bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tocolytic effectiveness of nifedipine versus ritodrine and follow‐up of newborns: a randomised controlled trial
Authors: VAN DE WATER M. , TIMMERMAN‐VAN KESSEL E. , DE KLEINE M.J. , OEI S.G. 
Published: February 2008

AbstractBackground. Several studies have demonstrated the superior tocolytic effectiveness of nifedipine over ritodrine. Only 1 trial conducted a long‐term follow‐up of newborns and found no difference in psychosocial and motor functioning. In a randomised, multicentre trial, we compared the tocolytic effectiveness of nifedipine and ritodrine and included a long‐term follow‐up of the newborns after 2 years of age. Methods. Patients with imminent preterm labour were randomised and received either nifedipine or ritodrine. Side‐effects, tocolytic effectiveness and neonatal outcome were studied. Development of the children was studied after the age of 2 years by a parental questionnaire. Results. Ninety‐three patients were included. Birth was postponed for an average of 4.3 weeks in the ritodrine group and 5.0 weeks in the nifedipine group (p = 0.4). Patients who received ritodrine experienced significantly more side‐effects compared to patients who received nifedipine (29 versus 4%, p<0.05). No significant differences were found in either group for average birth weight, Apgar scores after 1 min, neonatal intensive care unit (NICU) admission and neonatal complications. Parental questionnaires after 2 years had a response rate of 70%. Two‐thirds of the children had developed normally in both groups. In both groups, only a few children were severely retarded (n = 4). No significant differences in development were found between the 2 groups. Conclusions. Both nifedipine and ritodrine proved effective tocolytic drugs, however ritodrine caused significantly more maternal side‐effects. Neonatal outcome and long‐term development after 2 years of age were not significantly different. We favour nifedipine over ritodrine as a tocolytic drug.
Adenocarcinoma of the uterine cervix: prognostic significance of clinicopathologic parameters, flow cytometry analysis and HPV infection
Authors: DABIĆ MIRELA M. , NOLA MARIN , TOMIČIĆ IVANA , DOTLIĆ SNJEŽANA , PETROVEČKI MARKO , JUKIĆ STANKO 
Published: February 2008

AbstractBackground. This study was designed to determine the possible impact of status of human papillomavirus (HPV) infection (no infection, single, multiple infections) on the survival of patients with cervical adenocarcinoma, to correlate the HPV status with other clinicopathologic parameters, and to examine clinical, histological and flow cytometric parameters as predictors of survival in cervical adenocarcinoma. Methods. The clinical data of 51 patients with adenocarcinoma of the cervix who were treated at the Department of Gynecology and Obstetrics, Zagreb University School of Medicine, from 1978 to 2004 were analysed: age at presentation, menstrual status, clinical stage, relapse, survival. Exact histologic subtype, architectural grade and nuclear grade were determined. DNA flow cytometry was performed to determine DNA ploidy and proliferative index. Polymerase chain reaction (SPF primers), followed by reverse hybridisation for genotyping, was used to determine the HPV status. Results. The status of HPV infection had no impact on patient survival, and could not be correlated with any of the analysed clinicopathologic parameters. Univariate analysis showed significant association between patient survival and clinical stage (p = 0.002) and architectural grade (p = 0.033). Multivariate analysis confirmed both parameters as significantly associated with survival. Menstrual status, nuclear grade, DNA ploidy and proliferative activity had no impact on patient survival. Conclusion. Clinical stage and architectural grade are significant predictors for survival of patients with cervical adenocarcinoma. Status of HPV infection, flow cytometric parameters, nuclear grade and menstrual status do not predict patient survival.
Responding to Simulated Pandemic Influenza in San Antonio, Texas
Authors: Miller George , Randolph Stephen , Patterson Jan E. 
Published: February 2008

Objective.To describe the results of a simulation study of the spread of pandemic influenza, the effects of public health measures on the simulated pandemic, and the resultant adequacy of the surge capacity of the hospital infrastructure and to investigate the adequacy of key elements of the national pandemic influenza plan to reduce the overall attack rate so that surge capacity would not be overwhelmed.Design.We used 2 discrete-event simulation models: the first model simulates the contact and disease transmission process, as affected by public health interventions, to produce a stream of arriving patients, and the second model simulates the diagnosis and treatment process and determines patient outcomes.Setting.Hypothetical scenarios were based on the response plans, infrastructure, and demographic data of the population of San Antonio, Texas.Results.Use of a mix of strategies, including social distancing, antiviral medications, and targeted vaccination, may limit the overall attack rate so that demand for care would not exceed the capacity of the infrastructure. Additional simulations to assess social distancing as a sole mitigation strategy suggest that a reduction of infectious community contacts to half of normal levels would have to occur within approximately 7 days.Conclusions.Under ideal conditions, the mix of strategies may limit demand, which can then be met by community surge capacity. Given inadequate supplies of vaccines and antiviral medications, aggressive social distancing alone might allow for the control of a local epidemic without reliance on outside support.
From pull-down data to protein interaction networks and complexes with biological relevance
Authors: Zhang Bing , Park Byung-Hoon , Karpinets Tatiana , Samatova Nagiza F. 
Published: February 2008

Abstract
Motivation: Recent improvements in high-throughput Mass Spectrometry (MS) technology have expedited genome-wide discovery of protein–protein interactions by providing a capability of detecting protein complexes in a physiological setting. Computational inference of protein interaction networks and protein complexes from MS data are challenging. Advances are required in developing robust and seamlessly integrated procedures for assessment of protein–protein interaction affinities, mathematical representation of protein interaction networks, discovery of protein complexes and evaluation of their biological relevance.
Results: A multi-step but easy-to-follow framework for identifying protein complexes from MS pull-down data is introduced. It assesses interaction affinity between two proteins based on similarity of their co-purification patterns derived from MS data. It constructs a protein interaction network by adopting a knowledge-guided threshold selection method. Based on the network, it identifies protein complexes and infers their core components using a graph-theoretical approach. It deploys a statistical evaluation procedure to assess biological relevance of each found complex. On Saccharomyces cerevisiae pull-down data, the framework outperformed other more complicated schemes by at least 10% in F1-measure and identified 610 protein complexes with high-functional homogeneity based on the enrichment in Gene Ontology (GO) annotation. Manual examination of the complexes brought forward the hypotheses on cause of false identifications. Namely, co-purification of different protein complexes as mediated by a common non-protein molecule, such as DNA, might be a source of false positives. Protein identification bias in pull-down technology, such as the hydrophilic bias could result in false negatives.
Contact: samatovan@ornl.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes
Authors: Mrázek Jan , Xie Shaohua , Guo Xiangxue , Srivastava Anuj 
Published: February 2008

Abstract
Motivation: Genomes contain biologically significant information that extends beyond that encoded in genes. Some of this information relates to various short dispersed repeats distributed throughout the genome. The goal of this work was to combine tools for detection of statistically significant dispersed repeats in DNA sequences with tools to aid development of hypotheses regarding their possible physiological functions in an easy-to-use web-based environment.
Results: Ab Initio Motif Identification Environment (AIMIE) was designed to facilitate investigations of dispersed sequence motifs in prokaryotic genomes. We used AIMIE to analyze the Escherichia coli and Haemophilus influenzae genomes in order to demonstrate the utility of the new environment. AIMIE detected repeated extragenic palindrome (REP) elements, CRISPR repeats, uptake signal sequences, intergenic dyad sequences and several other over-represented sequence motifs. Distributional patterns of these motifs were analyzed using the tools included in AIMIE.
Availability: AIMIE and the related software can be accessed at our web site http://www.cmbl.uga.edu/software.html.
Contact: mrazek@uga.edu
Growth and biochemical responses of the offspring of mussels directly affected by the “Prestige” oil spill
Authors: Peteiro Laura G. , Filgueira Ramón , Labarta Uxío , Fernández-Reiriz María José 
Published: February 2008

Abstract
Peteiro, L. G., Filgueira, R., Labarta, U., and Fernández-Reiriz, M. J. 2008. Growth and biochemical responses of the offspring of mussels directly affected by the “Prestige” oil spill. – ICES Journal of Marine Science, 65: 509–513. We investigated whether perturbations to growth and biochemistry, detected in Mytilus galloprovincialis mussel seed cultured after the “Prestige” oil spill (2003), were evident in its offspring (2004). Sublethal effects in the 2003 mussels or, alternatively, direct exposure to remobilization of fuel on the seabed, might have detrimental effects on mussel juveniles in 2004. However, the absence of differences in lipid composition and growth performance between mussel seed gathered from the area most affected by the spill (Pindo) and the reference population (Miranda) seems to indicate the absence of sublethal effects related to hydrocarbon exposure in the offspring of mussels directly exposed to the “Prestige” oil spill.
Arabidopsis PPR40 Connects Abiotic Stress Responses to Mitochondrial Electron Transport
Authors: Zsigmond Laura , Rigó Gábor , Szarka András , Székely Gyöngyi , Ötvös Krisztina , Darula Zsuzsanna , Medzihradszky Katalin F. , Koncz Csaba , Koncz Zsuzsa , Szabados László 
Published: February 2008

AbstractOxidative respiration produces adenosine triphosphate through the mitochondrial electron transport system controlling the energy supply of plant cells. Here we describe a mitochondrial pentatricopeptide repeat (PPR) domain protein, PPR40, which provides a signaling link between mitochondrial electron transport and regulation of stress and hormonal responses in Arabidopsis (Arabidopsis thaliana). Insertion mutations inactivating PPR40 result in semidwarf growth habit and enhanced sensitivity to salt, abscisic acid, and oxidative stress. Genetic complementation by overexpression of PPR40 complementary DNA restores the ppr40 mutant phenotype to wild type. The PPR40 protein is localized in the mitochondria and found in association with Complex III of the electron transport system. In the ppr40-1 mutant the electron transport through Complex III is strongly reduced, whereas Complex IV is functional, indicating that PPR40 is important for the ubiqinol-cytochrome c oxidoreductase activity of Complex III. Enhanced stress sensitivity of the ppr40-1 mutant is accompanied by accumulation of reactive oxygen species, enhanced lipid peroxidation, higher superoxide dismutase activity, and altered activation of several stress-responsive genes including the alternative oxidase AOX1d. These results suggest a close link between regulation of oxidative respiration and environmental adaptation in Arabidopsis.
Iron-Induced Turnover of the Arabidopsis IRON-REGULATED TRANSPORTER1 Metal Transporter Requires Lysine Residues
Authors: Kerkeb Loubna , Mukherjee Indrani , Chatterjee Iera , Lahner Brett , Salt David E. , Connolly Erin L. 
Published: February 2008

AbstractIron is an essential micronutrient but is toxic if accumulated at high levels. Thus, iron uptake and distribution in plants are controlled by precise regulatory mechanisms. IRON-REGULATED TRANSPORTER1 (IRT1) is the major high affinity iron transporter responsible for iron uptake from the soil in Arabidopsis (Arabidopsis thaliana). Previously, we showed that IRT1 is subject to posttranscriptional regulation; when expressed from the constitutive cauliflower mosaic virus 35S promoter, IRT1 protein accumulates only in iron-deficient roots. IRT1 contains an intracellular loop that may be critical for posttranslational regulation by metals. Of particular interest are a histidine (His) motif (HGHGHGH) that might bind metals and two lysine residues that could serve as attachment sites for ubiquitin. We constructed a set of mutant IRT1 alleles: IRT1H154Q, IRT1H156Q, IRT1H158Q, IRT1H160Q, IRT14HQ (quadruple His mutant), IRT1K146R, IRT1K171R, and a double mutant (IRT1K146R,K171R). Mutation of the His or lysine residues did not eliminate the ability of IRT1 to transport iron or zinc. Expression of each of the IRT1 variants and an IRT1intact construct in plants from the 35S promoter revealed that either K146 or K171 is required for iron-induced protein turnover, and 35S-IRT1K146R,K171R plants contain higher levels of iron as compared to 35S-IRT1 and wild type. Furthermore, accumulation of metals in 35S-IRT1K146R,K171R plants was not associated with an increase in ferric chelate reductase activity; this result indicates that, at least under conditions when iron is abundant, reduction of ferric iron may not be the rate-limiting step in iron uptake by strategy I plants such as Arabidopsis.
Structural dependencies of protein backbone 2JNC′ couplings
Authors: Juranić Nenad , Dannenberg J.J. , Cornilescu Gabriel , Salvador Pedro , Atanasova Elena , Ahn Hee‐Chul , Macura Slobodan , Markley John L. , Prendergast Franklyn G. 
Published: February 2008

AbstractProtein folding can introduce strain in peptide covalent geometry, including deviations from planarity that are difficult to detect, especially for a protein in solution. We have found dependencies in protein backbone 2JNC′ couplings on the planarity and the relative orientation of the sequential peptide planes. These dependences were observed in experimental 2JNC′ couplings from seven proteins, and also were supported by DFT calculations for a model tripeptide. Findings indicate that elevated 2JNC′ couplings may serve as reporters of structural strain in the protein backbone imposed by protein folds. Such information, supplemented with the H‐bond strengths derived from h3JNC′ couplings, provides useful insight into the overall energy profile of the protein backbone in solution.
Effect of pronounced weight loss on visceral fat, liver steatosis and adiponectin isoforms
Authors: Engl J. , Sturm W. , Sandhofer A. , Kaser S. , Tschoner A. , Tatarczyk T. , Weiss H. , Tilg H. , Patsch J. R. , Ebenbichler C. F. 
Published: February 2008

ABSTRACTBackground  Weight loss induced by bariatric surgery is an effective method to reverse obesity and comorbidities. The aim of this prospective weight loss study was to investigate changes of body fat distribution in relation to adiponectin and its isoforms and further to investigate the influence of both body fat distribution and adiponectin on the degree of liver steatosis.Design  Fifteen severely obese female patients (body mass index 43·1 ± 4·1, mean age 34·5 ± 8·6 years) were examined before and after surgical treatment. Grading of fatty liver disease and the subcutaneous and visceral fat diameters were determined by abdominal ultrasonography. Metabolic parameters were determined using standard methods; serum total adiponectin and its isoforms were detected by enzyme immuno assay (EIA).Results  Mean weight loss was 28·3 kg, which was mostly due to a loss in fat mass, accompanied by an increase in total adiponectin and the high molecular weight (HMW) adiponectin isoform. Visceral adipose tissue (VAT) diameter was highly correlated with liver steatosis, even more strongly than the parameters of liver function. In addition, liver steatosis correlated negatively with HMW adiponectin and binary logistic regression revealed that changes in fat mass, HMW adiponectin and alanine aminotransferase (ALT) were the best predictors for changes in the degree of hepatic steatosis.Conclusions  Our results suggest that circulating HMW adiponectin is associated with both VAT and liver steatosis. In summary, the major findings were that the VAT diameter is highly correlated with liver steatosis, even stronger than the parameters of liver function and the association of HMW adiponectin with liver steatosis was better than with total adiponectin.
Prey location and prey choice by the freshwater leech Erpobdella octoculata using foraging kairomones
Authors: KREUTER KIRSTEN , BAIER BEATE , AßMANN CHRISTINE , STEIDLE JOHANNES L. M. 
Published: February 2008

Summary1. The freshwater leech, Erpobdella octoculata, is a generalist predator feeding on prey organisms such as Tubifex spp., Chironomus spp. and Asellus aquaticus. Using different experimental designs, we studied the use of foraging kairomones by the leeches for prey location.2. Leeches were attracted to living as well as to freshly killed larvae of Chironomus sp., to Tubifex sp., and to A. aquaticus offered in Petri dishes covered with gauze. The leeches also reacted to an extract of macerated Tubifex sp. presented in agar.3. Using ion exchange chromatography, the presence of histidine and glutamic acid was demonstrated in water contaminated by living larvae of Chironomus sp. and Tubifex sp. Agar blocks containing a synthetic mixture of these compounds at concentrations above 5 mg mL−1 were attractive to the leeches.4. Choice tests showed that leeches preferred chemical signals from Tubifex sp. over larvae of Chironomus sp. No difference was found between chemicals from Tubifex sp. and A. aquaticus, and A. aquaticus and larvae of Chironomus sp.5. The results demonstrate that E. octoculata uses specific foraging kairomones in searching for prey and indicate that amino acids serve as foraging kairomones.
Restoration of salt‐marsh vegetation in relation to site suitability, species pool and dispersal traits
Authors: Wolters Mineke , Garbutt Angus , Bekker Renée M. , Bakker Jan P. , Carey Peter D. 
Published: February 2008

Summary

Restoration of salt marshes on previously reclaimed land provides an excellent opportunity to study plant colonization and subsequent development of salt‐marsh vegetation. Insight into the process of salt‐marsh development can guide the design, implementation and evaluation of salt‐marsh restoration schemes and help determine appropriate management strategies.
We evaluated the process of salt‐marsh restoration at a species‐ and plant‐community level and investigated how the sequence of species establishment is related to site suitability, availability of the target species in the local and regional species pools and dispersal traits.
It took approximately 5 years for species diversity in the restoration site to become similar to a local reference marsh. The annual species Salicornia spp. and Suaeda maritima colonized and reached maximum abundance first. Perennial species (Puccinellia maritima, Aster tripolium, Spartina anglica, Spergularia media, Atriplex portulacoides and Limonium vulgare) only started to colonize or increase notably in abundance after 3 years of restoration.
Plant composition at the highest elevation of the restoration site developed from an annual Salicornia community into a Puccinellia maritima salt marsh, which was similar to the local reference marsh. After 8 years, the lower elevations were still covered by annual Salicornia salt marsh despite the potential for the development of a Puccinellia community.
Salt tolerance appeared to be much more important in explaining the sequence of species establishment than the availability of the species in the local or regional species pools or dispersal traits.
Synthesis and applications. The prospect of salt‐marsh restoration after de‐embankment is good, with target species establishing spontaneously and vegetation succession taking place. Because most salt‐marsh species are dispersed over short distances, it is important that a well‐developed salt marsh is adjacent to the restoration site. The rate of salt‐marsh development and species diversity appears to be affected mainly by surface elevation. Proper elevation in relation to tidal inundation is therefore a prerequisite for the successful restoration of salt‐marsh vegetation after de‐embankment.
Determination of paper filler Z‐distribution by low‐vacuum SEM and EDX
Authors: ROUX S. , FEUGEAS F. , BACH M. , FAGON M. , BETTINGER C. , MOURAD S. , CORNET A. 
Published: February 2008

SummaryPaper, mainly constituted of cellulose fibres, often contains mineral fillers. These fillers increase some of the properties of the paper (whiteness, printability, etc.) and are cheaper than the cellulose fibres. Nevertheless, the fillers reduce the mechanical properties of the sheet. Paper presents an anisotropy corresponding to three main directions. This anisotropy characterises the sheet mechanical properties, structure and filler distribution. Analyses of the cross section of the paper sheet with a low‐vacuum scanning electron microscope with an energy dispersive spectrometer analysis module can show this distribution. The procedure developed consists in analysing discrete profiles to build the mean profile known as filler Z‐distribution for each of the fillers. To develop this method, problems such as determination of the surface points, the number of points to analyse to define a cross section profile and the time required for the test, have been solved. Paper is sensitive to electron irradiation. In order to avoid deterioration of the material and to obtain satisfactory results, the time span for analyses is restricted to 40 s with a 12 kV electron beam accelerating voltage. Monte Carlo simulations are used to determine the diffusion cloud size and thus to determine the number of points that constitute a profile. The samples are gold sputtered and, with the aid of backscattered imaging, the coated surface allows determination of the sample surface points.