bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selectivity of an indolyl berberine derivative for tetrameric G‐quadruplex DNA
Authors: Gornall Karina C. , Samosorn Siritron , Talib Jihan , Bremner John B. , Beck Jennifer L. 
Published: May 2007

AbstractNegative ion electrospray ionization mass spectrometry (ESI‐MS) was used to compare the binding affinities and stoichiometries of the alkaloid berberine, a 13‐substituted indolyl berberine derivative, SS14, and the chemotherapeutic agent, daunomycin, for 16‐mer double‐stranded (ds) DNA (D1 and D2) and for an 8‐mer tetrameric quadruplex, Q1 (d(TTGGGGGT)4). Under the experimental conditions presented here, ESI mass spectra of Q1 showed that the major ions were from Q1 with three ammonium ions bound in the structure. Ions from Q1 with four ammonium ions were of lower abundance. In agreement with other work, there were multiple binding sites on the dsDNA and the quadruplex for daunomycin and berberine. The binding of SS14 to both dsDNA and Q1 was less extensive. Although the binding affinity of SS14 for Q1 was modest, this compound showed a clear preference for Q1 DNA over D1 or D2 DNA. Berberine and daunomycin bound with greater affinity to both types of DNA secondary structure, with the former showing a slight preference for Q1 over D1 while the latter showed a slight preference for D1 over Q1. While at least five berberine molecules bound to Q1, this quadruplex could accommodate only two SS14 molecules. These investigations show that SS14 is a promising lead compound for drugs that may selectively bind quadruplex over duplex DNA. Copyright © 2007 John Wiley & Sons, Ltd.
Energy‐variable collision‐induced dissociation study of 1,3,5‐trisubstituted 2‐pyrazolines by electrospray mass spectrometry
Authors: Kéki Sándor , Nagy Lajos , Török János , Tóth Katalin , Lévai Albert , Zsuga Miklós 
Published: May 2007

AbstractThe pathways of the ([M+H]+) ions generated from electrosprayed solutions of nine 1,3,5‐trisubstituted 2‐pyrazoline derivatives were studied using energy‐variable collision‐induced dissociation (CID) and pseudo‐MS3 (in‐source CID combined with MS/MS) methods. It was shown that under CID conditions several structurally important product ions such as the 2,4‐substituted azete and 1,2‐substituted aziridine ions were formed. The compositions of the product ions were unambiguously supported by accurate mass measurement (mass accuracy was within ± 8 ppm). The fragmentation pathways of 1,3,5‐trisubstituted 2‐pyrazolines were established by means of pseudo‐MS3. It was found that a substituent at the N‐1 position greatly affects the fragmentation pathways of the 2‐pyrazoline derivatives. The 1‐acetyl‐ and 1‐propionyl‐2‐pyrazoline derivatives dissociate mainly through formation of a pyrazolium cation, while in the case of 1‐phenyl‐2‐pyrazoline derivatives product ions arising from the consecutive fragmentation of 2,4‐substituted azete and 1,2‐substituted aziridine ions dominate. Another interesting finding is the formation of a radical cation from the 2,4‐substituted azete by loss of a methyl radical. The fragmentation yield as a function of the collision energy for each of the 1,3,5‐trisubstituted 2‐pyrazolines was determined. Based on the fragmentation yield versus collision energy curves the relative fragmentation stabilities for the 1,3,5‐trisubstituted 2‐pyrazoline derivatives were also evaluated. Copyright © 2007 John Wiley & Sons, Ltd.
Investigation of unknown related substances in commercial neomycin samples with liquid chromatography/ion trap tandem mass spectrometry
Authors: Li Bo , Van Schepdael Ann , Hoogmartens Jos , Adams Erwin 
Published: May 2007

AbstractThe characterization of unknown impurities present in neomycin sulfate by liquid chromatography (LC) coupled with ion trap mass spectrometry (ITMS) is described. The volatile LC method was developed using an evaporative light scattering detector due to its lower investment and operating costs, easier operation and less maintenance than mass spectrometry. The method shows separation of neomycin B from seven potential related substances reported in the European Pharmacopoeia and several other unknown impurities. The unknown impurities were further investigated by coupling the developed LC method with ITMS. Their structures were deduced based on the fragmentation patterns obtained from reference substances. Four unknowns were identified as isomers of paromamine, LP‐A, neamine and LP‐B. Copyright © 2007 John Wiley & Sons, Ltd.
Genetic evolution of enterovirus 71: epidemiological and pathological implications
Authors: Bible Jon M. , Pantelidis Panagiotis , Chan Paul K. S. , Tong C. Y. William 
Published: May 2007

AbstractSince its discovery in the 1970s, enterovirus 71 (EV71) has become one of the most pathogenic enterovirus serotypes causing recurrent outbreaks in different parts of the world. Three waves of outbreaks globally have been recorded over the last three decades and more recently active circulation of EV71 is evident amongst countries in South East Asia and beyond. There is evidence of a continuous evolution in its genetic make up which is likely to impact on its epidemiology and pathological potential. This review examines the molecular genetics and evolution of EV71 in relation to its epidemiological and pathological properties. A thorough understanding of the relationship between the genetic changes and the resulting host–virus interaction is essential for successful control. Copyright © 2007 John Wiley & Sons, Ltd.
Prediction of ectopic pregnancy in women with a pregnancy of unknown location
Authors: Condous G. , Van Calster B. , Kirk E. , Haider Z. , Timmerman D. , Van Huffel S. , Bourne T. 
Published: May 2007

AbstractObjectiveWe have previously published on the use of mathematical Model M1 to predict ectopic pregnancy in women with no signs of intra‐ or extrauterine pregnancy. The aim of this study was to improve on the performance of this model for the detection of developing ectopic pregnancies in women with pregnancies of unknown location (PULs). We therefore generated and evaluated a new logistic regression model from simple hormonal data and compared it with Model M1.MethodsData were collected prospectively from women classified as having a PUL. These women were followed until the diagnosis was established as: a failing PUL, an intrauterine pregnancy (IUP) or an ectopic pregnancy. A multinomial logistic regression model, Model M4, was developed on 201 training cases and it was tested prospectively on another 175 women with a PUL. M4 performance was evaluated using receiver–operating characteristics (ROC) curves and compared with Model M1 based on the human chorionic gonadotropin (hCG) ratio alone.ResultsA total of 376 women with a PUL were recruited into this study: 201 in the training set (109 (54.2%) with a failing PUL, 76 (37.8%) with an IUP and 12 (6.0%) with an ectopic pregnancy; four with a persisting PUL were excluded from analysis) and 175 in the test set (94 (53.7%) with a failing PUL, 64 (36.6%) with an IUP and 15 (8.6%) with an ectopic pregnancy; two with a persisting PUL were excluded from analysis). The log serum hCG average ((hCG 0 h + hCG 48 h)/2) and the hCG ratio (hCG 48 h/hCG 0 h) were encoded as variables following multivariate analysis of the basic data. The new Model M4 contained the log of the hCG average, the hCG ratio and its quadratic effect. In the prediction of ectopic pregnancy, M4 gave an area under the ROC curve (AUC) of 0.900 and M1 gave an AUC of 0.842 (P = 0.0303).ConclusionsAlthough Model M4 is superior to Model M1 when comparing the AUCs for prediction of developing ectopic pregnancies in a PUL population, in real terms this model did not result in substantially more pregnancies being classified correctly as developing ectopic pregnancies. Prospective multicenter studies are needed to assess the diagnostic performance of such models in different populations. Copyright © 2007 ISUOG. Published by John Wiley & Sons, Ltd.
Use of argentation column chromatography in the identification of fish oil fatty acids by GLC: Application to cod liver oil
Authors: Hoque M. , Ghosh Amitabha , Dutta J. 
Published: May 2007

AbstractThe fatty acid methyl esters from cod liver oil have been fractionated into seven fractions, depending on degree of unsaturation, by a silver nitratetreated silicic acid column. The fractions have been analyzed by gas liquid chromatography and the components identified by usual techniques.
Application of ternary equilibrium data to the production of fish protein concentrate
Authors: McPhee A. D. , Dubrow D. L. 
Published: May 2007

AbstractStandard chemical engineering techniques were applied to ternary equilibria data obtained from laboratory studies for the systems water‐isopropyl alcohol‐menhaden oil and water‐ethanol‐menhaden oil to obtain information for development and operation of a fish protein concentrate process. Theoretical minimum solvent ratios, the required number of theoretical stages, stage efficiency, effect of excess water in the solvent and the effect of temperature of extraction are reported. A comparison of the solvent, isopropyl alcohol (IPA) and ethanol, at an extraction temperature of 70 C, leaves no doubt that IPA is a superior solvent for the system studied.
Alkoxylation of N‐alkyl substituted ethylenediamine
Authors: Rosenblatt W. , Stefcik A. , Bluestein C. , Kim Y. K. 
Published: May 2007

AbstractThe alkoxylation of a new mixture of N‐alkylethylenediamines obtained by reacting C11.5 av. chloroparaffins and ethylenediamine was studied. Ethoxylation in both laboratory glassware or Parr autoclave equipment readily produced 20 mole adducts without alkaline catalysis. The reaction was initiated by the formation of the 3 mole adduct at 160 C and subsequent addition of the alkylene oxide at 90 C. The formation of adducts with mole ratios greater than 20 required an alkaline catalyst. The preparation of propoxylate derivatives necessitated the addition of 2.5–3.0 wt % of caustic catalyst. The preparative time was minimized by operating at 185–190 C and 40–50 psi. The surfactant properties of the alkoxylates were evaluated and correlated with structures and compositions. Data on solubility, surface tension, density, refractive index, pH and foam characteristics are presented. Polyurethane foams were prepared from several of the alkoxylates.
Effect of the initial concentration of emulsifying agents on the ultracentrifugal stability of oil‐in‐water emulsions
Authors: Mittal Kashmiri L. , Vold Robert D. 
Published: May 2007

AbstractThe rate of loss of oil from 50% Nujol‐50% water emulsions stabilized with varying concentrations of Tween 20 or Triton X‐100, and from 50% olive oil‐50% water emulsions stabilized with sodium dodecyl sulfate (SDS), was determined by ultracentrifugation at 39,460 rpm. In all cases the ultracentrifugal stability increased with increasing initial concentration of emulsifier, although, unlike the behavior of Nujol‐water‐SDS emulsions, the rate of separation of oil decreased with time. The quantity of olive oil separated after a given time of centrifugation decreased linearly with increasing concentration of SDS, reaching zero at a concentration of SDS somewhat below the critical micelle concentration, and at adsorption of SDS corresponding to only about half the saturation capacity. The ultracentrifugal stability of Nujol emulsions with Tween 20 or Triton X‐100 continued to increase slowly with increasing concentration of emulsifier, even at concentrations far greater than the critical micelle concentration.
Observational Teamwork Assessment for Surgery (OTAS): Refinement and Application in Urological Surgery
Authors: Undre Shabnam , Sevdalis Nick , Healey Andrew N. , Darzi Ara , Vincent Charles A. 
Published: May 2007

AbstractBackgroundTeamwork in surgical teams is at the forefront of good practice guidelines and empirical research as an important aspect of safe surgery. We have developed a comprehensive assessment for teamwork in surgery—the Observational Teamwork Assessment for Surgery (OTAS)—and we have tested it for general surgical procedures. The aim of the research reported here was to extend the assessment to urology procedures.MethodsAfter refining the original assessment, we used it to observe 50 urology procedures. The OTAS comprises a procedural task checklist that assesses patient, equipment/provisions, and communication tasks as well as ratings on five team behavior constructs (communication, cooperation, coordination, leadership, and monitoring). Teamwork was assessed separately in the surgical, anesthesia, and nursing subteams in the operating theater. We also assessed the reliability of the behavioral scoring.ResultsRegarding task completion, a number of communication and equipment/provisions tasks were not routinely performed during the operations we observed. Regarding teamwork‐related behaviors, adequate reliability was obtained in the scoring of behaviors. Anesthetists and nurses obtained their lowest scores on communication. Surgeons’ scores revealed a more complex pattern. In addition to low scores on communication, surgeons’ teamwork behaviors appeared to deteriorate as the procedures were finishing.ConclusionsOur findings suggest that OTAS is applicable to various branches of surgery. Separate assessment of the subteams in the operating theater provides useful information that can be used to build targeted teamwork training aiming to improve surgical patients’ safety and outcomes.
Agonist‐dependent consequences of proline to alanine substitution in the transmembrane helices of the calcitonin receptor
Authors: Bailey R J , Hay D L 
Published: May 2007

Background and purpose:Transmembrane proline (P) residues in family A G protein‐coupled receptors (GPCRs) form functionally important kinks in their helices. These residues are little studied in family B GPCRs but experiments with the VPAC1 receptor and calcitonin receptor‐like receptor (CL) show parallels with family A receptors. We sought to determine the function of these residues in the insert negative form of the human calcitonin receptor, a close relative of CL.Experimental approach:Proline residues within the transmembrane domains of the calcitonin receptor (P246, P249, P280, P326, P336) were individually mutated to alanine (A) using site‐directed mutagenesis. Receptors were transiently transfected into Cos‐7 cells using polyethylenimine and salmon and human calcitonin‐induced cAMP responses measured. Salmon and human calcitonin competition binding experiments were also performed and receptor cell‐surface expression assessed by whole cell ELISA.Key results:P246A, P249A and P280A were wild‐type in terms of human calcitonin‐induced cAMP activation. P326A and P336A had reduced function (165 and 12‐fold, respectively). In membranes, human calcitonin binding was not detectable for any mutant receptor but in whole cells, binding was detected for all mutants apart from P326A. Salmon calcitonin activated mutant and wild‐type receptors equally, although Bmax values were reduced for all mutants apart from P326A.Conclusions and Implications:P326 and P336 are important for the function of human calcitonin receptors and are likely to be involved in generating receptor conformations appropriate for agonist binding and receptor activation. However, agonist‐specific effects were observed, implying distinct conformations of the human calcitonin receptor.British Journal of Pharmacology (2007) 151, 678–687; doi:10.1038/sj.bjp.0707246
ChromatinDB: a database of genome-wide histone modification patterns forSaccharomyces cerevisiae
Authors: O’Connor Timothy R. , Wyrick John J. 
Published: May 2007

AbstractSummary: Covalent modifications to histone proteins play a critical role in regulating gene transcription. Previous studies have used chromatin immunoprecipitation (ChIP) based microarray assays to profile genomic regions that are enriched or depleted for a particular histone modification. Such studies have been conducted extensively in the yeast Saccharomyces cerevisiae, but currently no comprehensive data repositories or analysis tools are available for these data sets. For this reason, we have developed the ChromatinDB database, which contains genome-wide ChIP data for 22 different histones or histone modifications in S.cerevisiae. ChromatinDB provides novel tools to facilitate the visualization and statistical analysis of chromatin features for user-selected gene sets.Availability: http://www.bioinformatics2.wsu.edu/ChromatinDBContact: jwyrick@wsu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering
Authors: Xiang Zuoshuang , Qin Zhaohui S. , He Yongqun 
Published: May 2007

AbstractSummary: CRCView is a user-friendly point-and-click web server for analyzing and visualizing microarray gene expression data using a Dirichlet process mixture model-based clustering algorithm. CRCView is designed to clustering genes based on their expression profiles. It allows flexible input data format, rich graphical illustration as well as integrated GO term based annotation/interpretation of clustering results.Availability: http://helab.bioinformatics.med.umich.edu/crcview/Contact: yongqunh@umich.edu
Bioinformatics software for biologists in the genomics era
Authors: Kumar Sudhir , Dudley Joel 
Published: May 2007

AbstractMotivation: The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large datasets in comparative sequence analyses for making evolutionary, functional and translational inferences. However, the majority of the scientists at the forefront of experimental research are not bioinformaticians, so a gap exists between the user-friendly software needed and the scripting/programming infrastructure often employed for the analysis of large numbers of genes, long genomic segments and groups of sequences. We see an urgent need for the expansion of the fundamental paradigms under which biologist-friendly software tools are designed and developed to fulfill the needs of biologists to analyze large datasets by using sophisticated computational methods. We argue that the design principles need to be sensitive to the reality that comparatively small teams of biologists have historically developed some of the most popular biological software packages in molecular evolutionary analysis. Furthermore, biological intuitiveness and investigator empowerment need to take precedence over the current supposition that biologists should re-tool and become programmers when analyzing genome scale datasets.Contact: s.kumar@asu.edu
Management Considerations for Differentiated Thyroid Carcinoma Presenting as a Metastasis to the Skull Base
Authors: Mydlarz Wojciech K. , Wu Julie , Aygun Nafi , Olivi Alessandro , Carey John P. , Westra William H. , Tufano Ralph P. 
Published: May 2007

AbstractObjectives/Hypothesis: To characterize the salient features of skull base metastasis from differentiated thyroid carcinoma, discuss the diagnostic and treatment strategies, and propose rational management guidelines for such tumors.Study Design: Case report.Methods: Review of English literature from MEDLINE with the addition of our case.Results: Skull base metastasis from differentiated thyroid carcinoma is rare, with only 20 cases reported to date, including our case report. On the basis of a review of all reported cases, both follicular and papillary thyroid cancers can metastasize to the skull base. Our case is unique because the lesion extends locally into the cavernous sinus and beyond. Histopathologic diagnosis is limited by the remote location of lesions. Most tumors are highly vascular, and there is potential for significant morbidity and mortality associated with surgical resection. The overall survival ranges from less than one year to 10+ years from the discovery of the metastasis and is similar in both tumor subtypes. There is no clear consensus on the management strategy for skull base metastasis from differentiated thyroid carcinoma. Interestingly, surgical resection of both the primary and metastatic lesions yields similar survival when compared with resection of the primary tumor alone.Conclusions: Distant metastasis from differentiated thyroid carcinoma needs to be considered in the differential diagnosis of destructive skull base lesions, regardless of the patient's age. Histopathologic tissue diagnosis should always be attempted, followed by total thyroidectomy, radioiodine, or external beam radiation, and chronic thyroid‐stimulating hormone suppression. Surgical resection of the metastatic lesion should only be performed in carefully selected cases because it is associated with significant morbidity.
Algorithm for Reconstruction After Endoscopic Pituitary and Skull Base Surgery
Authors: Tabaee Abtin , Anand Vijay K. , Brown Seth M. , Lin Jerry W. , Schwartz Theodore H. 
Published: May 2007

AbstractIntroduction: The expanding role of endoscopic skull base surgery necessitates a thorough understanding of the indications, techniques, and limitations of the various approaches to reconstruction. The technique and outcomes of endoscopic skull base reconstruction remain incompletely described in the literature.Study Design and Methods: Patients undergoing endoscopic skull base surgery underwent an algorithmic approach to reconstruction based on tumor location, defect size, and presence of intraoperative cerebrospinal fluid (CSF) leak. A prospective database was reviewed to determine the overall efficacy of reconstruction and to identify risk factors for postoperative CSF leak.Results: The diagnosis in the 127 patients in this series included pituitary tumor in 70 (55%) patients, encephalocele in 16 (12.6%) patients, meningioma in 11 (8.7%) patients, craniopharyngioma in 9 (7.1%) patients, and chordoma in 6 (4.7%) patients. Successful reconstruction was initially achieved in 91.3% of patients. Eleven (8.7%) patients experienced postoperative CSF leak, 10 of which resolved with lumbar drainage alone. One (0.8%) patient required revision surgery. Correlation between postoperative CSF leak and study variables revealed a statistically significant longer duration of surgery (243 vs. 178 min, P = .008) and hospitalization (12.1 vs. 4.5 days, P < .0001) and a trend toward larger tumors (mean, 3.2 vs. 2.3 cm; P = .058) in patients experiencing postoperative CSF leak.Conclusion: The algorithm for reconstruction after endoscopic surgery presented in this study is associated with excellent overall efficacy. A greater understanding of risk factors for postoperative CSF leak is imperative to achieve optimal results.