bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association Between Aryl Hydrocarbon Receptor Genotype and Survival in Soft Tissue Sarcoma
Authors: Berwick Marianne , Matullo Giuseppe , Song Yan Shuang , Guarrera Simonetta , Dominguez Gemma , Orlow Irene , Walker Mary , Vineis Paolo 
Published: September 2004

Purpose Accumulating evidence shows that germline polymorphisms may affect survival in cancer. The purpose of this study was to investigate the association between polymorphisms in a group of candidate genes and survival with soft tissue sarcoma. Patients and Methods We measured single nucleotide polymorphisms in the metabolizing, detoxifying, and DNA repair pathways in 120 newly diagnosed patients with soft tissue sarcoma. We assessed polymorphisms in the aryl hydrocarbon receptor (AhR-Arg554Lys), null variants of the glutathione S-transferase superfamily (GSTM1 and GSTT1), x-ray repair cross-complementing 1 and 3, and Xeroderma pigmentosum, group D (XRCC1-Arg399Gln, XRCC3-Thr241Met, XPD-Lys751Gln). We followed the patients for survival for a median of 7.6 years. Results Cox proportional hazards models demonstrated that a polymorphism at codon 554 in exon 10 of the AhR was significantly and adversely associated with survival (hazard ratio, 2.2; 95% CI, 1.3 to 3.9; P < .01), even while accounting for major clinical characteristics such as tumor grade, tumor size, anatomic site, and patient age. Conclusion Further study of the role of the AhR polymorphism is warranted.
Enhanced Fluorescence from Rhodamine B Intercalated into Hydrophobized Graphite Oxides Containing Perfluoroalkyl Chains
Authors: Matsuo Yoshiaki , Fukunaga Takahiro , Fukutsuka Tomokazu , Sugie Yosohiro 
Published: October 2004

Abstract
Fluorescence from Rhodamine B in hydrophobized graphite oxide was greatly enhanced by perfluoroalkyl chains, likely due to the lower radiationless quenching by low vibrational C–F bonds.
Temporal Emergence of Giant Vesicles Accompanied by Hydrolysis of Ammonium Amphiphiles with a Schiff-base Segment
Authors: Toyota Taro , Takakura Katsuto , Sugawara Tadashi 
Published: October 2004

Abstract
An aqueous dispersion of the ammonium amphiphile with a Schiff-base segment exhibited the formation and decomposition of giant vesicles with diameters of several micrometers 2–4 h after the preparation. The time course trace of the morphological changes of the self-aggregates by means of light microscopy, electron microscopy and 1H NMR revealed that the temporal emergence of the giant vesicles was dependent on the progress of hydrolysis of the Schiff-base segment.
Bisphosphonates: Clinical Experience
Authors: Coleman Robert E. 
Published: September 2004

Abstract

Learning Objectives
After completing this course, the reader will be able to:
Explain the importance of bone disease in the common solid tumors of adulthood. Describe the pathophysiology of bone metastasis. List the specialized end points used in clinical trials assessing treatment of bone disease. Discuss the current standard for the treatment and prevention of bone complications that may arise in cancer and its treatment.
Access and take the CME test online and receive 1 hour of AMA PRA category 1 credit at CME.TheOncologist.com
Bone is a preferred site of metastasis for many solid tumors, and the complications associated with bone metastases can result in significant skeletal morbidity including severe bone pain, pathologic fracture, spinal cord compression, and hypercalcemia of malignancy (HCM). Bisphosphonates are the current standard of care for preventing skeletal complications associated with bone metastases. Clinical trials investigating the benefit of bisphosphonate therapy have used a composite end point defined as a skeletal-related event (SRE) or bone event, which typically includes pathologic fracture, spinal cord compression, radiation or surgery to bone, and HCM. Bisphosphonates have been shown to significantly reduce the incidence of these events in patients with bone metastases. Zoledronic acid (Zometa®; Novartis Pharmaceuticals Corp.; East Hanover, NJ), pamidronate (Aredia®; Novartis Pharmaceuticals Corp.), clodronate (Bonefos®; Anthra Pharmaceuticals; Princeton, NJ), and ibandronate (Bondronat®; Hoffmann-La Roche Inc.; Nutley, NJ) all have demonstrated efficacy superior to that of placebo in patients with breast cancer. Zoledronic acid is the only bisphosphonate that has been compared directly with pamidronate, and it was shown by multiple event analysis to be significantly more effective at reducing the risk of an SRE. In patients with prostate cancer, clodronate, etidronate (Didronel®; Procter and Gamble Pharmaceuticals, Inc.; Cincinnati, OH), and pamidronate have demonstrated transient palliation of bone pain. However, zoledronic acid is the only bisphosphonate to demonstrate both significant and sustained pain reduction and a significantly lower incidence and longer time to onset of SREs compared with placebo. Zoledronic acid is also the only bisphosphonate to demonstrate efficacy in patients with bone metastases from a variety of other solid tumors, including lung cancer and renal cell carcinoma. In conclusion, bisphosphonates effectively reduce skeletal complications in patients with bone metastases from breast cancer, and zoledronic acid has demonstrated the broadest clinical activity in patients with a wide variety of tumor types.
Safety of Intravenous and Oral Bisphosphonates and Compliance With Dosing Regimens
Authors: Conte PierFranco , Guarneri Valentina 
Published: September 2004

Abstract

Learning Objectives
After completing this course, the reader will be able to:
Describe the differences between oral and i.v. bisphosphonate therapy in terms of safety and side effects. Explain the renal effects of long-term i.v. bisphosphonate treatment. Discuss the importance of patient compliance in long-term disease management.
Access and take the CME test online and receive 1 hour of AMA PRA category 1 credit at CME.TheOncologist.com
Patients with advanced cancers—particularly breast and prostate cancers—are at high risk for bone metastasis, leading to accelerated bone resorption and clinically significant skeletal morbidity. Bisphosphonates are effective inhibitors of bone resorption and reduce the risk of skeletal complications in patients with bone metastases. The standard routes of administration for bisphosphonates used in clinical practice are either oral or i.v. infusion. Oral administration of bisphosphonates is complicated by poor bioavailability (generally &lt;5%) and poor gastrointestinal tolerability. First-generation bisphosphonates, such as clodronate (Bonefos®; Anthra Pharmaceuticals; Princeton, NJ), must be administered at high oral doses (1,600–3,200 mg/day) to achieve therapeutic effects, which leads to poor tolerability and compliance with oral dosing regimens. Infusion of bisphosphonates is associated with dose- and infusion-rate-dependent effects on renal function. In particular, high bisphosphonate doses (e.g., 1,500 mg clodronate) can cause severe renal toxicity unless infused slowly over many hours. In contrast, the newer, more potent bisphosphonates effectively inhibit bone resorption at micromolar concentrations, and the small doses required can be administered via relatively short i.v. infusions without adversely affecting renal function. Zoledronic acid (Zometa®; Novartis Pharmaceuticals Corp.; East Hanover, NJ) is a new generation bisphosphonate, and the recommended dose of 4 mg can be safely infused over 15 minutes. The 90-mg dose of pamidronate (Aredia®; Novartis Pharmaceuticals Corp.) and the 6-mg dose of ibandronate (Bondronat®; Hoffmann-La Roche Inc.; Nutley, NJ) require 1- to 4-hour infusions. Intravenous bisphosphonates require less frequent dosing (once a month) and are generally well tolerated with long-term use in patients with bone metastases. Zoledronic acid has demonstrated the broadest clinical activity in patients with bone metastases.
Characterization of GABA Receptors
Authors: Enna S. J. , McCarson Kenneth E. 
Published: September 2004

AbstractDescribed in this unit are ligand binding assays for GABAA, GABAB, and GABAC receptor recognition sites in brain tissue. These assays may also be used to determine the affinity of an unlabeled compound for the GABA binding sites. Not included in this unit are ligand binding assays for other components of the GABAA, receptor complex, such as the benzodiazepine or ion channel binding sites.
Electrophysiological Characterization of Recombinant and Native P2X Receptors
Authors: Niforatos Wende , Jarvis Michael F. 
Published: September 2004

AbstractATP acts as a fast neurotransmitter by activating a family of ligand‐gated ion channels, the P2X receptors. Functional homomeric P2X3 and heteromeric P2X2/3 receptors are highly localized on primary sensory afferent neurons that transmit nociceptive sensory information. Activation of these P2X3‐containing channels may provide a specific mechanism whereby ATP, released via synaptic transmission or by cellular injury, elicits pain. The experimental procedures described in this unit are useful for the electorphysiological characterization of P2X receptors. In addition, these protocols provide methods for the evaluation of ligands that interact with P2X receptors that are either natively expressed on excitable cells or cloned and expressed in heterologous cell systems. These methods are derived from standard electrophysiological principles and procedures that are applicable to a wide variety of ligand‐gated ion channels. Specific attention is given here to the reliable electrophysiological measurement of both quickly (P2X3) and more slowly (P2X2 and P2X2/3) desensitizing receptors.
DNASynthesis Without Base Protection
Authors: Sekine Mitsuo 
Published: September 2004

AbstractDNA synthesis can be achieved by using O‐selective methods for internucleotide bond formation. This greatly simplifies the synthesis of oligodeoxyribonucleotides by eliminating the need for nucleobase protection and deprotection steps. This unit describes strategies that can be used for DNA synthesis without base protection. The discussion includes synthesis of phosphoramidite andH‐phosphonate monomers, solid‐phase assembly by the phosphoramidite andH‐phosphonate methods, and future prospects for DNA synthesis using N‐unprotected approaches.
Oligodeoxyribonucleotide Analogs Functionalized with Phosphonoacetate and Thiophosphonoacetate Diesters
Authors: Dellinger Douglas J. , Yamada Christina M. , Caruthers Marvin H. 
Published: September 2004

AbstractOligodeoxyribonucleotides with phosphonoacetate or thiophosphonoacetate internucleotide linkages can be made in high yield by solid‐phase synthesis and possess many advantages. They are highly stable to nucleases, water‐soluble, and anionic at neutral pH. They form stable duplexes with DNA and RNA, and stimulate RNase H degradation of complementary RNA. The preparation of the N,N‐(diisopropylamino)phosphinyl acetate monomers from standard protected nucleosides is described here, followed by the synthesis of phosphonoacetate and thiophosphonoate oligodeoxyribonucleotides, as well as chimeric oligomers that have these modified linkages in combination with natural or phosphorothioate linkages. Purification and characterization of these oligomers is also presented.
Derivatization of Glass and Polypropylene Surfaces
Authors: Beier Markus , Hoheisel Jörg D. 
Published: September 2004

AbstractThis unit describes the derivatization of solid support media, particularly glass and polypropylene, with a linker system by an iterative process that forms a dendrimeric structure, thereby increasing stepwise the loading capacity of the surface. The procedure permits the production of various types of linkers whose characteristics can be tailored to the requirements of the eventual applications. The specific modifications described here are used either for attaching prefabricated DNA oligonucleotides, PCR products, and peptide nucleic acid (PNA) oligomers, or for in situ synthesis of DNA microarrays.
Synthesis and Polymerase Incorporation of 5′‐Amino‐2′,5′‐Dideoxy‐5′‐N‐Triphosphate Nucleotides
Authors: Wolfe Jia Liu , Kawate Tomohiko 
Published: September 2004

AbstractThis unit presents synthetic procedures for the preparation of 5′‐amino‐2′,5′‐dideoxy analogs of adenosine, cytidine, guanosine, and thymidine, as well as corresponding 5′‐N‐triphosphate nucleotides, using commercially available reagents. The modified nucleosides are prepared in high yields from naturally occurring 2′‐deoxynucleosides using robust chemical reactions including tosylation, azide exchange, and the Staudinger reaction. Efficient conversion of these 5′‐amino nucleosides to corresponding 5′‐N‐triphosphate nucleotides is achieved through a one‐step reaction with trimetaphosphate in Tris‐buffered aqueous solution. The 5′‐amino modification renders these nucleoside and nucleotide analogs markedly increased reactivity, which is useful for a variety of biochemical, pharmaceutical, and genomic applications. Also included in this unit are protocols for polymerase incorporation of the 5′‐amino nucleotides, either partially or completely replacing their naturally occurring counterparts, and subsequent sequence‐specific cleavage at the modified nucleotides under mildly acidic conditions.
Actin‐Based Motility Assay
Authors: Le Clainche Christophe , Carlier Marie‐France 
Published: September 2004

AbstractActin‐based movement can be reconstituted by using microspheres functionalized with the enzymes N‐WASP or ActA, which use the Arp2/3 complex and actin to catalyze the formation of a branched actin filament network that is maintained in rapid turnover by three proteins (capping protein, profilin, and ADF). The particles continuously initiate filament assembly at their surface and are propelled, mimicking bacteria or the leading edge of motile cells. This biomimetic assay offers advantages over approaches based on living cells and cell extracts, because the physical‐chemical parameters are under control. The biomimetic motility assay offers the opportunity to test the function of proteins involved in signaling pathways or actin dynamics. It is a powerful tool to understand the physical mechanism of force production and has the potential to support high‐throughput screens for drugs, inhibitors of motility, or therapeutic agents in metastatic states in which motility is impaired.
Fluorescence Localization After Photobleaching (FLAP)
Authors: Dunn Graham A. , Holt Mark R. , Soong Daniel Y. H. , Gray Colin , Zicha Daniel 
Published: September 2004

AbstractFluorescence localization after photobleaching is a new method for localized photolabeling and subsequent tracking of specific molecules within living cells. The molecular species to be located carries two different fluorophores that can be imaged independently but simultaneously by fluorescence microscopy. For the method to work, these two fluorophores should be accurately colocalized throughout the cell so that their images are closely matched. One of the fluorophores (the target fluorophore) is then rapidly photobleached at a chosen location. The unbleached (reference) fluorophore remains colocalized with the target fluorophore; thus, the subsequent fate of the photobleached molecules can be revealed by processing simultaneously acquired digital images of the two fluorophores. Here we demonstrate the simplicity and effectiveness of the FLAP method in revealing both fast and slow molecular dynamics in living cells using a Zeiss LSM 510 laser scanning confocal microscope.
Searching the NCBI Databases Using Entrez
Authors: Baxevanis Andreas D. 
Published: September 2004

AbstractOne of the most widely‐used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre‐existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two Basic Protocols describe simple, text‐based searches, illustrating the types of information that can be retrieved through the Entrez system. An Alternate Protocol builds upon the first Basic Protocol, using additional, built‐in features of the Entrez system, as well as providing alternative ways to issue the initial query. The Support Protocol reviews how to save frequently‐issued queries.
Analyzing and Visualizing Expression Data with Spotfire
Authors: Kaushal Deepak , Naeve Clayton W. 
Published: September 2004

AbstractThis unit assumes the reader is familiar with the Spotfire environment, has successfully installed Spotfire, and has uploaded and prepared data for analysis. It presents numerous methods for analyzing microarray data. Specifically, the first two protocols describe methods for identifying differentially expressed genes via the t‐test/ANOVA and the distinction calculation respectively. Another protocol discusses how to conduct a profile search. Additional protocols illustrate various clustering methods, such as hierarchical clustering, K‐means clustering, and principal components analysis. A protocol explaining coincidence testing allows the reader to compare the results from multiple clustering methods. Additional protocols demonstrate querying the Internet for information based on the microarray data, mathematically transforming data within Spotfire to generate new data columns, and exporting Spotfire visualizations.
Using the Reactome Database
Authors: Stein Lincoln D. 
Published: September 2004

AbstractThere is considerable interest in the bioinformatics community in creating pathway databases. The Reactome project (a collaboration between Cold Spring Harbor Laboratory and the European Bioinformatics Institute) is one such pathway database and collects structured information on all the biological pathways in the human. It is a curated collection of well‐documented molecular reactions that span the gamut from simple intermediate metabolism to complex cellular events. This information is supplemented with likely orthologous molecular reactions in mouse, rat, zebrafish, and other model organisms. This unit describes how to use the Reactome database to learn the steps of a biological pathway and see how one pathway interacts with another; navigate and browse through the Reactome database; identify the pathways in which a molecule of interest is involved; use the Pathfinder tool to search the database for possible connections within and between pathways.
Using Relational Databases for Improved Sequence Similarity Searching and Large‐Scale Genomic Analyses
Authors: Mackey Aaron J. , Pearson William R. 
Published: September 2004

AbstractRelational databases are designed to integrate diverse types of information and manage large sets of search results, greatly simplifying genome‐scale analyses. Relational databases are essential for management and analysis of large‐scale sequence analyses, and can also be used to improve the statistical significance of similarity searches by focusing on subsets of sequence libraries most likely to contain homologs. This unit describes using relational databases to improve the efficiency of sequence similarity searching and to demonstrate various large‐scale genomic analyses of homology‐related data. This unit describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. These include basic use of the database to generate a novel sequence library subset, how to extend and use seqdb_demo for the storage of sequence similarity search results and making use of various kinds of stored search results to address aspects of comparative genomic analysis.
Finding Protein Sequences Using PROWL
Authors: Beavis Ronald , Fenyö David 
Published: September 2004

AbstractPROWL is a collection of tools for the identification of protein sequences, using input data derived from mass spectrometry. Experimental data from various types of mass spectrometers can be input directly into PROWL's component software. This unit presents protocols for several of the individual PROWL tools. Specifically, PepFrag allows for the analysis of a single spectrum derived from tandem mass spectrometry. GPM, on the other hand, provides for the analysis of multiple MS/MS spectra. An additional protocol introduces ProFound for analyzing a single spectrum of peptide mass fingerprinting data.
Preparation and characterization of poly(methyl methacrylate) grafted sago starch using potassium persulfate as redox initiator
Authors: Qudsieh Isam Y. M. , Fakhru'l‐Razi A. , Muyibi Suleyman A. , Ahmad Mansor B. , Rahman M. Z. Ab. , Zin Wan Yunus Wan Md 
Published: September 2004

AbstractIn this article, the graft copolymerization of methyl methacrylate (MMA) onto sago starch (AGU) was carried out in aqueous medium using potassium persulfate (PPS) under nitrogen gas atmosphere. The maximum percentage of grafting achieved was 90% under optimized conditions of reaction temperature, monomer, PPS, AGU, and reaction period corresponding to 50°C, 47 mmol, 1.82 mmol, 6.17 × 10−3 mol L−1, and 1.5 h, respectively. The grafting of MMA onto sago starch was confirmed by the differences in infrared spectroscopy. The viscosity measurement and the average molecular weight determination were estimated using Huggin's and Mark Houwink's equations, respectively. This material may have application as a biodegradable plastic. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 94: 1891–1897, 2004
Recycling of carbon/epoxy composites
Authors: Liu Yuyan , Meng Linghui , Huang Yudong , Du Jianjun 
Published: September 2004

AbstractThe recycling of carbon fibers from carbon/epoxy composites was attempted with a solvent method in nitric acid solutions. Gel permeation chromatography and gas chromatography/mass spectrometry showed that the epoxy resin could entirely decompose into low‐molecular‐weight compounds, and the main components of the dissoluble decomposed compounds were 2,4‐dinitrophenol and 2‐nitro‐4‐carboxylphenol. Electron probe microscopy showed no damage to the recycled carbon fibers. The single‐fiber tension strength loss of the recycled carbon fibers was 1.1% under the following conditions: a decomposition temperature of 90 °C, a nitric acid solution concentration of 8M, and a ratio of the sample weight to the nitric acid solution volume of 6 g:100 mL. Through orthogonal experimentation, the recycling conditions for the carbon/epoxy composites were examined. The best combination was a decomposition temperature of 90°C, a nitric acid solution concentration of 8M, and a ratio of the sample weight to the nitric acid solution volume of 4g:100 mL. This method could liquefy raw materials for rocket engine shells reinforced with carbon fibers. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 95: 1912–1916, 2004
Cellulose acetate deacetylation in benzene/acetic acid/water systems
Authors: Olaru N. , Olaru Liliana 
Published: September 2004

AbstractAn unconventional system for cellulose acetate hydrolysis, consisting of homogeneous mixtures of benzene/acetic acid/water of different compositions, was investigated from the perspective of kinetics and also with respect to the degradation of the cellulosic chains during the process. It was observed that the decrease of the degree of substitution of the polymer occurs with higher reaction rate than that in the reference system, free of benzene, and depends on the composition of the reaction medium. A pseudo–first‐order kinetic law satisfactorily describes the deacetylation process performed in the presence of benzene. Also, the degradation of the polymeric chain during the process is dependent on the presence of the hydrocarbon and on the composition of the reaction system used. A lower degradation rate was found to characterize the first period of the process, compared with that produced in a benzene‐free system. These peculiarities were explained by the influence of benzene on the composition of solvent shell in the vicinity of macromolecules. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 94: 1965–1968, 2004