information: Updates, installation and configuration information are available at http://gaia.biotech.vt.edu/goat
Preferred in vivo ubiquitination sites
Authors: Catic André , Collins Cal , Church George M. , Ploegh Hidde L. 
Published: July 2004

Abstract
Motivation: The conjugation of ubiquitin to target molecules involves several enzymatic steps. Little is known about the specificity of ubiquitination. How E3 ligases select their substrate and which lysines are targeted for ubiquitin conjugation is largely an enigma. The object of this study is to identify preferred ubiquitination sites. Genetic approaches to study this question have proven difficult, because of the redundancy of ligases and the lack of strictly required motifs. However, a better understanding of acceptor site selection could help to predict ubiquitination sites and clarify yet unsolved structure–function relationships of the transfer reaction.
Results: In an effort to define preferences for ubiquitination, we systematically analyzed structure and sequence of 135 known ubiquitination sites in 95 proteins in Saccharomyces cerevisiae. The results show clear structural preferences for ubiquitin ligation to target proteins, and compartment-specific amino acid patterns in close proximity to the modified side chain.
Supplementary information: http://www.people.fas.harvard.edu/~catic
A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences
Authors: Bilgen Mehmet , Karaca Mehmet , Onus A. Naci , Ince Ayşe Gül 
Published: July 2004

Abstract
Motivation: One of the most interesting features of genomes (both coding and non-coding regions) is the presence of relatively short tandemly repeated DNA sequences known as tandem repeats (TRs). We developed a new PC-based stand-alone software analysis program, combining sequence motif searches with keywords such as organs, tissues, cell lines or development stages for finding exact, inexact and compound, TRs. Tandem Repeats Analyzer 1.5 (TRA) has several advanced repeat search parameters/options over other repeat finder programs as it does not only accept GenBank, FASTA and expressed sequence tag (EST) sequence files but also does analysis of multifiles with multisequences. Advanced user-defined parameters/options let the researchers use different motif lengths search criteria for varying motif lengths simultaneously. The outputs show statistical results to be evaluated by the user. The discovery of TRs in ESTs could be useful for both gene mapping and association studies and discovering TRs located in coding regions of important genes that are expressed under various conditions of environment, stress, organ, tissue and development stage.
Results: In this paper, we demonstrated applications of TRA using 175 899 ESTs sequences for three Arabidopsis spp. downloaded from GenBank. The EST-SSRs/ESTs ratios were found 43.1%, 15.3% and 2.34% in A.lyrata, A.thaliana and A.halleri, respectively. Analysis revealed that organs, tissues and development stages possessed different amounts of repeats and repeat compositions. This indicated that the distribution of TRs among the tissues or organs may not be random differing from the untranscribed repeats found in genomes.
Availability: The program can be obtained free by anonymous FTP from ftp.akdeniz.edu.tr/Araclar/TRA
An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites
Authors: Selivanov Vitaly A. , Puigjaner Joaquim , Sillero Antonio , Centelles Josep J. , Ramos-Montoya Antonio , Lee Paul W.-N. , Cascante Marta 
Published: July 2004

Abstract
Motivation: Analysis of the conversion of 13C glucose within the metabolic network allows the evaluation of the biochemical fluxes in interconnecting metabolic pathways. Such analyses require solving hundreds of equations with respect to individual isotopomer concentrations, and this assumes applying special software even for constructing the equations. The algorithm, proposed by others could be improved.
Method: A C-code linked to the program written in Mathematica (Wolfram Research Inc.), constructs and solves differential equations for all isotopomer concentrations, using the general enzyme characteristics (Km, equilibrium constant, etc.). This code uses innovative algorithm of determination for the isotopomers–products, thus essentially decreasing the computation time. Feasible metabolic fluxes are provided by the parameters of enzyme kinetics found from the data fitting.
Results: The software effectively evaluates metabolic fluxes based on the measured isotopomer distribution, as was illustrated by the analysis of glycolysis and pentose phosphate cycle. The mechanism of transketolase and transaldolase catalysis was shown to induce a specific kind of isotopomer re-distribution, which, despite the significance of its effect, usually is not taken into account.
Availability: The software could be freely downloaded from the site: http://bq.ub.es/bioqint/label_distribution/
GenePicker: replicate analysis of Affymetrix gene expression microarrays
Authors: Finocchiaro Giacomo , Parise Paola , Minardi Simone P. , Alcalay Myriam , Müller Heiko 
Published: July 2004

Abstract
Summary: GenePicker allows efficient analysis of Affymetrix gene expression data performed in replicate, through definition of analysis schemes, data normalization, t-test/ANOVA, Change-Fold Change-analysis and yields lists of differentially expressed genes with high confidence. Comparison of noise and signal analysis schemes allows determining a signal-to-noise ratio in a given experiment. Change Call, Fold Change and Signal mean ratios are used in the analysis. While each parameter alone yields gene lists that contain up to 30% false positives, the combination of these parameters nearly eliminates the false positives as verified by northern blotting, quantitative PCR in numerous independent experiments as well as by the analysis of spike-in data.
Availability: http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html
Supplementary information: http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html
Gene selection using a two-level hierarchical Bayesian model
Authors: Bae Kyounghwa , Mallick Bani K. 
Published: July 2004

Abstract
Summary: The fundamental problem of gene selection via cDNA data is to identify which genes are differentially expressed across different kinds of tissue samples (e.g. normal and cancer). cDNA data contain large number of variables (genes) and usually the sample size is relatively small so the selection process can be unstable. Therefore, models which incorporate sparsity in terms of variables (genes) are desirable for this kind of problem. This paper proposes a two-level hierarchical Bayesian model for variable selection which assumes a prior that favors sparseness. We adopt a Markov chain Monte Carlo (MCMC) based computation technique to simulate the parameters from the posteriors. The method is applied to leukemia data from a previous study and a published dataset on breast cancer.
Supplementary information: http://stat.tamu.edu/people/faculty/bmallick.html
DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions
Authors: Gisel Andreas , Panetta Maria , Grillo Giorgio , Licciulli Vito Flavio , Liuni Sabino , Saccone Cecilia , Pesole Graziano 
Published: July 2004

Abstract
Summary: DNAfan (DNA Feature ANalyzer) is a tool combining sequence-filtering and pattern searching. DNAfan automatically extracts user-defined sets of sequence fragments from large sequence sets. Fragments are defined by annotated gene feature keys and co- or non-occurring patterns within the feature or close to it. A gene feature parser and a pattern-based filter tool localizes and extracts the specific subset of sequences. The selected sequence data can subsequently be retrieved for analyses or further processed with DNAfan to find the occurrence of specific patterns or structural motifs. DNAfan is a powerful tool for pattern analysis. Its filter features restricts the pattern search to a well-defined set of sequences, allowing drastic reduction in false positive hits.
Availability: http://bighost.ba.itb.cnr.it:8080/Framework