bluuebunny/crossref_metadata_2025_split huggingface dataset:
A questionnaire for screening the micronutrient intake of economically active South African adults
Authors: Senekal Marjanne , Steyn Nelia P , Nel Johanna 
Published: March 2009

AbstractObjectiveThe aim of the present study was to develop (phase 1) and validate (phase 2) a screening questionnaire to assess the adequacy of micronutrient intake of economically active South African adults.DesignFor identification of indicator foods to be included in the screening questionnaire (phase 1), a comprehensive, eighty-six-item, quantified FFQ that reflected the food sources of thirteen selected micronutrients associated with the nutrition-related health status of South Africans was developed and completed by 554 adults of all four major ethnic groups. Resulting dietary data were subjected to stepwise regression analyses to identify indicator foods to be included in the final screening questionnaire. For validation of frequency of intake reporting of specific food items included in the screening questionnaire (phase 2), a sample of sixty-six African and eighty-four white adult volunteers of both genders completed a 7 d record as well as the screening questionnaire. The frequency of intake of specific food items derived from the two methods was then compared using Spearman correlation coefficients.ResultsPhase 1 identified thirty indicator foods that formed the basis of the screening questionnaire. In phase 2, significant correlations were found for the total group for twenty-two out of the thirty items in the questionnaire, with correlations being the best for white females and the poorest for African males and females.ConclusionsA screening questionnaire (thirty-item FFQ) that can be used by researchers and health professionals to assess an individual’s risk of inadequate micronutrient intake was developed and validated.
Smoking worsens the prognosis of mild abnormalities in cervical cytology
Authors: GUARISI RENATA , SARIAN LUIS OTAVIO , HAMMES LUCIANO SERPA , LONGATTO‐FILHO ADHEMAR , DERCHAIN SOPHIE F.M. , ROTELI‐MARTINS CECÍLIA , NAUD PAULO , ERŽEN MOJCA , BRANCA MARGHERITA , TATTI SÍLVIO , COSTA SILVANO , SYRJÄNEN STINA , BRAGANÇA JOANA F. , SYRJÄNEN KARI 
Published: March 2009

AbstractObjective. To examine the effect of smoking on the incidence of low‐ and high‐grade cervical intraepithelial neoplasia (CIN) in women with a baseline Pap smear of atypical squamous cells (ASC) or a low‐grade squamous intraepithelial lesion (LSIL). Design. Prospective study in which a cohort of women with normal colposcopy and ASC/LSIL at baseline were followed at 6‐month intervals of up to 36 months. Women were grouped in post‐hoc analysis according to their smoking behavior: never (or past) smokers and current smokers. Setting. This report was based on data from the Latin American Screening Study, conducted in São Paulo, Campinas, Porto Alegre (Brazil) and Buenos Aires (Argentina). Population. A subset of 150 women derived from a cohort of 1,011 women. Methods. Multivariate Cox analysis and Kaplan–Meier curves were used. Main outcome measures. Low‐ and high‐grade CIN during follow‐up. Results. The only factor related to an increased risk of developing CIN was the positive high‐risk (hr) HPV status (hazard ratio (HR) = 3.42; 95% CI: 1.11–9.43). A total of 21 cases of incident CIN were detected during follow‐up. Of these, 11 appeared in the group of 67 smokers and 10 among the 83 non‐smoker women (log‐rank, p = 0.33). Smoking status was not associated with the risk of developing CIN (HR = 0.73; 95% CI: 0.40–1.33). However, when restricting the analysis to high‐grade CIN only (11 cases), the probability of developing the disease was significantly higher among smokers (p = 0.04). Conclusions. Smoking contributes additional risk for developing high‐grade CIN in women with ASC or LSIL cytology but normal colposcopy.
Optimization of computed tomography urography protocol, 1997 to 2008: Effects on radiation dose
Authors: Dahlman P. , Jangland L. , Segelsjö M. , Magnusson A. 
Published: March 2009

Background: Since computed tomography (CT) urography began to replace excretory urography as the primary imaging technique in uroradiology, the collective radiation dose to the patients has increased. Purpose: To examine the changes in the CT urography protocol for investigating suspected urinary tract malignancy between the years 1997 and 2008, and how these changes have influenced the mean effective dose. Material and Methods: The study was based on 102 patients (mean age 66.1±14.8 years, range 31–89 years; 30 female, 72 male) divided into five groups (groups A–E) corresponding to the time points at which changes were made to the CT urography protocol. The mean effective doses were estimated using the ImPACT CT Patient Dosimetry Calculator. Results: The number of scan phases at CT urography was reduced from four to three in 1999, resulting in a reduction of the mean effective dose from 29.9/22.5 (female [F]/male [M]) mSv (group A) to 26.1/18.9 (F/M) mSv (group B). In 2001, mAs settings were adapted to patient size, and the mean effective dose was reduced to 16.8/12.0 (F/M) mSv (group C). In 2005, scans were performed with a multidetector-row CT equipped with automatic tube current modulation in the x- and y-axis (CARE Dose). The effective mAs was also lowered in the unenhanced and excretory phase, yet the mean effective dose increased to 18.2/13.1 (F/M) mSv (group D), since the effective mAs had to be increased in the corticomedullary phase to maintain image quality. In 2008, as tube current modulation in the x-, y-, and z-axis was introduced (CARE Dose4D), the mean effective dose was reduced to 11.7/8.8 (F/M) mSv (group E). Conclusion: This study shows that the individual mean effective dose to patients undergoing CT urography has decreased by 60%, from 29.9/22.5 (F/M) mSv in 1997 to 11.7/8.8 (F/M) mSv in 2008.
Magnetic resonance coronary angiography: Comparison between a Gd-BOPTA- and a Gd-DTPA-enhanced spoiled gradient-echo sequence and a non-contrast-enhanced steady-state free-precession sequence
Authors: Nassenstein K. , Breuckmann F. , Hunold P. , Barkhausen J. , Schlosser T. 
Published: March 2009

Background: Several studies have demonstrated that the administration of contrast agents is advantageous in magnetic resonance coronary angiography (MRCA). Purpose: To compare a non-contrast-enhanced steady-state free-precession (SSFP) with a contrast-enhanced inversion recovery spoiled gradient-echo (IR-GE) sequence using two different contrast agents for MRCA. Material and Methods: Eight healthy volunteers were examined on a 1.5T MR scanner. For non-contrast-enhanced MRCA, a breath-hold three-dimensional (3D) SSFP sequence (repetition/echo time [TR/TE] 3.9/1.7 ms, flip angle [FA] 65°) was used. Contrast-enhanced MRCA was performed repetitively in two imaging sessions over 30 min after injection of 0.2 mmol/kg body weight gadobenate dimeglumine (Gd-BOPTA) or gadolinium diethylenetriamine pentaacetic acid (Gd-DTPA) using a breath-hold 3D IR-GE sequence (TR/TE 4.1/1.7 ms, FA 15°). The signal-to-noise ratios (SNR) of the coronary arteries, as well as the contrast-to-noise ratios (CNR) between coronary arteries and perivascular tissue, were calculated for all images. Blood T1 values were repetitively estimated over 30 min using an SSFP sequence with incrementally increasing inversion times (TR/TE 2.4/1.0 ms, FA 50°). Results: Gd-BOPTA-enhanced images showed significantly ( P<0.05) higher SNR and CNR compared to Gd-DTPA-enhanced images for all times after contrast injection (SNR: 1 min post injection [PI] 26.4±4.2 vs. 16.2±3.1; CNR: 1 min PI 21.4±3.7 vs. 13.2±2.6). Compared to the SSFP images, the Gd-BOPTA-enhanced images showed higher CNR values for all times after injection (1 min PI 21.4±3.7 vs. 13.8±5.5; P<0.05), whereas the Gd-DTPA-enhanced images did not (1 min PI 13.2±2.6 vs. 13.8±5.5; P>0.05). Blood T1 estimates were not significantly different for either agent 1 min after administration ( P>0.05), but they were significantly lower for Gd-BOPTA ( P<0.05) from 7 to 25 min after injection. Conclusion: Compared to non-contrast-enhanced SSFP images, only Gd-BOPTA-enhanced images show a significantly improved contrast between the coronary arteries and the surrounding tissue.
Protection by Glycyrrhizin against Warm Ischemia‐Reperfusion–Induced Cellular Injury and Derangement of the Microcirculatory Blood Flow in the Rat Liver
Authors: MABUCHI AYAKO , WAKE KENJIRO , MARLINI MUHAMAD , WATANABE HITOMI , WHEATLEY ANTONY M. 
Published: March 2009

ABSTRACTBackground/Aim: The mechanism by which ischemia‐reperfusion (I/R)‐induced derangement of the hepatic microcirculation leads to tissue injury is not fully understood. We postulated that alterations to the hepatic microcirculation, including hemodynamic derangement and increased leukocyte‐endothelium interaction, play a role, and that glycyrrhizin exerts its hepatoprotective effects, in part, by reducing these microcirculatory changes. Materials and Methods: Wistar rats were subjected to 30–60 minutes segmental hepatic ischemia, followed by 120 minutes of reperfusion. Glycyrrhizin was administered prior to ischemia. Using intravital fluorescence microscopy, the administration of fluorescein isothiocyanate–conjugated erythrocytes allowed the measurement of erythrocyte‐velocity (RBCvel), lobular, and sinusoidal perfusion. Bleb formation was observed by electron microscopy. Blood and tissue were taken for the assessment of liver injury. Results: Glycyrrhizin reduced I/R‐induced liver injury (histology, liver enzymes) and reduced hepatocyte apoptosis (TUNEL, caspase‐3 activity). Glycyrrhizin inhibited hepatocyte bleb formation and reversed the I/R‐induced reductions in lobular perfusion and RBCvel. Leukocyte rolling and adherence in postsinusoidal venules and neutrophil infiltration were reduced by glycyrrhizin. I/R‐induced elevation in HMGB1 was prevented by glycyrrhizin. Conclusions: Early bleb formation with deranged microcirculatory flow and leukocyte‐endothelium interaction would appear to contribute to I/R‐induced hepatocellular injury. Glycyrrhizin exerts its hepatoprotective effect by preventing these changes, in addition to a direct cellular effect.
Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease
Authors: Chu Tianjiao , Bunce Kimberly , Hogge W. Allen , Peters David G. 
Published: March 2009

Abstract
There is currently great interest in the development of methods for the minimally invasive diagnosis of fetal genetic disease using cell-free DNA from maternal plasma samples obtained in the first trimester of pregnancy. With the rapid development of high-throughput sequencing technology, the possibility of detecting the presence of trisomy fetal genomes in the maternal plasma DNA sample has recently been explored. The major concern of this whole genome sequencing approach is that, while detecting the karyotype of the fetal genome from the maternal plasma requires extremely high accuracy of copy number estimation, the majority of the available high-throughput sequencing technologies require polymerase chain reaction (PCR) and are subject to the substantial bias that is inherent to the PCR process. We introduce a novel and sophisticated statistical model for the whole genome sequencing data, and based on this model, develop a highly sensitive method of Minimally Invasive Karyotyping (MINK) for the diagnosis of the fetal genetic disease. Specifically we demonstrate, by applying our statistical method to ultra high-throughput whole sequencing data, that trisomy 21 can be detected in a minor (‘fetal’) genome when it is mixed into a major (‘maternal’) background genome at frequencies as low as 5%. This observation provides additional proof of concept and justification for the further development of this method towards its eventual clinical application. Here, we describe the statistical and experimental methods that illustrate this approach and discuss future directions for technical development and potential clinical applications.
Contact: dgp6@pitt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates
Authors: Matthew Ward R. , Venner Eric , Daines Bryce , Murray Stephen , Erdin Serkan , Kristensen David M. , Lichtarge Olivier 
Published: March 2009

Abstract
Summary:The Evolutionary Trace Annotation (ETA) Server predicts enzymatic activity. ETA starts with a structure of unknown function, such as those from structural genomics, and with no prior knowledge of its mechanism uses the phylogenetic Evolutionary Trace (ET) method to extract key functional residues and propose a function-associated 3D motif, called a 3D template. ETA then searches previously annotated structures for geometric template matches that suggest molecular and thus functional mimicry. In order to maximize the predictive value of these matches, ETA next applies distinctive specificity filters—evolutionary similarity, function plurality and match reciprocity. In large scale controls on enzymes, prediction coverage is 43% but the positive predictive value rises to 92%, thus minimizing false annotations. Users may modify any search parameter, including the template. ETA thus expands the ET suite for protein structure annotation, and can contribute to the annotation efforts of metaservers.
Availability:The ETA Server is a web application available at http://mammoth.bcm.tmc.edu/eta/.
Contact: lichtarge@bcm.edu
KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor
Authors: Zhang Jitao David , Wiemann Stefan 
Published: March 2009

Abstract
Motivation: KEGG PATHWAY is a service of Kyoto Encyclopedia of Genes and Genomes (KEGG), constructing manually curated pathway maps that represent current knowledge on biological networks in graph models. While valuable graph tools have been implemented in R/Bioconductor, to our knowledge there is currently no software package to parse and analyze KEGG pathways with graph theory.
Results: We introduce the software package KEGGgraph in R and Bioconductor, an interface between KEGG pathways and graph models as well as a collection of tools for these graphs. Superior to existing approaches, KEGGgraph captures the pathway topology and allows further analysis or dissection of pathway graphs. We demonstrate the use of the package by the case study of analyzing human pancreatic cancer pathway.
Availability:KEGGgraph is freely available at the Bioconductor web site (http://www.bioconductor.org). KGML files can be downloaded from KEGG FTP site (ftp://ftp.genome.jp/pub/kegg/xml).
Contact: j.zhang@dkfz-heidelberg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
SBML2LaTEX: Conversion of SBML files into human-readable reports
Authors: Dräger Andreas , Planatscher Hannes , Motsou Wouamba Dieudonné , Schröder Adrian , Hucka Michael , Endler Lukas , Golebiewski Martin , Müller Wolfgang , Zell Andreas 
Published: March 2009

Abstract
Summary: The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g. unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2LaTEX, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, LaTEX and PDF, and provides many settings for customization.
Availability: Source code, documentation and a web service are freely available at http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX.
Contact: andreas.draeger@uni-tuebingen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Cathepsin D activity protects against development of type AA amyloid fibrils
Authors: Van Der Hilst J. C. H. , Kluve‐Beckerman B. , Van Der Meer J. W. M. , Simon A. 
Published: March 2009

AbstractBackground  The extracellular, fibrillar deposits of reactive (secondary) amyloidosis are composed of amyloid A (AA) protein, a proteolytically derived fragment of the acute phase protein serum amyloid A (SAA). While complete degradation of SAA precludes amyloid formation, limited cleavage which generates AA protein is considered part of the pathogenic mechanism.Materials and methods  In this study, we investigated SAA degradation by lysosomal enzymes cathepsins B, D, and K, and assessed the impact of cathepsin activity on AA amyloid formation in a cell culture model using peripheral blood mononuclear cells from healthy volunteers.Results  Lysates of human mononuclear cells were capable of degrading SAA. Degradation was significantly reduced by inhibition of cathepsin D with pepstatin A. Inhibition of cathepsin B or cathepsin K, however, had no effect. The SAA fragment pattern generated by mononuclear cell lysates was similar to that produced by incubating SAA with purified human cathepsin D. Consistent with in vitro findings, amyloid formation in human monocyte cultures was increased by 43% when cathepsin D was inhibited, but remained unaffected by inhibition of cathepsin B or cathepsin K.Conclusion  These data provide evidence that cathepsin D but not cathepsin B or cathepsin K is physiologically important in SAA degradation and hence in preventing SAA from accumulating and serving as precursor of AA amyloid fibrils.
Arabidopsis plant homeodomain finger proteins operate downstream of auxin accumulation in specifying the vasculature and primary root meristem
Authors: Thomas Carole L. , Schmidt Dominik , Bayer Emmanuelle M. , Dreos Rene , Maule Andrew J. 
Published: March 2009

SummaryIn Arabidopsis thaliana, auxin is a key regulator of tissue patterning in the developing embryo. We have identified a group of proteins that act downstream of auxin accumulation in auxin‐mediated root and vascular development in the embryo. Combined mutations in OBERON1 (OBE1) and OBERON2 (OBE2) give rise to obe1 obe2 double mutant seedlings that closely phenocopy the monopteros (mp) mutant phenotype, with an absence of roots and defective development of the vasculature. We show that, in contrast to the situation in mp mutants, obe1 obe2 double mutant embryos show auxin maxima at the root pole and in the provascular region, and that the SCFTIR1 pathway, which translates auxin accumulation into transcriptional activation of auxin‐responsive genes, remains intact. Although we focus on the impact of obe mutations on aspects of embryo development, the effect of such mutations on a broad range of auxin‐related gene expression and the tissue expression patterns of OBE genes in seedlings suggest that OBE proteins have a wider role to play in growth and development. We suggest that OBE1 and OBE2 most likely control the transcription of genes required for auxin responses through the action of their PHD finger domains.
Virus Resistance in Cereals: Sources of Resistance, Genetics and Breeding
Authors: Ordon Frank , Habekuss Antje , Kastirr Ute , Rabenstein Frank , Kühne Thomas 
Published: March 2009

AbstractIn cereals, soil‐borne viruses transmitted by the plasmodiophorid Polymyxa graminis (e.g., Barley mild mosaic virus, Barley yellow mosaic virus or Soil‐borne cereal mosaic virus), have increased in importance due to the increase of the acreage infested and because yield losses cannot be prevented by chemical measures. Due to global warming, it is also expected that insect transmitted viruses vectored by aphids (e.g., Barley yellow dwarf virus, Cereal yellow dwarf virus), leafhoppers (Wheat dwarf virus) or mites (e.g., Wheat streak mosaic virus), will become much more important even in cooler regions. The environmentally most sound and also most cost effective approach to prevent high yield losses caused by these viruses is breeding for resistance. Therefore, in contrast to other reviews on cereal viruses, this study briefly reviews present knowledge on cereal‐infecting viruses and emphasizes especially the sources of resistance or tolerance to these viruses and their use in molecular breeding schemes.
Streptococcus pneumoniae and Haemophilus influenzae at the initial stage of influenza
Authors: Takano Misao , Ozaki Kyoko , Nitahara Yoshiyuki , Higuchi Wataru , Takano Tomomi , Nishiyama Akihito , Yamamoto Tatsuo 
Published: March 2009

AbstractBackground:  Streptococcus pneumoniae and Haemophilus influenzae infections in children with influenza have been noted because of the severity of co‐infection. In Japan, vaccination against S. pneumoniae and H. influenzae infections has been listed in the vaccine program in 2008, but the characteristics of the two organisms, colonizing at the initial stage of influenza infection, have not been investigated in detail.Methods:  Nasopharyngeal swabs from children with influenza (flu+) (n= 236; mean age, 6.2 years) were examined for bacterial pathogens, including S. pneumoniae and H. influenzae. They were then examined for serotypes, drug susceptibilities, and resistance genes (or gene mutations). As a reference, children with upper respiratory tract infection (URTI+, flu‐; n = 189; mean age, 6.2 years) were also examined.Results:  S. pneumoniae, β‐streptococci (groups A, B, and G), methicillin‐susceptible and ‐resistant S. aureus, Moraxella catarrhalis, and H. influenzae were isolated. For S. pneumoniae, nine serotypes were detected with prevalent types of 3, 6, 19 and 23. Penicillin resistance was detected in types 19 and 23, while resistance to macrolide and clindamycin was found in various types. For H. influenzae, only b serotype was detected, with marked ampicillin resistance. The majority was non‐typeable. Very similar results were obtained even in URTI+ (flu‐) cases.Conclusion:  Multiple drug‐resistant S. pneumoniae with major serotypes, for example, 19 and 23 and H. influenzae with serotype b were already present at the initial stage of influenza infection, similar to URTI+ flu‐ cases. They could be prevented by current vaccines, but drug‐resistant non‐typeable H. influenzae is troubling.
Ingested foreign bodies causing complications and requiring hospitalization in European children: Results from the ESFBI study
Authors: Gregori Dario , Scarinzi Cecilia , Morra Bruno , Salerni Lorenzo , Berchialla Paola , Snidero Silvia , Corradetti Roberto , Passali Desiderio 
Published: March 2009

AbstractBackground:  In young children, particularly those aged 1–3 years, aerodigestive tract foreign bodies (FB) are a common pediatric problem. The aim of the present study was therefore to characterize the risk of complications and prolonged hospitalization due to FB in the upper digestive tract in terms of the characteristics of the injured patients (age, gender), typology and features of the FB, the circumstances of the accident and hospitalization details.Methods:  A retrospective study was done in 19 hospitals in 19 corresponding European countries of 186 cases of injury due to the presence of an FB in the mouth, esophagus and stomach (ICD935), out of the 2103 overall cases of FB reported in other locations.Results:  Complications arose in 14 cases and hospitalization was required in 164 cases. No deaths were observed. A higher incidence of hospitalization in male patients (61%) was observed. Median age for children who experienced complications was 2 years old. The most common FB removal technique was esophagoscopy. In the majority of cases the children were treated by the ENT Department. The most common FB were coins, batteries and fish bones among food.Conclusion:  Because batteries, as well as coins and fish bones among food were the most common type of FB encountered, and because recent development of technology has accelerated broad use of disk‐type batteries, parents should be aware of this hazard, and an educational campaign for public education for this serious problem is advisable.