bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA editing of human microRNAs
Authors: Blow Matthew J , Grocock Russell J , van Dongen Stijn , Enright Anton J , Dicks Ed , Futreal P Andrew , Wooster Richard , Stratton Michael R 
Published: April 2006

Abstract
Background
MicroRNAs (miRNAs) are short RNAs of around 22 nucleotides that regulate gene expression. The primary transcripts of miRNAs contain double-stranded RNA and are therefore potential substrates for adenosine to inosine (A-to-I) RNA editing.

Results
We have conducted a survey of RNA editing of miRNAs from ten human tissues by sequence comparison of PCR products derived from matched genomic DNA and total cDNA from the same individual. Six out of 99 (6%) miRNA transcripts from which data were obtained were subject to A-to-I editing in at least one tissue. Four out of seven edited adenosines were in the mature miRNA and were predicted to change the target sites in 3' untranslated regions. For a further six miRNAs, we identified A-to-I editing of transcripts derived from the opposite strand of the genome to the annotated miRNA. These miRNAs may have been annotated to the wrong genomic strand.

Conclusion
Our results indicate that RNA editing increases the diversity of miRNAs and their targets, and hence may modulate miRNA function.
New gasoline homogeneous charge compression ignition combustion system using two-state direct injection and assisted spark ignition
Authors: Wang Z , Wang J-X , Shuai S-J , Ma Q-J 
Published: April 2006

Homogeneous charge compression ignition (HCCI) combustion was studied in a four-stroke gasoline engine with a direct injection system. The spark ignition and electronically controlled two-stage gasoline injection system are adopted to control the mixture formation, ignition timing, and combustion rate in the HCCI engine. The engine could be operated in HCCI combustion mode in a range of loads from 1 to 5 bar indicated mean effective pressure (IMEP) and operated in SI combustion mode up to loads of 8 bar IMEP. The HCCI combustion characteristics were investigated under different air—fuel ratios, engine speeds, starts of injection, as well as spark ignition enabled or not. By introducing the second fuel injection in the compression stroke, the stratified concentration is formed and the mixture is cooled, which means that HCCI ignition timing can be controlled and the load range can be extended by tuning the mixture concentration and temperature. At a critical ignition temperature, especially in SI—HCCI combustion mode transition, assisted SI improves the stability of HCCI combustion. In order to understand better the physicochemical process in the cylinder, an improved three-dimensional computational fluid dynamics code has been utilized to simulate the intake, two-stage spray, compression, and combustion processes of the HCCI engine. The calculated results show that a homogeneous lean charge could be realized by single fuel injection in the intake stroke. With the help of the intake swirl and squish flow in the compression stroke, a rich mixture resulting from the second fuel injection can be formed near the spark. Hydroxyl ions (OH) reach to a maximum at the periphery of the fuel-rich zone; a great number of spots are ignited simultaneously. It works as an initiation to ignite the surrounding lean mixture zone.
Estimation and Application of Biological Variation of Urinary δ-Aminolevulinic Acid and Porphobilinogen in Healthy Individuals and in Patients with Acute Intermittent Porphyria
Authors: Aarsand Aasne K , Petersen Per Hyltoft , Sandberg Sverre 
Published: April 2006

Abstract
Background: Diagnosis of an attack of acute intermittent porphyria (AIP) is based on the demonstration of increased concentrations of porphobilinogen (PBG) and δ-aminolevulinic acid (ALA) in urine, but many AIP patients also have high baseline concentrations in remission. The aim of this study was to estimate the biological variations of ALA, PBG, and porphyrins in healthy individuals and AIP patients to improve interpretation of test results.
Methods: Fifteen healthy individuals and 15 AIP patients were included, and biological variations were calculated based on urine samples collected weekly for 10 consecutive weeks. For the AIP patients, long-term variations were also estimated based on 7 samples collected through a 2-year period.
Results: The porphyrin variances were inhomogeneously distributed; biological variations of porphyrins were therefore not calculated. The within-subject biological variations of ALA and PBG were 16%–20% in the short-term settings and for PBG, 25% in the long-term setting, giving reference change values of ∼50% and 70%, respectively. The probability of detecting a 100% real change in PBG was 97% in the short-term setting and 80% in the long-term setting.
Conclusions: In an AIP patient, a 2-fold increase in PBG, independent of the baseline concentration, will be detected with a probability &gt;80% and is most likely related to the patient’s disease and not caused only by analytical and biological variation. When PBG is used in the assessment of AIP-related symptoms, both the PBG concentration in remission and the length of time since the previous sample must be considered.
Significant Expansion ofVicia pannonicaGenome Size Mediated by Amplification of a Single Type of Giant Retroelement
Authors: Neumann Pavel , Koblížková Andrea , Navrátilová Alice , Macas Jiří 
Published: April 2006

AbstractAmplification and eventual elimination of dispersed repeats, especially those of the retroelement origin, account for most of the profound size variability observed among plant genomes. In most higher plants investigated so far, differential accumulation of various families of elements contributes to these differences. Here we report the identification of giant Ty3/gypsy-like retrotransposons from the legume plant Vicia pannonica, which alone make up ∼38% of the genome of this species. These retrotransposons have structural features of the Ogre elements previously identified in the genomes of pea and Medicago. These features include extreme size (25 kb), the presence of an extra ORF upstream of the gag–pol region, and a putative intron dividing the prot and rt coding sequences. The Ogre elements are evenly dispersed on V. pannonica chromosomes except for terminal regions containing satellite repeats, their individual copies show extraordinary sequence similarity, and at least part of them are transcriptionally active, which suggests their recent amplification. Similar elements were also detected in several other Vicia species but in most cases in significantly lower numbers. However, there was no obvious correlation of the abundance of Ogre sequences with the genome size of these species.
Decade of Experience With Vascular Rings at a Single Institution
Authors: Humphrey Carrie , Duncan Kim , Fletcher Scott 
Published: April 2006

OBJECTIVE. Over the past decade, the diagnostic workup of vascular rings has changed at our institution. Despite surgical intervention, we have observed long-term aerodigestive issues in some patients. In an effort to better characterize these pre- and postoperative issues, we reviewed a decade of experience at our institution.
METHODS. We performed a complete chart review of all patients identified as having surgical intervention for vascular ring between January 1993 and December 2003. A questionnaire was mailed to the family of each patient to ascertain a subjective assessment of long-term postoperative issues.
RESULTS. Thirty-eight patients were reviewed and categorized as to specific arch anomaly. Associated cardiac anomalies were present in 29% of patients. Chronic feeding difficulties persisted in 18% of patients, and airway issues remained in nearly half of the patients. Patients with underlying genetic syndromes had less resolution of symptoms compared with nonsyndromic children. Chronic respiratory symptoms were present in 80% of patients operated &lt;6 months, 15% if operated between 6 months and 3 years, and 42% of patients operated after 3 years of age.
CONCLUSIONS. Aerodigestive issues may persist after vascular ring division despite initial improvement. Accurate preoperative anatomic imaging is imperative to surgical planning.
Constitutive Expression of a High‐Affinity Sulfate Transporter in Indian Mustard Affects Metal Tolerance and Accumulation
Authors: Lindblom Stormy Dawn , Abdel‐Ghany Salah , Hanson Brady R. , Hwang Seongbin , Terry Norman , Pilon‐Smits Elizabeth A. H. 
Published: April 2006

ABSTRACTThe Stylosanthes hamata SHST1 gene encodes a high‐affinity sulfate transporter located in the plasma membrane. In this study the S. hamata SHST1 gene was constitutively expressed in Indian mustard [Brassica juncea (L.) Czern.] to investigate its importance for tolerance and accumulation of various oxyanions that may be transported by SHST1 and for cadmium, which is detoxified by sulfur‐rich compounds. The transgenic SHST1 lines SHST1‐12C and SHST1‐4C were compared with wild‐type Indian mustard for tolerance and accumulation of arsenate, chromate, tungstate, vanadate, and cadmium. As seedlings the SHST1 plants accumulated significantly more Cd and W, and somewhat more Cr and V. The SHST1 seedlings were less tolerant to Cd, Mo, and V compared to wild‐type plants. Mature SHST1 plants were less tolerant than wild‐type plants to Cd and Cr. SHST1 plants accumulated significantly more Cd, Cr, and W in their roots than wild‐type plants. In their shoots they accumulated significantly more Cr and somewhat more V and W. Shoot Cd accumulation was significantly lower than in wild‐type, and As levels were somewhat reduced. Compared to wild‐type plants, sulfur accumulation was enhanced in roots of SHST1 plants but not in shoots. Together these results suggest that SHST1 can facilitate uptake of other oxyanions in addition to sulfate and that SHST1 mediates uptake in roots rather than root‐to‐shoot translocation. Since SHST1 overexpression led to enhanced accumulation of Cr, Cd, V, and W, this approach shows some potential for phytoremediation, especially if it could be combined with the expression of a gene that confers enhanced metal translocation or tolerance.
Determining Phosphorus Release Rates to Runoff from Selected Alberta Soils Using Laboratory Rainfall Simulation
Authors: Wright Charles R. , Amrani Mohamed , Akbar Muhammad A. , Heaney Danial J. , Vanderwel Douwe S. 
Published: April 2006

ABSTRACTPhosphorus losses from agricultural land can cause accelerated eutrophication of surface water bodies. This study evaluated the use of soil test phosphorus (STP) levels to predict dissolved inorganic phosphorus (DIP) concentrations in runoff water from agricultural soils using laboratory rainfall simulation. The objectives of this study were to determine (i) to what extent STP concentrations can be used as a basis to predict P losses from Alberta soils and (ii) how extended rainfall simulation run times affected DIP losses. Soil samples collected from a total of 38 field sites, widely scattered throughout the southern half of Alberta, were subjected to rainfall simulation in the laboratory. The STP concentrations were determined using Miller–Axley, Norwest, Kelowna, Modified Kelowna Mehlich‐III, and distilled water extraction methods. Each rainfall simulation event lasted for at least 90 min. Runoff samples were collected in time series for the duration of each simulation, during two distinct runoff intervals: (i) for the first 30 min of continuous runoff (T30) and (ii) for 40 min during runoff equilibrium (Teq). For all the STP extractants and both runoff intervals, the relationship with DIP–flow‐weighted mean concentration (FWMC) was linear and highly significant withr2values ranging from 0.74 to 0.96. However, the slopes of the resulting regression lines were, on average, 1.85 times greater for theT30runoff interval over those computed for theTeqinterval. Thus experimental methodology greatly influenced regression parameters, suggesting that more work was needed to verify these relationships under natural conditions. In addition, with many of ther2values greater than 0.90 there would be little, if any, benefit derived by including soil properties in regression analysis.
Modeling Methyl Isothiocyanate Soil Flux and Emission Ratio from a Field following a Chemigation of Metam‐Sodium
Authors: Li Lin Ying , Barry Terrell , Mongar Kevin , Wofford Pamela 
Published: April 2006

ABSTRACTMetam‐sodium had become the most heavily used soil fumigant in recent years as the deadline approached for methyl bromide to phase out in January 2005. After application, metam‐sodium decomposes rapidly to methyl isothiocyanate (MITC), a highly toxic compound capable of killing a wide spectrum of soil‐borne pests. Inhalation risk of MITC ranked high among airborne agricultural pesticides in California. Information about off‐gassing intensity and percentage of emission is essential for exposure risk assessment and mitigation measures, but is limited, especially for new application methods such as drip chemigation. Air concentrations of MITC were monitored around a field treated with metam‐sodium through surface drip irrigation system. The field was tarped with plastic films before the chemigation. The air concentrations at receptor locations were simulated for the period of air monitoring with the Industrial Source Complex (ISC3) Dispersion Model, and soil flux density of MITC at various periods after chemigation was estimated through a back‐calculation procedure. The estimated soil flux density of MITC showed a diurnal pattern, with the daytime flux stronger than nighttime. However, the average air concentration at nighttime was higher than that at daytime. Soil flux density peaked at 4.30 μg m−2 s−1 in the first 12‐h period after chemigation, then declined with time. The MITC emission percentage in the first 60‐h was 2.65% of applied mass, of which 57% occurred in the first 24‐h after chemigation. The study indicated that the tarped bed drip application method of metam‐sodium had a relatively good control of MITC emission from soil.
Determination of Steroidal Estrogens in Flushed Dairy Manure Wastewater by Gas Chromatography‐Mass Spectrometry
Authors: Hanselman Travis A. , Graetz Donald A. , Wilkie Ann C. , Szabo Nancy J. , Diaz Carolyn S. 
Published: April 2006

ABSTRACTThere is a critical need to accurately measure the concentrations of natural steroidal estrogens in flushed dairy manure wastewater (FDMW) to assess any potential risk of waterway contamination resulting from land application. Estrogens are a concern because low concentrations (10‐100 ng L−1) in water can adversely affect aquatic vertebrate species such as fish, turtles, and frogs by disrupting the normal function of their endocrine systems. The objective of this study was to develop a sample preparation method that permits the quantification of four natural steroidal estrogens (17α‐estradiol, 17β‐estradiol, estrone, and estriol) in FDMW by gas chromatography‐mass spectrometry (GC‐MS). Solid‐phase extraction with graphitized carbon black was used for the bulk extraction of estrogens from FDMW and additional sample purification was accomplished with C‐18. The sample preparation method allowed estrogens to be detected accurately by GC‐MS in FDMW. Spiked recovery experiments indicated that the method is satisfactory for measuring the estrogens of interest in FDMW with average recovery of >90%. As expected in FDMW, characterization of the estrogen profile revealed a large abundance of 17α‐estradiol relative to 17β‐estradiol and estrone. Estriol was not detected in FDMW. The methodology developed in this research helps provide an analytical foundation for the quantification of steroidal estrogens in FDMW by GC‐MS.
Tillage and Field Scale Controls on Greenhouse Gas Emissions
Authors: Lee Juhwan , Six Johan , King Amy P. , van Kessel Chris , Rolston Dennis E. 
Published: April 2006

ABSTRACTThere is a lack of understanding of how associations among soil properties and management‐induced changes control the variability of greenhouse gas (GHG) emissions from soil. We performed a laboratory investigation to quantify relationships between GHG emissions and soil indicators in an irrigated agricultural field under standard tillage (ST) and a field recently converted (2 yr) to no‐tillage (NT). Soil cores (15‐cm depth) were incubated at 25°C at field moisture content and 75% water holding capacity. Principal component analysis (PCA) identified that most of the variation of the measured soil properties was related to differences in soil C and N and soil water conditions under ST, but soil texture and bulk density under NT. This trend became more apparent after irrigation. However, principal component regression (PCR) suggested that soil physical properties or total C and N were less important in controlling GHG emissions across tillage systems. The CO2 flux was more strongly determined by microbial biomass under ST and inorganic N content under NT than soil physical properties. Similarly, N2O and CH4 fluxes were predominantly controlled by NO3− content and labile C and N availability in both ST and NT soils at field moisture content, and NH4+ content after irrigation. Our study indicates that the field‐scale variability of GHG emissions is controlled primarily by biochemical parameters rather than physical parameters. Differences in the availability and type of C and N sources for microbial activity as affected by tillage and irrigation develop different levels and combinations of field‐scale controls on GHG emissions.
Liming Poultry Manures to Decrease Soluble Phosphorus and Suppress the Bacteria Population
Authors: Maguire R. O. , Hesterberg D. , Gernat A. , Anderson K. , Wineland M. , Grimes J. 
Published: April 2006

ABSTRACTStabilizing phosphorus (P) in poultry waste to reduce P losses from manured soils is important to protect surface waters, while pathogens in manures are an emerging issue. This study was conducted to evaluate CaO and Ca(OH)2 for killing manure bacterial populations (pathogens) and stabilizing P in poultry wastes and to investigate the influence on soils following amendment with the treated wastes. Layer manure and broiler litter varying in moisture content were treated with CaO and Ca(OH)2 at rates of 2.5, 5, 10, and 15% by weight. All treated wastes were analyzed for microbial plate counts, pH, and water‐soluble phosphorus (WSP), while a few selected layer manures were analyzed by phosphorus X‐ray absorption near edge structure (XANES). A loamy sand and a silt loam were amended with broiler litter and layer manure treated with CaO at rates of 0, 2.5, 5, 10, and 15% and soil WSP and pH were measured at times 1, 8, and 29 d. Liming reduced bacterial populations, with greater rates of lime leading to greater reductions; for example 10% CaO applied to 20% solids broiler litter reduced the plate counts from 793 000 to 6500 mL−1 Liming also reduced the WSP in the manures by over 90% in all cases where at least 10% CaO was added. Liming the manures also reduced WSP in soils immediately following application and raised soil pH. The liming process used successfully reduced plate counts and concerns about P losses in runoff following land application of these limed products due to decreased WSP.
Soil Microbial and Faunal Community Responses toBtMaize and Insecticide in Two Soils
Authors: Griffiths Bryan S. , Caul Sandra , Thompson Jacqueline , Birch A. Nicholas E. , Scrimgeour Charles , Cortet Jérôme , Foggo Andrew , Hackett Christine A. , Krogh Paul Henning 
Published: April 2006

ABSTRACTThe effects of maize (Zea maysL.), genetically modified to express the Cry1Ab protein (Bt), and an insecticide on soil microbial and faunal communities were assessed in a glasshouse experiment. Soil for the experiment was taken from field sites where the same maize cultivars were grown to allow comparison between results under glasshouse conditions with those from field trials. Plants were grown in contrasting sandy loam and clay loam soils, half were sprayed with a pyrethroid insecticide (deltamethrin) and soil samples taken at the five‐leaf stage, flowering, and maturity. The main effect on all measured parameters was that of soil type and there were no effects ofBttrait or insecticide on plant growth. TheBttrait resulted in more soil nematodes and protozoa (amoebae), whereas insecticide application increased plantBtconcentration and altered nematode community structure. The only significant effects on soil microbial community structure, microarthropods, and larvae of a nontarget root‐feeding Dipteran, were due to soil type and plant growth stage. The results indicate that, although there were statistically significant effects of theBttrait on soil populations, they were small. The relative magnitude of the effect could best be judged by comparison with the insecticide treatment, which was representative of current best practice. TheBttrait had no greater effect than the insecticide treatment. Results from this glasshouse experiment were in broad agreement with conclusions from field experiments using the same plant material grown in the same soils.
Elasticity Imaging
Authors: Insana Michael F. 
Published: April 2006

Abstract
Basic principles and examples of elasticity imaging are summarized. The chapter focuses on static ultrasonic methods, and it discusses the advantages and limitations of this approach in the context of dynamic methods and alternative imaging modalities from the literature. We review the physics of continuum deformations as a way to evaluate various experimental approaches. A general strategy for the design of ultrasonic elasticity imaging algorithms for static deformations is also described. The objective is to summarize and critically assess a subset of current approaches to this exciting new field.
Semiconductor‐Based Implantable Prosthetic Devices
Authors: Liu Wentai , Sivaprakasam Mohanasankar , Wang Guoxing , Zhou Mingcui , Humayun Mark S. 
Published: April 2006

AbstractSemiconductor‐based Implantable Prosthetic Devices are artificial devices embedded into the body to replace/rectify a functionality of a part of the body. The devices function as prosthetic devices by the operation of electronics, which is their core. This chapter describes such devices with specific emphasis to the design and functioning of the electronics. The chapter begins with an overview of existing implantable devices, both commercialized and those under development. The components of a generic implantable prosthetic device are described leading to a detailed discussion of the major components in the continuing sections. Design examples will be presented from an implantable retinal prosthetic device under development for replacing lost vision. The concluding section of the chapter presents a discussion on the challenges and future direction of these implantable devices.
Nernst Potential
Authors: Butera Robert 
Published: April 2006

Abstract
The Nernst potential is a voltage necessary to negate the diffusion of an ionic species from one well‐stirred compartment to another, resulting in zero net ionic flux. It is often called the reversal potential. This relationship between voltage and diffusion gradients is a fundamental mechanisms governing the flow of charged ions into and out of electrically excitable cells, such as neurons, muscle, and cardiac myocytes.