bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of Xenobiotic Carbonyl Reduction in Human Liver Fractions
Authors: Rosemond M. Jane Cox 
Published: September 2005

AbstractCarbonyl reducing enzymes are involved in the metabolism of endogenous as well as xenobiotic molecules. Enzymes that catalyze the reversible oxidoreduction of aldehyde and ketone moieties include alcohol dehydrogenases, aldo‐keto reductases, quinone reductases, and short‐chain dehydrogenases/reductases. These enzymes differ with respect to subcellular location, cofactor dependence, and susceptibility to chemical inhibitors. Thus, it is possible to assess the relative contributions of these enzyme systems in the hepatic metabolism of a particular xenobiotic through simple in vitro experiments with commercially available reagents. The approaches described in this unit assume the availability of analytical procedures for measuring the parent compound and metabolites, such as HPLC with radiochemical, UV, or MS detection. Thus, the purpose of this unit is to outline methods for the study of the enzymatic carbonyl reduction of a drug development candidate or other xenobiotic molecule of interest.
Overview of Behavioral Teratology
Authors: Branchi Igor , Bignami Giorgio , Alleva Enrico 
Published: September 2005

AbstractThe discipline of behavioral teratology is based on the study of behavior as a powerful tool to identify and disentangle noxious effects of compounds known or suspected to be potentially neurotoxic early during development. Indeed, because behavior is the ultimate output of the brain, behavioral assessments can provide critical information on the noxious actions exerted by selected chemicals—information which is different from, and complementary to, the information provided by neurochemical, cellular, and histological evaluations. In particular, behavioral assessments allow one to investigate the integrity of a number of brain processes, helping to identify selected structural and/or functional alterations. A large number of behavioral protocols are available which are rapid, simple, quantitative, easily replicable, and reliable as indices of brain dysfunction. This unit provides an overview of the field of behavioral teratology.
Statistical Analysis of Behavioral Data
Authors: Chiarotti Flavia 
Published: September 2005

AbstractThe statistical analysis of behavioral data follows the collection and checking of the data, and is aimed at assessing the effect of treatments on the observed behaviors. In this unit, different behavioral tests and the response variables collected in each test are briefly described, to introduce a detailed description of the strategies for the analysis of such data. The main purpose of this unit is to enable the reader to choose the appropriate procedure for the statistical analysis, based on the type of data and experimental design adopted. Moreover, conditions for the application of the most common parametric and nonparametric tests for the comparison among groups in regard to the measures of location are also presented. Finally, some suggestions on the presentation of results coming from the different statistical analyses are given.
Protein Charge Determination
Authors: Winzor Donald J. 
Published: September 2005

AbstractThe most popular current method of determining protein valence entails the calculation of net charge from amino acid sequence/composition. However, the inaccuracy of that approach was recognized long before the advent of the protein data banks and computer programs to facilitate its adoption. Capillary zone electrophoresis affords the simplest and most economical procedure for obtaining a reliable estimate of the net charge of a protein in the buffer system of interest. This unit explains the major pitfalls in the calculation of net charge from protein sequence data.
Preparation of Soluble Proteins fromEscherichia coli
Authors: Wingfield Paul T. 
Published: September 2005

AbstractPurification of human IL‐1β is used in this unit as an example of the preparation of soluble proteins fromE. coli. Bacteria containing IL‐1β are lysed, and IL‐1 β in the resulting supernatant is purified by anion‐exchange chromatography, salt precipitation and cation‐exchange chromatography, and then concentrated. Finally, the IL‐1 β protein is applied to a gel‐filtration column to separate it from remaining higher‐ and lower‐molecular‐weight contaminants, the purified protein is stored frozen or is lyophilized. The purification protocol described is typical for a protein that is expressed in fairly high abundance (i.e., >5% total protein) and accumulates in a soluble state.
Two‐Dimensional Gel Electrophoresis
Authors: Adams Lonnie D. , Gallagher Sean R. 
Published: September 2005

AbstractTwo‐dimensional gel electrophoresis is the combination of two high‐resolution electrophoretic procedures (isoelectric focusing and SDS‐polyacrylamide gel electrophoresis) to provide much greater resolution than either procedure alone. In the first‐dimension gel, solubilized proteins are separated according to their isoelectric point (pI) by isoelectric focusing. This gel is then applied to the top of an SDS‐slab gel and electrophoresed. The proteins in the first‐dimension gel migrate into the second‐dimension gel where they are separated on the basis of their molecular weight. The basic protocols in this unit are based on the type of equipment originally described by O'Farrell in 1975. For very basic or very acidic proteins, two alternate protocols are provided. A third alternate protocol describes how two‐dimensional electrophoresis can be performed using a minigel system. Protein sample preparation is presented in the support protocol.
Human Complement Components C4A and C4B Genetic Diversities: Complex Genotypes and Phenotypes
Authors: Chung Erwin K. , Wu Yee Ling , Yang Yan , Zhou Bi , Yu C. Yung 
Published: September 2005

AbstractThis unit describes methods that can accurately determine the genotypes and phenotypes of human complement components C4A and C4B. Specifically, they allow investigators to determine how many C4 genes are present in a diploid genome of a human subject and to quantify how many of them encode C4A proteins and how many of them encode C4B proteins. In addition, methods to determine how many long and short C4 genes are present in a diploid genome of a subject are described together with experimental strategies to determine haplotypes and order or configuration of these genes in the MHC. Finally, methods to assess the degree of polymorphism in C4A and C4B proteins and whether low protein levels of plasma C4 may be caused by low C4 gene dosages and/or by mutant C4 genes.
One‐Pot Conversion of Cephalosporin C to 7‐Aminocephalosporanic Acid in the Absence of Hydrogen Peroxide
Authors: Lopez‐Gallego Fernando , Batencor Lorena , Hidalgo Aurelio , Mateo Cesar , Fernandez‐Lafuente Roberto , Guisan Jose M. 
Published: September 2005

AbstractThe main drawback in the production of 7‐aminocephalosporanic acid (7‐ACA) at the industrial level is the inactivation of the enzymes implicated in the process due to the presence of hydrogen peroxide during the reaction. As an alternative, we have developed the conversion of cephalosporin C to 7‐ACA in a single reactor without the presence of hydrogen peroxide during the reaction, achieving more than 80% yield. In order to develop this process, D‐amino acid oxidase (DAAO) was co‐immobilized with catalase (CAT), which is able to fully eliminate in situ the hydrogen peroxide formed by the neighbouring DAAO molecules. Thus, the product of the reaction is only α‐ketoadipyl‐7‐ACA. This system prevents the inactivation of the oxidase by hydrogen peroxide, solving the main problem of the enzymatic process. Moreover, we have found that α‐ketoadipyl‐7‐ACA is recognized as a substrate by glutaryl acylase (GAC) and hydrolyzed as long as glutaric acid is absent from the reaction medium (because it is able to inhibit the hydrolysis). The low stability of α‐ketoadipyl‐7‐ACA justifies the use of a single reactor, in which glutaryl acylase is already present when this substrate is generated. Thus, the whole process may (and must) be performed in a single step, and in the absence of hydrogen peroxide that could affect the stabilities of the involved enzymes.
Synthesis of N‐Heteroaryl(trifluoromethyl)hydroxyalkanoic Acid Esters by Highly Efficient Solid Acid‐Catalyzed Hydroxyalkylation of Indoles and Pyrroles with Activated Trifluoromethyl Ketones
Authors: Abid Mohammed , Török Béla 
Published: September 2005

AbstractThe synthesis of N‐heteroaryl(trifluoromethyl)hydroxyalkanoic acid esters by solid acid‐catalyzed Friedel–Crafts hydroxyalkylation of indoles and pyrroles with ethyl 3,3,3‐trifluoropyruvate and ethyl 4,4,4‐trifluoroacetoacetate is described. The inexpensive and readily available K‐10 montmorillonite is found to be an efficient catalyst for the synthesis of a wide variety of trifluoromethylated indol‐3‐yl‐ and pyrrol‐2‐yl‐hydroxypropionic and ‐butanoic acid esters. Using a series of substituted indoles and pyrroles the corresponding products were isolated in excellent yield (up to 98%) and 100% selectivity under mild experimental conditions, during very short reaction times. Beyond these, the ease of product isolation, catalyst stability and handling make this process an attractive, environmentally benign alternative for the synthesis of the target compounds.
Ionic Liquid as Catalyst and Reaction Medium: A Simple, Convenient and Green Procedure for the Synthesis of Thioethers, Thioesters and Dithianes using an Inexpensive Ionic Liquid, [pmIm]Br
Authors: Ranu Brindaban C. , Jana Ranjan 
Published: September 2005

AbstractAn easily accessible and inexpensive room temperature ionic liquid, 1‐pentyl‐3‐methylimidazolium bromide, [pmIm]Br efficiently catalyzes the reaction of alkyl halides or acyl halides with thiols without any solvent at room temperature leading to the synthesis of thioethers and thioesters in high yields. This reaction has also been extended for the preparation of dithianes and transthioetherification. The ionic liquid is recovered and recycled for subsequent runs.
Runx2: A master organizer of gene transcription in developing and maturing osteoblasts
Authors: Schroeder Tania M. , Jensen Eric D. , Westendorf Jennifer J. 
Published: September 2005

AbstractRunx2 is essential for osteoblast development and proper bone formation. A member of the Runt domain family of transcription factors, Runx2 binds specific DNA sequences to regulate transcription of numerous genes and thereby control osteoblast development from mesenchymal stem cells and maturation into osteocytes. Although necessary for gene transcription and osteoblast development, Runx2 is not sufficient for optimal gene expression or bone formation. Runx2 cooperates with numerous proteins, including transcription factors and cofactors, is posttranslationally modified, and associates with the nuclear matrix to integrate a variety of signals and organize crucial events during osteoblast development and maturation. Consistent with its role as a master organizer, alterations in Runx2 expression levels are associated with skeletal diseases. Runx2 haploinsufficiency causes cleidocranial dysplasia, while Runx2 overexpression is common in many bone‐metastatic cancers. In this review, we summarize the molecular mechanisms by which Runx2 integrates signals through coregulatory interactions, and discuss how its role as a master organizer may shift depending on promoter structure, developmental cues, and cellular context. Birth Defects Research (Part C) 75:213–225, 2005. © 2005 Wiley‐Liss, Inc.
Muscle function and dysfunction in health and disease
Authors: Huh Michael S. , Smid Johnathan K. , Rudnicki Michael A. 
Published: September 2005

AbstractSkeletal muscles of the trunk and limbs developmentally originate from the cells of the dermomyotomal compartment of the somite. A wealth of knowledge has been accumulated with regard to understanding the molecular regulation of embryonic skeletal myogenesis. Myogenic induction is controlled through a complex series of spatiotemporal dependent signaling cascades. Secreted signaling molecules from surrounding structures not only initiate the myogenic program, but also influence proliferation and differentiation decisions. The proper coordination of these molecular events is thus critical for the formation of physiologically functional skeletal muscles. Hereditary congenital skeletal muscle defects arise due to genetics lesions in myogenic specific components. Understanding the mechanistic routes of congenital skeletal muscle disease therefore requires a comprehensive knowledge of the developmental system. Ultimately, the application of this knowledge will improve the diagnostic and therapeutic methodologies for such diseases. The aim of this review is to overview our current understanding of skeletal muscle development and associated human congenital diseases. Birth Defects Research (Part C) 75:180–192, 2005. © 2005 Wiley‐Liss, Inc.
Dlx genes, p63, and ectodermal dysplasias
Authors: Morasso Maria I. , Radoja Nadezda 
Published: September 2005

AbstractMany events in vertebrate morphogenesis and organogenesis develop from epithelial/mesenchymal interactions. These processes involve a series of sequential and reciprocal interactions between the thickened epithelial sheets and underlying mesenchymal cells. Much has been learned from in vitro assays and knockout experiments in mice on the early signaling molecules that regulate the initial stages of the epithelial/mesenchymal interactions. In this review, we discuss effectors of these initial signals, specifically the p63 and Dlx families of transcription factors, that play central roles in embryonic patterning and regulation of different developmental processes, and provide a review of some of the mutations in these genes that have been associated with ectodermal dysplasias (EDs). Birth Defects Research (Part C) 75:163–171, 2005. Published 2005 Wiley‐Liss, Inc.
Tendon and ligament: Development, repair and disease
Authors: Tozer Samuel , Duprez Delphine 
Published: September 2005

AbstractTendons and ligaments (T/L) are very similar fibrous tissues that respectively connect muscle to bone and bone to bone. They are comprised of fibroblasts that produce large amounts of extra‐cellular matrix, resulting in a dense and hypocellular structure. The complex molecular organization of T/L, together with high water content, are responsible for their viscoelastic properties, hence insuring their mechanical function. We will first review recent work on tendon embryology and discuss ligament formation, which has been less documented. We will next summarize our current knowledge of T/L molecular architecture, alterations of which are a major cause for disease. We will finally focus on T/L repair after injury and on genetic diseases responsible for T/L defects. Birth Defects Research (Part C) 75:226–236, 2005. © 2005 Wiley‐Liss, Inc.
Mechanisms of synovial joint and articular cartilage formation: Recent advances, but many lingering mysteries
Authors: Pacifici Maurizio , Koyama Eiki , Iwamoto Masahiro 
Published: September 2005

AbstractSynovial joints are elegant, critically important, and deceptively simple biomechanical structures. They are comprised of articular cartilage that covers each end of the opposing skeletal elements, synovial fluid that lubricates and nourishes the tissues, ligaments that hold the skeletal elements in check, and a fibrous capsule that insulates the joints from surrounding tissues. Joints also exhibit an exquisite arrays of shapes and sizes, best exemplified by the nearly spherical convex femoral head articulating into a nearly spherical concave hip acetabulum, or a phalangeal joint with two condyles on the distal side articulating in reciprocally‐shaped sockets on the opposing proximal side. Though few in number, joint tissues are highly specialized in structure and function. This is illustrated by articular cartilage with its unique extracellular matrix, unique biomechanical resilience, its largely avascular nature, and its ability to persist through life with minimal turnover of its cells and components. The fact that interest in synovial joints has remained unabated for decades is a reflection of their fundamental importance for organism function and quality of life, and for their susceptibility to a variety of acquired and congenital conditions, most importantly arthritis. This has led to many advances in this field that encompass molecular genetics to biomechanics to medicine. Regrettably, what continues to be poorly understood are the mechanisms by which synovial joints actually form in the developing embryo. If available, this information would be not only of indisputable biological interest, but would also have significant biomedical ramifications, particularly in terms of designing novel tissue regeneration or reconstruction therapies. This review focuses on recent advances in understanding the mechanisms of synovial joint formation in the limbs, and places and discusses the information within the context of classic studies and the many mysteries and questions that remain unanswered. Birth Defects Research (Part C) 75:237–248, 2005. © 2005 Wiley‐Liss, Inc.
Prediction of atomic structure from sequence for double helical DNA oligomers
Authors: Farwer Jochen , Packer Martin J. , Hunter Christopher A. 
Published: September 2005

AbstractDNA can adopt different conformations depending on the base sequence, solvent, electrolyte composition and concentration, pH, temperature, and interaction with proteins. Here we present a model for calculating the three‐dimensional atomic structure of double‐stranded DNA oligomers. A theoretical energy function is used for calculating the interactions within the base steps and an empirical backbone function is used to restrict the conformational space accessible to the bases and to account for the conformational coupling of neighboring steps in a sequence. Conformational searching on large structures or a large number of structures is possible, because each base step can be described by just two primary degrees of freedom (slide and shift). A genetic algorithm is used to search for low‐energy structures in slide–shift space, and this allows very rapid optimization of DNA oligomers. The other base step parameters have been previously optimized for all possible slide–shift sequence combinations, and a heuristic algorithm is used to add the atomic details of the backbone conformation in the final step of the calculation. The structures obtained by this method are very similar to the corresponding X‐ray crystal structures observed experimentally. The average RMSD is 2.24 Åfor a set of 20 oligomer structures. For 15 of these sequences, theX‐ray crystal structure is the global energy minimum. The other 5 are bistable sequences that have B‐form global energy minima but crystallize as A‐DNA. © 2005 Wiley Periodicals, Inc. Biopolymers 81: 51–61, 2006This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Dielectric characterization of neutralized and nonneutralized chitosan upon drying
Authors: Viciosa M. T. , Dionísio M. , Mano J. F. 
Published: September 2005

AbstractIsothermal dielectric loss spectra of neutralized and nonneutralized chitosan were acquired in successive runs from –130°C up to increasing final temperatures, in a frequency range between 20 Hz and 1 MHz. Essentially, three relaxation processes were detected in the temperature range covered: (i) a β‐wet process, detected when the sample has a higher water content that vanishes after heating to 150°C; (ii) a β process, which is located at temperatures below 0°C, becoming better defined and maintaining its location after annealing at 150°C independently of the protonation state of the amino side group; and (iii) a σ process that deviates to higher temperatures with drying, being more mobile in the nonneutralized form. Moreover, in dried neutralized chitosan, a fourth process was detected in the low frequency side of the secondary β process that diminishes after annealing. Whether this process is a distinct relaxation of the dried polymer or a deviated β‐wet process due to the loss of water residues achieved by annealing is not straightforward. Only β and σ processes persist after annealing at 150°C. The changes in molecular mobility upon drying of these two relaxation processes were evaluated. © 2005 Wiley Periodicals, Inc. Biopolymers 81: 149–159, 2006This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Prospective study of the effect of rectopexy on colonic motility in patients with rectal prolapse
Authors: Brown A J , Nicol L , Anderson J H , McKee R F , Finlay I G 
Published: September 2005

Abstract

Background
Patients with rectal prolapse have abnormal hindgut motility. This study examined the effect of rectal prolapse surgery on colonic motility.

Methods
Twelve patients undergoing sutured rectopexy were studied before and 6 months after surgery by colonic manometry, colonic transit study and clinical assessment of bowel function. The results were compared with those from seven control subjects.

Results
Before surgery colonic pressure was greater in patients than controls (P &lt; 0·050). Controls responded to a meal stimulus by increasing colonic pressure; this increase was absent in patients. After rectopexy, colonic pressure reduced towards control values and patients' colonic pressure response to a meal returned. High-amplitude propagated contractions (HAPCs) were seen in all controls but in only three patients before and two patients after surgery. Three patients had prolonged colonic transit before and eight after rectopexy.

Conclusion
Patients with rectal prolapse have abnormal colonic motility associated with reduced HAPC activity. Rectopexy reduces colonic pressure but fails to restore HAPCs, reduce constipation or improve colonic transit. These observations help explain the pathophysiology of constipation associated with rectal prolapse.
Feasibility of autonomic nerve-preserving surgery for advanced rectal cancer based on analysis of micrometastases
Authors: Matsumoto T , Ohue M , Sekimoto M , Yamamoto H , Ikeda M , Monden M 
Published: September 2005

Abstract

Background
Autonomic nerve preservation has been advocated as a means of preserving urinary and sexual function after surgery for rectal cancer, but may compromise tumour clearance. The aim of this study was to determine the incidence of micrometastasis in the connective tissues surrounding the pelvic plexus.

Methods
The study included 20 consecutive patients who underwent rectal surgery with bilateral lymph node dissection for advanced cancer. A total of 78 connective tissues medial and lateral to the pelvic plexus and 387 lymph nodes were sampled during surgery. All connective tissue samples and 260 lymph nodes were examined for micrometastases by reverse transcriptase–polymerase chain reaction (RT–PCR) after operation. All patients were followed prospectively for a median of 36·0 months.

Results
Of 245 histologically negative lymph nodes, 38 (15·5 per cent) were shown by RT–PCR to harbour micrometastases. However, micrometastases to tissues surrounding the pelvic plexus were detected in only two (3 per cent) of 78 tissues, that is in two of 20 patients. Clinical follow-up showed that the two patients had a poor prognosis owing to distant metastases.

Conclusion
Autonomic nerve-preserving surgery may be feasible for advanced rectal cancer, but study of more patients positive for micrometastases is required.