bluuebunny/crossref_metadata_2025 huggingface dataset:
Competition between weeds and wet season transplanted paddy rice for nitrogen use, growth and yield in the central and northern regions of Laos
Authors: INAMURA TATSUYA , MIYAGAWA SHUICHI , SINGVILAY OLAYVANH , SIPASEAUTH NIVONG , KONO YASUYUKI
Published: November 2003

To quantify the effect of weeds on the nitrogen (N) use, growth and yield of wet season paddy rice in the central and northern regions of Laos, we surveyed the paddy fields in these regions in October 1999 and November 2000. We found 13 weed species in total, but there were few major weeds abundant at the survey sites. In the infertile soils under rainfed conditions, weed growth was poor. Rough rice yield, the number of panicles, the number of seeds per square meter, the above‐ground biomass of paddy rice and the amount of N accumulated in the above‐ground biomass of paddy rice (amount of N in rice) were suppressed by competition with weeds. However, harvest index (HI) and nitrogen use efficiency (NUE) of paddy rice were not suppressed by competition with weeds. The amount of N in rice was suppressed by competition with weeds, the number of panicles decreased as the amount of N in rice decreased, and the number of seeds per square meter decreased as the number of panicles decreased. As a result, rough rice yield was suppressed by competition with weeds. The weeds competed with paddy rice for N uptake during the productive tillering stage. However, the ability of paddy rice to compete for N uptake with weeds was not reduced under rainfed lowland conditions. When the weeds were completely removed, the amount of N in rice increased. Rough rice yield may be increased by 10% under rainfed lowland conditions and by 17–19% under irrigated conditions.
Managerial Quality, Administrative Performance and Trust in Governance: Can We Point to Causality?
Authors: Vigoda Eran , Yuval Fany
Published: November 2003

The relationship between managerial quality, administrative performance and citizens' trust in government and in public administration systems is a field of study that so far has not received adequate scholarly attention. This article explores some interrelationships between these variables and empirically tests between causality, if it exists, between performance and trust. Applying a technique of structural equation modelling (SEM) with LISREL 8.3 the study examined a sample of 345 Israeli citizens and compared three alternative models. The second model that showed a quality → performance → trust relationship fitted the data best. However, the third model also had some advantages worthy of elaboration. Thus, we concluded that administrative performance may be treated as a precondition to trust in governance rather than trust serving as the precondition to performance. The article ends with further discussion of the findings and their meaning in light of the democratic, bureaucratic and new public management theory.
Reducing Aboriginal Over‐representation in Prison
Authors: Weatherburn Don , Fitzgerald Jackie , Hua Jiuzhao
Published: November 2003

The Royal Commission into Aboriginal Deaths in Custody attributed the high rate of Aboriginal deaths in custody to the over‐representation of Aboriginal people in prison. Most analyses of this over‐representation focus on the issue of systemic bias in policing, the law or the operation of the criminal justice system. The present article contends that, while discriminatory treatment of Aboriginal people by police and the court system is an historical fact, the leading current cause of Aboriginal over‐representation in prison is not systemic bias but high rates of Aboriginal involvement in serious crime. We argue that efforts to reduce Aboriginal imprisonment rates through policing or criminal justice system policy have failed and will continue to fail until they succeed in reducing crime in Aboriginal communities. Future efforts to bring down Aboriginal imprisonment rates should focus on this issue.
A Critical Evaluation of Virtual Local Government in Australia
Authors: Dollery Brian
Published: November 2003

The vigorous debate surrounding local government amalgamation in Australia remains unresolved. In an attempt to break the current stalemate Percy Allan (2001) has proposed a model of ‘virtual local government’ that seeks to combine the service appropriateness and effectiveness purportedly associated with demographically small councils with the service efficiency of large municipalities. This paper attempts to place his model in the context of the literature on the theory of public sector policy reform. It then goes on to examine virtual local government in the light of new institutional economics, public choice theory and the characteristics of Australian local government.
The Changing Public‐Private Infrastructure Mix: Economy‐wide Implications
Authors: Makin Tony
Published: November 2003

This article provides an economy‐wide perspective on the changing role of the public sector in developing economic and social infrastructure in Australia. It analyses the scale and macroeconomic significance of the key economic and social infrastructure sectors — communication services, electricity, gas and water supply, transport, education, health and community services, government administration and defence. It then canvasses the major policy issues that have arisen in the progression from public to private infrastructure provision and considers why concerns about the trend fall in traditional public works spending may be misplaced in light of recent economic and institutional changes.
Propagation of Nominal Shocks in Open Economies
Authors: Andersen Torben M. , Beier Niels C.
Published: November 2003

Empirical evidence documents substantial persistence in the adjustment process to nominal shocks. Existing open‐economy models either have failed to generate interesting dynamics or have found that the mechanisms are quantitatively weak. We consider the propagation of nominal shocks in a fully specified stochastic intertemporal open‐economy model with incomplete capital markets and staggered nominal wage contracts. It is shown that persistence depends on wage–price interdependences (spiral), which in turn in a general equilibrium setting depend on structural parameters characterizing both the demand and the supply side of markets. Parameter choices strengthening wage–price interdependences thus strengthen persistence as is demonstrated analytically and illustrated numerically. A further product of the paper is that it develops a method by which to solve explicitly for a stochastic intertemporal version of the ‘new open‐economy macroeconomics’ model in which the expenditure switching effect is effective.
Durable Goods, Commitment Power and Public Monopolies
Authors: Goering Gregory E. , Pippenger Michael K.
Published: November 2003

Since many publicly owned firms manufacture a durable product we examine a simple two‐period, constant returns technology, durability choice monopoly model under public ownership. Various types of firm commitment ability are analyzed. The model suggests that many of the standard results of public ownership are not obtained when output is durable. Product durability is shown to be an important factor for public firm subsidization that is independent of the traditional economies of scale rationale. We show that this durable goods subsidization problem is due solely to the public firm's potential commitment problems with buyers.
The Revenue Responsiveness of Income and Consumption Taxes in the UK
Authors: Creedy John , Gemmell Norman
Published: November 2003

This paper provides new estimates of the revenue elasticities of income and consumption taxes in the UK over the period 1989–2000. Using new analytical expressions for consumption taxes, these elasticities are estimated from information on relatively few parameters, almost all of which are readily available from published sources. Changes in consumption patterns over time, and income tax parameters, are found to be important for the magnitude of consumption tax elasticities.
Taking a Long Hard Look at Imprisonment
Authors: Reuss Anne
Published: November 2003

Abstract: This article takes a ‘look’ at prisons – why do we have them, what do people expect of them, what do they ‘do’ to people and should we have something else instead? Some of my observations have arisen from having carried out research and taught degree level sociology and social policy to maximum‐security prisoners for five years. Some of my thoughts and feelings about prisons have arisen out of long conversations held with my ‘students’ and other prison staff during that time. More lately and after teaching for a number of years in university on courses on crime, deviance and penal institutions, I have firmly decided that, in order to reserve and retain some semblance of sanity, the safest thing to do is ‘observe and comment when asked’. The following is an article, therefore, that I was invited to present to the Association of Visiting Committees for Scottish Penal Establishments at their annual 2002 conference in Dundee on ‘Prisons: Value for Money or are there Alternatives?’.
Prostitutes' Clients, Ken Livingstone and a New Trojan Horse
Authors: Brooks‐Gordon Belinda , Gelsthorpe Loraine
Published: November 2003

Abstract: Recent legislation has taken a tough line with the clients of prostitutes. This is interesting given that such approaches have been resisted in the past by, amongst others, civil liberties groups and Members of Parliament. In this article we take a look at the legal and social history of prostitutes' clients. We examine the shifting socio‐legal definitions of men who purchase sex from women, in order to make apparent the influences that underpin the recent legislation. Our discussion concludes with comment on the state of contemporary debate following the Home Office Review, Setting the Boundaries, as we look to the Sexual Offences Bill 2003, and with it the possibility of the creation of a new Trojan horse.
Prison Education in Northern Ireland: Learning from our Paramilitary Past
Authors: Irwin Tracy
Published: November 2003

Abstract:Northern Ireland has historically battled with a varied and unique prison population. The release of ‘paramilitary prisoners’ under the Good Friday Agreement has forced prison policy makers to evaluate critically all their programmes including educational provision. This article argues that we should not simply shut the door on our paramilitary past, but should extract exemplary practices developed throughout those turbulent times, assimilating them within a contemporary educational model. This article aims to explore the historical ‘paramilitary’ educational paradigm suggesting ways in which the past can inform current developments, suitable for the changing prison population now resident within our custodial establishments.
Comparative Efficacy of Eletriptan and Zolmitriptan in the Acute Treatment of Migraine
Authors: Steiner TJ , Diener H-C , MacGregor EA , Schoenen J , Muirhead N , Sikes CR
Published: November 2003

Eletriptan 40 mg and 80 mg have shown greater efficacy in acute migraine than oral sumatriptan 100 mg and naratriptan 2.5 mg. This study continues the systematic series of active comparator trials in the eletriptan clinical development programme. In a multicentre double-blind, double-dummy, parallel-groups trial, 1587 outpatients with migraine by IHS criteria were randomised in a 3 : 3 : 3 : 1 ratio to eletriptan 80 mg, eletriptan 40 mg, zolmitriptan 2.5 mg or placebo. Of these, 1312 treated a single migraine attack and recorded baseline and outcome data to be included in the intention-to-treat population. The primary analysis was between eletriptan 80 mg and zolmitriptan. For the primary efficacy end-point of 2-h headache response, rates were 74% on eletriptan 80 mg, 64% on eletriptan 40 mg, 60% on zolmitriptan ( P < 0.0001 vs. eletriptan 80 mg) and 22% on placebo ( P < 0.0001 vs. all active treatments). Eletriptan 80 mg was superior to zolmitriptan on all secondary end-points at 1, 2 and 24 h, in most cases with statistical significance. Eletriptan 40 mg had similar efficacy to zolmitriptan 2.5 mg in earlier end-points, and significantly ( P < 0.05) lower recurrence rate and need for rescue medication over 24 h. All treatments were well tolerated; 30-42% of patients on active treatments and 40% on placebo reported all-causality adverse events that were mostly mild and transient. On patients' global ratings of treatment, both eletriptan doses scored significantly better than zolmitriptan.
Ice-Cream Headache - A Large Survey of 8359 Adolescents
Authors: Fuh Jong-Ling , Wang Shuu-Jiun , Lu Shiang-Ru , Juang Kai-Dih
Published: November 2003

We conducted a self-administered questionnaire to investigate ice-cream headache in school adolescents aged 13-15 in Taiwan. The target population was 8789 students in 6 public junior high schools. A total of 8359 students completed the questionnaire (response rate 95.1%). The prevalence of ice-cream headache was 40.6%. It was significantly higher in boys than in girls, and increased with grade. Students with migraine had a higher frequency of ice-cream headache compared with the students without migraine (55.2% vs. 39.6%, P < 0.0001). The prevalence of ice-cream headache increased among students with more migrainous features. Approximately one third of students decreased their intake of ice cream, or abstained completely, especially the younger students. Our study suggests icecream headache is very common in Taiwanese adolescents, and it is more common in students who experienced migraine.
Out-Patient Detoxification in Chronic Migraine: Comparison of Strategies
Authors: Krymchantowski AV , Moreira PF
Published: November 2003

Chronic migraine (CM) patients frequently overuse symptomatic medications (SM). These medications may create a cycle of rebound, worsening of headache and withdrawal symptoms that perpetuate the headache itself. In addition, the overuse of such substances is believed to counteract the efficacy of preventive treatments. We conducted a prospective randomized open-label trial comparing approaches to out-patient management in 150 CM patients (125 women, 25 men; ages 18-80 years, mean 40.3 ± 13.8) with overuse of SM. In each group, 50 patients received education and orientation and were then abruptly withdrawn from all SM. Immediately following withdrawal, the first group took prednisone (60 mg/day 2 days, 40 mg/day 2 days and 20 mg/day 2 days) for 6 days, the second group did not have any regular medications to take and the third group took naratriptan (2.5 mg twice a day) during this initial period. All patients had similar profiles of headache characteristics and consumption (quality and quantity) of SM before initiation of the treatment, but most were not severe headache sufferers, heavy SM overusers or were overusing opioids. After 5 weeks the headache frequency and intensity, the prevalence and frequency of withdrawal symptoms and consumption of rescue medications during the first 6 days were compared between groups. In addition, adherence to treatment (who returned or not and for which reasons, between groups) and headache frequency, week by week, among the groups of patients were also compared. Forty-four (88%) patients from the prednisone group, 41 (82%) from the ‘nothing’ group and 35 (70%) from the naratriptan group adhered to the treatment and returned. The were no differences between groups with regard to treatment adherence ( P = 0.072), headache frequency as well as intensity ( P = 0.311) and decreasing of days with headache after 5 weeks and weekly ( P = 0.275). However, the incidence of withdrawal symptoms and consumption of rescue drugs was higher among the patients who did not take regular medications during the first 6 days ( P = 0.0001 and P = 0.006). We concluded that CM patients with moderate overuse of SM other than opioids may be detoxified on an out-patient basis regardless of the strategy adopted with regard to the use of regular drugs during the initial days of withdrawal, but prednisone and naratriptan may be useful for reducing withdrawal symptoms and rescue medication consumption. Further controlled studies are necessary to confirm these observations.
The contractile response of the mesenteric resistance arteries to prostaglandin F2α; effects of simultaneous hyperlipemia–diabetes
Authors: Georgescu Adriana , Popov Doina
Published: November 2003

The effect of hyperlipemia associated with diabetes on the contractility of resistance arteries to prostaglandin F2α (PGF2α) was investigated employing 4 weeks simultaneously hyperlipemic–diabetic (HD), hyperlipemic (H), diabetic (D) and normal hamsters (controls, C). The isometric force produced by explanted arteries in the presence of 10−8 to 10−5 m PGF2α was recorded by the myograph technique. The results showed that compared with controls, the contractile response to 10−5 m PGF2α was approx. 2 fold increased in HD group, and approx. 1.75 and 1.62‐fold enhanced in H and D groups, respectively. Activation of protein kinase C with 10−6 m phorbol 12‐myristate 13‐acetate increased the contractility to PGF2α in all groups and particularly in HD hamsters (approx. 10.16‐fold). Inhibition of cyclooxygenase by indomethacin increased approx. 1.81‐fold the arterial contractility to PGF2α in C group, whereas in H, D and HD hamsters had no effect. Blockage of Ca2+‐activated K+‐channels with 10−3 m tetraethylammonium augmented the contraction to PGF2α approx. 6.43‐fold in C group, and at significantly lower levels in H, D and HD groups, i.e. approx. 3.84, 3.72 and 3.33‐fold, respectively. The results validate two conclusions: (i) simultaneous insult of hyperlipemia‐hyperglycemia is associated with the highest contractility of the resistance arteries to PGF2α; the highest circulating glucose and cholesterol levels, and the enhancement in the protein kinase C pathway underlay the augmented contractility; (ii) no matter the pathology induced (hyperlipemia, diabetes or both simultaneously) a common dysfunctional response to PGF2α was installed; this consists in a reduced effect of cyclooxygenase inhibition, and a altered activity of Ca2+ dependent K+ channels.
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

Glyceryl 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

Alzheimer'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.
The Effect of Food and Ice Cream on the Adsorption Capacity of Paracetamol to High Surface Activated Charcoal: In vitro Studies
Authors: Hoegberg Lotte Christine Groth , Angelo Helle Riis , Christophersen Anne Bolette , Christensen Hanne Rolighed
Published: November 2003

Abstract: The effect of added food mixture (as if food was present in the stomach of an intoxicated patient) or 4 different types of ice cream (added as a flavouring and lubricating agent) on the adsorption of paracetamol (acetaminophen) to 2 formulations of activated charcoal was determined in vitro and compared with results from previous investigations showing a maximum adsorption capacity to the two activated charcoal‐water slurries at about 0.62–0.72 g paracetamol/g activated charcoal. Activated charcoal (Carbomix® or Norit Ready‐To‐Use), simulated gastric (pH 1.2) or intestinal (pH 7.2) fluid, and paracetamol were mixed with either food mixture or ice cream followed by one hr incubation. The maximum adsorption capacity of paracetamol to activated charcoal was calculated using Langmuirs adsorption isotherm. Paracetamol concentration was analyzed using high pressure liquid chromatography. In the presence of food, the paracetamol adsorption capacity of the 2 activated charcoals was reduced by max. 19% (P<0.05) for Carbomix® and by max. 11% (P<0.05) for Norit Ready‐to‐use compared to control without food (Hoegberg et al. 2002). Depending on which type of ice cream was mixed with the charcoal, the reductions compared to control (Hoegberg et al. 2002) varied between 11% and 26%. Even though a reduction in drug adsorption to activated charcoal was observed when food mixture or ice cream was added, the remaining adsorption capacity of both types of activated charcoal theoretically was still able to provide an effective gastrointestinal decontamination.
From genomics to proteomics: new directions in molecular neuropsychiatry
Authors: Eisener Amy F. , Pato Carlos N. , Dewan Mantosh , Pato Michele T.
Published: November 2003

Neuropsychiatry, like many other biomedical sciences, has been revolutionized by the advances in genomic technologies over the years. The advent of PCR (polymerase chain reaction) and the sequencing of the human genome have provided invaluable insights into the molecular genetics of the various psychiatric disorders through the study of candidate genes and linkage analyses. However, biological phenotype is dictated by protein expression, which has been shown to stray from the genetic blueprint designated by the genome. Consequently, the field of proteomics has recently emerged as a powerful means of exploring protein structure, function, and expression patterns. The ability to study disease at the gene and protein levels presents a tremendous opportunity for neuropsychiatric research, particularly in terms of the potential for developing therapeutic agents for novel protein targets.
Application of Information Visualization Techniques to the Design of a Mathematical Mindtool: A Usability Study
Authors: Sedig Kamran , Rowhani Sonja , Morey Jim , Liang Hai-Ning
Published: November 2003

One of the goals of information visualization is to support human thinking through the use of external visual aids. Mathematical mindtools can act as visual cognitive aids to enhance thinking and reasoning about mathematical objects and concepts. Although some mathematical mindtools incorporate information visualization techniques, the systematic use of these techniques in the design of these tools and their effect on users’ thinking and reasoning need to be investigated. A mathematical mindtool called PARSE (Platonic-Archimedean Solids Explorer) is presented in this paper. PARSE is intended to support the exploration and learning of a subset of geometric shapes. The mathematical objects and concepts embedded in PARSE have been enhanced using information visualization techniques. A usability study of PARSE and its information visualization techniques have been conducted and reported. The study shows that information visualization techniques enhance and support learning and exploration of mathematical concepts. The findings reported in this paper suggest that mathematical mindtools provide a fertile ground for investigating different information visualization techniques and their effectiveness in supporting learning tasks.
Using the Self-Organizing Map as a Visualization Tool in Financial Benchmarking
Authors: Eklund Tomas , Back Barbro , Vanharanta Hannu , Visa Ari
Published: November 2003

In this paper, we illustrate the use of the self-organizing map technique for financial performance analysis and benchmarking. We build a database of financial ratios indicating the performance of 91 international pulp and paper companies for the time period 1995–2001. We then use the self-organizing map technique to analyze and benchmark the performance of the five largest pulp and paper companies in the world. The results of the study indicate that by using the self-organizing maps, we are able to structure, analyze, and visualize large amounts of multidimensional financial data in a meaningful manner.
Co-Citation Count vs Correlation for Influence Network Visualization
Authors: Noel Steven , Chu Chee-Hung Henry , Raghavan Vijay
Published: November 2003

Visualization of author or document influence networks as a two-dimensional image can provide key insights into the direct influence of authors or documents on each other in a document collection. The influence network is constructed based on the minimum spanning tree, in which the nodes are documents and an edge is the most direct influence between two documents. Influence network visualizations have typically relied on co-citation correlation as a measure of document similarity. That is, the similarity between two documents is computed by correlating the sets of citations to each of the two documents. In a different line of research, co-citation count (the number of times two documents are jointly cited) has been applied as a document similarity measure. In this work, we demonstrate the impact of each of these similarity measures on the document influence network. We provide examples, and analyze the significance of the choice of similarity measure. We show that correlation-based visualizations exhibit chaining effects (low average vertex degree), a manifestation of multiple minor variations in document similarities. These minor similarity variations are absent in count-based visualizations. The result is that count-based influence network visualizations are more consistent with the intuitive expectation of authoritative documents being hubs that directly influence large numbers of documents.
Social Diffusion Patterns in Three-Dimensional Virtual Worlds
Authors: Börner Katy , Penumarthy Shashikant
Published: November 2003

This paper presents a visualization tool set that can be used to visualize the evolution of three-dimensional (3D) virtual environments, the distribution of their virtual inhabitants over time and space, the formation and diffusion of groups, the influence of group leaders, and the environmental and social influences on chat and diffusion patterns for small (1 – 100 participants) but also rather large user groups (more than 100 participants). The techniques are applied to analyze and visualize data recorded during events in virtual worlds, as well as simulated data, but are also applicable to real-world data. Resulting visualizations can and have been used to ease social navigation in 3D virtual worlds, help evaluate and optimize the design of virtual worlds, and provide a means to study the communities evolving in virtual worlds. The visualizations are particularly valuable for analyzing events that are spread out in time and/or space or events that involve a very large number of participants. The paper reviews and builds upon research in information visualization, scientific visualization, geography, architecture, and social science. It discusses intended user groups and their tasks and how the proposed techniques support those tasks. Three dimensional virtual world technologies are briefly described before the visualization tool set is explained in detail together with sample applications. The paper concludes with a discussion of results and an outlook for future work.
PDB file parser and structure class implemented in Python
Authors: Hamelryck Thomas , Manderick Bernard
Published: November 2003

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

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

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

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

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

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

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

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.