bluuebunny/crossref_metadata_2025_split huggingface dataset:
F18-FDG coincidence-PET in patients with suspected gynecological malignancy
Authors: Zor E. , Stokkel M. P. , Özalp S. , Vardarelİ E. , YalÇİn Tarik Ö. , Ak İ. 
Published: June 2006

Purpose: To assess the role of F18-FDG imaging with a dual-head coincidence mode gamma camera (Co-PET) in identifying malignant tumors in patients with a suspicious adnexal mass depicted by conventional imaging methods. Material and Methods: F18-FDG Co-PET was performed preoperatively in 18 women (mean age 56.38 years) with suspected malignant gynecologic tumors according to clinical and abdomino-pelvic/transvaginal ultrasound or computed tomography findings. Exploratory laparotomy was performed in all patients within the 10 days post-F18-FDG Co-PET study, and the definitive diagnosis of the adnexal masses was established by histopathological examination. Results: Histopathological examinations of the surgically excised adnexal masses revealed eight malignant, one borderline, and nine benign neoplastic tumors. Four benign tumors had no F18-FDG uptake, while the remaining five tumors, all leiomyomas, showed mild FDG accumulation. Eight malignant tumors showed intense F18-FDG uptake. Sensitivity, specificity, PPV, and NPV of F18-FDG co-PET in differentiating benign from malign adnexal masses were 88%, 44%, 61%, and 80%, respectively. Tumor to background ratios (T/B) in benign lesions (2.04 ± 0.27) were significantly lower than in malignant lesions (7.4 ± 0.99). Conclusion: F18-FDG Co-PET is of clinical value when assessing suspicious malignant adnexal masses. False-negative F18-FDG results might arise from borderline disease. Moderate F18-FDG uptake in leiomyomas can result false-positive, but T/B ratios may be helpful in such cases.
Radiation dose reduction to breast and thyroid during MDCT: effectiveness of an in-plane bismuth shield
Authors: Hohl C. , Wildberger J. E. , Süß C. , Thomas C. , Mühlenbruch G. , Schmidt T. , Honnef D. , Günther R. W. , Mahnken A. H. 
Published: June 2006

Purpose: To evaluate dose reduction and image deterioration using in-plane bismuth breast-shielding and thyroid-shielding for MDCT. Material and Methods: Skin and organ doses of thyroid and breast were measured with thermoluminescent dosimeters in a female Alderson-Rando Phantom with and without a 4-ply in-plane bismuth shield. Routine neck (120 kVp, 150 mAseff; 16×1.5 mm) and chest (120 kVp, 100 mAseff; 16×1.5 mm) scan protocols were simulated on a 16-row MDCT scanner in three different settings: without shielding, with the shield directly on the surface, and with a 1-cm-thick cotton spacer between surface and shield. Image noise was quantified and compared using the t test. Results: On average, shielding resulted in a 47% organ-dose reduction for the thyroid and 32% for the breast. Placement of the spacer between shield and surface had no significant impact on the measured doses, but significantly decreased the image noise ( P<0.05). Conclusion: In-plane bismuth breast and thyroid shielding significantly decreases radiation dose in MDCT without deteriorating image quality.
Inadvertent intra-arterial drug injections: the role of angiographic and clinical findings
Authors: Rautio R. , Keski-Nisula L. 
Published: June 2006

Purpose: To evaluate the angiographic findings of patients who have inadvertently injected oral formulations of drugs into an upper extremity artery. Material and Methods: The radiology files for the previous 4 years were analyzed retrospectively. Seven patients were referred from the Emergency Department for angiography and possible thrombolysis during that time period. Results: The worst clinical results were found among the patients whose angiographic examinations showed absent flow. Two patients who were treated with local thrombolysis had no better results compared to the other five patients. Conclusion: Findings of delayed flow and absent flow in angiography should lead to intensified conservative treatment, especially among patients who have clinical findings of delayed capillary refilling or/and impaired muscular strength.
Usefulness of measurement of the temporal stem on magnetic resonance imaging in the diagnosis of frontotemporal dementia
Authors: Hayashida Y. , Hirai T. , Korogi Y. , Kimura T. , Ishizuka K. , Kawanaka K. , Yamura M. , Kitajima M. , Ikushima I. , Yamashita Y. 
Published: June 2006

Purpose: To investigate whether measurements of brain structures on routine magnetic resonance (MR) images can be used to distinguish between normal subjects and patients with frontotemporal dementia (FTD) or Alzheimer's disease (AD). Material and Methods: MRI studies were performed on 30 patients with dementia (FTD, n = 15; AD, n = 15) and 15 age-matched controls. Width measurements, obtained at the corpus callosum, the cingulate gyri, the hippocampi, and the temporal stem of the anterior temporal lobes, were compared among FTD and AD patients and control subjects on oblique-coronal T2-weighted images. Results: The width of the temporal stem was significantly narrower in FTD than in AD patients and control subjects (6.3±1.3 mm, 7.8±1.1 mm, and 8.2±0.9 mm, respectively) ( P<0.05), although there was some overlapping between AD and FTD patients. All patients whose temporal stem width was <6 mm had FTD. While the width of the corpus callosum, cingulate gyri, and hippocampi was significantly narrower in patients with AD and FTD than in the controls, there was no significant difference between the AD and FTD patients. Conclusion: The width of the temporal stem was significantly narrower in patients with FTD than in those with AD and controls. The described measurements can easily be obtained and may be useful for the diagnosis of FTD.
ET viewer: an application for predicting and visualizing functional sites in protein structures
Authors: Morgan Daniel H. , Kristensen David M. , Mittelman David , Lichtarge Olivier 
Published: June 2006

Abstract
Summary: The Evolutionary Trace Viewer (ETV) provides a one-stop environment in which to run, visualize and interpret Evolutionary Trace (ET) predictions of functional sites in protein structures. ETV is implemented using Java to run across different operating systems using Java Web Start technology.
Availability: The ETV is available for download from our website at . This webpage also links to sample trace results and a user manual that describes ET Viewer functions in detail.
Contact: lichtarge@bcm.edu
A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-α
Authors: Li Lang , Cheng Alfred S. L. , Jin Victor X. , Paik Henry H. , Fan Meiyun , Li Xiaoman , Zhang Wei , Robarge Jason , Balch Curtis , Davuluri Ramana V. , Kim Sun , Huang Tim H.-M. , Nephew Kenneth P. 
Published: June 2006

Abstract
Motivation: To detect and select patterns of transcription factor binding sites (TFBSs) which distinguish genes directly regulated by estrogen receptor-α (ERα), we developed an innovative mixture model-based discriminate analysis for identifying ordered TFBS pairs.
Results: Biologically, our proposed new algorithm clearly suggests that TFBSs are not randomly distributed within ERα target promoters (P-value &lt; 0.001). The up-regulated targets significantly (P-value &lt; 0.01) possess TFBS pairs, (DBP, MYC), (DBP, MYC/MAX heterodimer), (DBP, USF2) and (DBP, MYOGENIN); and down-regulated ERα target genes significantly (P-value &lt; 0.01) possess TFBS pairs, such as (DBP, c-ETS1-68), (DBP, USF2) and (DBP, MYOGENIN). Statistically, our proposed mixture model-based discriminate analysis can simultaneously perform TFBS pattern recognition, TFBS pattern selection, and target class prediction; such integrative power cannot be achieved by current methods.
Availability: The software is available on request from the authors.
Contact: lali@iupui.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Domain organization within repeated DNA sequences: application to the study of a family of transposable elements
Authors: Tempel Sébastien , Giraud Mathieu , Lavenier Dominique , Lerman Israël-César , Valin Anne-Sophie , Couée Ivan , Amrani Abdelhak El , Nicolas Jacques 
Published: June 2006

Abstract
Motivation: The analysis of repeated elements in genomes is a fascinating domain of research that is lacking relevant tools for transposable elements (TEs), the most complex ones. The dynamics of TEs, which provides the main mechanism of mutation in some genomes, is an essential component of genome evolution. In this study we introduce a new concept of domain, a segmentation unit useful for describing the architecture of different copies of TEs. Our method extracts occurrences of a terminus-defined family of TEs, aligns the sequences, finds the domains in the alignment and searches the distribution of each domain in sequences. After a classification step relative to the presence or the absence of domains, the method results in a graphical view of sequences segmented into domains.
Results: Analysis of the new non-autonomous TE AtREP21 in the model plant Arabidopsis thaliana reveals copies of very different sizes and various combinations of domains which show the potential of our method.
Availability: DomainOrganizer web page is available at
Contact: DomainOrganizer@irisa.fr
Effects of replacing the unreliable cDNA microarray measurements on the disease classification based on gene expression profiles and functional modules
Authors: Wang Dong , Lv Yingli , Guo Zheng , Li Xia , Li Yanhui , Zhu Jing , Yang Da , Xu Jianzhen , Wang Chenguang , Rao Shaoqi , Yang Baofeng 
Published: June 2006

Abstract
Motivation: Microarrays datasets frequently contain a large number of missing values (MVs), which need to be estimated and replaced for subsequent data mining. The focus of the paper is to study the effects of different MV treatments for cDNA microarray data on disease classification analysis.
Results: By analyzing five datasets, we demonstrate that among three kinds of classifiers evaluated in this study, support vector machine (SVM) classifiers are robust to varied MV imputation methods [e.g. replacing MVs by zero, K nearest-neighbor (KNN) imputation algorithm, local least square imputation and Bayesian principal component analysis], while the classification and regression tree classifiers are sensitive in terms of classification accuracy. The KNNclassifiers built on differentially expressed genes (DEGs) are robust to the varied MV treatments, but the performances of the KNN classifiers based on all measured genes can be significantly deteriorated when imputing MVs for genes with larger missing rate (MR) (e.g. MR &gt; 5%). Generally, while replacing MVs by zero performs relatively poor, the other imputation algorithms have little difference in affecting classification performances of the SVM or KNN classifiers. We further demonstrate the power and feasibility of our recently proposed functional expression profile (FEP) approach as means to handle microarray data with MVs. The FEPs, which are derived from the functional modules that are enriched with sets of DEGs and thus can be consistently identified under varied MV treatments, achieve precise disease classification with better biological interpretation. We conclude that the choice of MV treatments should be determined in context of the later approaches used for disease classification. The suggested exclusion criterion of ignoring the genes with larger MR (e.g. &gt;5%), while justifiable for some classifiers such as KNN classifiers, might not be considered as a general rule for all classifiers.
Contact: guoz@ems.hrbmu.edu.cn; yangbf@ems.hrbmu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature
Authors: Grimes G. R. , Wen T. Q. , Mewissen M. , Baxter R. M. , Moodie S. , Beattie J. S. , Ghazal P. 
Published: June 2006

Abstract
Summary: PDQ Wizard automates the process of interrogating biomedical references using large lists of genes, proteins or free text. Using the principle of linkage through co-citation biologists can mine PubMed with these proteins or genes to identify relationships within a biological field of interest. In addition, PDQ Wizard provides novel features to define more specific relationships, highlight key publications describing those activities and relationships, and enhance protein queries. PDQ Wizard also outputs a metric that can be used for prioritization of genes and proteins for further research.
Availability: PDQ Wizard is freely available from
Contact: Graeme.Grimes@ed.ac.uk
Supplementary Information: Supplementary Data are available
Pathway analysis using random forests classification and regression
Authors: Pang Herbert , Lin Aiping , Holford Matthew , Enerson Bradley E. , Lu Bin , Lawton Michael P. , Floyd Eugenia , Zhao Hongyu 
Published: June 2006

Abstract
Motivation: Although numerous methods have been developed to better capture biological information from microarray data, commonly used single gene-based methods neglect interactions among genes and leave room for other novel approaches. For example, most classification and regression methods for microarray data are based on the whole set of genes and have not made use of pathway information. Pathway-based analysis in microarray studies may lead to more informative and relevant knowledge for biological researchers.
Results: In this paper, we describe a pathway-based classification and regression method using Random Forests to analyze gene expression data. The proposed methods allow researchers to rank important pathways from externally available databases, discover important genes, find pathway-based outlying cases and make full use of a continuous outcome variable in the regression setting. We also compared Random Forests with other machine learning methods using several datasets and found that Random Forests classification error rates were either the lowest or the second-lowest. By combining pathway information and novel statistical methods, this procedure represents a promising computational strategy in dissecting pathways and can provide biological insight into the study of microarray data.
Availability: Source code written in R is available from
Contact: hongyu.zhao@yale.edu
Supplementary Information: Supplementary Data are available at
SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs
Authors: Reumers Joke , Maurer-Stroh Sebastian , Schymkowitz Joost , Rousseau Frederic 
Published: June 2006

Abstract
Summary: Single nucleotide polymorphisms (SNPs) constitute the most fundamental type of genetic variation in human populations. About 75 000 of these reported variations cause an amino acid change in the translated protein. An important goal in genomic research is to understand how this variability affects protein function, and whether or not particular SNPs are associated to disease susceptibility. Accordingly, the SNPeffect database uses sequence- and structure-based bioinformatics tools to predict the effect of non-synonymous SNPs on the molecular phenotype of proteins. SNPeffect analyses the effect of SNPs on three categories of functional properties: (1) structural and thermodynamic properties affecting protein dynamics and stability (2) the integrity of functional and binding sites and (3) changes in posttranslational processing and cellular localization of proteins. The search interface of the database can be used to search specifically for polymorphisms that are predicted to cause a change in one of these properties. Now based on the Ensembl human databases, the SNPeffect database has been remodeled to better fit an automatically updatable structure. The current edition holds the molecular phenotype of 74 567 nsSNPs in 23 426 proteins.
Availability: SNPeffect can be accessed through
Supplementary Material: Statistics on the contents of the database, figures on the workflow used to create the database and information on the used sources and tools is available at .
Contact: joost.schymkowitz@vub.ac.be or frederic.rousseau@vub.ac.be
An iterative refinement algorithm for consistency based multiple structural alignment methods
Authors: Chen Yu , Crippen Gordon M. 
Published: June 2006

Abstract
Motivation: Multiple STructural Alignment (MSTA) provides valuable information for solving problems such as fold recognition. The consistency-based approach tries to find conflict-free subsets of alignments from a pre-computed all-to-all Pairwise Alignment Library (PAL). If large proportions of conflicts exist in the library, consistency can be hard to get. On the other hand, multiple structural superposition has been used in many MSTA methods to refine alignments. However, multiple structural superposition is dependent on alignments, and a superposition generated based on erroneous alignments is not guaranteed to be the optimal superposition. Correcting errors after making errors is not as good as avoiding errors from the beginning. Hence it is important to refine the pairwise library to reduce the number of conflicts before any consistency-based assembly.
Results: We present an algorithm, Iterative Refinement of Induced Structural alignment (IRIS), to refine the PAL. A new measurement for the consistency of a library is also proposed. Experiments show that our algorithm can greatly improve T-COFFEE performance for less consistent pairwise alignment libraries. The final multiple alignment outperforms most state-of-the-art MSTA algorithms at assembling 15 transglycosidases. Results on three other benchmarks showed that the algorithm consistently improves multiple alignment performance.
Availability: The C++ code of the algorithm is available upon request.
Contact: gcrippen@umich.edu
Setting priorities: global patterns of disaster risk
Authors: Dilley Maxx 
Published: June 2006

Natural disasters are caused by the exposure and vulnerabilities to natural hazards of people, infrastructure and economic activities. Analysis of these factors has permitted identification of countries and areas within them where disaster-related mortality and economic losses are likely in the future. These high-risk areas are candidates for increased attention to, and investment in, disaster risk identification, reduction and transfer.Plans are underway to further identify disaster risk levels and factors on national and subnational scales in high-risk countries to create evidence for improved risk management decision-making. In this paper, I review selected recent global and regional risk analyses to highlight findings, areas for improvement and next steps in the overall process of using disaster risk information for more effective risk management and cost-effective reduction of losses.
Influence of steel composition on strain induced corrosion cracking and other types of corrosion
Authors: Huijbregts W. , Leferink R. 
Published: June 2006

PurposeTo make clear that C‐steel can differ very much in corrosion resistance under practical conditions only because of differences in chemical composition of the steels.Design/methodology/approachIn the electricity generating industry, “mild” (i.e. “plain carbon”) and low‐alloyed steels are used in huge quantities, for instance, in boilers, steam generators, heat recovery boilers and waste incineration boilers. The resistance to strain induced corrosion cracking (SICC) was determined by measuring the “repassivation” behaviour of the steels at freshly ground surfaces with an electrochemical technique. The corrosion current measured with time was used to calculate the cracking rates of a compact tension specimen.FindingsA correlation was found between chemical composition, corrosion resistance to SICC and experiences under practical conditions. The results of early‐published papers on boiler corrosion (testing in FeCl2 solutions), erosion corrosion (testing in wet steam at 20 bar), nitrate stress corrosion cracking (testing in NH4NO3 solutions) and SICC together with those originating from in‐service failures, were compiled into a reference database. This paper is a compilation of this work too.Originality/valueThe database and formulas presented make clear there is often a direct correlation between chemical composition of ordinary C‐steel and mentioned types of corrosion failures. The paper is of importance to designers, failure analysts and researchers.
Evaluation of mild steel corrosion using a new surfactant inhibition model
Authors: Youp Ryu Dong , Free Michael L. 
Published: June 2006

PurposeTo evaluate mild steel corrosion using a new surfactant‐inhibition model which was derived, in part, from the concept of intermolecular energy and molecular separation distance.Design/methodology/approachA Gamry potentiostat was used for polarization resistance tests to determine corrosion rate and the level of adsorption of surfactant at the solution‐metal interface was determined using UV‐spectroscopy. The relationship between inhibition and surfactant adsorption as well as metal corrosion was investigated using a traditional surfactant‐inhibition model, which assumes inhibition is directly proportional to surfactant coverage and new model.FindingsThe comparison of adsorption data and corrosion inhibition data shows inhibition was not directly proportional to physical coverage as assumed by the traditional inhibition model. Instead, it was found that coverage was related to inhibition through a power‐law dependency that is similar to that used to determine molecular interaction energies.Research limitations/implicationsThe new model was evaluated only for dodecyl pyridinium chloride mild steel system. The evaluation of the new model for various surfactant‐metal systems is suggested for future research.Originality/valueThe new model was found to more accurately predict the relationship between inhibition and coverage rather than traditional models for dodecyl pyridinium chloride‐mild steel system.
Iron corrosion inhibition with dihydrobis‐ and hydrotris‐(1‐pyrazolyl)borates
Authors: Babić‐Samardžija Ksenija , Hackerman Norman 
Published: June 2006

PurposeThe objective in the present paper is a better understanding of acidic corrosion inhibition by polypyrazolylborates on iron electrodes. Structural and electronic effects of these compounds are discussed in relation to the inhibiting efficiencies and absorption.Design/methodology/approachTwo polypyrazolylborates, i.e. dihydrobis(1‐pyrazolyl) borate (Bp) and hydrotris(1‐pyrazolyl)borate (Tp) were investigated as corrosion inhibitors for iron in 1 mol/l HCl and in 0.5 mol/l H2SO4 using Tafel measurements, linear polarization resistance and electrochemical impedance spectroscopy. Theoretical explanation between molecular parameters of these compounds and inhibitor efficiency (IE) was made using the MNDO SCF‐MO method. Morphological changes of the reacted surfaces were monitored via SEM.FindingsResults obtained show higher inhibition effect of Bp than Tp. Inhibitors are more efficient in HCl than in H2SO4. Corrosion current and corrosion rate (CR) decrease with inhibitor concentration, while polarization and charge transfer resistance markedly increase from 10−4 to 10−2 mol/l inhibitor concentration range. All impedance data are modeled with an equivalent circuit model. The semicircular shape of Nyquist plots is indicative of a charge transfer process occurring via a parallel resistor and capacitor.Originality/valueThis study provides constructive information relative to corrosion inhibitor behavior of polypyrazolylborates in acids. Using the molecular modeling calculations, the compounds were characterized in terms of their structural properties and inhibition activity. It was noticed how exposure to the inhibitor solution changes the film morphology.