bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Amplification 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 <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.
Polarization reorientation in ferroelectric lead zirconate titanate thin films with electron beams
Authors: Li D.B. , Strachan D.R. , Ferris J.H. , Bonnell D.A.
Published: April 2006

Ferroelectric domain patterning with an electron beam is demonstrated. Polarization of lead zirconate titanate thin films is shown to be reoriented in both positive and negative directions using piezoresponse force and scanning surface potential microscopy. Reorientation of the ferroelectric domains is a response to the electric field generated by an imbalance of electron emission and trapping at the surface. A threshold of 500 μC/cm2 and a saturation of 1500 μC/cm2 were identified. Regardless of beam energy, the polarization is reoriented negatively for beam currents less than 50 pA and positively for beam currents greater than 1 nA.
Grain orientations and grain boundary networks of YBa2Cu3O7−δ films deposited by metalorganic and pulsed laser deposition on biaxially textured Ni–W substrates
Authors: Feldmann D.M. , Holesinger T.G. , Cantoni C. , Feenstra R. , Nelson N.A. , Larbalestier D.C. , Verebelyi D.T. , Li X. , Rupich M.
Published: April 2006

We report a detailed study of the grain orientations and grain boundary (GB) networks in YBa2Cu3O7-δ (YBCO) films ∼0.8 μm thick grown by both the in situ pulsed laser deposition (PLD) process and the ex situ metalorganic deposition (MOD) process on rolling-assisted biaxially textured substrates (RABiTS). The PLD and MOD growth processes result in columnar and laminar YBCO grain structures, respectively. In the MOD-processed sample [full-width critical current density Jc(0 T, 77 K) = 3.4 MA/cm2], electron back-scatter diffraction (EBSD) revealed an improvement in both the in-plane and out-of-plane alignment of the YBCO relative to the template that resulted in a significant reduction of the total grain boundary misorientation angles. A YBCO grain structure observed above individual template grains was strongly correlated to larger out-of-plane tilts of the template grains. YBCO GBs meandered extensively about their corresponding template GBs and through the thickness of the film. In contrast, the PLD-processed film [full width Jc(0 T, 77 K) = 0.9 MA/cm2] exhibited nearly perfect epitaxy, replicating the template grain orientations. No GB meandering was observed in the PLD-processed film with EBSD. Direct transport measurement of the intra-grain Jc(0 T, 77 K) values of PLD and MOD-processed films on RABiTS revealed values up to 4.5 and 5.1 MA/cm2, respectively. As the intra-grain Jc values were similar, the significantly higher full-width Jc for the MOD-processed sample is believed to be due to the improved grain alignment and extensive GB meandering.
Revelation of a functional dependence of the sum of two uniaxial strengths/hardness on elastic work/total work of indentation
Authors: Ma Dejun , Zhang Taihua , Ong Chung Wo
Published: April 2006

Dimensional and finite element analyses were used to analyze the relationship between the mechanical properties and instrumented indentation response of materials. Results revealed the existence of a functional dependence of (engineering yield strength σE,y+ engineering tensile strength σE,b)/Oliver & Pharr hardness on the ratio of reversible elastic work to total work obtained from an indentation test. The relationship links up the Oliver & Pharr hardness with the material strengths, although the Oliver & Pharr hardness may deviate from the true hardness when sinking in or piling up occurs. The functional relationship can further be used to estimate the sum σE,y+ σE,baccording to the data of an instrumented indentation test. The σE,y+ σE,bvalue better reflects the strength of a material compared to the hardness value alone. The method was shown to be effective when applied to aluminum alloys. The relationship can further be used to estimate the fatigue limits, which are usually obtained from macroscopic fatigue tests in different modes.
Solution-processed lanthanum zirconium oxide as a barrier layer for high Ic-coated conductors
Authors: Sathyamurthy Srivatsan , Paranthaman Mariappan , Heatherly Lee , Martin Patrick M. , Specht E.D. , Goyal Amit , Kodenkandath Thomas , Li Xiaoping , Rupich Martin W.
Published: April 2006

High-quality lanthanum zirconium oxide (La2Zr2O7 or LZO) films have been deposited and processed on Ni–W substrates using a sol-gel processing approach. It has been demonstrated that crack-free coatings with thicknesses up to 100 nm can be processed in a single step, while thicker coatings (200–225 nm) were processed using a multiple coating and annealing process. Using simulated metalorganic deposition (MOD)-YBa2Cu3O7−δ (YBCO) processing conditions, the barrier properties of the sol-gel LZO coating with a thickness of 120 nm were found to be comparable to that of the standard 3-layer buffer stack deposited using physical vapor deposition. Secondary ion mass spectroscopy depth profile analysis of LZO films annealed in oxygen-18 shows that LZO effectively stops the diffusion of Ni within the first 80–100 nm. Using MOD processes, a CeO2 cap layer and superconducting YBCO layer were deposited on sol-gel LZO/Ni–W. For the first time, using such an all-solution conductor architecture, a critical current (Ic) of 140 A/cm with a corresponding critical current density (Jc) of 1.75 MA/cm2 has been demonstrated. Using a very thin Y2O3 seed layer (∼10 nm) deposited by electron beam evaporation; improved texture quality in the LZO layers has been demonstrated. The performance of the LZO deposited on these samples was evaluated using a sputtered CeO2 cap layer and MOD YBCO layer. Critical currents of up to 255 A/cm (3.2 MA/cm2) with 0.8-μm-thick YBCO films have been demonstrated, comparable to the performance of films grown using physical vapor deposited yttria stabilized zirconia as a barrier layer. Similar experiments using an MOD-CeO2 cap layer and MOD-YBCO layer yielded critical currents of 200 A/cm (2.5 MA/cm2) with 0.8-μm-thick YBCO films.
Hydrogen behavior in Mg+-implanted graphite
Authors: Jiang W. , Shutthanandan V. , Zhang Y. , Thevuthasan S. , Weber W.J. , Exarhos G.J.
Published: April 2006

A graphite wafer has been implanted with Mg+to produce a uniform Mg concentration. Subsequent H+implantation covered the Mg+-implanted and -unimplanted regions. Ion-beam analysis shows a higher H retention in graphite embedded with Mg than in regions without Mg. A small amount of H diffuses out of the H+-implanted graphite during thermal annealing at temperatures up to 300 °C. However, significant H release from the region implanted with Mg+and H+ions occurs at 150 °C; further release is also observed at 300 °C. The results suggest that there are efficient H trapping centers and fast pathways for H diffusion in the Mg+-implanted graphite, which may prove highly desirable for reversible H storage.
Crystallization kinetics of homogeneously precipitated lead zirconate titanate using urea: Comparison with the conventional ammonia precipitated sample
Authors: Roy S. , Bysakh S. , Subrahmanyam J.
Published: April 2006

Ultrafine, PbZr0.53Ti0.47O3 powder was synthesized by homogeneous precipitation of metal ions in aqueous solution using urea. The results obtained from different characterization methods were compared with those obtained from the conventional precipitation method using ammonia in terms of crystallization, homogeneity, and microstructure. The as-dried precipitate converted to the single-phase crystalline lead zirconate titanate powder when calcined at 550 °C and above. The calcined powder showed smaller particle size, minimum agglomeration, and uniform shape. The growth of the particles was very little at higher temperatures. Powdered samples that precipitated using urea crystallized directly to rhombohedral lead zirconate titanate, without any intermediate pyrochlore phase formation. The NH3-precipitated powder converted to rhombohedral lead zirconate titanate via metastable pyrochlore and it showed phase segregation upon annealing at higher temperatures. The reaction kinetics has been studied by x-ray diffraction, differential thermal analysis, and differential scanning calorimetry.
Emerging anti-cancer molecular mechanisms of aminobisphosphonates
Authors: Caraglia Michele , Santini Daniele , Marra Monica , Vincenzi Bruno , Tonini Giuseppe , Budillon Alfredo
Published: April 2006

Bone metastases are common in patients with many types of cancer, especially breast and prostate cancer — in which the incidence is approximately 70% among patients with advanced metastatic disease. Aminobisphosphonates (NBPs) have entered clinical practice in the treatment of bone metastases from several neoplasms, including breast and prostate adenocarcinoma, as a result of their anti-resorption properties. However, evidence has accumulated on the direct anti-tumour effects of NBPs. This review describes the metabolic pathways that are putative molecular targets of NBPs and that are involved in the prenylation processes of several intracellular small GTP-binding proteins (ras family related proteins). The latter regulate the intracellular survival and proliferative pathways of tumour cells and could be the intracellular molecular targets of the NBPs responsible for the direct anti-cancer effects, even if definitive conclusions cannot be drawn at present. Different mechanisms have been reported to account for the anti-neoplastic action of NBPs, including: the induction of apoptosis; cell cycle perturbations; and anti-invasive, anti-migration and anti-angiogenic effects. Moreover, this review describes the most important clinical studies that demonstrate the activity of NBPs in preventing skeletal-related events induced by bone metastases. The main pharmacokinetic pitfalls of NBPs are described, and methods of overcoming these pitfalls through the use of liposome vehicles are proposed. Finally, the principal pre-clinical studies on the interaction between NBPs and other biological agents are also described; these studies may enable reductions in the in vivo NBP concentrations required to achieve anti-tumour activity. To date, however, the real molecular targets of NBPs are not completely known and new technological platforms are required in order to detect them and to develop new anti-cancer strategies based on the use of NBPs.
Molecular cloning and regulation of porcine SULT2A1: relationship between SULT2A1 expression and sulfoconjugation of androstenone
Authors: Sinclair P A , Gilmore W J , Lin Z , Lou Y , Squires E J
Published: April 2006

Hydroxysteroid sulfotransferase (SULT2A1) is a key enzyme in the testicular and hepatic metabolism of 5α-androstenone, which is a major component of the off-odor and off-flavor in pork known as boar taint. The goals of this study were to determine the role of testicular and hepatic SULT2A1 activity on plasma 5α-androstenone sulfate levels, the accumulation of 5α-androstenone in adipose tissue, and to gain insight into the regulatory control of SULT2A1. Testicular SULT2A1 activity was negatively correlated (r= −0.57; P<0.01) with 5α-androstenone concentrations in fat. The differences observed in SULT2A1 activity warranted investigation into potential genetic variation within porcine SULT2A1. The cDNA sequence of porcine Sult2A1 was determined to be >82% homologous to the human, mouse, and rat Sult2A1 genes. A single nucleotide polymorphism was detected within the coding region of the Sult2A1 from individual testes and liver samples; however, this did not affect the amino acid sequence of the enzyme. Western blot analysis determined that animals with high concentrations of 5α-androstenone in fat and low SULT2A1 activity had corresponding low levels of SULT2A1 protein compared with animals with low levels of 5α-androstenone in fat. Real-time PCR analysis indicated that Sult2A1 mRNA was increased 2.8-fold in animals with high levels of the protein relative to animals with low levels of the protein. Furthermore, we demonstrated the positive role of the nuclear receptors constitutive androstane receptor and pregnane X receptor, as well as the possible role of farnesoid X receptor in the regulation of testicular SULT2A1 activity. Together, the results of this study suggest that differences in SULT2A1 expression can influence 5α-androstenone accumulation in fat.
Identification and characterization of RanBPM, a novel coactivator of thyroid hormone receptors
Authors: Poirier Marie-Belle , Laflamme Liette , Langlois Marie-France
Published: April 2006

Thyroid hormone receptors (TRs) are transcription factor members of the nuclear receptor superfamily. The transcriptional activity of TRs is controlled by thyroid hormones and cell-specific coregulators. Using the yeast two-hybrid system, we identified RanBPM as a new protein partner for TRs. RanBPM was initially discovered as an interacting partner for Ran, and was also shown to be a protein partner and coactivator of the androgen receptor. The novel interaction between RanBPM and TR isoforms was addressed by glutathione-S-transferase (GST) pull-down assays and co-immunoprecipitation in intact mammalian cells, where RanBPM was shown to bind TRs in a ligand-independent fashion. We also studied the regions implicated in the interaction with deletion mutants: the principal interacting region of RanBPM is comprised within its carboxyl-terminal end and the TR DNA-binding domain is sufficient to mediate the interaction. To investigate the potential role of RanBPM in thyroid hormone action, transient transfections with luciferase reporter genes were performed in CV-1 cells. We found that the over-expression of RanBPM increases the activation of TRETK- and DR+4-positive thyroid hormone response elements. Interestingly, over-expression of the truncated protein RanBPM55, which lacks the N-terminal polyglutaminated region but binds TRs, decreased the fold activation by almost 80%. Furthermore, we performed competition assays using transient transfection of RanBPM and increasing amounts of RanBPM55. This revealed that the stimulating effect on TR transactivation by the full-length protein is inhibited in a dose-dependent fashion by RanBPM55. This suggests that although the polyglutaminated region of RanBPM is not required for the binding to TRs, it is required for the stimulation of TR transactivation. Taken together, our results provide evidence that RanBPM is a potent novel coactivator for thyroid hormone receptors.
Zebrafish arylalkylamine-N-acetyltransferase genes – targets for regulation of the circadian clock
Authors: Appelbaum L , Vallone D , Anzulovich A , Ziv L , Tom M , Foulkes N S , Gothilf Y
Published: April 2006

Daily rhythms of melatonin production are controlled by changes in the activity of arylalkylamine-N-acetyltransferase (AANAT). Zebrafish possess two aanats, aanat1 and aanat2; the former is expressed only in the retina and the latter is expressed in both the retina and the pineal gland. Here, their differential expression and regulation were studied using transcript quantification and transient and stable in vivo and in vitro transfection assays. In the pineal gland, the aanat2 promoter exhibited circadian clock-controlled activity, as indicated by circadian rhythms of Enhanced green fluorescent protein (EGFP) mRNA in AANAT2:EGFP transgenic fish. In vivo transient expression analyses of the aanat2 promoter indicated that E-box and photoreceptor conserved elements (PCE) are required for expression in the pineal gland. In the retina, the expression of both genes was characterized by a robust circadian rhythm of their transcript levels. In constant darkness, the rhythmic expression of retinal aanat2 persisted while the aanat1 rhythm disappeared; indicating that the former is controlled by a circadian clock and the latter is also light driven. In the light-entrainable clock-containing PAC-2 zebrafish cell line, both stably transfected aanat1 and aanat2 promoters exhibited a clock-controlled circadian rhythm, characteristic for an E-box-driven expression. Transient co-transfection experiments in NIH-3T3 cells revealed that the two, E-box- and PCE-containing, promoters are driven by the synergistic action of BMAL/CLOCK and orthehodenticle homeobox 5. This study has revealed a shared mechanism for the regulation of two related genes, yet describes their differential phases and photic responses which may be driven by other gene-specific regulatory mechanisms and tissue-specific transcription factor profiles.
Induction of steroidogenesis in immature rat Leydig cells by interleukin-1α is dependent on extracellular signal-regulated kinases
Authors: Renlund N , Jo Y , Svechnikova I , Holst M , Stocco D M , Söder O , Svechnikov K
Published: April 2006

Interleukin-1α (IL-1α) plays an important role in the regulation of immune responses as well as in non-inflammatory events in different types of cells. Here we have investigated the involvement of the extracellular signal-regulated kinase (ERK) cascade in IL-1α-induced steroidogenesis by primary cultures of immature rat Leydig cells. Our findings indicate that protein kinase C functions as an upstream component of signal transduction from the IL-1 receptor type I (IL-1RI) to the ERK cascade. It was observed that IL-1α upregulated both steroidogenic acute regulatory (StAR) protein expression and its phosphorylation when compared with controls. Selective inhibition of these mitogen-activated protein kinases (MAPKs) by UO126 enhanced both the expression and phosphorylation of the StAR protein, but suppressed androgen production by the immature Leydig cells as well as dissipating the mitochondrial electrochemical potential (Ψm) in these cells. The evidence that water-soluble cholesterol but not 22R-hydroxycholesterol-stimulated steroidogenesis was inhibited by UO126 suggested that an intact Ψm across the inner mitochondrial membrane is required for cholesterol translocation and is positively regulated by the ERK cascade. We propose that activation of ERKs by IL-1α plays a dual role in the regulation of steroidogenesis in immature Leydig cells: these MAPKs downregulate StAR expression and phosphorylation, while at the same time they support an intact Ψm across the inner mitochondrial membrane, thereby promoting translocation of cholesterol into the mitochondria of the Leydig cell.
Direct electrochemistry of human, bovine and porcine cytochrome P450c17
Authors: Johnson D L , Conley A J , Martin L L
Published: April 2006

The direct electrochemistry of human, bovine and porcine cytochrome P450c17 (CYP17) has been examined on an edge-oriented pyrolytic graphite electrode. The recombinant protein was immobilized on an electrode modified with a surfactant to simulate the environment of a biological membrane, and hence physiological electron-transfer conditions. The P450 enzymes all retained ‘electron-transfer’ activity while immobilized at the electrode surface as assessed by the presence of catalytic signals under aerobic conditions. The redox potentials for porcine P450c17 were more positive (anodic) than both the human and bovine forms, perhaps reflecting the differences in substrate specificity for these species. In addition, these enzymes were all influenced by pH, consistent with a single proton associated with the single electron-transfer event. Ionic strength of the buffer medium also shifted the redox potentials towards positive, suggesting that electrostatic forces contribute to the protein environment required for the electron-transfer process. The effect of substrate on the redox potential for each P450c17 was measured in the presence of pregnenolone, progesterone, 17α-hydroxypregnenolone and 17α-hydroxyprogesterone. However, no influence on the redox parameters was observed.
A high-speed railway through marshlands (CTRL)
Authors: Dyson S. W. , Kirk M. J. D.
Published: April 2006

Providing a high-speed railway from the Channel Tunnel to London St Pancras has brought a wide variety of engineering challenges. This paper describes some major features of contract 310 of the Channel Tunnel Rail Link (CTRL), where the challenge was the construction of a high-speed railway formation across marshlands adjacent to the River Thames. Contract 310 provided the main civils works from where the Thames tunnel emerges westward from under the Thames to the start of the London tunnel just to the west of Dagenham Dock Station leading to Stratford and St Pancras. The contract extends over 12 km on an alignment mostly at grade through Aveley, Wennington and Rainham Marshes where, for the most part, the railway formation is supported on concrete piled slabs. In some areas, ground strengthening has been used instead. Three significant viaducts carry the track over obstacles from roads, railways and rivers (Thurrock, Aveley and Rainham Creek Viaducts). Construction started in January 2002 and was completed in July 2005.
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

The 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

Phosphorus 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

Metam‐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

There 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

There 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

Stabilizing 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

The 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

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

Semiconductor‐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

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.
Robotic Surgery
Authors: Desai Jaydev P. , Yasha Kresh J. , Wechsler Andrew S. , Castellanos Andres E. , Meyers William C.
Published: April 2006

The development and growth of robotics in surgery has been significant within the last few years. Minimally invasive surgical procedures using long instruments deprive the surgeon of depth perception, dexterity, sense of touch, and the excellent hand‐eye coordination that they are so accustomed to in open procedures. What the surgeon loses presents excellent theoretical, experimental, and developmental opportunities for the engineer to develop “smarter” and more efficient systems for use in minimally invasive surgery, which consequently leads to better patient care and reduced morbidity. Recent advancements in the integration of robotic surgical systems in the operating room have led to improvements in minimally invasive surgery (MIS) by returning some of the lost faculties of surgeons, such as dexterity, improved 3‐D visualization of the surgical field, and better hand‐eye coordination. In addition, MIS procedures with robotic assistance can lead to a shorter hospital stay, reduced trauma, faster recovery times, and lower health‐care costs. This chapter will explore the innovations in robotics for surgery, such as deformation modeling for tool‐tissue interactions with soft tissues and organs, sensing and control, and model‐based teleoperation. Finally, the future direction of robotics in surgery will also be discussed.
Sepsis
Authors: Keith Scott L. , Conrad Steven A.
Published: April 2006

Sepsis is a state of systemic inflammation resulting from an unregulated and dysfunctional response of the innate immune system to an infectious stimulus. The sepsis response is initiated through cell surface signaling receptors that recognize specific microbial antigens, such as lipopolysaccharide, from gram‐negative bacteria. The signaling pathway activation results in increased activity of transcription factors in the cytoplasm, in particular nuclear factor
κ
B, followed by translocation to the nucleus and promotion of transcription of several early phase (proximal) inflammatory mediators, such as tumor necrosis factor‐
α
and interleukin‐1
β
. A number of later phase (distal) mediators are upregulated, producing activation of inflammation, anti‐inflammation, coagulation, and apoptotic pathways, with the endothelial cell playing a central role. This response is intended to function at a local level to contain the pathogenic process; however, systemic activation results in a systemic inflammatory response.

Therapies targeting single mediators of the sepsis response based on linear, reductionist approaches to sepsis pathophysiology have been largely ineffectual. The sepsis response is perhaps best approached as a nonlinear, redundant complex network. Mathematical models based on this approach are being developed and hold promise for better understanding of the sepsis response and for developing therapeutic targets. Recently described models include a mechanistic model based on ordinary differential equations describing the behavior of populations of cells and mediators, and an agent‐based model in which agents represent individual cells associated with the inflammatory response. Both of these models show promise in reproducing particular components of the sepsis response. Future successes in the treatment of sepsis will depend on improvements in modeling that will enable a better understanding of this complex process.
Software Engineering
Authors: Najarian Kayvan , Eichelberger Christopher
Published: April 2006

Software engineering theory, practice, and applications germane to biomedical engineering are presented.
State‐Space Methods
Authors: Jovičić Aleksandar , Stipanović Dušan M.
Published: April 2006

The theory and application of state‐space representations of linear‐time‐invariant systems is presented. Time‐domain representations, transfer functions, and canonical forms are described as well as how to obtain analytical solutions to systems of ordinary differential equations.
Stents
Authors: Lally C. , Kelly D.J. , Prendergast P.J.
Published: April 2006

Stents are devices implanted into vessels or ducts in the body to remove a constriction by holding the vessel or duct open. Deployment of stents is a major challenge; deployment is often performed by expanding a balloon onto which the stent has been crimped or by releasing a self‐expanding stent or a coiled stent from a restraining sheath. The expanding stent pushes the inner lumen radially outward to restore patency. Several biomechanical issues pertaining to stents exist, such as they should not overstress the vessel wall on expansion nor should they straighten a curved vessel, as that would generate high stresses at the ends of the stent. Restenosis (reformation of the original blockage) was always an issue with “bare metal stents” but this problem has, it seems, been largely overcome by coating the stents with an anti‐proliferative drug. A comprehensive description of the main cardiovascular stent designs is given and the main issues facing innovation in stent design in the future are outlined.
Tissue‐Engineered Cartilage
Authors: Pagnotto Michael R. , Chu Constance R.
Published: April 2006

The goal of cartilage tissue engineering is to recreate functional articular cartilage. The tissue must be able to fill chondral defects while maintaining the unique biomechanical characteristics that make articular cartilage functional. The goal may be accomplished either by inducing native repair cells to regenerate or through
ex vivo
techniques where cells are obtained from a patient and use to develop cartilage or pre‐cartilaginous constructs in the laboratory and then the constructs are surgically implanted back into the patient. As this chapter will demonstrate, extensive research continues to examine nearly every facet of cartilage tissue engineering.
Biochemical findings in common inborn errors of metabolism
Authors: Pasquali Marzia , Monsen Gavin , Richardson Leah , Alston Martha , Longo Nicola
Published: April 2006

The application of tandem mass spectrometry (MS/MS) to newborn screening has led to the detection of patients with a wider spectrum of inborn errors of metabolism. A definitive diagnosis can often be established early enough to start treatment before symptoms appear. Here, we review common biochemical findings in disorders caused by deficiency of 3‐methylcrotonyl‐CoA carboxylase, isobutyryl‐CoA dehydrogenase, 2‐methyl‐3‐hydroxybutyryl‐CoA dehydrogenase, 3‐ketothiolase, 2‐methylbutyryl‐CoA dehydrogenase, and medium chain acyl CoA dehydrogenase. The diagnosis of these disorders requires biochemical confirmation by measurement of plasma acylcarnitine profile, urine organic acids, and urine acylglycine profiles followed by measurement of enzyme activity or detection of causative mutations. Early treatment can improve the outcome of these disorders. © 2006 Wiley‐Liss, Inc.
Disorders of carnitine transport and the carnitine cycle
Authors: Longo Nicola , Amat di San Filippo Cristina , Pasquali Marzia
Published: April 2006

Carnitine plays an essential role in the transfer of long‐chain fatty acids across the inner mitochondrial membrane. This transfer requires enzymes and transporters that accumulate carnitine within the cell (OCTN2 carnitine transporter), conjugate it with long chain fatty acids (carnitine palmitoyl transferase 1, CPT1), transfer the acylcarnitine across the inner plasma membrane (carnitine‐acylcarnitine translocase, CACT), and conjugate the fatty acid back to Coenzyme A for subsequent beta oxidation (carnitine palmitoyl transferase 2, CPT2). Deficiency of the OCTN2 carnitine transporter causes primary carnitine deficiency, characterized by increased losses of carnitine in the urine and decreased carnitine accumulation in tissues. Patients can present with hypoketotic hypoglycemia and hepatic encephalopathy, or with skeletal and cardiac myopathy. This disease responds to carnitine supplementation. Defects in the liver isoform of CPT1 present with recurrent attacks of fasting hypoketotic hypoglycemia. The heart and the muscle, which express a genetically distinct form of CPT1, are usually unaffected. These patients can have elevated levels of plasma carnitine. CACT deficiency presents in most cases in the neonatal period with hypoglycemia, hyperammonemia, and cardiomyopathy with arrhythmia leading to cardiac arrest. Plasma carnitine levels are extremely low. Deficiency of CPT2 present more frequently in adults with rhabdomyolysis triggered by prolonged exercise. More severe variants of CPT2 deficiency present in the neonatal period similarly to CACT deficiency associated or not with multiple congenital anomalies. Treatment for deficiency of CPT1, CPT2, and CACT consists in a low‐fat diet supplemented with medium chain triglycerides that can be metabolized by mitochondria independently from carnitine, carnitine supplements, and avoidance of fasting and sustained exercise. © 2006 Wiley‐Liss, Inc.