bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct demonstration of nitric oxide formation in organs of rabbits treated by transdermal glyceryl trinitrate using an in vivo spin trapping technique
Authors: Clermont Gaëlle , Lecour Sandrine , Vergely Catherine , Zeller Marianne , Perrin Caroline , Maupoil Véronique , Bouchot Olivier , Rochette Luc 
Published: November 2003

AbstractGlyceryl trinitrate (GTN) is commonly delivered by a patch for the treatment of angina pectoris. The idea is now generally accepted that GTN requires a biotransformation process that activates the drug, in particular through nitric oxide (NO) generation. However, the pharmacokinetics of NO delivery from GTN still remains obscure. The objective of this study was to assess GTN‐derived NO formation in vascular tissues and organs in rabbit given GTN patches. NO levels were evaluated in rabbits after 3 h of treatment with a 10 mg GTN patch (GTN group; n = 7) or a placebo patch (CTL; n = 7). Nitrosylhaemoglobin (HbNO) was evaluated by electron spin resonance (ESR) spectroscopy in red cell suspension. In vivo spin trapping technique using FeMGD as a spin trap, associated with ESR was used to quantify NO in tissues. The NO‐spin trap complex, which is a relatively stable product, has been measured in several tissues. The ESR spectrum corresponding to HbNO was not found in red cell of GTN or CTL rabbits. The spectrum corresponding to the NO‐spin trap complex was observed in all analysed tissues of CTL rabbits. The signal was significantly increased in liver, renal medulla, heart left ventricle and spleen of GTN‐treated rabbits, and to a lesser extent in right ventricle and lung. No difference was shown between NO‐spin trap levels measured in aorta or inferior vena cava from GTN or CTL rabbits. These data suggest that GTN patch treatment induced NO release, and that tissue‐specific differences in transdermal GTN‐derived NO exist. The GTN–NO pathway appears to be largely involved in organs such as the liver, kidney and heart.
Clinical pharmacology of anti‐Alzheimer drugs
Authors: Pettenati Carla , Annicchiarico Roberta , Caltagirone Carlo 
Published: November 2003

AbstractAlzheimer's disease (AD) is a chronic neurodegenerative disorder characterized by a progressive loss of cognitive and functional abilities, associated with various degrees of behavioural disturbances, with a devastating impact on public health and on the whole society. Slowing of cognitive impairment, duration of disease, self‐sufficiency and behavioural disturbances represent the best outcomes of the pharmacologic therapy. Cholinesterase inhibitors (ChE‐I) have been shown to be effective in the treatment of the cognitive, behavioural, and functional deficits of AD. In addition to ChE‐I, a number of studies have been carried out to investigate the possible use of other compounds and pharmacologic strategies; more compounds, postsynaptic muscarinic and nicotinic receptor agonists, are under investigation. The standard suggested care for pharmacologic management of the cognitive and functional disabilities of AD at present consists of treatment with ChE‐I. Practice recommendations and treatment guidelines are derived from clinical trials.
PDB file parser and structure class implemented in Python
Authors: Hamelryck Thomas , Manderick Bernard 
Published: November 2003

Abstract
Summary: The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors.
Availability: The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org
GeneHuggers: database mining and application connectivity tools for subsequence analyses of the human genome
Authors: Iacovoni Jason S. 
Published: November 2003

Abstract
Summary: GeneHuggers is a collection of program modules that enables precise selection of subsequence regions from records of the RefSeq human genome database. Subsequence regions can be selected based on diverse criteria, including feature addresses, annotations from LocusLink and UniGene, and results obtained from analyses with homologous subsequence detection programs. GeneHuggers provides functionality to the UNIX operating system that allows customized bioinformatics program development.
Availability: GeneHuggers source code is available under the GNU general public license and can be downloaded from ftp://ftp.scripps.edu/pub/genehuggers/gh.tar.gz
BioWareDB: the biomedical software and database search engine
Authors: Matthiessen M. W. 
Published: November 2003

Abstract
Summary: A wealth of bioinformatics tools and databases has been created over the last decade and most are freely available to the general public. However, these valuable resources live a shadow existence compared to experimental results and methods that are widely published in journals and relatively easily found through publication databases such as PubMed. For the general scientist as well as bioinformaticists, these tools can deliver great value to the design and analysis of biological and medical experiments, but there is no inventory presenting an up-to-date and easily searchable index of all these resources. To remedy this, the BioWareDB search engine has been created. BioWareDB is an extensive and current catalog of software and databases of relevance to researchers in the fields of biology and medicine, and presently consists of 2800 validated entries.
Availability: BioWareDB is freely available over the Internet at http://www.biowaredb.org/
Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles
Authors: Eichler Gabriel S. , Huang Sui , Ingber Donald E. 
Published: November 2003

Abstract
Summary: Genome-wide expression profiles contain global patterns that evade visual detection in current gene clustering analysis. Here, a Gene Expression Dynamics Inspector (GEDI) is described that uses self-organizing maps to translate high-dimensional expression profiles of time courses or sample classes into animated, coherent and robust mosaics images. GEDI facilitates identification of interesting patterns of molecular activity simultaneously across gene, time and sample space without prior assumption of any structure in the data, and then permits the user to retrieve genes of interest. Important changes in genome-wide activities may be quickly identified based on ‘Gestalt’ recognition and hence, GEDI may be especially useful for non-specialist end users, such as physicians.
Availability: GEDI v1.0 is written in Matlab, and binary Matlab .dll files which require Matlab to run can be downloaded for free by academic institutions at http://www.chip.org/~ge/gedihome.html
Supplementary information: http://www.chip.org/~ge/gedihome.html
Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks
Authors: Husmeier Dirk 
Published: November 2003

Abstract
Motivation: Bayesian networks have been applied to infer genetic regulatory interactions from microarray gene expression data. This inference problem is particularly hard in that interactions between hundreds of genes have to be learned from very small data sets, typically containing only a few dozen time points during a cell cycle. Most previous studies have assessed the inference results on real gene expression data by comparing predicted genetic regulatory interactions with those known from the biological literature. This approach is controversial due to the absence of known gold standards, which renders the estimation of the sensitivity and specificity, that is, the true and (complementary) false detection rate, unreliable and difficult. The objective of the present study is to test the viability of the Bayesian network paradigm in a realistic simulation study. First, gene expression data are simulated from a realistic biological network involving DNAs, mRNAs, inactive protein monomers and active protein dimers. Then, interaction networks are inferred from these data in a reverse engineering approach, using Bayesian networks and Bayesian learning with Markov chain Monte Carlo.
Results: The simulation results are presented as receiver operator characteristics curves. This allows estimating the proportion of spurious gene interactions incurred for a specified target proportion of recovered true interactions. The findings demonstrate how the network inference performance varies with the training set size, the degree of inadequacy of prior assumptions, the experimental sampling strategy and the inclusion of further, sequence-based information.
Availability: The programs and data used in the present study are available from http://www.bioss.sari.ac.uk/~dirk/Supplements
Metabolomics spectral formatting, alignment and conversion tools (MSFACTs)
Authors: Duran Anthony L. , Yang Jian , Wang Liangjiang , Sumner Lloyd W. 
Published: November 2003

Abstract
Motivation: The amplified interest in metabolic profiling has generated the need for additional tools to assist in the rapid analysis of complex data sets.
Results: A new program; metabolomics spectral formatting, alignment and conversion tools, (MSFACTs) is described here for the automated import, reformatting, alignment, and export of large chromatographic data sets to allow more rapid visualization and interrogation of metabolomic data. MSFACTs incorporates two tools: one for the alignment of integrated chromatographic peak lists and another for extracting information from raw chromatographic ASCII formatted data files. MSFACTs is illustrated in the processing of GC/MS metabolomic data from different tissues of the model legume plant, Medicago truncatula. The results document that various tissues such as roots, stems, and leaves from the same plant can be easily differentiated based on metabolite profiles. Further, similar types of tissues within the same plant, such as the first to eleventh internodes of stems, could also be differentiated based on metabolite profiles.
Availability: Freely available upon request for academic and non-commercial use. Commercial use is available through licensing agreement http://www.noble.org/PlantBio/MS/MSFACTs/MSFACTs.html.
libsequence: a C++ class library for evolutionary genetic analysis
Authors: Thornton Kevin 
Published: November 2003

Abstract
Summary: A C++ class library is available to facilitate the implementation of software for genomics and sequence polymorphism analysis. The library implements methods for data manipulation and the calculation of several statistics commonly used to analyze SNP data. The object-oriented design of the library is intended to be extensible, allowing users to design custom classes for their own needs. In addition, routines are provided to process samples generated by a widely used coalescent simulation.
Availability: The source code (in C++) is available from http://www.molpopgen.org
Silent DNA: speaking RNA language?
Authors: Vinogradov Alexander E. 
Published: November 2003

Abstract
The sequence of silent DNA in the human genome (intergenic spacers, introns and synonymous codon positions of protein-coding genes) was found here to have the higher thermostability of corresponding RNA/RNA and RNA/DNA duplexes as compared with randomized sequence. This difference increased with elevation of GC content. The revealed effect was not due to correlation of RNA/RNA and RNA/DNA thermostabilities with thermostability of the DNA/DNA duplex, which, on the contrary, was lower than in the randomized sequence and lagged behind the elevation of GC content. The same picture was observed in the genomes of other warm-blooded vertebrates but not in the lower organisms. This finding suggests that RNA–RNA and RNA–DNA interactions could be involved in the putative function of silent DNA.
ε-aminocaproic Acid in Coronary Artery Bypass Graft Surgery
Authors: Kluger Roman , Olive David J. , Stewart Andrew B. , Blyth Carolyn M. 
Published: November 2003

Background
Epsilon-aminocaproic acid (epsilon-ACA), an antifibrinolytic agent, is used in cardiac surgery to decrease postoperative bleeding. Theoretical concerns exist about the potential for epsilon-ACA to contribute to thrombotic complications. For this reason epsilon-ACA administration is sometimes delayed until after heparinization. This study investigated the impact of the timing of epsilon-ACA administration on its efficacy.

Methods
In this double-blind study, 90 patients undergoing primary coronary artery bypass graft surgery were prospectively randomized to receive either epsilon-ACA commencing prior to skin incision (bolus 150 mg/kg, followed by an infusion at 15 mg x kg(-1) x hr(-1), epsilon-ACA commencing after heparin (same doses), or placebo. All infusions were terminated at the end of cardiopulmonary bypass. Criteria for the transfusion of blood products were standardized. Postoperative chest tube drainage (at 6 h, 12 h, and at chest tube removal) and blood transfusion requirements of the three groups were compared.

Results
At all time intervals, the placebo group had significantly greater chest tube drainage than either of the two epsilon-ACA groups (P < 0.005). At no time did a significant difference exist between the two epsilon-ACA groups. A trend existed for the placebo group to require more blood products than either epsilon-ACA group.

Conclusions
Epsilon-ACA produces a reduction in chest tube drainage in patients undergoing primary coronary artery bypass graft surgery. This effect is similar whether the drug is given prior to incision or following anticoagulation. Given the similar hemostatic efficacy and the theoretical potential for thrombotic complications, it may be prudent to administer epsilon-ACA following anticoagulation.
Sleep Arousal after Lower Abdominal Surgery and Relation to Recovery from Respiratory Obstruction
Authors: Wu Aihua , Drummond Gordon B. 
Published: November 2003

Background
Hypoxemic episodes occur during sleep after abdominal surgery, possibly caused by airway obstruction. The authors found arousals from sleep more often than respiratory disturbances, so they related changes in sleep state (short arousals from sleep and longer periods of wakening) to the sudden increase in respiratory flow that indicates relief from complete or partial respiratory obstruction.

Methods
Sleep state and nasal flow were studied in 16 patients receiving patient-controlled morphine and oxygen by facemask on the night after routine gynecologic surgery. Traces were analyzed separately for sleep events and for sudden increases in respiratory flow. The authors noted sleep events (arousals from sleep and transition from sleep to wake) that occurred within 12 s of relief of obstruction.

Results
Sleep quality was poor, with only stage 2 sleep in most patients. Median sleep duration was 70% of the study period, with 15 arousals and 6 awakenings per hour of sleep. Only 30% of arousals and awakenings were associated with relief of obstruction. Relief of obstruction also occurred without arousal from sleep, with a median frequency of 38 (30-62) in each night. Relief of obstruction was more frequently associated with arousal from sleep after benzodiazepine premedication (33% vs. 28%; P = 0.012), but this allocation was not randomized.

Conclusions
Arousals from sleep are frequent after abdominal surgery and mostly not related to respiratory disturbance. Relief of respiratory obstruction can occur during sleep without sleep arousal and during wakefulness.
Mild Hypercapnia Induces Vasodilation via Adenosine Triphosphate-sensitive K+Channels in Parenchymal Microvessels of the Rat Cerebral Cortex
Authors: Nakahata Katsutoshi , Kinoshita Hiroyuki , Hirano Yusei , Kimoto Yoshiki , Iranami Hiroshi , Hatano Yoshio 
Published: November 2003

Background
Carbon dioxide is an important vasodilator of cerebral blood vessels. Cerebral vasodilation mediated by adenosine triphosphate (ATP)-sensitive K+ channels has not been demonstrated in precapillary microvessel levels. Therefore, the current study was designed to examine whether ATP-sensitive K+ channels play a role in vasodilation induced by mild hypercapnia in precapillary arterioles of the rat cerebral cortex.

Methods
Brain slices from rat cerebral cortex were prepared and superfused with artificial cerebrospinal fluid, including normal (Pco2 = 40 mmHg; pH = 7.4), hypercapnic (Pco2 = 50 mmHg; pH = 7.3), and hypercapnic normal pH (Pco2 = 50 mmHg; pH = 7.4) solutions. The ID of a cerebral parenchymal arteriole (5-9.5 microm) was monitored using computerized videomicroscopy.

Results
During contraction to prostaglandin F2alpha (5 x 10(-7) m), hypercapnia, but not hypercapnia under normal pH, induced marked vasodilation, which was completely abolished by the selective ATP-sensitive K+ channel antagonist glibenclamide (5 x 10(-6) m). However, the selective Ca2+-dependent K+ channel antagonist iberiotoxin (10(-7) m) as well as the nitric oxide synthase inhibitor NG-nitro-L-arginine methyl ester (10(-4) m) did not alter vasodilation. A selective ATP-sensitive K+ channel opener, levcromakalim (3 x 10(-8) to 3 x 10(-7) m), induced vasodilation, whereas this vasodilation was abolished by glibenclamide.

Conclusion
These results suggest that in parenchymal microvessels of the rat cerebral cortex, decreased pH corresponding with hypercapnia, but not hypercapnia itself, contributes to cerebral vasodilation produced by carbon dioxide and that ATP-sensitive K+ channels play a major role in vasodilator responses produced by mild hypercapnia.
Isoflurane Enhances the Expression and Activity of Glutamate Transporter Type 3 in C6 Glioma Cells
Authors: Huang Yueming , Zuo Zhiyi 
Published: November 2003

Background
Glutamate transporters play an important role in maintaining extracellular glutamate homeostasis. Volatile anesthetics have been shown to affect glutamate transporter activity acutely (within minutes after the exposure). It is not known whether volatile anesthetics affect the expression of glutamate transporters.

Methods
Rat cultured C6 glioma cells that express excitatory amino acid transporter type 3 (EAAT3) were exposed to isoflurane at various concentrations (0.5-4.0%) or for different periods (1-24 h) at 37 degrees C. EAAT3 mRNA, proteins, and activity were quantified.

Results
Isoflurane induced a time- and concentration-dependent increase in the mRNA and protein levels of EAAT3 in C6 cells. The maximal increase was induced by 2% isoflurane, and the cells incubated with 2% isoflurane for 3 and 7 h expressed the highest levels of EAAT3 mRNA and proteins, respectively. Similarly, glutamate uptake was higher in C6 cells exposed to 2% isoflurane for 7 h than in control cells. Actinomycin D and cycloheximide, inhibitors for mRNA and protein synthesis, respectively, did not affect the isoflurane-induced increase in EAAT3 mRNA and protein expression. Phorbol 12-myristate 13-acetate, a protein kinase C activator, also enhanced EAAT3 expression. The combination of 2% isoflurane and phorbol 12-myristate 13-acetate caused a higher level of EAAT3 expression than that induced by 2% isoflurane alone. Neither staurosporine, a protein kinase C inhibitor, nor wortmannin, a phosphatidylinositol 3 kinase inhibitor, inhibited the isoflurane-induced increase in EAAT3 expression.

Conclusions
The results of this study suggest that isoflurane increases the expression and activity of EAAT3 by stabilizing EAAT3 mRNA and proteins via protein kinase C- and phosphatidylinositol 3 kinase-independent pathways.
Current Transfusion Practices of Members of the American Society of Anesthesiologists
Authors: Nuttall Gregory A. , Stehling Linda C. , Beighley Christopher M. , Faust Ronald J. 
Published: November 2003

Background
The last published survey of transfusion practices among members of the American Society of Anesthesiologists (ASA) was conducted in 1981. The ASA Committee on Transfusion Medicine conducted a new transfusion survey in 2002.

Methods
The survey was mailed to 2,500 randomly selected active ASA members. The previous survey was modified to incorporate questions based on the ASA Practice Guidelines for Blood Component Therapy. The chi-square test was used for comparisons. Two-tailed P values of 0.05 or less were considered as nonchance differences.

Results
A total of 862 survey responses were completed by anesthesiologists who provided or directly supervised anesthesia for patients who may have required transfusion. In a given week, 62% rarely or never transfused 3 or more units of blood to the same patient. The percentage of anesthesiologists who responded that it is never or rarely (1% or less of the time) necessary to cancel elective surgery because of unavailability of blood products was 96% in 2002. In 1981, 92% responded that it was rarely necessary, and 8% said that it was occasionally necessary. The percentage of anesthesiologists who required patients undergoing elective surgery to have a hemoglobin concentration of at least 10 g/dl decreased from 65% to 9% (P < 0.001). Before intraoperative erythrocyte transfusion, 89% of respondents performed hemoglobin or hematocrit determinations routinely or sometimes. Intraoperative autologous transfusion equipment availability increased from 39% to 95% (P < 0.001). Awareness of the ASA Guidelines was 72%.

Conclusions
Transfusion practices have changed considerably since 1981. Current transfusion practices are, in general, consistent with the ASA Guidelines.
Disciplining Society through the City: The Genesis of City Planning in Brazil and Argentina (1894–1945)
Authors: Outtes Joel 
Published: November 2003

This paper looks at the genesis of a discourse on urbanismo (city planning) in Brazil and Argentina between 1894 and 1945 using the ideas of Michel Foucault on discipline and his concept of bio–power. The demographic pattern of the major cities in both countries from 1890 onwards and the renewals of the centres of these cities are also discussed. Other sections are dedicated to the plans proposed for the same cities in the 1920s and to urban representations, such as ideas about social reform, the role of hygiene as a point of departure for planning, and the relationship of ideas on Taylorism (scientific management) and the city. The paper also discusses the planners opposition to elections, when they claimed that they were the only ones qualified to deal with urban problems and therefore they should be employed in the state apparatus.Other concerns of the paper are the use of planning as an element of nation building and ideas defining eugenics (race ‘betterment’) as an important aspect of city planning. I conclude by arguing that, if implemented, city planning was a way of creating an industrial culture, disciplining society through the city, although the industrial proletariat has never made up the majority of the population in Brazil or Argentina. Even if many aspects of the plans proposed for both countries were not implemented, the discourse of planners can be seen as a will to discipline society through the city. This discipline would affect the freedom of movement of human bodies, and is therefore approached through Foucault's concepts of bio–power and discipline