bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of selected risk factors on quality-adjusted life expectancy in Denmark
Authors: Brønnum-Hansen Henrik , Juel Knud , Davidsen Michael , Sørensen Jan
Published: September 2007

Aims: The construct quality-adjusted life years (QALYs) combines mortality and overall health status and can be used to quantify the impact of risk factors on population health. The purpose of the study was to estimate the impact of tobacco smoking, high alcohol consumption, physical inactivity, and overweight on QALYs. Methods: Life tables for each level of exposure to the risk factor were constructed mainly on the basis of the Danish National Cohort Study. QALYs were estimated for exposed and unexposed by Sullivan's method, by combining life tables, EQ-5D self-classified health status from the Danish Health Survey 2000, and Danish EQ-5D values. Results: The quality-adjusted life expectancy of 25-yearolds was 10—11 QALYs shorter for heavy smokers than for those who never smoke. The difference in life expectancy was 9— 10 years. Men and women with high alcohol consumption could expect to lose about 5 and 3 QALYs, respectively. Sedentary persons could expect to have about 7 fewer QALYs than physically active persons. Obesity shortened QALYs by almost 3 for men and 6 for women. Conclusions: Smoking, high alcohol consumption, physical inactivity, and obesity strongly reduce life expectancy and health-related quality of life. These results could be used by health policy-makers to evaluate the potential gains in public health due to interventions against these risk factors, when the prevalence of exposure to the risk factor is available.
Preschool children's sickness absenteeism from Norwegian regular and outdoor day care centres: A comparative study
Authors: Moen Kari H. , Bakke Hjørdis K. , Bakke Øyvind , Fors Egil A.
Published: September 2007

Aims: To examine whether there are any differences in sickness absenteeism between children in outdoor day care centres and regular day care centres and also to investigate whether other variables predict sickness absenteeism. Methods: Data on sickness absence during a 4-week period together with several explanatory variables of 531 children in 32 regular and 37 outdoor day care centres were collected and included in the analysis. The data were analysed by generalized linear modelling. Results: The overall frequency of sickness absence was 5.1%. There was no general significant difference between sickness absenteeism in regular and outdoor day care centres. Of the other possible explanatory variables only two were found to contribute significantly: age, with a negative relationship, and the interaction effect of a child with a chronic disease or disability going to an outdoor day care centre, with a positive relationship. Conclusions: The present study indicates that sickness absenteeism of a child without a chronic disease or disability is not affected by whether the child attends a regular or an outdoor day care centre. There seem to be no health benefits for children with chronic diseases or disabilities to attend outdoor day care centres — there is in fact evidence that sickness absence for those children is higher in outdoor centres.
Patients retrieving additional information via the Internet: A trend analysis in a Swedish population, 2000—05
Authors: Rahmqvist Mikael , Bara Ana-Claudia
Published: September 2007

Aims: To examine the trends over five years for patients' seeking online additional health information about their disease/ health problem to what the doctor has been giving, and investigate any differences in information-seeking behaviour according to age, gender, self-perceived health status, living area, and type of medical encounter. Methods: Data from three independent surveys conducted in 2000, 2002, and 2005 of a population with a recent experience of outpatient care[n]typesetter: please remove blue shading here and elsewhere[/n], including 24,800 respondents aged between 20 and 95, were analysed in a trend analysis and a logistic regression regarding background factors that may influence the seeking behaviour. Results: During the study period, there was a significant increase in Internet use in most age groups. The total use among men 20—95 years old increased from 7% in 2000 to 18% in 2005 and from 9% to 25% for women respectively. The predictors for using the Internet as a source of information were: age, gender, self-perceived health status, living area, and the type of medical encounter (first or repeated). In 2005, women aged 20—49 used the Internet as a source to a significantly greater extent than men, even when all background factors were controlled for (OR 1.46 and CI 1.21—1.77). Conclusions: Swedish patients, especially the young and middle-aged, are to a substantial degree using the Internet to gather additional information on their disease. The benefits of this increase include more informed patients; however, there are inherent quality issues that require strategies for ensuring public access to high-quality health information online.
Prevalence of hearing loss among 18-year-old Swedish men during the period 1971—1995
Authors: Muhr Per , Rasmussen Finn , Rosenhall Ulf
Published: September 2007

Aims: To study the hearing of 18-year-old men by using screening audiograms obtained at military conscription. Methods: The study group comprised 301,873 Swedish men belonging to six age cohorts born from 1953 to 1977 who had been screened at age 18 years from 1971 to 1995. The prevalence of mild to moderate hearing loss was investigated. Results: Of the entire study group, 13.1% had elevation of one or more pure tone thresholds. In most cases, 11.9%, the elevation was situated in the high-frequency region. High-frequency hearing loss was more common in the left ear (7.5%) than in the right ear (6.2%). The prevalence of hearing loss decreased during the period 1971 to 1981 from 15.7% to 8.3%. During the last part of the study period, 1986 to 1995, the prevalence increased from 9.8% to 16.3%. The increase included mild to moderate degrees of hearing loss with thresholds below 35 dB HL. The prevalence of threshold elevations was highest in sparsely populated areas of Sweden and lowest in large, metropolitan areas of Sweden from 1971 to 1986. During the last part of the study period the geographical differences decreased or disappeared. Conclusions: The total prevalence of hearing loss was in accordance with other reports. The frequency 6 kHz was most affected by threshold elevations. The prevalence of hearing loss decreased in the first part of the study period, and increased at the end of the study period. Hearing loss was most commonly seen in rural areas.
Social predictors of non-attendance in an urban mammographic screening programme: A multilevel analysis
Authors: Zackrisson Sophia , Lindström Martin , Moghaddassi Mahnaz , Andersson Ingvar , Janzon Lars
Published: September 2007

Objective: Rate of non-attendance following invitation for breast cancer screening is related to several socioeconomic conditions. To what extent this reflects differences with regard to individual and environmental circumstances, respectively, has received little attention. The purpose of this study was to investigate the effect of individual socioeconomic and area-level determinants on variations in non-attendance among geographic areas in an urban mammographic service screening programme. Methods: The study population consisted of 32,119 women invited for mammographic screening in 1990—93, residing in 97 neighbourhoods in the city of Malmö in Sweden. The influence of the individual factors age, marital status, education, housing accommodation, household income, and area-level circumstances, e.g. rate of migration and rate of being gainfully employed, on the rate of non-attendance was assessed by multilevel analysis. Results: Area rates of non-attendance ranged from 18% to 63%. Of the total variability in non-attendance, 4.3% was between neighbourhoods. This effect was significantly reduced when adjusting for the individual factors. The area-level factors, migration, and rate of being gainfully employed reduced and almost erased the neighbourhood variance in non-attendance. Conclusion: In addition to individual socioeconomic factors, area-level factors seem to be important determinants of neighbourhood rates of non-attendance in an urban mammographic screening programme. In a public health perspective neighbourhoods may be targeted in order to affect the problem of non-attendance in mammographic screening.
The NORPEQ patient experiences questionnaire: Data quality, internal consistency and validity following a Norwegian inpatient survey
Authors: Oltedal Sigve , Garratt Andrew , Bjertnæs Øyvind , Bjørnsdottìr Margrét , Freil Morten , Sachs Magna
Published: September 2007

Aims: This article describes the development of a questionnaire designed for comparisons of patient experiences of hospital care within the Nordic countries. The results of testing for data quality, reliability, and validity are presented following a Norwegian survey. Methods: Following a literature review and consultation within an expert group six items were developed measuring patient experiences together with two items assessing global satisfaction and perception of incorrect treatment. The questions were included in a questionnaire that was mailed to 500 patients randomly selected from patients receiving inpatient treatment at a large university hospital in Norway. Principal component analysis was used to assess dimensionality. Reliability was assessed by the internal consistency and test—retest methods. Construct validity was assessed by the scale's correlation with variables known to be related to patient experiences. Results: A total of 244 (48.8%) patients responded. Levels of missing data ranged from 0.4% to 2.5%. The six items in the questionnaire that measured important aspects of patient experiences with the services contributed to a single scale with item-total correlations in the range 0.59—0.71 and a Cronbach's alpha of 0.85. The test—retest intraclass correlation was 0.88. Conclusions: The NORPEQ is a brief measure of patient experiences that covers important aspects of the healthcare encounter. It shows good evidence of reliability and validity and is relatively easy to apply alongside existing national surveys.
Urban—rural differences in BMI, overweight and obesity in Norway (1990 and 2001)
Authors: Svensson Elisabeth , Reas Deborah L. , Sandanger Inger , Nygård Jan F.
Published: September 2007

Aim: The aim of this study was to examine body mass index and the prevalence of overweight and obesity in 1990 and 2001 in Oslo and Lofoten, Norway. Methods: A randomly selected study population of 1,924 individuals (OsLof) underwent a structured personal interview in 1990. In 2001, 1,629 individuals underwent the same interview. These samples were analysed as two cross-sectional datasets. Results: Overall mean BMI in 1990 was 24.7 for men and 22.9 for women, increasing significantly in 2001 to 26.1 and 24.6, respectively. In 1990, 37% of men and 20% of women were overweight, while 5% of men and 4% of women were obese. The corresponding figures for 2001 were 48% and 27% for overweight, and 12% and 11% for obesity, respectively. Discussion: The greatest increases in average BMI occurred for the youngest (18—34 years) for both genders and geographic regions. In 1990, urban—rural differences existed for mean BMI and proportion overweight for both genders, although geographic differences persisted only for women 10 years later.
Functional connections and pathways of coenzyme Q10‐inducible genes: An in‐silico study
Authors: Döring Frank , Schmelzer Constance , Lindner Inka , Vock Christina , Fujii Kenji
Published: September 2007

Coenzyme Q10 (CoQ10, ubiquinone) is an essential cofactor in the electron transport chain, serves as a potent antioxidant in mitochondria and lipid membranes, and is often used as a dietary supplement for a number of diseases including cardiovascular diseases. Recently, we obtained evidence that CoQ10 (Kaneka Q10™) affects the expression of hundreds of human genes. To decipher the functional and regulatory connections of these genes, a literature search combined with transcription factor binding site analysis was performed using Genomatix BiblioSphere and MatInspector. This in‐silico analysis revealed 17 CoQ10‐inducible genes which are functionally connected by signalling pathways of G‐protein coupled receptors, JAK/STAT, integrin, and beta‐arrestin. Promoter analysis of these CoQ10‐inducible genes showed one group of NFκ B‐regulated genes, namely IL5, thrombin, vitronectin receptor and C‐reactive protein (CRP). Furthermore, a common promoter framework containing binding sites of the transcription factor families EVI1, HOXF, HOXC, and CLOX was identified in the promoters of IL5, CRP, and vitronectin receptor. The identified CoQ10‐inducible genes and pathways play an important role in inflammatory response. Since these effects are based on an in‐vitro study, the effect of CoQ10 on vascular health in vivo needs to be addressed in further animal and/or human intervention studies. IUBMB Life, 59: 628‐633, 2007
Implication of PKC in the seasonal variation of the immune response of the hemocytes of Mytilus galloprovincialis Lmk. and its role in interleukin‐2‐induced nitric oxide synthesis
Authors: Novas Ana , Barcia Ramiro , Ramos‐Martínez Juan Ignacio
Published: September 2007

The hemocytes are the cells responsible for the immune response in marine mollusks. The role of NO in processes related to the activation of the hemocytes has turned out evident over the late years. In the case of the mussel Mytilus galloprovincialis Lmk., hemocyte NO basal production varies throughout the year, showing a maximum in summer and a minimum in winter. IL‐2 reverts the low winter NO basal production through a process mediated by cAMP‐dependent protein kinase and by an apparent side effect of protein kinase C. The seasonal variation of NO production in the presence of the PKC inhibitor bisindolylmaleimide (BSM) allows suggesting a model in which PKC would modulate the activity of the enzymes responsible for nitric oxide production. IUBMB Life, 59: 659‐663, 2007
Identification of six new box C/D snoRNA gene clusters from rice
Authors: Li Wei , Jiang Ge , Zeng Dabo , Jin Youxin
Published: September 2007

Here we have identified 18 different box C/D snoRNAs encoded in six new gene clusters by the screening of Oryza sativa (rice) genome sequences using a computer program that we have designed to search for non‐canonical box C and D sequences. Among this snoRNA collection, five are homologues of snoRNAs previously reported in other plants. One snoRNA is implicated to guide methylation at a corresponding site also modified in yeast rRNA but not in any other plants species yet examined. The other 12 snoRNAs are implicated in guiding 12 completely novel rRNA 2′‐O‐ribose methylation sites. We have verified the methylation of these rRNA sites by dNTP‐concentration dependent primer extension assay. The expression of all snoRNAs reported here was experimentally confirmed by primer extension assay. Polycistronic precursor transcripts from the gene clusters have been demonstrated by RT‐PCR. Thus it is highly likely that each of the rice snoRNA gene clusters identified here is transcribed in a polycistronic way, regardless of whether or not they are encoded within introns. This indicates that the mode of polycistronic expression of snoRNA clusters is widespread in rice, as is the case in Arabidopsis thaliana. IUBMB Life, 59: 664‐674, 2007
Sulfation of nitrotyrosine: Biochemistry and functional implications
Authors: Liu Ming‐Cheh , Yasuda Shin , Idell Steven
Published: September 2007

Nitration of tyrosine, in both protein‐bound form and free amino acid form, can readily occur in cells under oxidative/nitrative stress. In addition to serving as a biomarker of oxidative/nitrative stress, elevated levels of nitrotyrosine have been shown to cause DNA damage or trigger apoptosis. An important issue is whether the human body is equipped with mechanisms to counteract the potentially harmful effects of nitrotyrosine. Sulfate conjugation, as mediated by the cytosolic sulfotransferases (SULTs), is widely used for the biotransformation and disposal of a variety of drugs and other xenobiotics, as well as endogenous thyroid/steroid hormones and catecholamine neurotransmitters. Recent studies have revealed that the sulfation of nitrotyrosine occurs in cells under oxidative/nitrative stress, and have pinpointed the SULT1A3 as the responsible SULT enzyme. In this review, we summarized the available information concerning the biochemistry of nitrotyrosine sulfation and the effects of genetic polymorphisms on the nitrotyrosine sulfating activity of SULT1A3. Functional implications of the sulfation of nitrotyrosine are discussed. IUBMB Life, 622‐627, 2007
Comparative RNomics and Modomics in Mollicutes: Prediction of Gene Function and Evolutionary Implications
Authors: de Crécy‐Lagard Valérie , Marck Christian , Brochier‐Armanet Céline , Grosjean Henri
Published: September 2007

Stable RNAs are central to protein synthesis. Ribosomal RNAs make the core of the ribosome and provide the scaffold for accurate translation of mRNAs by a set of tRNA molecules each carrying an activated amino acid. To fulfill these important cellular functions, both rRNA and tRNA molecules require more than the four canonical bases and have recruited enzymes that introduce numerous modifications on nucleosides. Mollicutes are parasitic unicellular bacteria that originated from gram‐positive bacteria by considerably reducing their genome, reaching a minimal size of 480 kb in Mycoplasma genitalium. By analyzing the complete set of tRNA isoacceptors (tRNomics) and predicting the tRNA/rRNA modification enzymes (Modomics) among all sequenced Mollicutes (15 in all), our goal is to predict the minimal set of RNA modifications needed to sustain accurate translation of the cell's genetic information. Building on the known phylogenetic relationship of the 15 Mollicutes analyzed, we demonstrate that the solutions to reducing the RNA component of the translation apparatus vary from one Mollicute to the other and often rely on co‐evolution of specific tRNA isoacceptors and RNA modification enzymes. This analysis also reveals that only a few modification enzymes acting on nucleotides of the anticodon loop in tRNA (the wobble position 34 as well as in position 37, 3′‐adjacent to anticodon) and of the peptidyltransferase center of 23S rRNA appear to be absolutely essential and resistant to gene loss during the evolutionary process of genome reduction. IUBMB Life, 634‐658, 2007
Identification and biochemical properties of Dps (starvation‐induced DNA binding protein) from cyanobacterium Anabaena sp. PCC 7120
Authors: Wei Xiong , Mingjia He , Xiufeng Li , Yang Gao , Qingyu Wu
Published: September 2007

DNA‐binding Proteins from Starved cells (Dps) are anti‐stress iron proteins preserving bacteria from oxidative damage. Based on sequence alignment, a 564‐bp open reading frame (all1173) encoding product in Anabaena sp. PCC 7120 shared high similarity with Dps family proteins. RT‐PCR showed all1173 is active at transcriptional level in Anabaena sp. PCC 7120 cells. We accordingly cloned the all1173 into prokaryotic expression system, purified the corresponding recombinant protein (Dps1173) and characterized its properties in vitro. According to CD spectrum and non‐denaturing electrophoresis assays, recombinant Dps1173 was alpha helix riched, and was likely to form dodecametric oligomer under native conditions. Fluorescence titration experiment revealed two major iron binding sites within Dps1173 monomer, indicating its potential ferroxidase activity. Although phenomena of direct DNA binding was not observed in Electrophoretic mobility shift assay, Dps1173 could also protect DNA from H2O2 stress for its iron scavenging capacity. This is the first description of Dps from heterocystous cyanobacterium Anabaena sp. PCC 7120. IUBMB Life, 59: 675‐681, 2007
Marsupial oocytes, fertilization and embryonic development can provide useful tools to study developmental mechanisms
Authors: Selwood Lynne
Published: September 2007

An analysis of several features of marsupial oocytes and developmental stages from the zygote to the neonate shows the advantages of studying these to answer questions about mammalian development in general. Marsupials make good model systems providing that species have well established breeding and husbandry protocols, a detailed time table of embryonic development associated with appropriate monitoring to collect desired stages and an induced ovulation protocol to allow collection of normal oocytes and developmental stages. One of the specific features of marsupial development that would provide further insight into problems in mammalian development is distinct oocyte and/or zygote polarity. Additionally, because the conceptus is transparent, cell‐cell associations can be studied until well after the hypoblast is formed. These combined features mean that lineage allocation and axis formation can be more easily studied and related to oocyte/zygote polarity and the order of cell division in these conceptuses. Another feature is the ability to collect normal unattached embryonic and fetal stages in some species and to culture conceptuses from the primitive streak stage to within a few hours of birth. This ability means that stages of organogenesis in most organ systems are readily accessible without the complications of implantation. IUBMB Life, 59: 617‐621, 2007
Developing a Virtual Library for 44,000 chemists
Authors: LEES Nigel
Published: September 2007

This article describes how the Royal Society of Chemistry's library is making the transition from being a largely traditional print‐based library to one that offers remote‐access resources to its widespread membership. Key to its strategy is working with publishers and other content providers in a proactive and innovative way. Examples, case studies and difficulties faced are outlined alongside some of the solutions employed to facilitate the delivery of content.
Fighting plagiarism and IPR violation: why is it so important?
Authors: KULATHURAMAIYER Narayanan , MAURER Hermann
Published: September 2007

Plagiarism and intellectual property rights (IPR) violations have become a serious concern for many institutions and organizations. The revolutionary development of the Web presents numerous opportunities for such infringements to become even more widespread. This situation creates the risk of introducing a ‘culture of mediocrity'. This paper discusses these issues and proposes means of addressing the concerns by applying viable technological solutions.
Moving out of Oldenbourg's long shadow: what is the future for society publishing?
Authors: ARMBRUSTER Chris
Published: September 2007

The Internet and the rise of e‐Science alter the conditions for scholarly communication. In signing declarations against open access mandates, society publishers indicate that they feel most threatened by the emergence of institutional repositories and the self‐archiving mandates that these make possible. More attention should be paid to the impact of e‐Science, the rise of Internet‐based guild publishers, and the entrance of players from the new economy. Society journals should stop aspiring to such functions as registration and archiving and should shed electronic dissemination, while enhancing certification and investing in (new) navigation services.
Open access developments in France: the HAL Open Archives System
Authors: BARUCH Pierre
Published: September 2007

This article presents an overview of open access publishing and open access archiving in France. In natural sciences, most articles are published in international journals; authors must therefore comply with the policies of their publishers, irrespective of their nationality. For humanities and social sciences, where publication tends to be distributed among many small journals, portals have been created to provide electronic publishing, with varied access policies. Open archives repositories have been in existence in France since 2001; from 2006, a proactive policy led the main research agencies and universities to coordinate their actions towards a common archiving platform, HAL (Hyper Articles on Line), operated by CNRS (Centre National pour la Recherche Scientifique), with individual portals, either thematic or institutional. HAL stores now the majority of open access records – presently some 10–15% of French output – and is growing almost exponentially.
Launching an online‐only journal
Authors: STALKER Matt
Published: September 2007

In May 2006, the Institution of Chemical Engineers (IChemE) launched its first exclusively online journal, Education for Chemical Engineers (http://www.icheme.org/ece). The author describes the editorial and marketing strategy behind the successful launch of the new title and the challenges facing a publisher when launching an ‘online‐only’ title. The article discusses how IChemE's established presence in the chemical engineering community benefited the new journal's launch and concludes with a list of key points to remember when launching a new product – with particular relevance to online titles.
Mapping the journal publishing landscape: how much do we know?
Authors: MORRIS Sally
Published: September 2007

In debates about journals, their publishers and the future of both, it is important to be clear about what we are discussing. In this article, the sparse existing literature is surveyed, and original sources examined to provide further detail. The membership lists of six leading publishing associations, and the websites of their members, were also studied. More than half of all peer‐reviewed journals in Ulrich's are published by or on behalf of/in association with nonprofit organizations. Other than the top few commercial publishers, there is little difference in size between the two types; the ‘long tail’ of publishers are small and therefore vulnerable, and yet most are not represented by any trade association. The majority of journals come from the USA or the UK. Nonprofits launch fewer new journals, but are also less likely to close journals. The quality advantage of nonprofit journals may be reducing, but nonprofit journals still predominate among the most highly cited journals.
Rotationally Resolved Vacuum Ultraviolet Pulsed Field Ionization-Photoelectron Vibrational Bands for H2+ (X2g+,v+=0-18)
Authors: Chang Chao , Ng Cheuk-Yiu , Stimson S. , Evans M. , Hsu C. W.
Published: September 2007

We have obtained a rotationally resolved vacuum ultraviolet pulsed field ionization-photoelectron (VUV-PFI-PE) spectrum of H2 in the energy range of 15.30-18.09 eV, covering the ionization transitions {H2}+(X2g+, v+=0-18, N+=0-5)H2(X1g+, v=0, J=0-4). The assignment of the rotational transitions resolved in the VUV-PFI-PE vibrational bands for {H2}+(X2g+, v+=0-18) and their simulation using the Buckingham-Orr-Sichel (BOS) model are presented. Only the N=N+ - J=0 and 2 rotational branches are observed in the VUV-PFI-PE spectrum of H2. However, the vibrational band is increasingly dominated by the N=0 rotational branch as v+ is increased. The BOS simulation reveals that the perturbation of VUV-PFI-PE rotational line intensities by near-resonance autoionizing Rydberg states is minor at v+ 6 and decreases as v+ is increased. Thus, the rotationally resolved PFI-PE bands for {H2}+(v+ 6) presented here provide reliable estimates of state-to-state cross sections for direct photoionization of H2, while the rotationally resolved PFI-PE bands for {H2}+(v+ 5) are useful data for fundamental understanding of the near resonance autoionizing mechanism. On the basis of the rovibrational assignment of the VUV-PFI-PE spectrum of H2, the ionization energies for the formation of {H2}+(X2g+, v+=0-18, N+=0-5) from {H2}+(X1g+, v=0, J=0-4), the vibrational constants (e, ee, !US!eye, and !US!eze), the rotational constants (Bv+, Dv+, Be, and e), and the vibrational energy spacings G(v++1/2) for {H2}+(X2g+, v+=0-18) are determined. With a significantly higher photoelectron energy resolution achieved in the present study, the precisions of these spectroscopic values are higher than those obtained in the previous photoelectron studies. As expected, the spectroscopic results for {H2}+(X2g+, v+=0-18) derived from this VUV-PFI-PE study are in excellent agreement with high-level theoretical predictions.
Time-dependent Quantum Wave Packet Study of F+HCl and F+DCl Reactions
Authors: Sun Zhi-gang , Lee Soo Y. , Zhang Dong-hui
Published: September 2007

The F+HCl and F+DCl reactions are studied by the time-dependent quantum wave packet method, using the most recent potential energy surface reported by Deskevich et al.. Total reaction probabilities for a number of initial ro-vibrational states of HCl and DCl diatomic moiety are presented in the case of total angular momentum J=0. It is found that for both reactions the initial rotational excitation of the diatomic moiety enhances greatly the reaction probabilities but this effect is more significant for F+HCl system. This is mainly due to larger rotational constant of the HCl reagent. The initial vibrational excitation of the diatomic moiety has little effect on the reactivity for both systems except shifting down the collision energy threshold. The results indicate that the reaction coordinates for these two systems are effectively along rotational freedom degree. More quantum phenomena, such as tunneling and resonance, are observed in F+HCl reaction than F+DCl reaction, and for the initial states studied, the reactivity of the later is lower. Different skewing angles of these two systems account for these isotopic differences.
Experimental Study of C2Cl3+NO2 Reaction
Authors: Xiang Tian-cheng , Liu Kun-hui , Su Hong-mei
Published: September 2007

The free radical reaction of C2Cl3 with NO2 was investigated by step-scan time-resolved FTIR (TR-FTIR) emission spectroscopy. Due to the vibrationally excited products of Cl2CO, NO, and CO, strong IR emission bands were observed with high resolution TR-FTIR spectra. Four reaction channels forming C2Cl3O+NO, CCl3CO+NO, CO+NO+CCl3, and ClCNO+Cl2CO were elucidated, respectively. Spectral fitting showed that the product CO was highly vibrationally excited with the nascent average vibrational energy of {60.2 kJ/mol}. Possible reaction mechanism via intermediates C2Cl3NO2 and C2Cl3ONO was proposed.
Experimental Observables and Macroscopic Susceptibility/Microscopic Polarizability Tensors for Third and Fourth-Order Nonlinear Spectroscopy of Ordered Molecular System
Authors: Wang Yuan , Cui Zhi-feng , Wang Hong-fei
Published: September 2007

There has been emerging needs for the quantitative polarization analysis for the Coherent Anti-stokes Raman Spectroscopy and Coherent Anti-stokes Hyper-raman Spectroscopy, as the experimental studies with coherent anti-stokes raman spectroscopy and coherent anti-stokes hyper-raman spectroscopy for the interface and membrane studies being growing. Recently we have demonstrated that orientational analysis of linear and nonlinear spectroscopy from the ordered molecular system, such as molecular interfaces and films, can be carried out with the formulation of the orientational function in simple functional forms. Applications of such formulation for the second order spectroscopy, namely, the Second Harmonic Generation and Sum Frequency Generation Vibrational Spectroscopy, have helped to understand spectral and orientational details of the molecular interfaces and films. In order to employ this formulation for the higher order coherent nonlinear spectroscopy, the detailed expressions of the experimental observables and the macroscopic susceptibility/microscopic polarizability tensors for the third and fourth-order nonlinear spectroscopy for the interface or film is presented with the rotational symmetry. General expressions for the typical third and fourth order spectroscopy, such as the Third Harmonic Generation, the degenerated coherent anti-stokes raman spectroscopy, the Fourth Harmonic Generation and the degenerated coherent anti-stokes hyper-raman spectroscopy, are presented for their future applications. The advantages and limitations of the third and fourth order spectroscopic techniques are also discussed.
Spectroscopic Characteristics of Hyperbranched Conjugated Polymers Studied by One- and Two-Photon Excitations
Authors: Yang Zhi , Li Na , Xia An-dong , He Qing-guo , Lin Hong-zhen , Bai Feng-lian
Published: September 2007

Spectroscopic properties of new hyperbranched conjugated polymers functionalized in periphery with N,N-dimethylaniline and tert-butyl-benzene as terminal groups are investigated by one- and two-photon excitations. The absorption, fluorescence excitation and emission spectra are examined in chloroform and N,N-dimethylformamide. The two-photon excitation measurements show that the new hyperbranched conjugated polymer possesses large two-photon excitation cross section which makes it a very attractive candidate for the potential application as nonlinear optical materials. As an example, the two-photon induced three-dimensional data storage is also demonstrated.
Fun&Co: identification of key functional differences in transcriptomes
Authors: Gamberoni Giacomo , Lamma Evelina , Lodo Gianluca , Marchesini Jlenia , Mascellani Nicoletta , Rossi Simona , Storari Sergio , Tagliavini Luca , Volinia Stefano
Published: September 2007

Motivation: Microarray and other genome-wide technologies allow a global view of gene expression that can be used in several ways and whose potential has not been yet fully discovered. Functional insight into expression profiles is routinely obtained by using gene ontology terms associated to the cellular genes. In this article, we deal with functional data mining from expression profiles, proposing a novel approach that studies the correlations between genes and their relations to Gene Ontology (GO). We implemented this approach in a public web-based application named Fun&Co. By using Fun&Co, the user dissects in a pair-wise manner gene expression patterns and links correlated pairs to gene ontology terms. The proof of principle for our study was accomplished by dissecting molecular pathways in muscles. In particular, we identified specific cellular pathways by comparing the three different types of muscle in a pairwise fashion. In fact, we were interested in the specific molecular mechanisms regulating the cardiovascular system (cardiomyocytes and smooth muscle cells).

Results: We applied here Fun&Co to the molecular study of cardiovascular system and the identification of the specific molecular pathways in heart, skeletal and smooth muscles (using 317 microarrays) and to reveal functional differences between the three different kinds of muscle cells.

Availability: Application is online at http://tommy.unife.it.

Contact:  s.volinia@unife.it

Supplementary information: Supplementary data are available at Bioinformatics online.
TreeSnatcher: coding trees from images
Authors: Laubach Thomas , von Haeseler Arndt
Published: September 2007

Summary: TreeSnatcher is a GUI-driven JAVA application for the semi-automatic recognition of multifurcating phylogenetic trees in pixel images. The program accepts an image file as input and analyzes the topology and the metrics of a tree depicted. The analysis is carried out in a multiple-stage process using algorithms from image analysis. In the end, TreeSnatcher produces a Newick tree code that represents the tree structure optionally including branch lengths. TreeSnatcher can process trees with 100 leaves or more in a few seconds.

Availability: TreeSnatcher was developed in JAVA under Mac OS X and is executable on UNIX/Linux, Windows and Mac OS X systems. The application and its documentation can be freely downloaded from http://www.cibiv.at/software/treesnatcher.

Contact:  arndt.von.haeseler@univie.ac.at
The high-level similarity of some disparate gene expression measures
Authors: Raghavan Nandini , De Bondt An M. I. M. , Talloen Willem , Moechars Dieder , Göhlmann Hinrich W. H. , Amaratunga Dhammika
Published: September 2007

Probe-level data from Affymetrix GeneChips can be summarized in many ways to produce probe-set level gene expression measures (GEMs). Disturbingly, the different approaches not only generate quite different measures but they could also yield very different analysis results. Here, we explore the question of how much the analysis results really do differ, first at the gene level, then at the biological process level. We demonstrate that, even though the gene level results may not necessarily match each other particularly well, as long as there is reasonably strong differentiation between the groups in the data, the various GEMs do in fact produce results that are similar to one another at the biological process level. Not only that the results are biologically relevant. As the extent of differentiation drops, the degree of concurrence weakens, although the biological relevance of findings at the biological process level may yet remain.

Contact: damaratu@prdus.jnj.com

Supplementary information: Supplementary data are available at Bioinformatics online.
Idiographica: a general-purpose web application to build idiograms on-demand for human, mouse and rat
Authors: Kin Taishin , Ono Yukiteru
Published: September 2007

Summary: We have launched a web server, which serves as a general-purpose idiogram rendering service, and allows users to generate high-quality idiograms with custom annotation according to their own genome-wide mapping/annotation data through an easy-to-use interface. The generated idiograms are suitable not only for visualizing summaries of genome-wide analysis but also for many types of presentation material including web pages, conference posters, oral presentations, etc.

Availability: Idiographica is freely available at http://www.ncrna.org/idiographica/

Contact:  kin-taishin@aist.go.jp
Inferring transcriptional regulatory networks from high-throughput data
Authors: Wang Rui-Sheng , Wang Yong , Zhang Xiang-Sun , Chen Luonan
Published: September 2007

Motivation: Inferring the relationships between transcription factors (TFs) and their targets has utmost importance for understanding the complex regulatory mechanisms in cellular systems. However, the transcription factor activities (TFAs) cannot be measured directly by standard microarray experiment owing to various post-translational modifications. In particular, cooperative mechanism and combinatorial control are common in gene regulation, e.g. TFs usually recruit other proteins cooperatively to facilitate transcriptional reaction processes.

Results: In this article, we propose a novel method for inferring transcriptional regulatory networks (TRN) from gene expression data based on protein transcription complexes and mass action law. With gene expression data and TFAs estimated from transcription complex information, the inference of TRN is formulated as a linear programming (LP) problem which has a globally optimal solution in terms of L1 norm error. The proposed method not only can easily incorporate ChIP-Chip data as prior knowledge, but also can integrate multiple gene expression datasets from different experiments simultaneously. A unique feature of our method is to take into account protein cooperation in transcription process. We tested our method by using both synthetic data and several experimental datasets in yeast. The extensive results illustrate the effectiveness of the proposed method for predicting transcription regulatory relationships between TFs with co-regulators and target genes.

Availability: The software TRNinfer is available from http://intelligent.eic.osaka-sandai.ac.jp/chenen/TRNinfer.htm

Contact:  chen@eic.osaka-sandai.ac.jp and zxs@amt.ac.cn

Supplementry information: Supplementary data are available at Bioinformatics online.
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees
Authors: Soria-Carrasco Víctor , Talavera Gerard , Igea Javier , Castresana Jose
Published: September 2007

Summary: We introduce a new phylogenetic comparison method that measures overall differences in the relative branch length and topology of two phylogenetic trees. To do this, the algorithm first scales one of the trees to have a global divergence as similar as possible to the other tree. Then, the branch length distance, which takes differences in topology and branch lengths into account, is applied to the two trees. We thus obtain the minimum branch length distance or K tree score. Two trees with very different relative branch lengths get a high K score whereas two trees that follow a similar among-lineage rate variation get a low score, regardless of the overall rates in both trees. There are several applications of the K tree score, two of which are explained here in more detail. First, this score allows the evaluation of the performance of phylogenetic algorithms, not only with respect to their topological accuracy, but also with respect to the reproduction of a given branch length variation. In a second example, we show how the K score allows the selection of orthologous genes by choosing those that better follow the overall shape of a given reference tree.

Availability:  http://molevol.ibmb.csic.es/Ktreedist.html

Contact:  jcvagr@ibmb.csic.es
The Poisson Index: a new probabilistic model for protein–ligand binding site similarity
Authors: Davies J.R. , Jackson R.M. , Mardia K.V. , Taylor C.C.
Published: September 2007

Motivation: The large-scale comparison of protein–ligand binding sites is problematic, in that measures of structural similarity are difficult to quantify and are not easily understood in terms of statistical similarity that can ultimately be related to structure and function. We present a binding site matching score the Poisson Index (PI) based upon a well-defined statistical model. PI requires only the number of matching atoms between two sites and the size of the two sites—the same information used by the Tanimoto Index (TI), a comparable and widely used measure for molecular similarity. We apply PI and TI to a previously automatically extracted set of binding sites to determine the robustness and usefulness of both scores.

Results: We found that PI outperforms TI; moreover, site similarity is poorly defined for TI at values around the 99.5% confidence level for which PI is well defined. A difference map at this confidence level shows that PI gives much more meaningful information than TI. We show individual examples where TI fails to distinguish either a false or a true site paring in contrast to PI, which performs much better. TI cannot handle large or small sites very well, or the comparison of large and small sites, in contrast to PI that is shown to be much more robust. Despite the difficulty of determining a biological ‘ground truth’ for binding site similarity we conclude that PI is a suitable measure of binding site similarity and could form the basis for a binding site classification scheme comparable to existing protein domain classification schema.

Availability: PI is implemented in SitesBase www.modelling.leeds.ac.uk/sb/

Contact:  r.m.jackson@leeds.ac.uk
A District General Hospital pain management programme
Authors: LUSCOMBE F. E. , WALLACE L. , WILLIAMS J. , GRIFFITHS D. P. G.
Published: September 2007

A pain management programme was set up in a large District General Hospital to improve the management of the many patients with chronic non‐malignant pain who do not respond to interventional medicine. Outcome measures studied were depression, anxiety, disability, pain locus of control, illness behaviour and patient satisfaction with the programme. The first five of these measures showed statistically significant improvements whilst patient satisfaction with the programme was high at both assessments. In addition, there were marked decreases in the consumption of analgesics and sedative drugs. We conclude that a multidisciplinary pain management programme is a cost effective and constructive way of treating patients whose pain does not respond to interventional management.
The intensive care treatment of convulsive status epilepticus in the UK
Authors: WALKER M. C. , SMITH S. J. M. , SHORVON S. D.
Published: September 2007

Six hundred and ninety–four members of the Intensive Care Society working in the UK were surveyed by postal questionnaire between May and November 1993 to determine their management of convulsive status epilepticus resistant to initial therapy with intravenous diazepam and phenytoin. Four hundred and eight forms were completed and returned (58.8%). The survey revealed that, following failure of initial management, a benzodiazepine infusion (35%) or anaesthetic induction agent (32%) were the preferred second lines of treatment in intensive care units. In paediatric intensive care units, phenobarbitone (31 %) was the agent of choice. Most respondents (57%) gave anaesthetic induction agents within 60min of the start of status epilepticus, the majority choosing thiopentone (82%). Patients were usually monitored using clinical assessment only (45%), except in paediatric intensive care units and specialist neurological or neurosurgical units where the majority used a cerebral function monitor. Only 12%> of the respondents were aware of a protocol for status epilepticus in their intensive care units. The most frequently used therapeutic and monitoring strategies in the management of refractory status epilepticus in the UK are insufficient and need re–evaluation.
A comparison of three variable performance devices for postoperative oxygen therapy
Authors: McBRIEN M. E. , SELLERS W. F. S.
Published: September 2007

Eleven patients in the intensive care unit following major abdominal surgery with a nasogastric tube in situ and receiving oxygen via facemask were allocated to receive in a random sequence oxygen at 4l.min‐1 via a Hudson mask, nasal cannulae or a nasal catheter with foam collar at the distal end. A significantly greater Pao2 was achieved using both the nasal catheter with foam collar (p < 0.01) and Hudson mask (p < 0.05) compared to the nasal cannulae. There were no significant differences in the PacO2 or SpO2 values obtained between the devices. In the majority of postoperative patients in whom a variable performance device is indicated, nasal devices appear preferable in terms of patient comfort and compliance. The nasal catheter with foam collar produced a significantly greater PaQ2 than nasal cannulae in patients with a nasogastric tube in situ.
Maternal hypoxaemia during labour and delivery: the influence of analgesia and effect on neonatal outcome
Authors: Griffin R. P. , Reynolds F.
Published: September 2007

The effect of analgesia on the incidence of hypoxaemia was assessed in an unrandomised trial in 51 parturients from the last hour of the first stage of labour until delivery. Women were retrospectively divided into four groups: no analgesia, pethidine with intermittent Entonox, extradural bupivacaine (either infusion of 0.125% or top‐ups of 10ml of 0.25%): and extradural infusion of 0.1% bupivacaine with 2 μg.ml ‐1fentanyl. The lowest median incidence of desaturation (Spo2< 94%) was in the extradural bupivacaine group: 0 min.h‐1 in the last hour of the first stage and 0.1 min.h‐1 in the second stage. The incidence was significantly lower than in the pethidine I Entonox group (1.4min.h‐1) in the last hour of the first stage (p < 0.001) and the extradural bupivacaine /fentanyl group (0.9 min.h‐1 and no analgesia group (3min.h‐1) in the second stage (p < 0.05 in both cases). There was no correlation between maternal oxygenation during the second stage and measures of neonatal outcome including Apgar score and umbilical artery and vein blood gases.