cssi/SciSciGPT-SciSciNet huggingface dataset:
Expanding the use and effectiveness of dose-volume histograms for 3-D treatment planning I: Integration of 3-D dose-display

Abstract Purpose : A technique is presented for overcoming a major deficiency of histogram analysis in three-dimensional (3-D) radiotherapy treatment planning; the lack of spatial information. Methods and Materials : In this technique, histogram data and anatomic images are displayed in a side-by-side fashion. The histogram curve is used as a guide to interactively probe the nature of the corresponding 3-D dose distribution. Regions of dose that contribute to a specific dose bin or range of bins are interactively highlighted on the anatomic display as a window-style cursor is positioned along the dose-axis of the histogram display. This dose range highlighting can be applied to two-dimensional (2-D) images and to 3-D views which contain anatomic surfaces, multimodality image data, and representations of radiation beams and beam modifiers. Additionally, as a range of histogram bins is specified, dose and volume statistics for the range are continually updated and displayed. Results : The implementation of these techniques is presented and their use illustrated for a nonaxial three field treatment of a hepatic tumor. Conclusion : By integrating displays of 3-D doses and the corresponding histogram data, it is possible to recover the positional information inherently lost in the calculation of a histogram. Important questions such as the size and location of hot spots in normal tissues and cold spots within target volumes can be more easily uncovered, making the iterative improvement of treatment plans more efficient.
Influence of phenylbutazone on gastric secretion of mucus.

SummaryThis study was undertaken in an attempt to clarify the mechanism by which the therapeutic use of phenylbutazone sometimes causes gastric mucosal injury in the form of hemorrhage, erosions or frank ulcerations. Mucoid secretions from gastricantral pouches of dogs were studied before, during and after the oral administration of phenylbutazone in doses of 100 mg/kg of body weight. This drug decreased the rate of mucus secretions and the carbohydrate to protein ratio in non-dialyzable mucosubstance. The data suggest that gastric mucosal injury by phenylbutazone may be due to altered mucosal defense mechanisms.
Perchance to dream: solving the mystery of sleep through genetic analysis.

Sleep has been identified in all mammals and nonmammalian vertebrates that have been critically evaluated. In addition, sleep-like states have also been identified and described in several invertebrates. Despite this prevalence throughout the animal kingdom, the function of sleep remains a mystery. The completion of several genome sequencing projects has led to the expectation that fundamental aspects of sleep can be elucidated through genetic dissection. Indeed, studies in both the mouse and fly have begun to reveal tantalizing suggestions about the underlying principles that regulate sleep homeostasis. In this article we will review recent studies that have used genetic techniques to evaluate sleep in the fruit fly and the mouse.
Supersonic flux-split procedure for second moments of turbulence

A finite volume procedure which combines flux-difference splitting and flux-vector splitting is presented in this paper. The diffusive fluxes are treated explicitly to preserve the upwinding structure of the split Euler fluxes. This procedure is extended in this paper from its essentially laminar or eddy viscosity form to include the equations for the six components of the Reynolds stress tensor and an additional equation for the solenoidal dissipation. The models used for the unclosed terms are presented as are the extensions of the numerical procedures to cover the turbulence equations. To validate the proposed procedures, a compressible turbulent flow over a flat plate at Mach number M∞ = 2.87 and Reynolds number per unit length Re/m of 6.5X10 7 was calculated and compared with experimental measurements. Also simulated was the case when the foregoing boundary-layer flow was made to pass over a ramp. A strong adverse pressure gradient case in which boundary-layer thickness-to-curvature ratio (δ/R c ) is 0.1 was considered. In this case, the supersonic turbulent boundary layer experiences the combined effects of an adverse pressure gradient, bulk compression, and concave streamline curvature.
Capillary electrophoresis of anions at high salt concentrations

It is commonly thought that even a moderately high ionic concentration in the background electrolyte (BGE) would lead to Joule heating and serious peak distortion. However, we obtained very satisfactory separations of both inorganic and organic anions in electrolyte solutions as high as 5 M sodium chloride using direct photometric detection. Samples containing a 0.5 M concentration of a salt can be analyzed directly by making the BGE concentration of the same salt even higher to obtain electrostacking. The temperature in the center of the capillary was calculated to be 49 degrees C when the current is at its maximum of 280 microA. The effect of various salts on electrophoretic and electroosmotic mobility is discussed. Several examples are given of capillary electrophoresis under high-salt conditions.
Multi-rate model predictive control of particle size distribution in a semibatch emulsion copolymerization reactor

Abstract A multi-rate model predictive controller algorithm is presented for the in-batch closed-loop control of the full particle size distribution (PSD) in a semibatch emulsion copolymerization system. The lack of frequent measurements of the PSD and the measurement delay of these measurements are addressed through the use of frequent density measurements from which the current conditions of the system are estimated. The high dimensionality of the discretized full PSD is reduced by the use of model order reduction based on principal component analysis. This method effectively reduces the size of the problem while preserving the main characteristics of the population balance system. Disturbances that perturb the surfactant and monomer amounts inside the semibatch vinyl acetate–butyl acrylate reactor are considered to demonstrate the performance of the proposed control algorithm.
Use of Established Nomograms to Predict Non-Sentinel Lymph Node Metastasis

Sentinel node biopsy has replaced routine axillary node dissection for women with clinically node-negative breast cancer. The development of nomograms, predictive models that enable individualized risk estimation, has enabled identification of women that are at low or high risk of residual non-sentinel node disease after a positive sentinel node biopsy, and have been widely validated. Furthermore, such models have been shown to predict risk of regional recurrence, risk of non-sentinel node involvement after neoadjuvant chemotherapy, and risk of four or more positive axillary nodes. Together with the panoply of other data, these mathematical models contribute to optimum and individualized decision making for a woman with breast cancer.
Dynamical faceting and nanoscale lateral growth of GaAs by molecular beam epitaxy

Abstract Dynamical faceting during homoepitaxial growth of GaAs on nanoscale-patterned surfaces by molecular beam epitaxy is examined. Selective deposition on open GaAs(1 0 0) surfaces with lateral dimensions ranging from 130 to 250 nm, separated by 15–80 nm-wide (25-nm-thick) SiO 2 stripes aligned along the [0 1 1] direction results in facet formation and lateral growth over the SiO 2 mask. At the early stage of growth, (3 1 1) facets appear on sidewalls near the boundary between an open GaAs surface and SiO 2 mask, these are replaced by (1 1 1) facets starting from SiO 2 boundaries as growth continues. After complete replacement, growth proceeds laterally in the direction perpendicular to [0 1 1] retaining the (1 1 1) facets until coalescence occurs between adjacent triangular cross-sectioned GaAs stripes. Nanoscale fabrication nonuniformity results in dynamical formation and retention of multiple (3 1 1) facets even for growth thicknesses much greater than the thickness of the SiO 2 mask stripes. This dynamical faceting is interpreted by minimization of total surface free energy based on equilibrium crystal shape, in qualitative agreement with our experimental results.
Introduction to the cell broadband engine architecture

This paper provides an overview of the Cell Broadband Engine™ Architecture (CBEA). The CBEA defines a revolutionary extension to a more conventional processor organization and serves as the basis for the development of microprocessors targeted at the computer entertainment, multimedia, and real-time market segments. In this paper, the organization of the architecture is described, as well as the instruction set, commands, and facilities defined in the architecture. In many cases, the motivation for these facilities is explained and examples are provided to illustrate their intended use. In addition, this paper introduces the Software Development Kit and the software standards for a CBEA-compliant processor.
Electrochemical studies of a hexaarylbiimidazole

Abstract The electrochemical behavior of the hexaarylbiimidazole derived from 2-(2-chlorophenyl)-4,5-diphenylimidazole (o-Cl-HABI or L2) has been studied in acetonitrile. Reduction proceeds in an overall two-electron process that is presumed to occur by an ECE process in which the initially formed radical anion L−·2 undergoes a fast cleavage reaction to give the corresponding anion of the triarylimidazole L− and the triarylimidazoyl radical L·, which is subsequently reduced to the anion. The purported radical anion intermediate could not be detected by fast-scan (104 V s−1) cyclic voltammetry, putting a lower limit of 4 × 104 s−1 on the rate constant for the cleavage reaction. The product of controlled-potential reduction was L−. On the positive-going sweep of a cyclic voltammogram of L2, the L− that was formed at the main cathodic peak is oxidized to L· that dimerizes to form the original o-Cl-HABI with a dimerization rate constant of 1.1 × 104 M−1s−1 at 298 K. The reversible potential for the L · L − couple was found to be −0.15 V vs. the ferrocene/ferrocenium potential. Analysis of the voltammetric data from 0.02 to 10 V s−1 allowed the establishment of limits for the parameters of the ECE reaction. Namely, the reversible potential for the L 2 L −· 2 couple falls between −1.83 and −1.91 V vs. ferrocene, the standard heterogeneous electron transfer rate constant lies between 0.03 and 0.2 cm s−1 and the rate constant for cleavage of L−·2 falls in the range from 4 × 104 to 1 × 107 s−1.
312 DEVELOPMENT OF SERUM HEXOSAMINIDASE (HEX) IN INFANTS

Serum activity of hexosaminidases A and B has been measured to identify patients with Tay-Sachs and Sandhoff's diseases, and may also be affected in other clinical conditions including neonatal necrotizing enterocolitis (NEC). Data utilizing serum HEX as a marker for NEC is difficult to interpret because normal developmental patterns have not been characterized. We have measured serum activity of total HEX and Hex B in 61 neonates of 27 to 40 weeks gestation who did not have NEC. These infants were followed from birth until 4 to 8 weeks of age. The infants were divided into 2 gestational age groups (≤34 weeks and >35 weeks) since enzyme activities were similar within each of these 2 groups. Total serum HEX activity, increased with postnatal (PN) age and was greater in the older gestational age group (ANOVA p<0.01). Factors associated with increased total serum HEX include enteral feeding, parenteral nutrition and unexplained hematochezia. Serum HEX activity in infants with clinical conditions that may influence serum activity of this enzyme must be compared to that in normal infants of similar gestational and postnatal ages.
Total Physical Response: A Technique for Teaching all Skills in Spanish

ABSTRACT Research in foreign language learning continues to reveal positive effects of an initial listening period with a delay in oral production. Studies have shown that use of Asher's “Total Physical Response” strategy, through which students internalize meaning initially by physically responding to oral commands, results in better listening comprehension, speaking, and reading performance. Despite TPR's acclaimed success, many teachers hesitate to adopt the entire method, because of the lack of explicit guidelines and materials for its use and because of the constraints of traditional language programs. This paper presents a strategy for utilizing an expanded version of TPR as one tool for teaching listening, speaking, reading, and writing in Spanish. Ways are suggested to implement the technique within the language curriculum. Although examples are given for Spanish, the guidelines are applicable to any foreign language program.
Mature habitats associated with genetic divergence despite strong dispersal ability in an arthropod.

Populations may be bound by contemporary gene flow, selective sweeps, and extinction-recolonization processes. Indeed, existing molecular estimates indicate that species with low levels of gene flow are rare. However, strong priority effects and local selective regimes may hinder gene flow (despite dispersal) sending populations on independent evolutionary trajectories. In this scenario (the monopolization hypothesis), population differentiation will increase with time and genealogical evidence should yield ample private haplotypes. Cyclical parthenogens (e.g. rotifers and cladocerans such as Daphnia) have an increased capacity for rapid local adaptation and priority effects because sexual reproduction is followed by multiple generations of clonal selection and massive egg bank formation. We aimed to better understand the history of population differentiation and ongoing gene flow in Daphnia rosea s.l., by comparing population and regional divergences in mature unglaciated areas and younger previously glaciated areas. We also examined the timing and paths of colonization of previously-glaciated areas to assess the dispersal limitations of D. rosea s.l. We used DNA sequence variation (84 populations and >400 individuals) at the mitochondrial ND2 and nuclear HSP90 loci from Holarctic populations for our genetic analyses. The genetic evidence indicated pronounced historical structure. Holarctic mtDNA phylogenies of D. rosea s.l. revealed three geographically restricted and divergent clades: European, Siberian and Japanese/American. The Japanese/American clade showed marked population genetic structure (F ST > 0.8) that was weakly associated with geographic distance, and a high proportion of private haplotypes. Populations from older unglaciated habitats (i.e., Japan) showed higher DNA sequence divergences than populations from presumed younger habitats (i.e. non-Beringian North America) with nDNA and with mtDNA. Mismatch analyses of mtDNA and nDNA were consistent with a single rapid post-glacial expansion of D. rosea that covered most of the New World. Our evidence agrees with negligible gene flow after founding, and the accumulation of genetic divergence with habitat age. Existing direct evidence and our mismatch analyses indicate that the pronounced population differentiation is unlikely to be due to dispersal limitation. Instead, priority effects and local selection regimes may play a role in limiting gene flow. The results challenge the notion that lacustrine populations of cladocerans are generally unified by contemporary gene flow.
Single-cell dynamics of T-cell priming.

The recent application of in vivo imaging to characterize the dynamics of T-cell activation by dendritic cells (DCs) has reshaped long-held beliefs of how adaptive immune responses are initiated. However, to improve our fundamental understanding, these new observations must be synthesized with the diverse theories and paradigms in the field, many of which were established before the advent of the cutting-edge techniques in a modern immunologist's toolbox. A number of factors have been investigated that combine to determine the ability of the DC to activate a naive T cell: the rules that govern the ability of a T cell to find antigen-bearing DCs; the parameters that define the dose and quality of the antigenic signal; and the mechanisms used by the T cell to interpret a given antigenic signal. Considering T-cell activation to be determined by the sum of interdependent factors might allow us to integrate seemingly disparate observations and hypotheses and to formulate testable predictions for further experimentation.
Effects of Substrate Pre-deposition Annealing and Deposition Parameters on the Properties of RF Sputter-deposited ZnO Films

Zinc Oxide thin films were deposited on sapphire substrates by radio frequency (RF) magnetron sputtering from an ultra-high purity ZnO solid target. The ZnO films were deposited on sapphire substrates heated in oxygen and/or in vacuum prior to deposition. Additional parameters investigated included the substrate temperature varied from 25 °C to 600 °C, the deposition gas pressure varied from 5 mTorr to 40 mTorr and the gas flow rate varied from 5 to 30 standard cubic centimeter per minute (sccm). The resulting films were annealed using a rapid thermal processor in N2 gas at 900 °C for 5 min. Analyses carried out using photoluminescence spectroscopy (PL) and X-ray diffraction (XRD) measurements indicate that films deposited at 300 °C using Ar:O2 (1:1) had the best optical and microstructure qualities. Pre-heating the sapphire substrate in oxygen prior to deposition was found to create a smoother sapphire surface, and this produced a ZnO film with greatly improved qualities. This film had a luminescence peak at 3.362 eV with a full-width-half maximum (FWHM) value of 15.3 meV when measured at 11 K. The XRD 29-scans had peaks at 34.4° with the best FWHM value of only 0.10°. Production of high quality ZnO materials is a necessary step towards realizing highly conductive p-type doped ZnO materials which is currently a major goal in research efforts on ZnO.
Precision GPR measurements: assessing and compensating for instrument drift

Recognizing the contributions that ground penetrating radar (GPR) is making to a broad range of near surface geophysical applications, including geotechnical, agricultural and watershed management activities, our group has undertaken a series of studies to identify the precision and accuracy with which GPR traveltimes, velocities and interval properties can be estimated under controlled conditions. We have recently reported on the analysis of a sequence of high quality common mid-point (CMP) soundings collected on eight different days at a single location on "clean" (low attenuating) stratified glacial drift in Southern New England. The results indicated that the two-way traveltime and velocity may be optimally estimated with precisions of ± 0.7 ns and ± 0.001 m/ns at the 95% confidence level. The high degree of precision in that dataset made it possible to observe that there may be non-random patterns in the differences between estimates of the same parameter, suggesting possible systematic biases in the data. Since one source of such a bias might be due to timing errors in the instrumentation, this report addresses the issue of time base drift; namely, ways to identify its presence, to assess its influence on estimating GPR parameters, and to compensate for its effect. Drift effects can be readily identified and compensated for. An invariant condition in a GPR survey is that the true velocity of the direct air phase should be the velocity of an electromagnetic pulse in free space. Thus, upon carefully determining the observed velocity of the air phase, and using the ratio between it and 0.29979 m/ns , one can correct the entire time base of a radargram. We illustrate this compensation procedure using two CMPs from the same site that exhibit a 14.7% difference in direct air phase velocity, and the depth estimates differ by 0.5 m. After correcting the time base, the difference between the depth estimates improves to 0.05 m.
Rebuttal to Wolfe's comments on modeling the human component in computer-based business simulations

Algorithmic adequacy is vital in computer-based games because designers control algorithms, because users cannot safely change algorithms, because elegant algorithms reduce programming errors, and because intrinsically valid algorithms increase a game's flexibility. Although algorithmic errors can remain unnoticed, this is generally more true of errors deliberately introduced by a researcher than of errors inadvertently made by a programmer. Besides being valid, good algorithms are comprehensible and clearly structured. When comprehensible algorithms are accompanied by configurable parameters, instructors can readily adapt the game, and create strategic decision-making situations, thereby opening new possibilities for learning and research.
Patterns of frequency in species-rich vegetation in pine savannas: Effects of soil moisture and scale

Our principal objective was to document dominant plant composition and the species frequency pattern in a plant community type, longleaf pine savanna, known for its extraordinary number of vascular plant species. We also tested whether an important habitat factor, soil moisture, affected the resulting patterns, and whether the patterns were scale-dependent. We began with a collection of 120 sample plots (1- × 1-m) in a wet coastal plain savanna. These plots contained 126 plant species. The 3 dominant species by cover were Rhynchospora gracilenta (15.37%), Schizachyrium tenerum (13.36%), and Scleria pauciflora (10.07%). The species frequency distribution was a skewed unimodal pattern with most species occurring infrequently, in less than 10% of the plots. There was no evidence for bimodality. To test whether soil moisture affected species frequency patterns, we sorted the plots into 2 groups: 60 representing wetter conditions and 60 representing drier conditions. Measured by percent cover, the dominants in the wetter plots were R. gracilenta, Dichanthelium scabriusculum, and S. pauciflora, whereas in the drier area they were S. tenerum, Ilex glabra, and D. dichotomum. The species frequency pattern was similar for both wet and dry plots (χ2 = 8.97, P > 0.05). To explore possible effects of sample area on this pattern, we sampled a further 75 plots in a larger tract of similar habitat in De Soto National Forest, using 4 sample areas of 0.1, 1, 10, and 100 m2. Again, the species frequency distributions all had a skewed unimodal pattern. These patterns are consistent with other studies of savannas but do not appear consistent with the bimodal patterns reported from some grasslands. Further studies of frequency will determine the degree of generality of such patterns and their relationship to mechanistic processes in plant communities.
Sorghum as a Gift of Self: the Jie Harvest Ritual Through Time

The purpose of this paper is to present an interpretation of sorghum as the dominant metaphor of self among the Jie people, and the offering of sorghum to the Turkana women by the Jie women as a gift. The literature on food as self is extensive, emerging from various key theorists who have defined the field of food and the semiotics of food (Ohnuki-Tierney 1993; Parry 1985; Raheja 1988). These scholars are keenly aware of the symbolic utility of food as constitutive features of self identity, and they have examined the interplay between self and food and tropes. For Ohnuki-Tierney, for instance, food and food production, and their associations with metaphors, define and produce meaning. Her interpretation of rice grain as one of the foundational categories of the Japanese traditional polity explicates the role commensality of rice plays in defining boundaries between people who share the commensal food and those who do not. As each member of the commensal consume the food, the food becomes a part of his or her body. The food embodied in each individual “…operates as a metonym by being part of the self” (Ohnuki-Tierney 1993:130). In this paper I extend Ohnuki-Tierney's theoretical model in understanding the role sorghum symbolism and metaphors play in producing identities and social relations of power in the Jie society and in the Jie people's interethnic relationship with their Turkana neighbors.
Jumping switched reluctance motor operating as a hoist

The motor discussed in the paper utilizes the attraction force that an electromagnet exerts on a ferromagnetic yoke. Constituting the motor is a spring placed between the electromagnet and the ferromagnetic yoke, which is located on a guiding track. This arrangement travels in a jumping manner. Presented in the paper is an analysis of the motor's performance based on the results obtained from a computer simulation of a dynamic model of the motor. Having measured the parameters of the mechanical system and the winding, calculations were performed considering the actual object. The motor's operation depends on the supply conditions. In this paper, the motor operates as a switched reluctance motor that drives the hoist, i.e. a steady gravity load force and a mass are attached to the yoke. The simulation results show that the motor performs the highest efficiency equal to 23.4%
Semi-automated literature mining to identify putative biomarkers of disease from multiple biofluids.

Computational methods for mining of biomedical literature can be useful in augmenting manual searches of the literature using keywords for disease-specific biomarker discovery from biofluids. In this work, we develop and apply a semi-automated literature mining method to mine abstracts obtained from PubMed to discover putative biomarkers of breast and lung cancers in specific biofluids. A positive set of abstracts was defined by the terms ‘breast cancer’ and ‘lung cancer’ in conjunction with 14 separate ‘biofluids’ (bile, blood, breastmilk, cerebrospinal fluid, mucus, plasma, saliva, semen, serum, synovial fluid, stool, sweat, tears, and urine), while a negative set of abstracts was defined by the terms ‘(biofluid) NOT breast cancer’ or ‘(biofluid) NOT lung cancer.’ More than 5.3 million total abstracts were obtained from PubMed and examined for biomarker-disease-biofluid associations (34,296 positive and 2,653,396 negative for breast cancer; 28,355 positive and 2,595,034 negative for lung cancer). Biological entities such as genes and proteins were tagged using ABNER, and processed using Python scripts to produce a list of putative biomarkers. Z-scores were calculated, ranked, and used to determine significance of putative biomarkers found. Manual verification of relevant abstracts was performed to assess our method’s performance. Biofluid-specific markers were identified from the literature, assigned relevance scores based on frequency of occurrence, and validated using known biomarker lists and/or databases for lung and breast cancer [NCBI’s On-line Mendelian Inheritance in Man (OMIM), Cancer Gene annotation server for cancer genomics (CAGE), NCBI’s Genes & Disease, NCI’s Early Detection Research Network (EDRN), and others]. The specificity of each marker for a given biofluid was calculated, and the performance of our semi-automated literature mining method assessed for breast and lung cancer. We developed a semi-automated process for determining a list of putative biomarkers for breast and lung cancer. New knowledge is presented in the form of biomarker lists; ranked, newly discovered biomarker-disease-biofluid relationships; and biomarker specificity across biofluids.
Observer-based control of model following systems using LMI

This paper presents a technique to design an observer-based control law that will stabilize a linear model following system. We assume that the model dynamics are completely known and has the same order as the plant. The linear matrix inequality approach is utilized in the design of observer-based controller. The controller developed in this investigation is linear and under certain assumptions this controller forces the plant states to follow the states of a model. The controller also guarantees that every system response is asymptotically stable. An example is provided to demonstrate the efficiency of the proposed method.
A micro-computed tomography-based method for the measurement of pulmonary compliance in healthy and bleomycin-exposed mice.

Micro-computed tomography (microCT) is being increasingly used to examine small animal models of pulmonary injury. We have developed a microCT technique suitable for the determination of pulmonary compliance in injured mice. Lung volumes in normal mice were radiographically determined at end-inspiration and end-expiration and pulmonary compliance was calculated at two timepoints 2 weeks apart, while a second group of mice were given bleomycin and imaged 3 weeks following drug administration. Compliance measurements were validated using a commercially available ventilator system. MicroCT pulmonary compliance measurements are suitable for longitudinal measurements, and correlate with physiologic measurements of pulmonary compliance.
International perspective: characterisation of United States Department of Agriculture and Meat Standards Australia systems for assessing beef quality

The intent, in this manuscript, is to characterise the United States Department of Agriculture (USDA) and Meat Standards Australia (MSA) systems for assessing beef quality and to describe the research evidence that supports the principles involved in grade application. USDA beef quality grading standards rely on carcass-trait-only assessments of approximate age of the animal at harvest and amount of intramuscular fat (as marbling) inside the muscles. USDA beef quality grading started 82 years ago. Then, as now, because no traceability system was in place, each animal’s history (exact age, feeding regimen, management practices, etc.) was incomplete; those who assigned quality grades used indicators of age (physiological maturity) and plane of nutrition (amount of marbling), and they do so still. Since 1926, research studies have identified a multitude of palatability-determining live-animal factors (e.g. genetics, use of hormonal growth promotants, high-energy diet finishing) and carcass-treatment factors (e.g. electrical stimulation, tenderstretch carcass suspension, postmortem aging) that cannot be incorporated into a carcass-trait-only quality assessment system. The USA beef industry has depended on development of more than 100 beef brands – some using palatability assurance critical control point plans, total quality management (TQM) philosophies, USDA certification and process verification programs, or combinations of live-animal factors, carcass-treatment factors and carcass-trait constraints – to further differentiate fresh beef products. The MSA grading system is a TQM grading approach that incorporates animal-specific traits (e.g. genetics, sex, age), control of certain pre-harvest and post-harvest processes in the beef chain, cut-specific quality differences and consumer preferences, into a beef pricing system. A unique aspect of the MSA grading system is that the grades are assigned to cuts or muscles, not carcasses; cuts or muscles from the same carcass are assigned individual (and in many cases, different) grades that reflect differences in expected eating quality performance among the various cuts of beef further adjusted to reflect the influence of cut or muscle aging and alternative cooking methods. The MSA grading system is still being modified and refined (using results of an extensive, ongoing consumer testing program), but it represents the best existing example of a TQM grading approach for improving beef quality and palatability. Research studies have shown that the accuracy of palatability-level prediction by use of the two systems – USDA quality grades for US customers and consumers and MSA grades for Australian customers and consumers – is sufficient to justify their continued use for beef quality assessment.
Molecular dosimetry of endogenous and ethylene oxide-induced N7-(2-hydroxyethyl) guanine formation in tissues of rodents.

The formation of N7-(2-hydroxyethyl)guanine (7-HEG) in DNA was investigated previously in target and non-target tissues of F-344 rats and B6C3F1 mice exposed to >/=ISOdia>/=10 p.p.m. concentrations of ethylene oxide (EO) using fluorescence-linked high-performance liquid chromatography [V.E. Walker et al. (1992) Cancer Res., 52, 4238-4334]. In order to study the dose-responses for 7-HEG at lower exposures, a highly sensitive and specific gas chromatography coupled with high-resolution mass spectrometry (GC-HRMS) assay was developed. DNA was extracted from liver, brain, lung and spleen of B6C3F1 mice and F-344 rats exposed to 0, 3, 10, 33 or 100 p.p.m. EO for 4 weeks (6 h/day, 5 days/week). Analysis of DNA from control rodents showed that endogenous 7-HEG varied from 0.2 +/- 0.1 to 0.3 +/- 0.2 pmol/micromol guanine in tissues of rats and mice. 7-HEG exhibited tissue- and species-specific dose-response relationships in EO-exposed animals. Linear dose-response relationships were evident in mouse liver, brain and spleen at exposures between 3 and 100 p.p.m. Mouse lung exhibited a slightly sublinear response between 33 and 100 p.p.m. EO. The relationships were linear in liver and spleen of rats between 3 and 100 p.p.m. EO, but were slightly sublinear in brain and lung between 33 and 100 p.p.m. EO. The number of 7-HEG adducts present in rats exposed to 3 p.p.m. EO was 5.3-12.5 times higher than endogenous 7-HEG in unexposed controls. In contrast, mice exposed to 3 p.p.m. EO only had 1.3- to 2.5-fold greater numbers of 7-HEG adducts. The factors driving the exposure-response relationships are also likely to affect carcinogenic and mutagenic responses of rodents to EO. Likewise, a better understanding of the relationships between 7-HEG derived from low exposures to EO and endogenously formed 7-HEG may be important for the accurate extrapolation of risk to humans.
A methodology for improved circuit simulation efficiency via topology-based variable accuracy device modeling

We have developed a general and efficient preprocessing algorithm which can increase circuit simulation efficiency. The algorithm identifies significant devices based upon circuit topology. Device model complexity and error tolerances are varied based upon device significance which results in a reduction in the required model evaluation time.
Fatal Canine Adenoviral Pneumonia in Two Litters of Bulldogs

Five Bulldog pups, 4 weeks of age or younger, were presented over a 2-day period for postmortem examination and diagnostic evaluation. The pups originated from 2 different litters but had been cared for at a common facility since their birth. All 5 pups died after exhibiting symptoms consisting of lethargy, dyspnea, nasal discharge, anorexia, vomiting, diarrhea, and abdominal pain. Necropsy examination revealed locally extensive to diffusely red, firm, consolidated lungs in all pups. Histopathologically, the lungs were variably effaced by multifocal areas of necrosis. The alveolar lumens contained fibrin, edema fluid, macrophages, and neutrophils. Many of the bronchioles contained cellular debris and neutrophils admixed with sloughed bronchiolar epithelium, which often contained large intranuclear amphophilic inclusion bodies that peripherally displaced chromatin. Fluorescent antibody testing was positive for Canine adenovirus. An adenovirus isolated via cell culture was positive on direct fluorescent antibody test and was identified as Canine adenovirus serotype 2 via polymerase chain reaction. Electron microscopy revealed typical viral inclusions within bronchiolar epithelial cells. Hemolytic Escherichia coli was also isolated from the lungs in 3 of the 5 pups. The current case demonstrates a natural and rare fatal infection with a viral agent that is typically associated with immunosuppression in both animals and humans.
Further Properties of Reliability Importance for Continuum Structure Functions

A continuum structure function (CSF) is a nondecreasing mapping from the unit hypercube to the unit interval. The Kim-Baxter definition of the reliability importance of component i in a CSF at system level α, R i (α), say, is reviewed. Conditions under which R i (α) is positive, under which R i (α) is a continuous function of α, and under which R i (α) ≥ R j (α) uniformly in α are presented. A simple algorithm for evaluating R i (α) is described.
Complex Ligand-Induced Conformational Changes in tRNAAsp Revealed by Single-Nucleotide Resolution SHAPE Chemistry†

RNA conformation is both highly dependent on and sensitive to the presence of charged ligands. Mono- and divalent ions stabilize the native fold of RNA, whereas other polyvalent cationic ligands can act to both stabilize or disrupt native RNA structure. In this work, we analyze the effects of two ligands, Mg (2+) and tobramycin, on the folding of S. cerevisiae tRNA (Asp) transcripts using single nucleotide resolution SHAPE chemistry. Surprisingly, reducing the Mg (2+) concentration favors a structural rearrangement in which the D- and variable loops pair. The tobramycin polycation binds to loops in tRNA (Asp) and induces RNA unfolding in two distinct transitions: the loss of tertiary interactions between the T- and D-loops followed by complete unfolding of the D-stem. Although Mg (2+) and tobramycin are relatively simple ligands, both modulate tRNA (Asp) folding in unanticipatedly complex ways, neither of which is consistent with simple hierarchical folding or unfolding of this RNA. Monitoring the structural consequences of ligand binding to RNA at single nucleotide resolution makes it possible to define intermediate structures that contribute to the complex energy landscapes often observed for RNA folding processes and lays the groundwork for a significantly improved understanding of the interactions between RNA and its solution environment.
Teaching Introductory Stem with the Marble Game

Recently there has been a call for curricular reform to plot a “learning progression” for students through the curriculum. In response, I offer the Marble Game. It provides a conceptual framework for quantitative scientific modeling skills that are useful across the science, technology, engineering and math (STEM) disciplines - at many levels. The approach actively engages students in a process of directed scientific discovery. In a SALG survey, students identified this approach as producing “great gains” in their understanding of real world problems and scientific research. Students build a conceptual framework that applies directly to random molecular-level processes in biology such as diffusion and interfacial transport. It is also isomorphic with a reversible first-order chemical reaction providing conceptual preparation for chemical kinetics. The computational and mathematical framework can also be applied to investigate the predictions of physics topics ranging from Newtonian mechanics (addressing student misconceptions by using a process of scientific discovery) through RLC circuits. To test this approach, students were asked to derive a novel theory of osmosis. The test results confirm that they were able to successfully apply the conceptual framework to a new situation under final exam conditions. DUE-0836833 http://circle4.com/biophysicsView Large Image | View Hi-Res Image | Download PowerPoint Slide
The order independence of iterated dominance in extensive games

Shimoji and Watson (1998) prove that a strategy of an extensive game is rationalizable in the sense of Pearce if and only if it survives the maximal elimination of conditionally dominated strategies. Briefly, this process iteratively eliminates conditionally dominated strategies according to a specific order, which is also the start of an order of elimination of weakly dominated strategies. Since the final set of possible payoff profiles, or terminal nodes, surviving iterated elimination of weakly dominated strategies may be order-dependent, one may suspect that the same holds for conditional dominance. We prove that, although the sets of strategy profiles surviving two arbitrary elimination orders of conditional dominance may be very different from each other, they are equivalent in the following sense: for each player i and each pair of elimination orders, there exists a function φi mapping each strategy of i surviving the first order to a strategy of i surviving the second order, such that, for every strategy profile s surviving the first order, the profile (φi(si))i induces the same terminal node as s does. To prove our results, we put forward a new notion of dominance and an elementary characterization of extensive-form rationalizability (EFR) that may be of independent interest. We also establish connections between EFR and other existing iterated dominance procedures, using our notion of dominance and our characterization of EFR.
Below-ground architectural and mycorrhizal responses to elevated CO2 in Betula alleghaniensis populations

1. Replicate populations of crowded, regenerating stands of Betula alleghaniensis were grown in ambient and elevated (700p.p.m.) atmospheric CO2 concentrations in monoliths of forest soil. Early in the second year the seedlings were harvested and detailed measurements of individual plant root architectural parameters and ectomycorrhizal colonization were made. 2. Comparing the average responses of individual plants within the populations, elevated CO2 had no significant effects on architectural parameters that improve a plant’s ability to forage for and acquire soil resources. In contrast, the intensity and magnitude of mycorrhizal colonization, and whole plant C/N ratios were significantly enhanced with elevated CO2. 3. The allometric scaling relationship between total plant biomass and root biomass was not affected by CO2, suggesting that relative allocation between roots and shoots was not affected. However, the allometric scaling relationships between root architectural parameters and plant biomass, and between fine root biomass and woody root biomass were significantly altered by elevated CO2. For all of these relationships, elevated CO2 reduced the ‘size bias’ of architectural components in relation to plant size within the populations; in elevated CO2 root architectural size (e.g. root length) per unit biomass was more similar between the smallest and largest individuals within the population than was the case for ambient CO2. 4. Overall, the results of this study suggest that the average individual seedling biomass and architectural growth responses within populations of plants exposed to elevated atmospheric CO2 levels may be unresponsive, but that mycorrhizal responses and interactions among plants within populations may be altered significantly. These findings have important implications for how we make predictions about plant growth responses to elevated CO2 in natural ecosystems. Significant increases in mycorrhizal infection rates and architecture–biomass allometries suggest that below-ground competitive interactions within plant populations may be reduced in elevated CO2. Alterations in competitive interactions may lead to shifts in productivity and plant population structure.
The role of immigration status in heavy drinking among Asian Americans.

We examined the role of Asian Americans’ immigration status in their heavy drinking, using a national sample of 3,574 Asian American adults during 2008 to 2011 when surveyed by the National Health Interview Survey. Our results, with relevant social structural factors controlled, show that U.S.-born Asian Americans exhibited the highest heavy-drinking levels, followed by long-time-resident Asian immigrants, then recent-resident Asian immigrants (our three main subsamples). The higher heavy-drinking levels characterizing U.S.-born Asians who were male and younger, as compared to immigrant Asians who were male and younger, helped explain differential heavy-drinking levels across subsamples. The study's limitations are noted.
Experimental study of thickness-shear vibration of AT-Cut quartz resonators loaded with microparticles

We study experimentally thickness-shear (TSh) vibrations of an AT-cut quartz resonator loaded with a thin layer of microparticles. The effects of the particles on TSh resonant frequencies are examined. The inertia of the particles lowers the frequencies as expected. However, the frequency shift is found to be dependent on the particle size, and it may also be nonlinear in the particle layer thickness.
Open reduction, ulnar osteotomy and external fixation for chronic anterior dislocation of the head of the radius

We reviewed 15 patients, nine girls and six boys, with chronic anterior dislocation of the radial head which was treated by ulnar osteotomy, external fixation and open reconstruction of the elbow joint but without repair of the annular ligament. Their mean age was 9.5 years (5 to 15) and the mean interval between the injury and reconstruction was 22 months (2 months to 7 years).All radial heads remained reduced at a mean follow-up of 20 months (6 months to 5 years). Normal ranges of movement for flexion, extension, pronation and supination were unchanged in 96.1% (49/51) and worse in 3.9% (2/51). Limited ranges of movement were improved in 77.8% (7/9), unchanged in 11% (1/9) and further decreased in 11% (1/9).There were two superficial pin-track infections and two cases of delayed union but with no serious complications. Reconstruction of the radiocapitellar joint is easier using external fixation since accurate correction of the ulna can be determined empirically and active functional exercises started i...
Infectivity of Microsporidia Spores Stored in Water at Environmental Temperatures

To determine how long spores of Encephalitozoon cuniculi, E. hellem, and E. intestinalis remain viable in seawater at environmental temperatures, culture-derived spores were stored in 10, 20, and 30 ppt artificial seawater at 10 and 20 C. At intervals of 1, 2, 4, 8, and 12 wk, spores were tested for infectivity in monolayer cultures of Madin Darby bovine kidney cells. Spores of E. hellem appeared the most robust, some remaining infectious in 30 ppt seawater at 10 C for 12 wk and in 30 ppt seawater at 20 C for 2 wk. Those of E. intestinalis were slightly less robust, remaining infectious in 30 ppt seawater at 10 and 20 C for 1 and 2 wk, respectively. Spores of E. cuniculi remained infectious in 10 ppt seawater at 10 and 20 C for 2 wk but not at higher salinities. These findings indicate that the spores of the 3 species of Encephalitozoon vary in their ability to remain viable when exposed to a conservative range of salinities and temperatures found in nature but, based strictly on salinity and temperature, can potentially remain infectious long enough to become widely dispersed in estuarine and coastal waters.
Design for Hardware Trust

Toward further enhancing the effectiveness of postfabrication hardware Trojan detection solutions and alleviating their limitations, as discussed in previous chapters, several methods which rely on modifying the current IC design flow have been developed by the hardware security and trust community. Collectively termed design for hardware trust [1], these Trojan prevention methods aim to prevent insertion and facilitate simple detection of hardware Trojans. In contrast to Trojan detection methods which passively test chips anticipating that the inserted Trojans will be identified based on their abnormal behavior, Trojan prevention methods take a proactive step by changing the circuit structure itself in order to prevent the insertion of Trojans. In order to achieve this goal, the entire IC supply chain needs to be revisited. The resulting modified IC supply chain emphasizes design security to counter Trojan threats and provide a solution for trusted IC design.