bluuebunny/crossref_metadata_2025_split huggingface dataset:
Congenital Adrenal Hyperplasia: The Molecular Basis of 21-Hydroxylase Deficiency in H-2aw18 Mice
Authors: Riepe Felix G. , Tatzel Stephan , Sippell Wolfgang G. , Pleiss Jürgen , Krone Nils 
Published: February 2005

AbstractThe mouse strain H-2aw18 shows typical characteristics of 21-hydroxylase deficiency (21-OHD). A deletion of the active Cyp21a1 gene has been postulated; however, the changes on the nucleotide level are still unknown. To investigate whether this animal model, the only one available, is suitable for studying congenital adrenal hyperplasia in man, a detailed analysis of the Cyp21 locus has been performed to ascertain the genetic cause of 21-OHD in H-2aw18 mice. We demonstrate that 21-OHD is caused by unequal crossing over between the active Cyp21a1 gene and the pseudogene resulting in a hybrid Cyp21a1-Cyp21a2-p gene including a partial deletion of Cyp21a1. Next to several pseudogene-specific point mutations, various novel missense mutations and a nonsense mutation are present. Enzyme activity for each point mutation has been determined in vitro and the structure-function relationship has been studied by sequence conservation analysis and a three-dimensional murine 21-hydroxylase protein (Cyp21) structure model. The mutations are classified in three classes: I, no or minor decrease in enzyme activity: R238Q, P465L, R361K, A362V, P458L; II, loss of enzyme activity caused by inefficient electron flux: R346H, R400C; III, loss of activity due to deficient substrate binding: I462F, L464F. The combination of in vitro protein expression and three-dimensional structure modeling provides a valuable tool to understand the role of the different mutations and polymorphisms on the resulting enzyme activity. The underlying genetic mechanisms are also known to be responsible for 21-OHD in humans, so rodent 21-OHD turns out to be an excellent genetic model for studying the human disease.
Blockade of Rapid Versus Prolonged Extracellularly Regulated Kinase 1/2 Activation Has Differential Effects on Insulin-Induced Gene Expression
Authors: Keeton Adam B. , Bortoff Katherine D. , Franklin J. Lee , Messina Joseph L. 
Published: February 2005

AbstractIn the present work, insulin’s regulation of expression of activating transcription factor 3 (ATF-3), the putative transcription factor proline-rich induced protein (Pip)92, and insulin-inducible gene-1 (Insig-1) (an ER resident protein involved in regulation of sterol-responsive element-binding protein 1 activation) have been examined in a liver-derived cell line (rat H4IIE hepatoma cells). We report that: 1) insulin-induced transcription of ATF-3, Pip92, and Insig-1 required MEK-ERK activation; 2) insulin-induced transcription of ATF-3 and Pip92 reached maximum levels within 15 min and was blocked by wortmannin but not LY294002; 3) in contrast, the maximum level of insulin-induced transcription of Insig-1 was delayed and was not blocked by either wortmannin or LY294002; 4) insulin activated ERK1/2 in two distinct phases, a rapid peak and a later plateau; 5) the delayed plateau phase of insulin-induced ERK1/2 activation was partially phosphatidylinositol 3-OH-kinase dependent; and 6) however, the rapid, insulin-induced peak of ERK1/2 activation was blocked by wortmannin but not LY294002.
Hydrothermal Synthesis of Highly Crystallized Lepidocrocite Nanosheets of TiO2 under Low Temperature
Authors: Wang Fumin , Jiu Jinting , Pei Lihua , Nakagawa Keizo , Isoda Seiji , Adachi Motonari 
Published: February 2005

Abstract
The highly crystallized lepidocrocite nanosheets of TiO2 was synthesized by hydrothermal methods at low temperature by using dodecanediamine (DDA) as a surfactant. The above structural features of the titanium oxide nanosheets were confirmed by transmission electron microscopy (TEM), selected area electron diffraction (SAED), X-ray diffraction (XRD) and UV–vis optical spectra analysis.
Scintillation Proximity Assay
Authors: Kahl Steven D. , Felder Christian C. 
Published: February 2005

AbstractScintillation proximity assay technologies provide a rapid non‐separation method to measure common biological interactions using radioactively tagged molecules. This unit identifies potential uses of the technology for the measurement of receptor‐ligand binding, cAMP accumulation, GTP binding to heterotrimeric G proteins, protease activity and cellular uptake.
Defensive Responses to Predator Threat in the Rat and Mouse
Authors: Blanchard D. Caroline , Blanchard Robert J. , Griebel Guy 
Published: February 2005

AbstractDefensive responses include an array of specific behaviors, including flight, freezing, risk assessment, and defensive threat/attack, that are elicited by unconditioned threat stimuli such as predators or predator odors. Some individual defensive behaviors are selectively responsive to drugs effective against generalized anxiety disorder or panic, providing a rationale for their use in investigation of compounds that may be useful in treating these disorders. In addition, defensive behaviors toward predators and some predator odors show rapid conditioning to contextual stimuli, whereas other predator odors do not, although they too elicit defensiveness. This pattern suggests that the ability of a predator odor to predict danger may be a determinant of the degree to which that odor supports aversive conditioning. Predators and predator odors are also increasingly used in studies of brain systems potentially related to emotionality. These factors indicate the need for selective, reliable, and convenient tests of defensiveness to predators and predator odors using rat and mouse subjects.
Difference Gel Electrophoresis (DIGE) Using CyDye DIGE Fluor Minimal Dyes
Authors: Chakravarti Bulbul , Gallagher Sean R. , Chakravarti Deb N. 
Published: February 2005

AbstractOne‐ and two‐dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1‐ and 2‐D SDS‐PAGE) have been widely used for the separation and quantitative estimation of proteins. Following electrophoresis, the gels are stained appropriately to visualize the proteins. Difference gel electrophoresis (DIGE) is a new technique in which different protein samples, individually labeled with specific CyDyes, are combined together followed by electrophoresis and post electrophoretic co‐detection and co‐analysis on the same gel. CyDye DIGE fluor minimal dyes, which consist of three different CyDyes with different spectral characteristics, have been widely used for such purposes. The technique is highly sensitive with a wide dynamic range for detection of proteins and compatible with state‐of‐the‐art protein identification techniques using mass spectrometry. Although DIGE is mainly used to compare differential expression of various protein samples using 2‐D SDS‐PAGE, 1‐D DIGE also has important applications in quantitative proteomic studies.
Micrococcal Nuclease Analysis of Chromatin Structure
Authors: Zaret Ken 
Published: February 2005

AbstractThis unit describes methodology for using micrococcal nuclease to investigate the presence of nucleosomes at a particular location in chromatin and to map the positions of nucleosomes at various levels of resolution. The approaches are readily adaptable to other probes of chromatin structure that cause DNA cleavage. Results obtained from such chromatin studies provide a structural view of the molecular environment of gene in their native context in cells.
Chromatin Immunoprecipitation for Determining the Association of Proteins with Specific Genomic Sequences In Vivo
Authors: Aparicio Oscar , Geisberg Joseph V. , Sekinger Edward , Yang Annie , Moqtaderi Zarmik , Struhl Kevin 
Published: February 2005

AbstractChromatin immunoprecipitation (ChIP) is a powerful and widely applied technique for detecting the association of individual proteins with specific genomic regions in vivo. Live cells are treated with formaldehyde to generate protein‐protein and protein‐DNA cross‐links between molecules that are in close proximity on the chromatin template in vivo. DNA sequences that cross‐link with a given protein are selectively enriched, and reversal of the formaldehyde cross‐linking permits recovery and quantitative analysis of the immunoprecipitated DNA. As formaldehyde inactivates cellular enzymes essentially immediately upon addition to cells, ChIP provides snapshots of protein‐protein and protein‐DNA interactions at a particular time point, and hence is useful for kinetic analysis of events occurring on chromosomal sequences in vivo. In addition, ChIP can be combined with microarray technology to identify the location of specific proteins on a genome‐wide basis. in this unit describes the ChIP procedure for Saccharomyces cerevisiae; describes the corresponding steps for mammalian cells.
Pattern Discovery in Expression Profiling Data
Authors: Katagiri Fumiaki , Glazebrook Jane 
Published: February 2005

AbstractIn expression profiling studies, it is often necessary to identify groups of genes with similar expression profiles in a variety of samples, and/or groups of samples with similar expression profiles. Each profile can be expressed as a single data point in a space with the same number of dimensions as there are parameters in the profiles. In this way, pattern discovery among expression profiles is translated into pattern discovery in the spatial distribution of data points. Hierarchical clustering is useful for clustering similarly behaving genes or samples at local levels and for displaying the results in a simple color‐coded manner. K‐means clustering can be used for discovery of well‐defined clusters. Principal component analysis and self‐organizing maps can be used for dimensionality reduction, thereby facilitating visualization of major trends in data sets.
High‐Resolution FISH Analysis
Authors: Heng Henry H.Q. , Windle Bradford , Tsui Lap‐Chee 
Published: February 2005

AbstractMap order, orientation, and gap or overlap distance of closely linked DNA probes may be determined using fluorescent hybridization to decondensed DNA. The linear arrangement of released chromatin fibers not only simplifies the task of gene ordering, but also provides higher resolution with probes separated by greater distances than can be achieved in FISH with intact interphase nuclei. Theof this unit describes an alkaline lysis procedure for generating free chromatin from cultured cells for FISH analysis. A support protocol describes an empirical approach to optimize conditions for preparation of free chromatin. Anprovides a method for producing free chromatin from cultured lymphocytes with drug treatment. The, high‐resolution FISH mapping with free chromatin, is a modification of the method used for FISH mapping of interphase nuclei.
Morphology Antibody Chromosome Technique for Determining Phenotype and Genotype of the Same Cell
Authors: Knuutila Sakari 
Published: February 2005

AbstractThe morphology antibody chromosome (MAC) technique is a powerful combination of methods that permits analysis of both phenotype and genotype on a single interphase or mitotic cell as a basis for lineage analysis of neoplastic and normal cells. This unit describes MAC with sequential phenotypic analysis using antibody and an alkaline phosphatase anti‐alkaline phosphatase (APAAP) complex and genotypic analysis using in situ hybridization with either enzymatic or fluorescence detection. Alternate methods for phenotypic analysis are also described, which include the use of horseradish peroxidase‐conjugated antibodies, fluorochrome‐conjugated antibodies, May‐Grunwald‐Giemsa cytochemical staining, and Sudan black B cytochemical staining. An additional protocol describes G‐ and C‐banding as alternatives to in situ hybridization (ISH) for genotyping MAC specimens. Support protocols describe methods for preparing specimenscytospin preparations, in situ cultures, paraffin‐embedded or cryostat sections, and blood and bone marrow smears. describes a procedure for chromosome painting of previously GTG‐banded slides.
Gene Expression Analysis of a Single or Few Cells
Authors: Klein Christoph A. , Zohlnhöfer Dietlind , Petat‐Dutter Karina , Wendler Nicole 
Published: February 2005

AbstractThe need to analyze rare cells is based on the nature of tissue differentiation and regeneration, the initiation and propagation of disease processes in multicellular organisms, and the functional diversity of individual cells. Gene transcription is the most important regulatory mechanism by which a phenotype and functional state of a cell is determined. Therefore, procedures for the qualitative and quantitative assessment of mRNA abundance are important. This unit presents a protocol for semi‐quantitative analysis of gene expression of a single cell and quantitative representation of expressed genes from >10 to 30 cells. A basic protocol for array hybridization on nylon filters is provided because such filters are available in every laboratory. Tissue samples contain many different cell types in variable amounts, so their analysis may require microdissection; a protocol for obtaining cryosections is given. Finally, a simple procedure to prepare the data for statistical analysis is also provided.
Comparative Overview of Flow and Image Cytometry
Authors: Robinson J. Paul 
Published: February 2005

AbstractThis unit considers the issues of which tool to use—flow cytometry or imaging—and under what conditions. In particular, it compares the advantages and disadvantages of flow and image cytometry and provides examples illustrating the proper choice of each technology. The result is a better understanding of why the two technologies are complementary in many applications. It is clear that many scientists use the tools that are familiar to them, often in preference to the best tool. In cases where very advanced and rather expensive technologies are concerned, this is not surprising. However, there are clearly times when one form of cytometry is definitely superior to another. What then constitute the criteria for a decision when both flow cytometry and imaging are available? This unit addresses some of these concerns.
Modern Confocal Microscopy
Authors: Rajwa Bartek 
Published: February 2005

AbstractThis unit re‐examines confocal microscopy from a current perspective. It outlines many of the most modern applications of confocal microscopy and the issues surrounding them. The expanding applications of confocal microscopy demand both minor and major modifications of the technology to enhance imaging capabilities for a growing variety of samples. Techniques of interest such as FRET, FLIP, FRAP, and IFRAP are described. The unit includes a discussion on multispectral imaging, potentially the most exciting innovation in the field of biological imaging. The other area that is beginning to have considerable impact on biology, medicine, and pharmacology comprises high‐content screening (HCS) and high‐throughput screening (HTS). This unit also introduces programmable array microscopes (PAMs), which are based upon a technique in which spatial modulators are placed in the imaging plane of a microscope and used to generate patterns of illumination and/or detection.
Accuracy verification of spaceborne radar estimates of rain rate
Authors: Amitai E. , Liao L. , Llort X. , Meneghini R. 
Published: February 2005

AbstractThe distribution of rain rate is of great concern for many hydrological applications. Probability distribution functions (pdf) of rain rate can now be obtained from spaceborne radar observations. Effort to evaluate these pdfs using ground observations is described. Copyright © 2005 Royal Meteorological Society
Very short period quantitative precipitation forecasting
Authors: Fox Neil I. , Wilson James W. 
Published: February 2005

AbstractThis article presents an overview of the state of the art of very short period quantitative precipitation forecasting. The authors draw primarily on work presented during the sessions on ‘Nowcasting’ held at the 6th Symposium on the Hydrological Applications of Weather Radar, in Melbourne, Australia, from 2nd to 4th February 2004, and also include some other work in order to give a more complete picture of the field. Copyright © 2005 Royal Meteorological Society
Combining radar and rain gauge rainfall estimates using conditional merging
Authors: Sinclair Scott , Pegram Geoff 
Published: February 2005

AbstractThe Hydrologist's traditional tool for measuring rainfall is the rain gauge. Rain gauges are relatively cheap, easy to maintain and provide a direct and suitably accurate estimate of rainfall at a point. What rain gauges fail to capture well is the spatial variability of rainfall with time, an important aspect for the credible modelling of a catchment's response to rainfall. This spatial variability is particularly evident at short timescales of up to several days. As the period of accumulation increases, the expected spatial variability is reduced and rain gauges provide improved spatial rainfall estimates. Because of the fractal variability of rainfall in space, simple interpolation between rain gauges does not provide an accurate estimate of the true spatial rainfall field, at short time scales.Weather radar provides (with a single instrument) a highly detailed representation of the spatial structure and temporal evolution of rainfall over a large area. Estimated rainfall rates are derived indirectly from measurements of reflectivity and are therefore subject to a combination of systematic and random errors.This article describes a recently proposed merging technique and presents an application to simulated rainfall fields. The technique employed is Conditional Merging (Ehret, 2002), which makes use of Kriging to extract the optimal information content from the observed data. A mean field based on the Kriged rain gauge data is adopted, while the spatial detail from the radar is retained, reducing bias, but keeping the spatial variability observed by the radar. The variance of the estimate is reduced in the vicinity of the gauges where they are able to provide good information on the true rainfall field. Copyright © 2005 Royal Meteorological Society
Correction of the bright band using dual‐polarisation radar
Authors: Rico‐Ramirez M. A. , Cluckie I. D. , Han D. 
Published: February 2005

AbstractThis article presents an algorithm to correct the increase in reflectivity in the melting layer using weather radars. The correction starts with a fuzzy logic system (FLS) to classify rain, snow and melting snow using the reflectivity factor, the differential reflectivity, the linear depolarisation ratio and the height of the measurement from the ground surface. Using the output of the FLS, a correction is performed on the bright band contaminated reflectivity data assuming an idealised vertical reflectivity profile typical from stratiform precipitation and obtained from a considerable number of observations at S‐band frequencies. Copyright © 2005 Royal Meteorological Society
Assessing error in hydrological and hydraulic model output flows
Authors: Robbins Gavin L. , Collier Chris. G. 
Published: February 2005

AbstractA hydraulic model of an urban drainage system with a Bayesian post processor is used to assess the uncertainty in model output flows associated with the use of measurements of rainfall made using raingauges, microwave link attenuation measurements and weather radar. Copyright © 2005 Royal Meteorological Society
Colour remediation of pulp mill effluent using purified fungal cellobiose dehydrogenase: Reaction optimisation and mechanism of degradation
Authors: Wingate Kathryn G. , Stuthridge Trevor , Mansfield Shawn D. 
Published: February 2005

AbstractCellobiose dehydrogenase purified from two different fungal sources was assessed for its ability to remove and/or reduce colour from pulp mill bleach plant effluent. Cellobiose dehydrogenase purified from Phanerochaete chrysosporium was shown to prefer acidic conditions and was consequently used to treat the acid effluent stream discharged from a pulp mill bleach plant, while an analogous enzyme originating from Humicola insolens preferred alkaline conditions, and was applied to the effluent discharged from the caustic sewer of the bleach plant. Both enzyme preparations were able to remove colour from their respective effluent sources to a comparable extent. Up to 50% of the effluent colour was removed within 4 days when treated under optimised conditions. Furthermore, it was also shown that this enzymatic approach was effective at removing colour generated by both softwood and hardwood resources. Mechanistically, it was shown that colour was removed from all molecular weight fractions, and the higher molecular weight material (>300 kDa) was concurrently preferentially degraded. Cellobiose dehydrogenase treatment of effluent did not target phenolic, stilbene, or α‐carbonyl structures, but did affect the quinone content. Further investigations using model compounds confirmed these results, and subsequently showed that only the para‐quinones with low substitution were reduced with cellobiose dehydrogenase. © 2005 Wiley Periodicals, Inc.
Object combining: a new aggressive optimization for object intensive programs
Authors: Veldema Ronald , Jacobs Ceriel J. H. , Hofman Rutger F. H. , Bal Henri E. 
Published: February 2005

AbstractObject combining tries to put objects together that have roughly the same life times in order to reduce strain on the memory manager and to reduce the number of pointer indirections during a program's execution. Object combining works by appending the fields of one object to another, allowing allocation and freeing of multiple objects with a single heap (de)allocation. Unlike object inlining, which will only optimize objects where one has a (unique) pointer to another, our optimization also works if there is no such relation. Object inlining also directly replaces the pointer by the inlined object's fields. Object combining leaves the pointer in place to allow more combining. Elimination of the pointer accesses is implemented in a separate compiler optimization pass. Unlike previous object inlining systems, reference field overwrites are allowed and handled, resulting in much more aggressive optimization. Our object combining heuristics also allow unrelated objects to be combined, for example, those allocated inside a loop; recursive data structures (linked lists, trees) can be allocated several at a time and objects that are always used together can be combined. As Java explicitly permits code to be loaded at runtime and allows the new code to contribute to a running computation, we do not require a closed‐world assumption to enable these optimizations (but it will increase performance). The main focus of object combining in this paper is on reducing object (de)allocation overhead, by reducing both garbage collection work and the number of object allocations. Reduction of memory management overhead causes execution time to be reduced by up to 35%. Indirection removal further reduces execution time by up to 6%. Copyright © 2005 John Wiley & Sons, Ltd.