bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic Analysis of the Major Envelope and Nucleocapsid Proteins of White Spot Syndrome Virus
Authors: Xie Xixian , Xu Limei , Yang Feng 
Published: October 2006

ABSTRACT

White spot syndrome virus (WSSV) virions were purified from the tissues of infected
Procambarus clarkii
(crayfish) isolates. Pure WSSV preparations were subjected to Triton X-100 treatment to separate into the envelope and nucleocapsid fractions, which were subsequently separated by 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The major envelope and nucleocapsid proteins were identified by either matrix-assisted laser desorption ionization-time of flight mass spectrometry or defined antibody. A total of 30 structural proteins of WSSV were identified in this study; 22 of these were detected in the envelope fraction, 7 in the nucleocapsid fraction, and 1 in both the envelope and the nucleocapsid fractions. With the aid of specific antibodies, the localizations of eight proteins were further studied. The analysis of posttranslational modifications revealed that none of the WSSV structural proteins was glycosylated and that VP28 and VP19 were threonine phosphorylated. In addition, far-Western and coimmunoprecipitation experiments showed that VP28 interacted with both VP26 and VP24. In summary, the data obtained in this study should provide an important reference for future molecular studies of WSSV morphogenesis.
Integrative missing value estimation for microarray data
Authors: Hu Jianjun , Li Haifeng , Waterman Michael S , Zhou Xianghong Jasmine 
Published: October 2006

Abstract

Background
Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples.

Results
We present the integrative Missing Value Estimation method (iMISS) by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS) imputation algorithm by up to 15% improvement in our benchmark tests.

Conclusion
We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.
Genepi: a blackboard framework for genome annotation
Authors: Descorps-Declère Stéphane , Ziébelin Danielle , Rechenmann François , Viari Alain 
Published: October 2006

AbstractBackgroundGenome annotation can be viewed as an incremental, cooperative, data-driven, knowledge-based process that involves multiple methods to predict gene locations and structures. This process might have to be executed more than once and might be subjected to several revisions as the biological (new data) or methodological (new methods) knowledge evolves. In this context, although a lot of annotation platforms already exist, there is still a strong need for computer systems which take in charge, not only the primary annotation, but also the update and advance of the associated knowledge. In this paper, we propose to adopt a blackboard architecture for designing such a systemResultsWe have implemented a blackboard framework (called Genepi) for developing automatic annotation systems. The system is not bound to any specific annotation strategy. Instead, the user will specify a blackboard structure in a configuration file and the system will instantiate and run this particular annotation strategy. The characteristics of this framework are presented and discussed. Specific adaptations to the classical blackboard architecture have been required, such as the description of the activation patterns of the knowledge sources by using an extended set of Allen's temporal relations. Although the system is robust enough to be used on real-size applications, it is of primary use to bioinformatics researchers who want to experiment with blackboard architectures.ConclusionIn the context of genome annotation, blackboards have several interesting features related to the way methodological and biological knowledge can be updated. They can readily handle the cooperative (several methods are implied) and opportunistic (the flow of execution depends on the state of our knowledge) aspects of the annotation process.
Noninvasive Prenatal Detection of Fetal Trisomy 18 by Epigenetic Allelic Ratio Analysis in Maternal Plasma: Theoretical and Empirical Considerations
Authors: Tong Yu K , Ding Chunming , Chiu Rossa WK , Gerovassili Ageliki , Chim Stephen SC , Leung Tak Y , Leung Tse N , Lau Tze K , Nicolaides Kypros H , Lo YM Dennis 
Published: October 2006

Abstract
Background: The discovery of cell-free fetal DNA in maternal plasma has opened up new possibilities for noninvasive prenatal diagnosis. However, the use of maternal plasma fetal DNA for the direct detection of fetal chromosomal aneuploidies has not been reported. We postulate that the aneuploidy status of a fetus could be revealed by an epigenetic allelic ratio approach, i.e., by analyzing the allelic ratio of a single-base variation present within DNA molecules exhibiting a placental-specific epigenetic signature in maternal plasma.
Methods: Placental-derived fetal-specific unmethylated maspin (SERPINB5) promoter sequences on human chromosome 18 were detectable in placental–maternal DNA mixtures and in maternal plasma by bisulfite modification followed by methylation-specific PCR (MSP) and primer extension. The ratios between the extension products of the 2 alleles were calculated for heterozygous placentas, placental–maternal blood cell DNA mixtures, and maternal plasma samples. The allelic ratios were compared between pregnancies carrying trisomy 18 and euploid fetuses.
Results: The epigenetic allelic ratios of all tested trisomy 18 samples deviated from the reference range obtained from euploid samples (placental DNA, 1.135 to 2.052; placental–maternal DNA mixtures, 1.170 to 1.985; maternal plasma, 0.330 to 3.044; without skew correction on the raw mass spectrometric data). A theoretical model was established and validated that predicted that a minimum of 200 copies of genomic DNA after bisulfite conversion were required for distinguishing euploid and aneuploid fetuses with confidence.
Conclusion: Epigenetic allelic ratio analysis of maternal plasma DNA represents a promising approach for noninvasive prenatal diagnosis of fetal chromosomal aneuploidies.
Enantioselective Catalysis over Chiral Imidazolidin‐4‐one Immobilized on Siliceous and Polymer‐Coated Mesocellular Foams
Authors: Zhang Yugen , Zhao Lan , Lee Su Seong , Ying Jackie Y. 
Published: October 2006

AbstractA highly efficient and enantioselective organocatalyst, imidazolidin‐4‐one, has been successfully immobilized on siliceous MCF and polymer‐coated MCF. The resulting heterogenized catalyst demonstrated excellent catalytic performance and recyclability for Friedel–Crafts alkylation and Diels–Alder cycloaddition. The performance of the supported catalysts in relation to the surface environment of siliceous MCF was examined. It was found that partially pre‐capping the MCF with TMS groups enabled us to attain well‐dispersed catalysts on the siliceous support with optimal performance. We have also developed a polymer‐coated MCF, which retained the porous structure of MCF without the surface silanol groups. High reactivity and excellent recyclability were achieved by the organocatalyst immobilized on polymer‐coated MCF.
Productivity of Selective Electroenzymatic Reduction and Oxidation Reactions: Theoretical and Practical Considerations
Authors: Ruinatscha Reto , Höllrigl Volker , Otto Katja , Schmid Andreas 
Published: October 2006

AbstractThe volumetric productivities, final product concentration and total process times, of electroenzymatic processes comprising reductive electrochemical cofactor regeneration coupled to dehydrogenase or oxygenase catalyzed redox reactions determine process performance. Exemplified for the production of fine chemicals, operational windows were defined to consider these parameters. This theoretical approach allows the identification of limiting process parameters and promising process developments. Several biocatalytic processes for syntheses of specialty chemicals are already in a performance range of technical relevance. Electroenzymology thus evolved to a strong additional technology in the toolbox of biocatalysis and organic chemistry.
Terminal Alkyne Metathesis: A Further Step Towards Selectivity
Authors: Coutelier Olivier , Mortreux André 
Published: October 2006

AbstractTerminal alkyne metathesis has been improved by addition of quinuclidine as an external ligand to the (t‐BuO)3WCBu‐t carbyne complex, giving a yield of 80 % during hept‐1‐yne metathesis. Extension of this system to the co‐metathesis of terminal and disubstituted alkynes affords the expected cross‐reaction products.
Enzymatic Conversion of Unnatural Amino Acids by Yeast D‐Amino Acid Oxidase
Authors: Caligiuri Antonio , D'Arrigo Paola , Rosini Elena , Tessaro Davide , Molla Gianluca , Servi Stefano , Pollegioni Loredano 
Published: October 2006

AbstractUnnatural amino acids, particularly synthetic α‐amino acids, are becoming crucial tools for modern drug discovery research. In particular, this application requires enantiomerically pure isomers. In this work we report on the resolution of racemic mixtures of the amino acids d,l‐naphthylalanine and d,l‐naphthylglycine by using a natural enzyme, D‐amino acid oxidase from the yeast Rhodotorula gracilis. A significant improvement of the bioconversion is obtained using a single‐point mutant enzyme designed by a rational approach. With this D‐amino acid oxidase variant the complete resolution of all the unnatural amino acids tested was obtained: in this case, the bioconversion requires a shorter time and a lower amount of biocatalyst compared to the wild‐type enzyme. The simultaneous production of the corresponding α‐keto acid, a possible precursor of the amino acid in the L‐form, improves the significance of the procedure.
Facile Preparation of an Enzyme‐Immobilized Microreactor using a Cross‐Linking Enzyme Membrane on a Microchannel Surface
Authors: Honda Takeshi , Miyazaki Masaya , Nakamura Hiroyuki , Maeda Hideaki 
Published: October 2006

AbstractThe enzyme microreactor has considerable potential for use in biotechnological syntheses and analytical studies. Simplifying the procedure of enzyme immobilization in a microreactor is attractive, and it is achievable by utilizing enzyme immobilization techniques and taking advantage of the characteristics of microfluidics. We previously developed a facile and inexpensive preparation method for an enzyme‐immobilized microreactor. The immobilization of enzymes can be achieved by the formation of an enzyme‐polymeric membrane on the inner wall of the microchannel through cross‐linking polymerization in a laminar flow. However, this method is unsuitable for use in conjunction with electronegative enzymes. Therefore, a novel preparation method using poly‐L‐lysine [poly(Lys)] as a booster and an adjunct for the effective polymerization of electronegative enzymes was developed in this study. Using aminoacylase as a model for an electronegative enzyme, the reaction conditions for the enzyme‐cross‐linked aggregation were optimized. On the basis of the determined conditions, an acylase‐immobilized tubing microreactor was successfully prepared by cross‐linking polymerization in a concentric laminar flow. The resulting microreactor showed a higher stability against heat and organic solvents compared to those of the free enzyme. The developed method using poly(Lys) was applicable to various enzymes with low isoelectric points, suggesting that this microreactor preparation utilizing a cross‐linked enzyme in a laminar flow could be expanded to microreactors in which a broad range of functional proteins are employed.
Sustained increased risk of adverse cardiac events over 5 years after implantation of gold‐coated coronary stents
Authors: Pache Jürgen , Dibra Alban , Schaut Christian , Schühlen Helmut , Dirschinger Josef , Mehilli Julinda , Kastrati Adnan , Schömig Albert 
Published: October 2006

AbstractObjective: To study the 5‐year outcome of patients treated with gold‐coated stent placement. Background: We have previously shown in the setting of a randomized trial that gold‐coated stents are associated with worse mid‐term outcome, mainly because of an increased risk of restenosis, compared to uncoated stents. The long‐term outcome and, in particular, mortality risk after implantation of gold‐coated stents are not known. Methods: A total of 731 patients with symptoms or signs of ischemia received randomly either a gold‐coated (n = 367) or an uncoated steel stent (n = 364) of identical design. Patients were clinically followed‐up at 1 and 5 years. The primary endpoint of the study was the composite of major cardiac events (death, myocardial infarction, or target vessel revascularization (TVR)). The incidence of death was a secondary endpoint. Results: Five‐year follow‐up was available in 97.5% of the patients. The composite of death, myocardial infarction, or TVR occurred in 51% of the patients treated with gold‐coated stents and 40% of the patients treated with uncoated stents (P = 0.005). Of note, there was a marked increase in the absolute difference in mortality between patients in the gold‐coated and uncoated stent groups, from 1.6% at 1 year to 4.9% after 5‐year follow‐up (P = 0.09). A multivariate analysis showed that gold‐coated stent implantation was independently associated with 5‐year mortality (hazard ratio, 1.46; 95% confidence interval, 1.02–2.09; P = 0.04). Conclusions: Gold‐coated stents are associated with a sustained increased overall risk for major cardiac events, and notably, they may increase the long‐term mortality risk. © 2006 Wiley‐Liss, Inc.
Late migration of a Sideris buttoned device for occlusion of atrial septal defect
Authors: Cotts Timothy , Strouse Peter J. , Graziano Joseph N. 
Published: October 2006

AbstractWe describe a 17‐year‐old patient with an atrial septal defect who underwent device closure with a second generation Sideris buttoned device at 4 years of age. She presented 13 years after the procedure with the acute onset of chest discomfort, at which time a chest radiograph showed migration of the wire of the right atrial counter‐occluder to the lateral aspect of the right atrial wall, with an associated right atrial perforation. The patient underwent uneventful surgical device retrieval and atrial septal defect closure. Late migration of a portion of the Sideris buttoned device can occur, suggesting the need for continued follow up, and a high index of suspicion for device failure should a patient become symptomatic. © 2006 Wiley‐Liss, Inc.
Achieving fine‐grained access control in virtual organizations
Authors: Zhang N. , Yao L. , Nenadic A. , Chin J. , Goble C. , Rector A. , Chadwick D. , Otenko S. , Shi Q. 
Published: October 2006

AbstractIn a virtual organization environment, where services and data are provided and shared among organizations from different administrative domains and protected with dissimilar security policies and measures, there is a need for a flexible authentication framework that supports the use of various authentication methods and tokens. The authentication strengths derived from the authentication methods and tokens should be incorporated into an access‐control decision‐making process, so that more sensitive resources are available only to users authenticated with stronger methods. This paper reports our on‐going efforts in designing and implementing such a framework to facilitate multi‐level and multi‐factor adaptive authentication and authentication strength linked fine‐grained access control. The proof‐of‐concept prototype is designed and implemented in the Shibboleth and PERMIS infrastructures, which specifies protocols to federate authentication and authorization information and provides a policy‐driven, role‐based, access‐control decision‐making capability. Copyright © 2006 John Wiley & Sons, Ltd.
Synthesis and Structural Characterization of Sandwich‐Type Keggin‐γ‐Lacunary Silicotungstates with an Open Wells–Dawson‐Like Structure
Authors: Liu Hongsheng , Peng Jun , Su Zhongnin , Chen Yanhui , Dong Baoxia , Tian Aixiang , Han Zhangang , Wang Enbo 
Published: October 2006

AbstractThree novel [γ‐SiW10O36]8– dimers, [{K(H2O)}2{(μ3‐H2O)M(H2O)}(γ‐Si2W20O70)]8– (M = Mn2+, 1; Co2+, 2; Ni2+, 3), are isolated from an aqueous acidic medium without isomerization, which is different from most reactions of [γ‐SiW10O36]8– with first‐row transition metals. They are isomorphous and crystallize in the orthorhombic system, space group Pnma. These species are the first examples of imidazole–potassium mixed salts of Keggin‐γ‐type dimers having an analogous open structure related to the Wells–Dawson anionic cluster. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
The Reaction of Hyperforin with Hydride Reducing Agents
Authors: Verotta Luisella , Sterner Olov , Appendino Giovanni , Bombardelli Ezio , Pilati Tullio 
Published: October 2006

AbstractAs part of a study aimed at generating analogues of hyperforin (1), the reaction of this prenylated phloroglucinol with various hydride reducing agents was investigated. Hyperforin contains two β‐dicarbonyl systems, one of which is non‐enolizable, and it was interesting to assess the relative reactivity of these structural elements in the highly compact framework of the natural product. Depending on the reducing agent employed, a surprising range of compounds could be obtained, sometimes in synthetically useful yields. The stereochemistry of the LiAlH4‐reduced product was secured by X‐ray analysis and served as a base for elucidating the configuration of a series of reduced and deoxygenated analogues obtained with other reducing agents. The chemoselectivity observed in these reactions is apparently the result of a combination of metal‐chelation and hydrogen‐bonding effects. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Hippocampal contributions to recollection in retrograde and anterograde amnesia
Authors: Gilboa Asaf , Winocur Gordon , Rosenbaum R. Shayna , Poreh Amir , Gao Fuqiang , Black Sandra E. , Westmacott Robyn , Moscovitch Morris 
Published: October 2006

AbstractLesions restricted to the hippocampal formation and/or extended hippocampal system (hippocampal formation, fornix, mammillary bodies, and anterior thalamic nuclei) can disrupt conscious recollection in anterograde amnesia, while leaving familiarity‐based memory relatively intact. Familiarity may be supported by extra‐hippocampal medial temporal lobe (MTL) structures. Within‐task dissociations in recognition memory best exemplify this distinction in anterograde amnesia. The authors report for the first time comparable dissociations within recognition memory in retrograde amnesia. An amnesic patient (A.D.) with bilateral fornix and septal nuclei lesions failed to recognize details pertaining to personal past events only when recollection was required, during recognition of episodic details. His intact recognition of generic and semantic details pertaining to the same events was ascribed to intact familiarity processes. Recollective processes in the controls were reflected by asymmetrical Receiver's Operating Characteristic curves, whereas the patient's Receiver's Operating Characteristic was symmetrical, suggesting that his inferior recognition performance on episodic details was reliant on familiarity processes. Anterograde and retrograde memories were equally affected, with no temporal gradient for retrograde memories. By comparison, another amnesic person (K.C.) with extensive MTL damage (involving extra‐hippocampal MTL structures in addition to hippocampal and fornix lesions) had very poor recognition and no recollection of either episodic or generic/semantic details. These data suggest that the extended hippocampal system is required to support recollection for both anterograde and retrograde memories, regardless of their age. © 2006 Wiley‐Liss, Inc.
Fertility among female hodgkin lymphoma survivors attempting pregnancy following ABVD chemotherapy
Authors: Hodgson David C. , Pintilie Melania , Gitterman Leah , DeWitt Beth , Buckley Carol‐Ann , Ahmed Sameera , Smith Katherine , Schwartz Amanda , Tsang Richard W. , Crump Michael , Wells Woodrow , Sun Alexander , Gospodarowicz Mary K. 
Published: October 2006

AbstractAlthough ABVD (doxorubicin, bleomycin, vinblastine, dacarbazine) chemotherapy is infrequently associated with premature amenorrhea, little is known about the success rate of women attempting pregnancy following ABVD. In the present study females treated for HL with ABVD chemotherapy without pelvic radiation therapy (RT) and who were alive without relapse ≥3 years after treatment were identified from a clinical database and screened for inclusion. Using a standardized questionnaire, we determined the pregnancy rate (i.e. time‐to‐pregnancy, TTP) among survivors who had become pregnant, tried to become pregnant, or who had been sexually active for over 2 months without using contraception at any time following ABVD. The cumulative incidence of pregnancy was calculated using the Kaplan–Meier method. Cox proportional hazards models were constructed to compare the pregnancy rate among HL survivors to that reported by friend or sibling controls. Thirty‐six female HL survivors, who had attempted pregnancy after ABVD treatment, and 29 controls, completed the survey. Eighteen patients (50%) received 2–4 cycles of ABVD, 16 (44%) received 4–6 cycles, and 2 (6%) received >6 cycles. The median TTP among both HL survivors and controls was 2.0 months. The 12‐month pregnancy rates were 70% and 75%, respectively. The fertility ratio (FR) for HL survivors versus controls was 0.94 (95%CI = 0.53–1.66; p = 0.84) after adjusting for age and frequency of intercourse (where FR < 1 indicates subfertility). Age at treatment and the number of cycles of chemotherapy were not associated with pregnancy rate among HL survivors. Female HL patients who had survived without recurrence ≥3 years and who had attempted pregnancy after ABVD did not experience significant sub‐fertility. Copyright © 2006 John Wiley & Sons, Ltd.