bluuebunny/crossref_metadata_2025 huggingface dataset:
Recombinant Rift Valley fever vaccines induce protective levels of antibody in baboons and resistance to lethal challenge in mice
Authors: Papin James F. , Verardi Paulo H. , Jones Leslie A. , Monge-Navarro Francisco , Brault Aaron C. , Holbrook Michael R. , Worthy Melissa N. , Freiberg Alexander N. , Yilma Tilahun D.
Published: August 2011

Rift Valley fever (RVF) is a zoonotic disease endemic in Africa and the Arabian Peninsula caused by the highly infectious Rift Valley fever virus (RVFV) that can be lethal to humans and animals and results in major losses in the livestock industry. RVF is exotic to the United States; however, mosquito species native to this region can serve as biological vectors for the virus. Thus, accidental or malicious introduction of this virus could result in RVFV becoming endemic in North America. Such an event would likely lead to significant morbidity and mortality in humans, and devastating economic effects on the livestock industry. Currently, there are no licensed vaccines for RVF that are both safe and efficacious. To address this issue, we developed two recombinant RVFV vaccines using vaccinia virus (VACV) as a vector for use in livestock. The first vaccine, vCOGnGc, was attenuated by the deletion of a VACV gene encoding an IFN-γ binding protein, insertional inactivation of the thymidine kinase gene, and expression of RVFV glycoproteins, Gn and Gc. The second vaccine, vCOGnGcγ, is identical to the first and also expresses the human IFN-γ gene to enhance safety. Both vaccines are extremely safe; neither resulted in weight loss nor death in severe combined immunodeficient mice, and pock lesions were smaller in baboons compared with the controls. Furthermore, both vaccines induced protective levels of antibody titers in vaccinated mice and baboons. Mice were protected from lethal RVFV challenge. Thus, we have developed two safe and efficacious recombinant vaccines for RVF.
Ion implantation induced modification of structural and magnetic properties of perpendicular media
Authors: Gaur Nikita , Piramanayagam S N , Maurer S L , Nunes R W , Steen S , Yang H , Bhatia C S
Published: August 2011

This study reports the effects of implanting various doses of boron (11B+) and argon (40Ar+) ions into the recording layer and the soft underlayer of CoCrPt–SiO2-based perpendicular recording media. Implantation of a lower dose of boron ions (1011 ions cm−2) in the recording layer was found to reduce the out-of-plane coercivity, whereas no changes in the coercivity were observed when they were implanted into the soft underlayer. In the case of argon ions, lower dose implantation did not show any changes in the coercivity, irrespective of the implanted layer. However, higher dose implantations (1016 ions cm−2) of all the species were found to cause a reduction in coercivity, irrespective of the implanted layer. The reduction in coercivity was more significant when the ions were implanted in the recording layer compared with the case of implantation in the soft underlayer. X-ray diffraction (XRD) results on samples where argon was implanted in the recording layer showed a strong shift in the position of Co (0 0 .2) peaks, indicating an increase in the ‘c’ parameter. The shift is explained, on the basis of x-ray photoelectron spectroscopy, to be arising from intra-layer mixing at the CoCrPt–SiO2/Ru interface. Magnetic force microscopy images indicated an increase in domain size arising from the ion implantation.
AlxGa1−xN/GaN heterostructures on a thin silicon-on-insulator substrate for metal–semiconductor–metal photodetectors
Authors: Lin Vivian Kaixin , Dolmanan Surani-bin , Teo Siew Lang , Kim Hui Hui , Alarcon-Llado Esther , Dadgar Armin , Krost Alois , Tripathy Sudhiranjan
Published: August 2011

The authors demonstrate epitaxial growth of two-dimensional-electron-gas (2DEG)-based Al
x
Ga1−x
N/GaN heterostructures on a thin silicon-on-insulator (SOI) substrate. Cross-sectional transmission electron microscopy, high-resolution x-ray diffraction, photoluminescence, atomic force microscopy and ultraviolet (UV) micro-Raman spectroscopy measurements are performed to address the structural and interface properties of the epilayers on such a Si-based composite substrate. Device processing of Schottky metal–semiconductor–metal UV photodetectors is carried out to test the applicability of such a thin Al
x
Ga1−x
N layer on a GaN/SOI template for UV sensors. The high sensitivity response of such a 2DEG Al
x
Ga1−x
N/GaN heterostructure in the UV spectral range shows high potential for integration with SOI-based electronics and photonics.
A diffraction-based technique for determination of interband absorption coefficients in bulk 3C-, 4H- and 6H-SiC crystals
Authors: Ščajev Patrik , Kato Masashi , Jarašiūnas Kęstutis
Published: August 2011

Knowledge of absorption coefficient values for wavelengths above the bandgap and the injected carrier density profile is an important issue for analysis of carrier dynamics in highly excited semiconductors, e.g. for evaluation of the carrier density in photoexcited layer, density-dependent recombination rate and diffusivity. In this work we present a novel way for determining the interband absorption coefficient α for SiC crystals in a wide temperature range. The proposed method is based on recording of a transient free carrier grating in a bulk semiconductor by strongly absorbed light and measurements of probe beam diffraction efficiencies on the grating for the Bragg and symmetric anti-Bragg directions. The method was applied for 3C-, 6H-, 4H-SiC polytypes at 351 nm wavelength and revealed 3 to 10-fold increase in the interband absorption coefficients in the 80–800 K temperature range. Increase in absorption coefficients with temperature was simulated by bandgap shrinkage and increase in phonon density. A good agreement of the determined α values with a priori known room-temperature data verified validation of this technique.
Relationship Between the Application of Foliar Chemicals to Reduce Common Scab Disease of Potato and Correlation with Thaxtomin A Toxicity
Authors: Tegg Robert S. , Corkrey Ross , Wilson Calum R.
Published: August 2011

Production of the phytotoxin thaxtomin A by pathogenic Streptomyces spp. is essential for induction of common scab disease in potato. The disease can be significantly reduced by a range of chemicals applied as foliar sprays before tuber initiation. We tested a range of chemicals that had previously demonstrated varying capacities to reduce common scab for both disease suppression and their ability to inhibit thaxtomin A toxicity in both ‘Desiree’ and ‘Russet Burbank’ potato. Our results for disease suppression generally supported previous studies. Our tuber slice assays with thaxtomin A showed a strong correlation between the ability of the chemical to suppress common scab symptom development and the ability of the chemical to inhibit thaxtomin A toxicity. A Bayesian measurement error linear regression model was derived for each cultivar and trial and demonstrated a clear positive relationship between disease and thaxtomin-A-induced necrosis. The relationships obtained were much stronger than would have been obtained without adjustment for measurement error. This demonstrates that disease mitigation using chemical foliar sprays is strongly correlated with the ability of the chemical to inhibit thaxtomin A toxicity, suggesting this mechanism as a key mode of action for understanding this novel disease control strategy.
Toxicity and Resistance Potential of Selected Fungicides to Galactomyces and Penicillium spp. Causing Postharvest Fruit Decays of Citrus and Other Crops
Authors: McKay A. H. , Förster H. , Adaskaveg J. E.
Published: August 2011

A diverse collection of isolates of Galactomyces citri-aurantii and G. geotrichum, the causal pathogens of sour rots of citrus and other fruit crops, respectively, was evaluated for sensitivity to demethylation-inhibiting (DMI) fungicides of the triazole group. Propiconazole was found to be highly effective in reducing mycelial growth of both species in vitro. For 139 isolates of G. citri-aurantii, a mean effective concentration for 50% reduction of mycelial growth (EC50 value) of 0.34 μg/ml was determined; whereas, for 33 isolates of G. geotrichum, this value was 0.14 μg/ml. In a comparison of additional DMI fungicides, mean EC50 values for 60 isolates of G. citri-aurantii and 20 isolates of G. geotrichum, were 0.27 and 0.17 μg/ml for cyproconazole, 0.25 and 0.14 μg/ml for metconazole, and 1.16 and 0.73 μg/ml for tebuconazole, respectively. Propiconazole was also highly active against mycelial growth of imazalil-sensitive isolates of Penicillium digitatum, the pathogen that causes green mold of citrus, with a mean EC50 value of 0.008 μg/ml for 63 isolates. Imazalil-resistant isolates of this fungus were cross-resistant to propiconazole. When G. citri-aurantii and P. digitatum were grown at selected pH values between 3 and 9, inhibition by propiconazole occurred over the entire pH range. The fungicide was most effective at pH 5 when compared with the non-fungicide-amended control grown at the same pH. In laboratory mass platings of single-spore isolates sensitive to propiconazole onto selective media, isolates with an up to 81.6-fold decrease in sensitivity to the fungicide were recovered for P. digitatum. For G. geotrichum, isolates with an approximately twofold decrease in sensitivity were obtained. No isolates with reduced sensitivity were recovered for G. citri-aurantii. Propiconazole is currently being registered for postharvest use on citrus and other crops, and the information provided will be valuable in monitoring of fungicide resistance and in designing effective fungicide application strategies.
Whole-Genome QTL Analysis of Stagonospora nodorum Blotch Resistance and Validation of the SnTox4–Snn4 Interaction in Hexaploid Wheat
Authors: Abeysekara Nilwala S. , Faris Justin D. , Chao Shiaoman , McClean Phillip E. , Friesen Timothy L.
Published: August 2011

Necrotrophic effectors (also known as host-selective toxins) are important determinants of disease in the wheat–Stagonospora nodorum pathosystem. To date, five necrotrophic effector–host gene interactions have been identified in this system. Most of these interactions have additive effects while some are epistatic. The Snn4–SnTox4 interaction was originally identified in a recombinant-inbred population derived from a cross between the Swiss winter wheat cultivars ‘Arina’ and ‘Forno’ using the S. nodorum isolate Sn99CH 1A7a. Here, we used a recombinant-inbred population consisting of 121 lines developed from a cross between the hexaploid land race Salamouni and the hexaploid wheat ‘Katepwa’ (SK population). The SK population was used for the construction of linkage maps and quantitative trait loci (QTL) detection using the Swiss S. nodorum isolate Sn99CH 1A7a. The linkage maps developed in the SK population spanned 3,228 centimorgans (cM) and consisted of 441 simple-sequence repeats, 9 restriction fragment length polymorphisms, 29 expressed sequence tag sequence-tagged site markers, and 5 phenotypic markers. The average marker density was 6.7 cM/marker. Two QTL, designated QSnb.fcu-1A and QSnb.fcu-7A on chromosome arms 1AS and 7AS, respectively, were associated with disease caused by the S. nodorum isolate Sn99CH 1A7a. The effects of QSnb.fcu-1A were determined by the Snn4–SnTox4 interaction and accounted for 23.5% of the phenotypic variation in this population, whereas QSnb.fcu-7A accounted for 16.4% of the phenotypic variation for disease but was not associated with any known effector sensitivity locus. The effects of both QTL were largely additive and collectively accounted for 35.7% of the total phenotypic variation. The results of this research validate the effects of a compatible Snn4–SnTox4 interaction in a different genetic background, and it provides knowledge regarding genomic regions and molecular markers that can be used to improve Stagonospora nodorum blotch resistance in wheat germplasm.
Comments Regarding the Binary Power Law for Heterogeneity of Disease Incidence
Authors: Turechek W. W. , Madden L. V. , Gent D. H. , Xu X.-M.
Published: August 2011

The binary power law (BPL) has been successfully used to characterize heterogeneity (overdispersion or small-scale aggregation) of disease incidence for many plant pathosystems. With the BPL, the log of the observed variance is a linear function of the log of the theoretical variance for a binomial distribution over the range of incidence values, and the estimated scale (κ) and slope (b) parameters provide information on the characteristics of aggregation. When b = 1, the interpretation is that the degree of aggregation remains constant over the range of incidence values observed; otherwise, aggregation is variable. In two articles published in this journal in 2009, Gosme and Lucas used their stochastic simulation model, Cascade, to show a multiphasic (split-line) relationship of the variances, with straight-line (linear) relationships on a log-log scale within each phase. In particular, they showed a strong break point in the lines at very low incidence, with b considerably >1 in the first line segment (corresponding to a range of incidence values usually not observed in the field), and b being ≈1 in the next segment (corresponding to the range of incidence values usually observed). We evaluated their findings by utilizing a general spatially explicit stochastic simulator developed by Xu and Ridout in 1998, with a wide range of median dispersal distances for the contact distribution and number of plants in the sampling units (quadrats), and through an assessment of published BPL results. The simulation results showed that the split-line phenomenon can occur, with a break point at incidence values of ≈0.01; however, the split is most obvious for short median dispersal distances and large quadrat sizes. However, values of b in the second phase were almost always >1, and only approached 1 with extremely short median dispersal distances and small quadrat sizes. An appraisal of published results showed no evidence of multiple phases (although the minimum incidence may generally be too high to observe the break), and estimates of b were almost always >1. Thus, it appears that the results from the Cascade simulation model represent a special epidemiological case, corresponding primarily to a roughly nearest-neighbor population-dynamic process. Implications of a multiphasic BPL property may be important and are discussed.
Evolutionary dynamics of taxonomic structure
Authors: Foote Michael
Published: August 2011

The distribution of species among genera and higher taxa has largely untapped potential to reveal among-clade variation in rates of origination and extinction. The probability distribution of the number of species within a genus is modelled with a stochastic, time-homogeneous birth–death model having two parameters: the rate of species extinction,μ, and the rate of genus origination,γ, each scaled as a multiple of the rate of within-genus speciation,λ. The distribution is more sensitive toγthan toμ, althoughμaffects the size of the largest genera. The species : genus ratio depends strongly on bothγandμ, and so is not a good diagnostic of evolutionary dynamics. The proportion of monotypic genera, however, depends mainly onγ, and so may provide an index of the genus origination rate. Application to living marine molluscs of New Zealand shows that bivalves have a higher relative rate of genus origination than gastropods. This is supported by the analysis of palaeontological data. This concordance suggests that analysis of living taxonomic distributions may allow inference of macroevolutionary dynamics even without a fossil record.
The evolutionary palaeoecology of species and the tragedy of the commons
Authors: Roopnarine Peter D. , Angielczyk Kenneth D.
Published: August 2011

The fossil record presents palaeoecological patterns of rise and fall on multiple scales of time and biological organization. Here, we argue that the rise and fall of species can result from a tragedy of the commons, wherein the pursuit of self-interests by individual agents in a larger interactive system is detrimental to the overall performance or condition of the system. Species evolving within particular communities may conform to this situation, affecting the ecological robustness of their communities. Results from a trophic network model of Permian–Triassic terrestrial communities suggest that community performance on geological timescales may in turn constrain the evolutionary opportunities and histories of the species within them.
Models in palaeontological functional analysis
Authors: Anderson Philip S. L. , Bright Jen A. , Gill Pamela G. , Palmer Colin , Rayfield Emily J.
Published: August 2011

Models are a principal tool of modern science. By definition, and in practice, models are not literal representations of reality but provide simplifications or substitutes of the events, scenarios or behaviours that are being studied or predicted. All models make assumptions, and palaeontological models in particular require additional assumptions to study unobservable events in deep time. In the case of functional analysis, the degree of missing data associated with reconstructing musculoskeletal anatomy and neuronal control in extinct organisms has, in the eyes of some scientists, rendered detailed functional analysis of fossils intractable. Such a prognosis may indeed be realized if palaeontologists attempt to recreate elaborate biomechanical models based on missing data and loosely justified assumptions. Yet multiple enabling methodologies and techniques now exist: tools for bracketing boundaries of reality; more rigorous consideration of soft tissues and missing data and methods drawing on physical principles that all organisms must adhere to. As with many aspects of science, the utility of such biomechanical models depends on the questions they seek to address, and the accuracy and validity of the models themselves.
Statistical analysis of nonlinear dynamical systems using differential geometric sampling methods
Authors: Calderhead Ben , Girolami Mark
Published: August 2011

Mechanistic models based on systems of nonlinear differential equations can help provide a quantitative understanding of complex physical or biological phenomena. The use of such models to describe nonlinear interactions in molecular biology has a long history; however, it is only recently that advances in computing have allowed these models to be set within a statistical framework, further increasing their usefulness and binding modelling and experimental approaches more tightly together. A probabilistic approach to modelling allows us to quantify uncertainty in both the model parameters and the model predictions, as well as in the model hypotheses themselves. In this paper, the Bayesian approach to statistical inference is adopted and we examine the significant challenges that arise when performing inference over nonlinear ordinary differential equation models describing cell signalling pathways and enzymatic circadian control; in particular, we address the difficulties arising owing to strong nonlinear correlation structures, high dimensionality and non-identifiability of parameters. We demonstrate how recently introduced differential geometric Markov chain Monte Carlo methodology alleviates many of these issues by making proposals based on local sensitivity information, which ultimately allows us to perform effective statistical analysis. Along the way, we highlight the deep link between the sensitivity analysis of such dynamic system models and the underlying Riemannian geometry of the induced posterior probability distributions.
Direct evidence of phospholipids in gecko footprints and spatula–substrate contact interface detected using surface-sensitive spectroscopy
Authors: Hsu Ping Yuan , Ge Liehui , Li Xiaopeng , Stark Alyssa Y. , Wesdemiotis Chrys , Niewiarowski Peter H. , Dhinojwala Ali
Published: August 2011

Observers ranging from Aristotle to young children have long marvelled at the ability of geckos to cling to walls and ceilings. Detailed studies have revealed that geckos are ‘sticky’ without the use of glue or suction devices. Instead, a gecko's stickiness derives from van der Waals interactions between proteinaceous hairs called setae and substrate. Here, we present surprising evidence that although geckos do not use glue, a residue is transferred on surfaces as they walk—geckos leave
footprints
. Using matrix-free nano-assisted laser desorption-ionization mass spectrometry, we identified the residue as phospholipids with phosphocholine head groups. Moreover, interface-sensitive sum-frequency generation spectroscopy revealed predominantly hydrophobic methyl and methylene groups and the complete absence of water at the contact interface between a gecko toe pad and the substrate. The presence of lipids has never been considered in current models of gecko adhesion. Our analysis of gecko footprints and the toe pad–substrate interface has significant consequences for models of gecko adhesion and by extension, the design of synthetic mimics.
Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment
Authors: Ebeling Martin , Küng Erich , See Angela , Broger Clemens , Steiner Guido , Berrera Marco , Heckel Tobias , Iniguez Leonardo , Albert Thomas , Schmucki Roland , Biller Hermann , Singer Thomas , Certa Ulrich
Published: August 2011

The long-tailed macaque, also referred to as cynomolgus monkey (Macaca fascicularis), is one of the most important nonhuman primate animal models in basic and applied biomedical research. To improve the predictive power of primate experiments for humans, we determined the genome sequence of a Macaca fascicularis female of Mauritian origin using a whole-genome shotgun sequencing approach. We applied a template switch strategy that uses either the rhesus or the human genome to assemble sequence reads. The sixfold sequence coverage of the draft genome sequence enabled discovery of about 2.1 million potential single-nucleotide polymorphisms based on occurrence of a dimorphic nucleotide at a given position in the genome sequence. Homology-based annotation allowed us to identify 17,387 orthologs of human protein-coding genes in the M. fascicularis draft genome, and the predicted transcripts enabled the design of a M. fascicularis–specific gene expression microarray. Using liver samples from 36 individuals of different geographic origin we identified 718 genes with highly variable expression in liver, whereas the majority of the transcriptome shows relatively stable and comparable expression. Knowledge of the M. fascicularis draft genome is an important contribution to both the use of this animal in disease models and the safety assessment of drugs and their metabolites. In particular, this information allows high-resolution genotyping and microarray-based gene-expression profiling for animal stratification, thereby allowing the use of well-characterized animals for safety testing. Finally, the genome sequence presented here is a significant contribution to the global “3R” animal welfare initiative, which has the goal to reduce, refine, and replace animal experiments.
Generation of Signaling Specificity in Arabidopsis by Spatially Restricted Buffering of Ligand–Receptor Interactions
Authors: Abrash Emily B. , Davies Kelli A. , Bergmann Dominique C.
Published: August 2011

Core signaling pathways function in multiple programs during multicellular development. The mechanisms that compartmentalize pathway function or confer process specificity, however, remain largely unknown. In Arabidopsis thaliana, ERECTA (ER) family receptors have major roles in many growth and cell fate decisions. The ER family acts with receptor TOO MANY MOUTHS (TMM) and several ligands of the EPIDERMAL PATTERNING FACTOR LIKE (EPFL) family, which play distinct yet overlapping roles in patterning of epidermal stomata. Here, our examination of EPFL genes EPFL6/CHALLAH (CHAL), EPFL5/CHALLAH-LIKE1, and EPFL4/CHALLAH-LIKE2 (CLL2) reveals that this family may mediate additional ER-dependent processes. chal cll2 mutants display growth phenotypes characteristic of er mutants, and genetic interactions are consistent with CHAL family molecules acting as ER family ligands. We propose that different classes of EPFL genes regulate different aspects of ER family function and introduce a TMM-based discriminatory mechanism that permits simultaneous, yet compartmentalized and distinct, function of the ER family receptors in growth and epidermal patterning.
Liquid Leak Predictions in Micro- and Nanoporous Gaskets
Authors: Grine Lotfi , Bouzid Abdel-Hakim
Published: August 2011

In recent years, quite few experimental and theoretical studies have been conducted to predict gas leak rate through gaskets. However, a very limited work is done on liquid leak rates through gaskets. The slip flow model is used to predict liquid flow through porous gaskets based on measurements of gas flow at different pressures. In fact, an extrapolation of the porosity parameter approach (Grine, L., and Bouzid, A., 2009, “Correlation of Gaseous Mass Leak Rates Through Micro and Nano-Porous Gaskets,” ASME Paper No. PVP2009-77205) used to correlate leak rates between different gases is used to predict liquid leak rates. In the present article, an analytical-computational methodology based on the number and pore size to predict liquid micro- and nanoflows in the slip flow regime through gaskets is presented. The formulation is based on the Navier–Stokes equations associated with slip boundary condition at the wall. The mass leak rates through a gasket considered as a porous media under various experimental conditions of fluid media, pressure, and gasket stress were conducted on a special gasket test rig. Gaseous and liquid leaks are measured and comparisons with the analytical predictions are made.
Temperature Control of a Cutting Process Using Fractional Order Proportional-Integral-Derivative Controller
Authors: Tavakoli-Kakhki Mahsan , Haeri Mohammad
Published: August 2011

In this paper, the fractionalized differentiating method is implemented to reduce commensurate fractional order models complexity. The prominent properties of this method are its simplicity and guarantee of preserving the stability of a specific class of fractional order models in their reduced counterparts. The presented reduction method is employed in simplifying complicated fractional order controllers to a fractional order PID (FOPID) controller and proposing tuning rules for its parameters adjustment. Finally, the efficiency of the FOPID tuning rule obtained based on the proposed reduction method is shown in the temperature control of a cutting process.
A Simple Experiment to Explore Standing Waves in a Flexible Corrugated Sound Tube
Authors: Amorim Maria Eva , Sousa Teresa Delmira , Carvalho P. Simeão , Sousa Adriano Sampaioe
Published: August 2011

Sound tubes, pipes, and singing rods are used as musical instruments and as toys to perform amusing experiments. In particular, corrugated tubes present unique characteristics with respect to the sounds they can produce; that is why they have been studied so intensively, both at theoretical and experimental levels.1–4 Experimental studies usually involve expensive and sophisticated equipment that is out of reach of school laboratory facilities.3–6 In this paper we show how to investigate quantitatively the sounds produced by a flexible sound tube corrugated on the inside by using educational equipment readily available in school laboratories, such as the oscilloscope, the microphone, the anemometer, and the air pump. We show that it is possible for students to study the discontinuous spectrum of sounds produced by a flexible corrugated tube and go even further, computing the speed of sound in air with a simple experimental procedure.
The “Green Lab”: Power Consumption by Commercial Light Bulbs
Authors: Einsporn James A. , Zhou Andrew F.
Published: August 2011

Going “green” is a slogan that is very contemporary, both with industry and in the political arena. Choosing more energy-efficient devices is one way homeowners can “go green.” A simple method is to change home lighting from hot incandescent bulbs to compact fluorescent lights (CFLs). But do they really save energy? How do their illuminations compare? Even if the CFLs are more energy efficient, they still add to our pollution problem because of the mercury inside them. Light-emitting diodes (LEDs) could be the answer, but they are not available at our local stores. Can LEDs be made to screw right into a standard socket? How expensive are they? What are the power consumptions of so-called “60-W” and “100-W” CFL and LED light bulbs? These are the questions that are answered during this lab activity. Students measure the voltage and current for each of the three types of bulbs, and then calculate the electrical power required by each. An optional experiment is to set the light outputs of each bulb so they are equal in intensity, and then determine the power consumed. While not practical in the home, this experiment gives students an understanding of value for their buck.
Motivating Calculus-Based Kinematics Instruction with Super Mario Bros
Authors: Nordine Jeffrey C.
Published: August 2011

High-quality physics instruction is contextualized, motivates students to learn, and represents the discipline as a way of investigating the world rather than as a collection of facts and equations.1 Inquiry-oriented pedagogy, such as problem-based instruction, holds great promise for both teaching physics content and representing the process of doing real science.2 A challenge for physics teachers is to find instructional contexts that are meaningful, accessible, and motivating for students. Today's students are spending a growing fraction of their lives interacting with virtual environments, and these environments—physically realistic or not—can provide valuable contexts for physics explorations3–5 and lead to thoughtful discussions about decisions that programmers make when designing virtual environments. In this article, I describe a problem-based approach to calculus-based kinematics instruction that contextualizes students' learning within the Super Mario Bros. video game—a game that is more than 20 years old, but still remarkably popular with today's high school and college students.
Blue-CHIP Diagnostics
Authors: Nyendak Melissa
Published: August 2011

“Lab on a chip” technology is used for rapid diagnosis of HIV and syphilis in a resource-poor setting.
Population Genetics of Vibrio cholerae from Nepal in 2010: Evidence on the Origin of the Haitian Outbreak
Authors: Hendriksen Rene S. , Price Lance B. , Schupp James M. , Gillece John D. , Kaas Rolf S. , Engelthaler David M. , Bortolaia Valeria , Pearson Talima , Waters Andrew E. , Prasad Upadhyay Bishnu , Devi Shrestha Sirjana , Adhikari Shailaja , Shakya Geeta , Keim Paul S. , Aarestrup Frank M.
Published: August 2011

Cholera continues to be an important cause of human infections, and outbreaks are often observed after natural disasters, such as the one following the 2010 earthquake in Haiti. Once the cholera outbreak was confirmed, rumors spread that the disease was brought to Haiti by a battalion of Nepalese soldiers serving as United Nations peacekeepers. This possible connection has never been confirmed. We used whole-genome sequence typing (WGST), pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility testing to characterize 24 recent
Vibrio cholerae
isolates from Nepal and evaluate the suggested epidemiological link with the Haitian outbreak. The isolates were obtained from 30 July to 1 November 2010 from five different districts in Nepal. We compared the 24 genomes to 10 previously sequenced
V. cholerae
isolates, including 3 from the Haitian outbreak (began July 2010). Antimicrobial susceptibility and PFGE patterns were consistent with an epidemiological link between the isolates from Nepal and Haiti. WGST showed that all 24
V. cholerae
isolates from Nepal belonged to a single monophyletic group that also contained isolates from Bangladesh and Haiti. The Nepalese isolates were divided into four closely related clusters. One cluster contained three Nepalese isolates and three Haitian isolates that were almost identical, with only 1- or 2-bp differences. Results in this study are consistent with Nepal as the origin of the Haitian outbreak. This highlights how rapidly infectious diseases might be transmitted globally through international travel and how public health officials need advanced molecular tools along with standard epidemiological analyses to quickly determine the sources of outbreaks.

IMPORTANCE
Cholera is one of the ancient classical diseases and particularly prone to cause major outbreaks following major natural disasters, such as earthquakes and hurricanes, where the normal separation between sewage and drinking water is destroyed. This was the case following the 2010 earthquake in Haiti. Rumors spread that the disease was brought to Haiti by a battalion of Nepalese soldiers serving as United Nations peacekeepers. This possible connection has never been confirmed. Sequencing the genomes of bacteria can give detailed information on whether isolates from different sites share a common origin. We used this technology to sequence isolates of
Vibrio cholerae
from Nepal, identify single-nucleotide polymorphisms (SNPs), and compare these high-resolution genotypes to the complete genome sequences of isolates from the Haiti outbreak. We provide support for the hypothesis that the isolates were brought to Haiti from Nepal.
2-Thiozebularine: base modified nucleoside fully constrained in C3′-endo conformation in solution
Authors: Ebenryter Katarzyna , Jankowski Stefan , Karolak-Wojciechowska Janina , Fruziński Andrzej , Kaźmierczak-Baranska Julia , Nawrot Barbara , Sochacka Elzbieta
Published: August 2011

2-Thiopyrimidinone ribofuranoside (2-thiozebularine, s2zeb) was synthesized by the adaptation of silyl method of N-glycosidic bond formation and using thionation of protected 2-oxonucleoside derivative (zebularine, zeb) with Lawesson reagent. The X-ray crystal structure of s2zeb and NMR determined conformations of s2zeb and zeb in solution were compared with structures of 2-thiouridine (s2U) and uridine (U). In the solid state s2zeb molecule adopts conformation typical for ribonucleosides: C3′-endo C2′-exo twist type of ribofuranose pucker, anti of N-glycosidic bond and trans around C4′–C5′ bond. In aqueous solution, however, almost 100% population of s2zeb exhibits C3′-endo ribofuranose pucker. The population of N-conformer of s2zeb is about 20% higher than for zeb (analogously to pair of s2U and U nucleosides) indicating similar influence of steric effect of bulky sulfur atom on stabilization of N-type ribose conformation. Interestingly, the absence of 4-carbonyl function in zeb and s2zeb raises the population of C3′-endo conformation by about 30% in comparison to U and s2U as a result of significant anomeric effect. Additive action of both effects makes the 2-thiozebularine almost fully constrained in C3′-endo conformation in aqueous solution. Cytotoxic properties of s2zeb are less pronounced in comparison to zebularine, with IC50 > 100 mM for HeLa and K562 cancer cells and for HUVEC non-cancerous cells.
Review of bacterial and fungal culture and sensitivity results from reptilian samples submitted to a UK laboratory
Authors: Cushing A. , Pinborough M. , Stanford M.
Published: August 2011

Reptiles are increasingly kept as pets in the UK and the majority of animals presented for veterinary attention have conditions with a bacterial basis, either as a primary infection or secondary to husbandry deficiencies. Culture and sensitivity tests can provide useful information for selecting treatment protocols, but the lack of published data reviewing the normal reptilian microflora means interpretation of results is subjective. This study publishes the results of culture and sensitivity results from all reptilian samples provided to a commercial pathology laboratory over a 24‐month period and compares these data with the published literature to assist clinicians to determine appropriate treatment protocols. Results provided a wide range of cultured organisms, although trends were seen for varying anatomical locations, species and time of year. In addition, antibiotic sensitivity revealed some concerning trends.
Abdominal radiographic and ultrasonographic findings in ferrets (Mustela putorius furo) with systemic coronavirus infection
Authors: Dominguez E. , Novellas R. , Moya A. , Espada Y. , Martorell J.
Published: August 2011

Ferret systemic coronavirus infection (FSCV) is a systemic disease in ferrets that clinically and pathologically resembles the dry form of FIP. The present study describes abdominal imaging features of 11 ferrets with FSCV. Abdominal survey radiographs were available for eight ferrets and ultrasound examination for all cases. Loss of lumbar musculature, decreased peritoneal detail, presence of mid‐abdominal soft‐tissue masses and splenomegaly were the most significant radiographic signs in these patients. Ultrasonographic findings including peritonitis, abdominal lymphadenopathy, splenomegaly, abdominal soft‐tissue masses, nephromegaly and changes in the renal cortex echogenicity were recorded in the majority of cases with FSCV. As an imaging modality, ultrasound is superior to radiology when abdominal contrast is reduced, as it frequently occurs in these cases. However, although imaging techniques provide additional information in the antemortem diagnosis, they can not replace the definitive diagnosis based on histological and immunohistochemical results.
Influence of housing system and design on bone strength and keel bone fractures in laying hens
Authors: Wilkins L. J. , McKinstry J. L. , Avery N. C. , Knowles T. G. , Brown S. N. , Tarlton J. , Nicol C. J.
Published: August 2011

The main objectives of the study were to provide an accurate assessment of current levels of old breaks in end‐of‐lay hens housed in a variety of system designs and identify the important risk factors. Sixty‐seven flocks housed in eight broad subcategories were assessed at the end of the production period. Within each flock, the presence of keel fractures was determined and the tibia, humerus and keel bones dissected for measurement of breaking strength. For each house, variations in internal design and perching provision were categorised and the effective heights of the differing structures recorded. All systems were associated with alarmingly high levels of keel damage although variation in mean prevalence between systems was evident with flocks housed in furnished cages having the lowest prevalence (36 per cent) despite also having significantly weaker bones and flocks housed in all systems equipped with multilevel perches showing the highest levels of damage (over 80 per cent) and the highest severity scores.
Reducing the oxygen concentration of gases delivered from anaesthetic machines unadapted for medical air
Authors: Clutton R. E. , Schoeffmann G. , Chesnil M. , Gregson R. , Reed F. , Lawson H. , Eddleston M.
Published: August 2011

High fractional concentrations of inspired oxygen (FiO2) delivered over prolonged periods produce characteristic histological changes in the lungs and airway of exposed animals. Modern medical anaesthetic machines are adapted to deliver medical air (FiO2 =0.21) for the purpose of reducing FiO2 ; anaesthetic machines designed for the veterinary market have not been so adapted. Two inexpensive modifications that allow medical air to be added to the gas flow from veterinary anaesthetic machines are described. The advantages and disadvantages of each modification are discussed.
Protective effects of diosmetin extracted from Galium verum L. on the thymus of U14-bearing mice
Authors: Zhao Rui , Chen Zhibao , Jia Guiyan , Li Jian , Cai Yaping , Shao Xingyue
Published: August 2011

Diosmetin (DGVL) extracted from the traditional Chinese herb Galium verum L. has been found to have anticancer activity. In this study, the effects of DGVL on the thymus of U14-bearing mice were investigated. Using flow cytometry, peripheral blood lymphocytes were characterized based on the expression of surface markers for T helper cells (CD4+) and T suppressor cells (CD8+). Serum levels of tumor necrosis factor α (TNF-α), interleukin-2 (IL-2), IL-10, and transforming growth factor β1 (TGF-β1) and a cell proliferation assay were determined with an enzyme-linked immunosorbent assay. The expression of Fas and Fas ligand (FasL) on the thymus was determined by Western blotting. Our results showed that DGVL inhibited tumor growth and significantly increased the thymus weight compared with the control. Also, DGVL elevated serum levels of IL-2 and significantly reduced levels of TNF-α, TGF-β1, and IL-10 in a dose-dependent manner. Histological study and terminal dUTP nick end labeling staining results showed that DGVL protected thymus tissue against the onslaught of tumor growth by inhibiting thymus lymphocyte apoptosis. The cell proliferation assay revealed that DGVL might promote more thymus lymphocytes towards proliferation. Furthermore, the ratio of CD4+/CD8+ T lymphocytes was significantly increased from 0.69 to 2.29 by treatment with DGVL. Immunoblotting analyses revealed that the expression of Fas and FasL on the thymus was lower in mice in the DGVL treatment group than in the control mice. In conclusion, DGVL can inhibit tumor growth and protect tumor-induced apoptosis of the thymus, and the mechanism is closely associated with reduced cell death in the thymus and a Fas–FasL-dependent pathway.
Characterization of excitatory and inhibitory motor neurons to the human gastric clasp and sling fibers
Authors: Liu Jun-Feng , Sun Jian , Drew Paul A
Published: August 2011

The aim of this study was to determine the morphology and position of the excitatory and inhibitory motor neurons to the human gastric sling and clasp fibers. Motor neurons were identified by retrograde staining with 1,1′-didodecyl 3,3,3′,3′-indocarbocyanine perchlorate (DiI), and choline acetyltransferase (ChAT) or nitric oxide synthase (NOS) immunoreactivity was then determined in these motor neurons. In the sling preparations, 46% of the DiI-stained cells were aboral motor neurons, 43% were local motor neurons, and only 10% were descending motor neurons. Overall, 58% were immunoreactive for ChAT, and 36% for NOS (P = 0.042). Sixty-two percent of local, and 66% of aboral DiI-stained motor neurons were immunoreactive for ChAT. In the clasp preparations, 52% of the DiI-stained cells were descending motor neurons, 45% were local motor neurons, and only 3% were aboral neurons. Overall, 31% were immunoreactive for ChAT and 65% for NOS (P = 0.039). Eighty-five percent of the DiI-stained descending motor neurons were immunoreactive for NOS. All of the cells that were labeled adequately had a single axon and a number of filamentous or flattened lobular dendrites, and fitted into the broad category of Dogiel type I neurons. In conclusion, the majority of the motor neurons to the sling fibers were ChAT-positive excitatory neurons from the myenteric plexus of the stomach and the local region, and to the clasp were predominantly NOS-positive inhibitory neurons from the esophagus.
Delineating the receptor mechanisms underlying the rapid vascular contractile effects of aldosterone and estradiol
Authors: Gros Robert , Ding Qingming , Davis Mark , Shaikh Rasha , Liu Bonan , Chorazyczewski Jozef , Pickering J. Geoffrey , Feldman Ross D.
Published: August 2011

It is increasingly appreciated that steroid hormones such as aldosterone and estradiol can mediate important cardiovascular effects. Many of these effects occur over a time course not consistent with the genomic actions of these hormones acting through classical nuclear receptors / transcription factors. Further, multiple receptors have been implicated in mediating these rapid effects of both aldosterone and estradiol, including a newly appreciated G-protein-coupled receptor, GPR30. In previous studies we demonstrated that both aldosterone and estradiol mediate contraction in vascular smooth muscle cells, as assessed in single cell assays. However, the receptor mechanisms underlying these effects remained unclear. Therefore, we studied the actions of estradiol and aldosterone on rat aortic vascular smooth muscle cells. Both aldosterone and estradiol mediated a concentration-dependent increase in contraction, as assessed in substrate deformation assays with EC50s in the range of nanomoles per litre. These effects paralleled increased myosin light chain phosphorylation. The effects of aldosterone were inhibited by the mineralocorticoid selective antagonist eplerenone. Further, aldosterone’s contractile effects were enhanced by increased expression of the mineralocorticoid receptor. The contractile effects of estradiol were inhibited by estrogen receptor (ER)-selective antagonists, tamoxifen, and ICI 182780, as well as eplerenone. Further, estradiol’s effects were enhanced by the increased expression of both ERα and the mineralocorticoid receptor (MR). To assess the potential role of GPR30 in mediating the effects of aldosterone and estradiol, GPR30 was re-introduced, since these cells lose endogenous GPR30 expression in culture. Re-expression of GPR30 enhanced both estradiol- and aldosterone-mediated contraction. These studies demonstrate that in rat aortic vascular smooth muscle cells, both aldosterone and estradiol mediate vascular smooth muscle contraction and that these effects can be mediated by MR, ERα, and by GPR30.
Transient middle cerebral artery occlusion and reperfusion alters inducible NOS expression within the ventrolateral medulla and modulates cardiovascular function during static exercise
Authors: Ally Ahmmed , Maher Timothy J.
Published: August 2011

A major cause of stroke is cerebral ischemia in regions supplied by the middle cerebral artery (MCA). In this study, we hypothesized that compromised cardiovascular function during static exercise may involve altered expression of inducible NOS (iNOS) protein within the rostral ventrolateral medulla (RVLM) and caudal ventrolateral medulla (CVLM). We compared cardiovascular responses and iNOS protein expression within the left and right sides of both RVLM and CVLM in sham-operated rats and in rats with a 90 min left-sided MCA occlusion (MCAO) followed by 24 h of reperfusion. Increases in blood pressure during a static muscle contraction were attenuated in MCAO rats compared with sham-operated rats. Also, iNOS expression within the left RVLM was augmented compared with the right RVLM in MCAO rats and compared with both RVLM quadrants in sham-operated rats. In contrast, compared with sham-operated rats and the right CVLM of MCAO rats, iNOS expression was attenuated in the left CVLM in left-sided MCAO rats. These data suggest that the attenuation of pressor responses during static exercise in MCAO rats involves overexpression of iNOS within the ipsilateral RVLM and attenuation in iNOS within the ipsilateral CVLM. Differential expression of iNOS within the medulla plays a role in mediating cardiovascular responses during static exercise following stroke.
SUBFACTORS OF INDEX LESS THAN 5, PART 4: VINES
Authors: PENNEYS DAVID , TENER JAMES E.
Published: August 2011

We eliminate 39 infinite families of possible principal graphs as part of the classification of subfactors up to index 5. A number-theoretic result of Calegari–Morrison–Snyder, generalizing Asaeda–Yasuda, reduces each infinite family to a finite number of cases. We provide algorithms for computing the effective constants that are required for this result, and we obtain 28 possible principal graphs. The Ostrik d-number test and an algebraic integer test reduce this list to seven graphs in the index range (4,5) which actually occur as principal graphs.