bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New Apparatus for Measuring Oxygen Diffusion and Water Retention in Soils
Authors: MacKay PL , Yanful EK , Kerry Rowe R , Badv K 
Published: February 2009

Abstract
A new apparatus developed for measuring the diffusion of oxygen, or any gas, through a soil sample is described. The apparatus uses nitrogen pressure to change a soil sample's degree of saturation and can therefore minimize the effects of structural changes due to remixing and packing. As a consequence, some innovative methods are employed to simulate oxygen concentration versus time data obtained with the apparatus. A one-dimensional semianalytic diffusion model is used to back-calculate diffusion coefficients based on laboratory data. Results for a local silt and a sand are presented to illustrate the utility of the apparatus. The apparatus is shown to perform well and provide gas diffusion coefficients similar to those reported by other researchers. The major advantage of the apparatus over other published methods lies in the fact that both the soil-water characteristic curve and oxygen diffusion coefficient at any degree of saturation can be obtained on the same soil sample in a single suite of tests. These two parameters are required for several geotechnical and geoenvironmental engineering designs involving unsaturated soils, such as the use of soil covers for mitigating acid drainage in sulfide-bearing mine waste.
Centrifuge Testing of Fixed-Head Laterally Loaded Battered and Plumb Pile Groups in Sand
Authors: McVay MC , Shang T-I , Casper R 
Published: February 2009

Abstract
Centrifuge tests were conducted on driven in-flight fixed-head plumb and battered 3 × 3 pile groups at three-diameter (3D) and five-diameter (5D) spacings. The piles simulated 430-mm-diameter by 13-m-long pipe piles founded in medium loose (Dr = 33%) and medium dense (Dr = 55%) sands. The battered groups were in an A frame arrangement, i.e., each pile in a given row battered the same. Results of the tests showed that fixed-head plumb groups have a 30 to 55% higher lateral resistance than free-headed piles depending on soil density and pile spacing. For the battered 3D-spaced group, the lateral resistance was greater by 20 to 50% than the fixed-head plumb response in the medium dense sand; however, in the medium loose sand, the battered and plumb fixed-head group response was very similar. The latter is attributed to the limited axial tension capacity of the piles in the medium loose sand (Dr = 33%). Increasing the dead load on a battered group to 45% of its axial capacity resulted in a 30% increase in the group's lateral resistance. The lateral resistance of the 5D-spaced battered groups were in all cases greater than their 3D counterparts.
Laboratory Testing Apparatus for Slopes Stabilized by Anchored Geosynthetics
Authors: Ghiassian H , Hryciw RD , Gray DH 
Published: February 2009

Abstract
A laboratory testing apparatus is described for examining slopes subjected to seepage and stabilized by anchored geosynthetics (AGS). The AGS technique can increase the stability of cohesionless slopes such as coastal dunes against surficial erosion and shallow mass failure caused by wave action and seepage forces. In the AGS, a geosynthetic fabric is placed on the face of the slope and tensioned via anchorage to the ground. The required tension is achieved through frictional or pullout resistance of earth anchors that are fastened to the fabric and driven into the underlying soil mass. In the laboratory testing apparatus, however, AGS tensioning is provided by thin wires connected to rigid steel tubes that exert line loads on the fabric. The wires in turn are connected to dead weights “beneath” the slope that simulate anchor loads. The prototype slopes are failed by uniformly decreasing anchor loads while maintaining the seepage gradient and orientation constant. Very good agreement was observed between experimental results and theoretical predictions of the failure mode and the average AGS loads at failure.
Low Strain Measurements Using Random Noise Excitation
Authors: Cascante G , Santamarina C 
Published: February 2009

Abstract
Low-strain wave propagation velocity and attenuation are effective measures of state in particulate media. The standard resonant column test procedure is modified to facilitate the study of wave propagation at low strains. The system uses band-limited random noise excitation in combination with signal averaging to control the signal-to-noise ratio. This procedure is efficiently implemented by replacing typical peripheral devices with a signal analyzer and computer control. The methodology permits testing at very low strains (γ ≈ 10−8). The effect of non-linear system response on computed transfer functions is addressed. Other results include the analytical treatment of coupling between torsional and transverse modes, the evaluation of local low-strain shear parameters from solid specimens tested in torsion, and the use of multi-mode testing for the evaluation of field parameters.
Relationships among Swimming Ability, Current Velocity Association, and Morphology for Freshwater Lotic Fishes
Authors: Leavy Tracy R. , Bonner Timothy H. 
Published: February 2009

Abstract
We determined swimming ability for 37 warmwater stream fishes in Texas and Louisiana and assessed relationships among swimming ability, habitat selection, and fish morphology. Mean absolute speeds (cm/s) were 17.8–81.9 cm/s for Cyprinidae, 50.9 cm/s for Characidae, 70.0 cm/s for Ictaluridae, 33.0 cm/s for Cichlidae, 40.0 cm/s for Percidae, 30.7–43.4 cm/s for Cyprinodontidae, 30.2 cm/s for Atherinidae, 15.7–18.6 cm/s for Poeciliidae, and 23.4–40.5 cm/s for Centrarchidae. Absolute swimming speeds were correlated (P &lt; 0.01) to reported habitat descriptions (i.e., sloughs, lakes, streams, and rivers) of fishes. Absolute swimming speeds also were good predictors of spatial (i.e., runs, pools, and riffles) distributions of fishes from Independence Creek, Texas (P = 0.03), and Banita Creek, Texas (P = 0.06). Multivariate ordination of nine morphological attributes identified the linear combination of relative body depth, dorsal fin length, and caudal span width as an adequate predictor (P &lt; 0.01) of swimming speed; however, several exceptions were noted. Understanding interactions between current velocity and swimming ability in fishes is critical to species conservation and to maintaining instream flow requirements for fishes.
A Simulation Study of the Effects of Spatially Complex Population Structure for Gulf of Maine Atlantic Cod
Authors: Reich Danielle Ameen , DeAlteris Joseph Thomas 
Published: February 2009

Abstract
There is growing evidence that numerous fish stocks consist of several smaller, reproductively isolated units that vary in their ability to produce new recruits each year because of a mismatch with environmental conditions. It has been suggested that spawning aggregations exist for the Gulf of Maine stock of Atlantic cod Gadus morhua and that approximately one-half of the historic aggregations are locally depleted. We developed a spatially explicit, age-based projection model to investigate the effects of complex population structure and spatially variable recruitment on Gulf of Maine Atlantic cod. The results of this study demonstrate that there are significant disparities in the estimates of spawning stock biomass, annual yield, and annual recruitment when a stock with a complex population structure is treated as a single stock. In addition, treating a stock with a complex population structure as a single stock can mask a steady decline in the values of these variables as the spawning aggregations gradually become depleted. To achieve rebuilding of the simulated Gulf of Maine Atlantic cod stock within 10 years, we determined that F = 0 would be required. Because continued bycatch mortality in other fisheries would prevent this even with the closure of the Gulf of Maine cod fishery, it may not be possible to rebuild this particular stock in a short time frame. When fishing mortality is removed, the stock only rebuilds to one-half of the initial carrying capacity because about 50% of the reproductive capacity of the stock has been lost. Without recolonization, the simulated stock has lost its biological capacity to return to the original unfished condition. Based on the simulations in this study, the behavior of the Gulf of Maine Atlantic cod stock is more consistent with that of a stock with a complex population structure than with that of a truly single stock. In light of this, the management measures for this stock and other stocks with the potential for complex population structure should be carefully evaluated. Managing such stocks as single units may be inappropriate and lead to both inadequate protection of the resource and reduced fishery yields.
Variable Responses of Channel Catfish Populations to Stocking Rate: Density-Dependent and Lake Productivity Effects
Authors: Michaletz Paul H. 
Published: February 2009

Abstract
Put–grow–take fisheries for channel catfish Ictalurus punctatus are popular in many small impoundments but are costly because fingerling (&gt;175 mm total length [TL]) stockings are usually necessary to maintain these fisheries. Stocking the appropriate number of fish is important for making efficient use of these hatchery products and for creating desirable fisheries. The effect of stocking rate on channel catfish populations was evaluated by examining 60 small impoundments that had been assigned to one of three annual stocking rates (12, 37, or 74 fingerlings/ha). As channel catfish stocking rate increased, catch per unit effort (CPUE, number of fish per 3-d tandem hoop-net series) and total annual mortality increased, while proportional size distribution (PSD, formerly proportional stock density), PSD for fish 508 mm or longer, relative weight, and annual growth increments decreased; these results suggest that density-dependent processes were important. However, 10-fold differences in CPUE and threefold differences in size structure indices and growth increments were common among lakes stocked at the same rate. Further analysis revealed that CPUE and lake productivity (indexed by chlorophyll-a concentration) were important variables in explaining differences in size structure, condition, and growth among populations. Because of the highly variable response, appropriate stocking rates need to be determined for each lake. I propose comparing growth increments of individuals within a lake to a statewide standard to determine the relative growth rate for the lake. Stocking rates should be reduced for channel catfish populations that are growing slowly but could be increased for fast-growing populations.
Dangers of predicting bird species distributions in response to land‐cover changes
Authors: Vallecillo Sara , Brotons Lluís , Thuiller Wilfried 
Published: February 2009

Land‐cover changes from the last decades are leading to important declines in habitat quality, giving rise to changes in bird species distribution all over the world. However, land‐cover changes result from a variety of different processes, and it is not clear how effective species distribution models are in capturing species responses to these changes. In this study, we evaluated our ability to predict the effects of land‐cover changes on shifts in species distributions at large spatial and temporal scales using Mediterranean landscapes and early‐successional, open‐habitat birds as study models. Based on presence–absence data from the second Catalan Breeding Bird Atlas (1999–2002), we applied six different species distribution modeling techniques for 10 bird species using climate, topographic, and land‐cover data as predictor variables. Then we back‐projected the models on land‐cover conditions from 1980 to evaluate the projections with field observation data from the first Catalan Breeding Bird Atlas (1975–1983). Finally, we assessed if, in addition to changes in habitat suitability resulting from land‐cover shifts, descriptors of fire impact contributed to further explain species distribution dynamics: colonization and local extinction.We developed accurate model projections of current and past global patterns of species distribution, but our ability to predict species distribution dynamics was reduced. Colonization dynamics were generally more strongly related to fire descriptors than to changes in overall habitat suitability derived from land‐cover changes. Our results warn of the dangers of projecting species distribution models onto future conditions if processes behind species distribution dynamics are not explicitly included. Consideration of ecologically meaningful processes for species (i.e., fire disturbance) when modeling species' distribution might contribute to a better explanation of species' colonization dynamics.
Glycemic Variability Correlates Strongly With Postprandialβ-Cell Dysfunction in a Segment of Type 2 Diabetic Patients Using Oral Hypoglycemic Agents
Authors: Kohnert Klaus-Dieter , Augstein Petra , Zander Eckhard , Heinke Peter , Peterson Karolina , Freyse Ernst-Joachim , Hovorka Roman , Salzsieder Eckhard 
Published: February 2009

OBJECTIVE
Glucose fluctuations trigger activation of oxidative stress, a main mechanism leading to secondary diabetes complications. We evaluated the relationship between glycemic variability and β-cell dysfunction.

RESEARCH DESIGN AND METHODS
We conducted a cross-sectional study in 59 patients with type 2 diabetes (aged 64.2 ± 8.6 years, A1C 6.5 ± 1.0%, and BMI 29.8 ± 3.8 kg/m2[mean ± SD]) using either oral hypoglycemic agents (OHAs) (n = 34) or diet alone (nonusers). As a measure of glycemic variability, the mean amplitude of glycemic excursions (MAGE) was computed from continuous glucose monitoring data recorded over 3 consecutive days. The relationships between MAGE, β-cell function, and clinical parameters were assessed by including postprandial β-cell function (PBCF) and basal β-cell function (BBCF) obtained by a model-based method from plasma C-peptide and plasma glucose during a mixed-meal test as well as homeostasis model assessment of insulin sensitivity, clinical factors, carbohydrate intake, and type of OHA.

RESULTS
MAGE was nonlinearly correlated with PBCF (r = 0.54, P &lt; 0.001) and with BBCF (r = 0.31, P = 0.025) in OHA users but failed to correlate with these parameters in nonusers (PBCF P = 0.21 and BBCF P = 0.07). The stepwise multiple regression analysis demonstrated that PBCF and OHA combination treatment were independent contributors to MAGE (R2 = 0.50, P &lt; 0.010), whereas insulin sensitivity, carbohydrate intake, and nonglycemic parameters failed to contribute.

CONCLUSIONS
PBCF appears to be an important target to reduce glucose fluctuations in OHA-treated type 2 diabetes.
Impact of Carbohydrate Counting on Glycemic Control in Children With Type 1 Diabetes
Authors: Mehta Sanjeev N. , Quinn Nicolle , Volkening Lisa K. , Laffel Lori M.B. 
Published: February 2009

OBJECTIVE
To study the association between parent carbohydrate counting knowledge and glycemic control in youth with type 1 diabetes.

RESEARCH DESIGN AND METHODS
We assessed 67 youth ages 4–12 years with type 1 diabetes (duration ≥1 year). Parents estimated carbohydrate content of children's meals in diet recalls. Ratios of parent estimates to computer analysis defined carbohydrate counting knowledge; the mean and SD of these ratios defined accuracy and precision, respectively. A1C defined glycemic control.

RESULTS
Greater accuracy and precision were associated with lower A1C in bivariate analyses (P &lt; 0.05). In a multivariate analysis (R2= 0.25, P = 0.007) adjusting for child age, sex, and type 1 diabetes duration, precision (P = 0.02) and more frequent blood glucose monitoring (P = 0.04), but not accuracy (P = 0.9), were associated with lower A1C. A1C was 0.8% lower (95% CI −0.1 to −1.4) among youth whose parents demonstrated precision.

CONCLUSIONS
Precision with carbohydrate counting and increased blood glucose monitoring were associated with lower A1C in children with type 1 diabetes.
Measurement of In Vitro Cytochrome P450 2B6 Activity
Authors: Walsky Robert L. , Obach R. Scott 
Published: February 2009

AbstractCytochrome P450 2B6 (CYP2B6) is responsible for the metabolism of a number of therapeutically relevant drugs and environmental chemicals. While not as frequently involved in xenobiotic metabolism as other more commonly studied P450 enzymes such as CYP3A, CYP2D6, or CYP2C9, its importance is becoming increasingly realized. Bupropion hydroxylase activity is an excellent indicator of in vitro CYP2B6 activity, and the metabolite formed is easily measured by HPLC/MS/MS. This assay allows the use of very low concentrations of human liver microsomes or recombinant enzyme, and it represents a selective, sensitive approach to assessing in vitro CYP2B6 activity, with minimal sample preparation.Curr. Protoc. Toxicol. 39:4.27.1‐4.27.11. © 2009 by John Wiley & Sons, Inc.
Measurement of Isoprostanes as Markers of Oxidative Stress in Neuronal Tissue
Authors: Milatovic Dejan , Aschner Michael 
Published: February 2009

AbstractOxidative stress is implicated in the pathogenesis of a variety of human diseases, including neurodegenerative disease, atherosclerosis, and cancer, as well as progressive and even normal aging processes. Increased generation of free radicals derived primarily from molecular oxygen has also been associated with neuronal damage induced by a variety of environmental agents. However, measuring oxidative stress in biological systems is complex and requires accurate quantification of either free radicals or damaged biomolecules. One method for quantifying oxidative injury is to measure lipid peroxidation caused by free radicals. One group of these peroxidation products, F2‐isoprostanes (F2‐IsoPs), is derived by free‐radical peroxidation of arachidonic acid (AA). These prostaglandin F2‐like compounds are currently the most accurate measure of oxidative damage in vivo. This unit summarizes current methodology for quantifying F2‐IsoPs and discusses the utility of these and other prostaglandin (PG)‐like compounds as in vivo biomarkers for oxidative stress in neuronal tissues.Curr. Protoc. Toxicol. 39:12.14.1‐12.14.12. © 2009 by John Wiley & Sons, Inc.
Analysis of Oxidative Modification of Proteins
Authors: Yan Liang‐Jun 
Published: February 2009

AbstractProteins are targets of oxidative modification. This unit describes detailed procedures for the analysis of popular indices of protein oxidation including protein carbonyl formation, loss of protein thiols, and nitrotyrosine and dityrosine formation, as well as isoaspartate formation. Procedures are detailed for the analysis of protein carbonyls labeled with 2,4‐dinitrophenylhydrazine, tritiated sodium borohydride, and biotin‐hydrazide, followed by detection measurements that are based on the distinguishing feature of each labeling chemical. Methods are outlined for the determination of protein cysteine oxidation by quantifying the loss of free protein thiols using radiolabeled [14C]‐iodoacetamide. Protocols are described for the measurement of protein dityrosine by gas chromatography/mass spectrometry, as are the details for the detection of protein nitrotyrosine by a competitive ELISA approach. Finally, methods are described for the quantification of protein‐bound isoaspartate using protein‐L‐isoaspartyl methyltransferase that converts aberrant L‐isoaspartyl residues in peptides and proteins to normal aspartyl residues. Curr. Protoc. Protein Sci. 55:14.4.1‐14.4.27. © 2009 by John Wiley & Sons, Inc.
Tandem Affinity Purification of Proteins
Authors: Günzl Arthur , Schimanski Bernd 
Published: February 2009

AbstractTandem affinity purification (TAP) is a very efficient method to isolate proteins, protein complexes, or ribonucleoprotein particles from crude extracts. The method depends on the expression of one protein component fused N‐ or C‐terminally to a TAP tag in the organism of interest. The TAP tag is a composite tag consisting of two different epitope domains and a protease cleavage site, and it facilitates the purification of the tagged protein in two consecutive, high‐affinity chromatography steps. Combined, the two steps are typically so efficient that a protein complex can be purified virtually to homogeneity without the need for protein overexpression. If the tag does not interfere with protein function, TAP is likely to yield an intact protein complex because all steps of the procedure are carried out under nondenaturing conditions. In this unit, a TAP procedure is detailed which employs a novel epitope combination termed PTP. Curr. Protoc. Protein Sci. 55:19.19.1‐19.19.16. © 2009 by John Wiley & Sons, Inc.
Skin Allograft Rejection
Authors: McFarland Hugh I. , Rosenberg Amy S. 
Published: February 2009

AbstractSkin allograft rejection is a test of the competence of T lymphocytes to mediate in vivo tissue destruction, which in turn reflects their role in critical functions such as anti‐viral and tumor immunity. The tail‐skin graft procedure described in this unit is useful predominantly because of the ease of preparation and resistance to ischemic (nonspecific) necrosis. Additionally, it is not necessary to sacrifice the donor mouse. However, rejection of tail‐skin grafts should not be used to test for genetic homogeneity in breeding experiments or to detect minor histocompatibility (minor‐H) antigens because tail skin is less sensitive than trunk skin in detecting such differences. Curr. Protoc. Immunol. 84:4.4.1‐4.4.13. © 2009 by John Wiley & Sons, Inc.
Human Natural Killer Receptors, Co‐Receptors, and Their Ligands
Authors: Biassoni Roberto 
Published: February 2009

AbstractIn the last 20 years, the study of human natural killer (NK) cells has moved from the first molecular characterizations of very few receptor molecules to the identification of a plethora of receptors displaying surprisingly divergent functions. Our laboratory has contributed to the description of inhibitory receptors and their signaling pathways, important in fine regulation in many cell types, but unknown until their discovery in the NK cells. Inhibitory function is central to regulating NK‐mediated cytolysis, with different molecular structures evolving during speciation to assure its persistence. Only in the last ten years has it become possible to characterize the NK triggering receptors mediating natural cytotoxicity, leading to an appreciation of the existence of a cellular interaction network between effectors of both natural and adaptive immunity. This report reviews the contemporary history of molecular studies of receptors and ligands involved in NK cell function, characterizing the ligands of the triggering receptor and the mechanisms for finely regulating their expression in pathogen‐infected or tumor cells. Curr. Protoc. Immunol. 84:14.10.1‐14.10.40. © 2009 by John Wiley & Sons, Inc.
Molecular Cloning and Characterization of MHC Class I– and II–Restricted Tumor Antigens Recognized by T Cells
Authors: Wang Rong‐Fu 
Published: February 2009

AbstractT cells play a central role in cancer immunosurveillance, autoimmune, and infectious diseases. Identification of MHC class I– and II–restricted T cell peptides is a critical step for the development of effective vaccines against cancer and infectious diseases. This unit describes a cDNA expression system and a genetic targeting expression system for the cloning of genes encoding for MHC class I– and II–restricted antigens recognized by antigen‐specific CD8+ and CD4+ T cells. Curr. Protoc. Immunol. 84:20.10.1‐20.10.29. © 2009 by John Wiley & Sons, Inc.