bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated On-Line Solid-Phase Extraction Coupled with HPLC for Measurement of 5-Hydroxyindole-3-acetic Acid in Urine
Authors: Mulder Erik J , Oosterloo-Duinkerken Alida , Anderson George M , De Vries Elisabeth GE , Minderaa Ruud B , Kema Ido P 
Published: July 2005

Abstract
Background: Quantification of 5-hydroxyindole-3-acetic acid (5-HIAA) in urine is useful in diagnosing and monitoring of patients with carcinoid tumors and in the study of serotonin (5-hydroxytryptamine) metabolism in various disorders. We describe an automated method that incorporates on-line solid-phase extraction (SPE) and HPLC to measure urinary 5-HIAA.
Methods: Automated prepurification of urine was accomplished with HySphere-resin GP SPE cartridges containing strong hydrophobic polystyrene resin. The analyte (5-HIAA) and internal standard [5-hydroxyindole-3-carboxylic acid (5-HICA)] were eluted from the SPE cartridge, separated by reversed-phase HPLC, and detected fluorometrically with a total cycle time of 20 min. Urinary excretion of 5-HIAA was measured in a group of patients with known and suspected carcinoid tumors (n = 63) and in 20 patients with autism.
Results: The internal standard (5-HICA) and 5-HIAA were recovered in high yields (87.2%–114%). Within- and between-series CVs for the measurement of 5-HIAA in urine ranged from 1.2% to 3.9% and 3.2% to 7.6%, respectively. For urine samples from patients with known or suspected carcinoid tumors, results obtained by the automated method were highly correlated (r = 0.988) with those from an established manual extraction method. For samples from autistic patients, urinary excretion of 5-HIAA was similar to that reported for healthy individuals.
Conclusion: This SPE-HPLC method demonstrated lower imprecision and time per analysis than the manual solvent extraction method.
DNA
methylation in epigenetics, development, and imprinting
Authors: Sasaki Hiroyuki 
Published: July 2005

Abstract
DNA methylation is a key epigenetic mechanism that controls developmental gene expression, transposon silencing, and genome integrity. In vertebrates, methylation occurs at the cytosine of CpG dinucleotides, and this provides the basis for heritability of methylation patterns through replication. The DNA methyltransferases and methyl‐CpG‐binding proteins cooperate with chromatin modification enzymes to silence genes. Although some organisms such as yeast and nematode live happily without methylation, mammals are heavily dependent on it: loss of methylation in mice causes early embryonic death. Genomic imprinting, an epigenetic phenomenon crucial for normal mammalian development, is also controlled by methylation.
Rapidly evolving imprinted loci
Authors: Kim Joomyeong , Stubbs Lisa 
Published: July 2005

Abstract

Most imprinted genes are highly conserved, encoding proteins with similar structure and function in all mammals; some are even well conserved in nonmammalian vertebrates in which imprinting does not exist. These genes are likely to participate in well‐established pathways defining shared embryological and adult traits. However, certain imprinted genes vary in form, function, and tissue‐specific regulation in different mammalian species. One imprinted domain, located in human chromosome 19 and proximal mouse chromosome 7, is exceptional in that all of the resident genes are of this evolutionarily unstable type. Five of the six genes in this region encode SCAN‐ and KRAB‐containing
Kruppel‐
type zinc‐finger (ZNF) genes, and are therefore members of rapidly evolving, vertebrate‐specific gene families. The recent advent of these genes may help explain their unusual level of evolutionary instability. However, because of their predicted function as transcription factors, the lineage‐specific loss and divergence of these loci may have far‐reaching effects on development, morphology, and behavior that define distinguishing traits in different mammals.
Gene mapping, imprinting, and epigenetics
Authors: Strauch Konstantin 
Published: July 2005

Abstract
In this review, methods for linkage and association analysis are presented that take imprinting into account. This epigenetic factor is also known as the parent‐of‐origin effect. Here, it is described why it is important to adequately model imprinting in the context of gene mapping. Tests for linkage that account for imprinting are contrasted with tests for imprinting. Furthermore, the confounding between sex differences in recombination fractions and imprinting is mentioned, as well as how such confounding can be avoided in a mapping study.
Gene identification in common disorders: a tutorial
Authors: Goodarzi Mark O. , Rotter Jerome I. 
Published: July 2005

Abstract
The task of identifying genes that predispose to common disorders presents unique challenges because, unlike rare genetic disorders, a number of genes may contribute to a common condition, each gene with a mild/moderate effect. This necessitates the study of large cohorts of subjects and families with and without the disorder of interest. These studies must establish the inherited nature of the condition, using a precise and reproducible method of defining the disorder. Intermediate phenotypes, thought to represent the earliest stages of the condition, may also prove useful in identifying genetic determinants in those at risk, as well as to subclassify affected individuals. In the past, linkage and association studies relied heavily on the use of single nucleotide polymorphisms and microsatellites as genetic markers; currently, interest is growing in the use of haplotypes, which are collections of marker alleles inherited together on a chromosome. By providing coverage across large regions of the genome, haplotypes may increase the ability to identify genetic determinants.
Single molecule array‐based sequencing
Authors: Bennett Simon T. , Smith Tony J. 
Published: July 2005

Abstract

Single molecule array‐based sequencing permits simultaneous analysis of potentially hundreds of millions of single molecules of DNA per cm
2
in an array‐based format. In this massively parallel approach to DNA sequence acquisition, reagents are utilized in an extremely efficient manner to achieve unprecedented levels of cost reduction and increased throughput. Ultimately, single molecule array (SMA)‐based sequencing will enable analysis of individual whole human genomes in a single experiment.
UsingESTsfor genome annotation – predicting the transcriptome
Authors: Eyras Eduardo 
Published: July 2005

AbstractExpressed sequence tags (ESTs) provide a quick and cost‐effective way to obtain information about the collection of expressed genes in a genome. They can also provide information about the expression of genes, alternative splicing, polymorphisms, and untranslated regions, complementing other standard methods of annotation and ab initio gene prediction. Here we describe some of the advantages and problems of the usage of ESTs for genome annotation, emphasizing their utility for describing alternative splicing.
Expression and localization of proteins in mammalian cells
Authors: Stow Jennifer L. , Teasdale Rohan D. 
Published: July 2005

AbstractThe transfer of genes and expression of recombinant proteins is one of the main methods for discovery in the quest for understanding as biology moves from genomes through to proteomes, and finally to working cells and organisms. The techniques and tools for the transfer and engineering of genetic material and for the detection and analysis of expressed proteins are evolving rapidly alongside the burgeoning databases they have to explore. Physical, chemical, and biologically based vectors increasingly enable gene transfer into mammalian cells for research and therapeutic purposes. The emergence of fluorescent protein tags now allows sophisticated tracking and functional analysis of expressed proteins. In this review, we summarize the methods and scientific tools contributing to this technology. Finally, the push is on to develop high‐throughput and computational methods for large‐scale protein expression, localization, and analysis, and here we set the stage by providing updates on the coming technology in these fields.
The promise of gene signatures in cancer diagnosis and prognosis
Authors: Sung Jimmy C. , Lee Alice Y. , Yeatman Timothy J. 
Published: July 2005

Abstract
Gene‐expression profiling is a relatively new technology that has promise for developing mathematical models that might be useful in predicting diagnoses and prognoses for a number of different cancer types. While the promise of this approach has not yet been realized, there is accumulating evidence that this approach is feasible. Extensive validation of all molecular classifiers with large independent test sets will be necessary prior to clinical application.
Protein microarrays as an emerging tool for proteomics
Authors: Qiu Ji , Hanash Sam 
Published: July 2005

Abstract
The emerging technology of protein microarrays has a far‐reaching potential to meet the needs for measuring not just the abundance of protein constituents but also their functional states and their interactions with other biomolecules, with the requisite high throughput and high sensitivity. While protein microarrays still present some challenging problems, recent progress makes it likely that it will be possible soon to interrogate proteins at a proteome scale, using protein microarrays, analogous to DNA microarrays, thus making a substantial impact on biomedical research.
Seven years of yeast microarray analysis
Authors: Sherlock Gavin , Spellman Paul T. 
Published: July 2005

Abstract

Since the advent of microarray technology in the mid‐1990s, and finishing of the complete genome sequence of the yeast
Saccharomyces cerevisiae
in 1996, yeast has been at the forefront of genomic biology. In this article, we review the uses of microarrays to investigate yeast biology, and the wide range of applications that they have been used for. While, typically, people think of microarrays for generating large‐scale expression measurements, we discuss several different experimental approaches that have used microarrays to probe almost every facet of a living yeast cell.
Small molecule fluorescent probes for protein labeling and their application to cell‐based imaging (including
Fl
As
H
etc.)
Authors: Cass Tony 
Published: July 2005

Abstract
The fluorescent imaging of live cells has benefited tremendously from the development of new types of highly specific protein reagents. Three broad approaches to introducing fluorescent proteins into live cells have been described; ex vivo labeling followed by the introduction of the labeled proteins into cells, heterologous expression of inherently fluorescent proteins as fusions to other proteins and heterologous expression of a tagged protein followed by labeling with a reagent that reacts specifically with the tag. This last approach will be the subject of this review, and both the principles of the method and some applications will be described.
History and future of
X
‐ray structure determination
Authors: Jaeger Joachim , Dennis Caitriona 
Published: July 2005

Abstract
Single crystal X‐ray diffraction was first applied at the beginning of the twentieth century and to this day remains the most commonly used and highly productive technique to elucidate macromolecular structures at the atomic level. Recent developments in the theoretical background and in computational methods, dramatic improvements in experimental designs of synchrotron beamlines and insertion devices, and technical advances in high‐throughput methods combined with robotics have had a major impact on the analysis of macromolecular structure. Combination of cryogenic imaging techniques (EM) with multidimensional NMR, X‐ray, and electron diffraction studies will lead to unprecedented, new insights into the structure–function relationships of biological macromolecules.
Repeatfinding
Authors: Sucgang Richard 
Published: July 2005

Abstract
Finding repeats in biological sequences is a necessary first step in recognizing patterns and biologically relevant motifs. Given the inexact nature of biological repeats, the software required to detect, identify, classify, and curate them have grown not only in variety but in sophistication as well, accommodating increases both in amount of data and available computing power. Open source and free‐for‐academic‐use programs implementing repeat finding algorithms, as well as databases that curate known biological repeat motifs are surveyed in this section.
Algorithms for sequence errors
Authors: Andersson Björn , Tammi Martti T. 
Published: July 2005

Abstract
There are many obvious reasons why we would want to use error‐free DNA sequence data. For example, computer assembly of sequence fragments would be algorithmically much simpler and the cost of genome sequencing would be lower, since less sequence redundancy would be required. Unfortunately, we cannot get perfect data, but we can measure the accuracy of the sequence. The accuracy measures or error probabilities help us correct sequence data.
Measuring evolutionary constraints as protein properties reflecting underlying mechanisms
Authors: Neuwald Andrew F. , Liu Jun S. 
Published: July 2005

AbstractSelective constraints are revealed in protein multiple sequence and structural alignments as conserved residues and corresponding atomic interactions. These patterns of conservation contain implicit information about underlying protein mechanisms, just as crystalline X‐ray diffraction patterns contain implicit information about a protein's structure. Contrast hierarchical alignment and interaction network (CHAIN) analysis measures and characterizes selective constraints on the basis of co‐conserved patterns and fits mechanistic models to these and other constraints. Just as the quantity and quality of X‐ray diffraction patterns determines how well one can fit an atomic model to the inferred electron density, the quantity and quality of co‐conserved patterns determines how well one can fit possible mechanisms to these inferred constraints. In principle, given sufficient data, biological mechanisms may be identified with high certainty. Nevertheless, even at “low resolution”, this information can prune the possibilities down to a manageable number for further experimental follow‐up.
Silicon Compounds: Anthropogenic Silicas and Silicates
Authors: Falcone James 
Published: July 2005

AbstractSynthetic akali silicates, M2O·mSiO2·nH2O, where M = Li, Na, and K, are manufactured as liquids or glasses that readily dissolve in water to form alkaline solutions. These silicates contain a complex mixture of polymeric species that vary as a function of modulus,m, of the material, solution concentration, impurities content, and pH value. The polymer chemistry of silicates influences the properties and function of these materials in a variety of applications including detergency, water treatment, mineral beneficiation, bleach stabilization, and as a raw material for the syntheses of silica sols, gels and precipites, zeolites, clays, and other siliceous materials. The speciation and structure of silicates have been studied using a broad variety of analytical methods including Fourier transform infrared, ft–nmr, laser Raman, and X‐ray photoelectron spectroscopic techniques. The current article discusses the properties of the synthetic alkali silicates that determine their function in a variety of commercial applications. Economic, manufacturing, regulatory and environmental aspects of silicate production and usage are reviewed.
The Drainage: Impacts, Plant Growth, and Water Table Levels
Authors: Madramootoo Chandra 
Published: July 2005

Abstract
Every soil has some degree of natural drainage. However, if the rates of precipitation or irrigation exceed the natural drainage rate of the soil, the high water table conditions will impair crop growth, because of a lack of oxygen in the root zone. Artificial, or tile drainage, is therefore required to remove excess soil water and to lower the water table, to maintain an optimum soil–air environment within the crop root zone. Most of the world's highly productive agricultural soils require either surface drainage or tile drainage, or a combination of both, to maintain stable crop yields. It is estimated that there are about 200 million hectares of cropland worldwide with improved drainage.
Pesticide Chemistry in the Environment
Authors: Miglioranza Karina S.B. , Gonzalez Mariana , Aizpún De Moreno Julia E. , Moreno Víctor J. 
Published: July 2005

AbstractThe use of pesticides has resulted in increased crop production but also raised concerns about potential adverse effects on the environment. The knowledge of pesticide environmental behavior, like soil adsorption, leaching, and volatility, is necessary to asses the risk to the environment and humans. The properties of pesticides, such as herbicides, insecticides, and fungicides, combined with the amount applied, determine how many pesticides can be transported along each route into the environment. Among insecticides, the monitoring of organochlorine pesticides (OCP) with low water solubility and high environmental persistence is highly recommended. Field studies determined that soil characteristics, topographic position, and land uses influence in OCP accumulation. The accumulation pattern represent a dynamic balance between deposition and erosion in association with wind‐induced circulation, tillage management practices, and effects by natural processes, such as rainfall and flooding periods, according to different soils. Moreover, the use of pesticides on agricultural land may have a negative effect on nearby aquatic ecosystems. This effect is determined by the specific chemicals used, the place and methods of application of the chemicals, and the various mechanisms available for transporting compounds to the waterbodies, with soil erosion being a major pathway. Hydrophobicity and persistence are the main properties of pesticides that control their accumulation in sediment and aquatic biota. Thus, this fact confirms the current necessity of OCP monitoring in natural areas.
Water Pollution from Fish Farms
Authors: Bergheim Asbjørn , Brinker Alexander 
Published: July 2005

Abstract
Wastes from aquaculture plants include all materials used in the process that are not removed from the system during harvest. The principle wastes from aquaculture are uneaten feed, excreta, chemicals, and therapeutics. In addition, the term “waste” can also refer to pathogens and dead or escaped fish.

Generally, the quantity of waste is closely connected to the culture system used.
Intensive
farm systems, typically monoculture of carnivorous finfish in the temperate zone reliant on artificial feed, may cause serious local pollution. So‐called semi‐intensive farm systems are supplied natural feed sources, such as vegetation, oil cakes, cereal bran, and organic‐chemical fertilizers. The latter systems dominate the tropical/subtropical production of herbivorous or omnivorous fish, e.g., the major production of carps and tilapia, and the waste output to the surrounding waters is much lower than from intensive fish farms.
Deep‐Well Turbine Pumps
Authors: Hanson Blaine 
Published: July 2005

Abstract
Deep‐well turbine pumps are used to pump groundwater. They consist of a housing or bowl, impellers, and a shaft, all of which are installed in the well. Impeller types include closed and semi‐open impellers. Submersible pumps are a modification of deep‐well turbines for which the electric motor is installed in the well, instead of at the ground surface. Performance curves, developed by pump manufacturers, describe relationships between total head and capacity, pump efficiency and capacity, and horsepower demand and capacity. These curves can select new pumps and evaluate existing pumps. A common cause of declining pump efficiency with time is wear caused by sand in the pumped water.
Nitrate Pollution Prevention
Authors: Maticic Brane 
Published: July 2005

Abstract
Groundwater and springwater are sources used for water supply in many countries. The pollution of surface and groundwater is caused mostly by the chemicals used in industry, urban wastes, and agriculture. The pollution of groundwater by nitrates, as well as the pollution of crops that we consume, is one of the most serious environmental concerns in most countries. Drinking water and eating vegetables with high amounts of nitrate and nitrite are toxic, especially for children and babies. It is not nitrate that is toxic, but the compounds derived from it, nitrites and nitrosamines.
To identify nitrogen surpluses (that may influence pollution of groundwater and surface waters) due to agricultural technology used in different countries, it is advisable to demonstrate a “mineral (nitrogen) balance” on regional and farm levels using a normative approach. In the most intensive arable region with a high intensity of animal husbandry (>2 LU/ha), nitrate surpluses are supposed to be found in the soil, crops and groundwater. These regions can be identified as vulnerable for nitrogen leaching into groundwater. In regions with limited growing conditions for agricultural plants (climate, soil depth), a small increase in livestock density can cause high nitrogen surpluses (karst regions).
To reduce mineral (nitrogen) surpluses in agriculture and to meet the standards of nitrate and nitrite in drinking water and crops, it is necessary to control water and food quality in connection with nitrates and nitrites and to exact certain regulations regarding change in agriculture, especially animal excrement management.
The regulations should give and follow different norms such as: the maximum allowed intensity of raising animals, proper timing for the application of organic manure on soil, the highest quantities of mineral fertilizers allowed per hectare, and suitably built dung yards and cesspools.
When the world is going through many changes regarding exploitation of its natural resources and environmental protection, new ideas for efficient and sustainable water management of agricultural land are very important to protect the quality of groundwater and water in rivers, as well as crops that we consume.
Biofuel Alternatives to Fossil Fuels
Authors: Reijnders Lucas 
Published: July 2005

Abstract
There is increased advocacy for replacing fossil fuels by biofuels by using advanced conversion technology. Increased use of biofuels has direct and indirect effects on water. Indirect effects are mediated by the impact of biofuels on climate. Specific biofuels may be linked to quite different inputs of fossil fuels, and effects on biogenic carbon stocks and are not necessarily “climate neutral.” Availability of water may be a limiting factor in biofuel production, making water efficiency an important matter. Peak flows, storm flows, and groundwater levels may be influenced by biofuel crops. The biofuel life cycle may mobilize large amounts of substances that may impact water. Biofuel crop production may be associated with silting, downstream channel instability, and increased concentrations of minerals and plant nutrients in surface water. Biofuel life cycle emissions of acidifying substances, persistent organic pollutants, heavy metals, and other hazardous elements may be significant. There are measures to limit the impact of substances mobilized during the biofuel life cycle.