Miracle-dz/UniFAR-FTUs huggingface dataset:
Symplectic integration of high-dimensional Hamiltonian systems with slowly varying quadratic stiff potentials

We propose a symplectic multiscale integrator for (possibly high-dimensional) Hamiltonian systems with slowly varying quadratic stiff potentials. This integrator is based on a generalization of the impulse method via a specific splitting of the vector field that guarantees uniform convergence. The proposed method does not require the exponentiation or diagonalization of the (possibly high-dimensional) stiffness matrix, but only needs $n+1$ matrix multiplication operations at each coarse time step for a preset fixed small number $n$.
Development of a behaviour-based scale to measure acute pain in dogs

A composite scale for assessing pain in dogs in a hospital setting has been developed on the basis of observations of their behaviour. Initially, 279 words and expressions suggested by 69 veterinary surgeons were reduced into 47 words and expressions which were allocated into seven behaviour categories: demeanour and response to people, posture, mobility, activity, response to touch, attention to painful area and vocalisation. Three statistical methods, hierarchical agglomerative cluster analysis, Cronbach's alpha coefficient, and analysis of variance with multiple comparisons and empirical cumulative distributions, were used to validate these procedures, and a questionnaire accompanied by a list of definitions was designed around the expressions. The new composite scale is more detailed than previously reported scales for assessing pain in dogs on the basis of their behaviour, and the methods used in its development are based on sound scientific principles.
Validation of Single Nucleotide Polymorphisms Associated with Carcass Traits in a Commercial Hanwoo Population

Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous genome-wide association study (GWAS) with the four carcass traits in a commercial Hanwoo population. We genotyped 83 SNPs distributed across all 29 autosomes in 867 steers from a Korean Hanwoo feedlot. Six SNPs, namely ARS-BFGL-NGS-22774 (Chr4, Pos:4889229), ARS-BFGL-NGS-100046 (Chr6, Pos:61917424), ARS-BFGL-NGS-39006 (Chr27, Pos:38059196), ARS-BFGL-NGS-18790 (Chr10, Pos:26489109), ARS-BFGL-NGS-43879 (Chr9, Pos:39964297), and BTB-00775794 (Chr20, Pos:20476265), were found to be associated with CW, EMA, BF, and MS. The ARS-BFGL-NGS-22774, BTB-00775794, and ARS-BFGL-NGS-39006 markers accounted for 1.80%, 1.72%, and 1.35% (p<0.01), respectively, of the phenotypic variance in the commercial Hanwoo population. Many genes located in close proximity to the significant SNPs identified in this study were previously reported to have roles in carcass traits. The results of this study could be useful for marker-assisted selection programs.
Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors

The steadily increasing number of sequenced fungal and oomycete genomes has enabled detailed studies of how these eukaryotic microbes infect plants and cause devastating losses in food crops. During infection, fungal and oomycete pathogens secrete effector molecules which manipulate host plant cell processes to the pathogen's advantage. Proteinaceous effectors are synthesized intracellularly and must be externalized to interact with host cells. Computational prediction of secreted proteins from genomic sequences is an important technique to narrow down the candidate effector repertoire for subsequent experimental validation. In this study, we benchmark secretion prediction tools on experimentally validated fungal and oomycete effectors. We observe that for a set of fungal SwissProt protein sequences, SignalP 4 and the neural network predictors of SignalP 3 (D-score) and SignalP 2 perform best. For effector prediction in particular, the use of a sensitive method can be desirable to obtain the most complete candidate effector set. We show that the neural network predictors of SignalP 2 and 3, as well as TargetP were the most sensitive tools for fungal effector secretion prediction, whereas the hidden Markov model predictors of SignalP 2 and 3 were the most sensitive tools for oomycete effectors. Thus, previous versions of SignalP retain value for oomycete effector prediction, as the current version, SignalP 4, was unable to reliably predict the signal peptide of the oomycete Crinkler effectors in the test set. Our assessment of subcellular localization predictors shows that cytoplasmic effectors are often predicted as not extracellular. This limits the reliability of secretion predictions that depend on these tools. We present our assessment with a view to informing future pathogenomics studies and suggest revised pipelines for secretion prediction to obtain optimal effector predictions in fungi and oomycetes.
Multi-objective optimization of microwave couplers using corrected domain patching

Practical design of microwave components and circuits is a compromise between various, often conflicting objectives. In case of compact structures, the trade-offs are typically concerned with the circuit size and its electrical performance. Comprehensive information about the best possible trade-offs can be obtained by means of multi-objective optimization. In this paper, we propose a computationally efficient technique for identifying a Pareto front representation for miniaturized microstrip couplers. We exploit a sequential domain patching technique that constructs a path between the extreme Pareto-optimal designs (found by single-objective optimization runs). This stage is executed using coarse-discretization EM simulation models. Selected non-dominated designs from the path are subsequently corrected in order to fulfill prescribed design constraints (in particular, equal power split at the operating frequency), and refined in order to obtain the final Pareto set representation at the level of high-fidelity EM simulation model of the structure at hand. The proposed technique is demonstrated using a miniaturized microstrip rat-race coupler.
A motivação para aprender de estudantes em cursos de formação de professores Students learning motivation in teachers training courses

Based on the Sociocognitive theories of Motivation, the objectives of the present study were to identify the type of motivation to learn of 225 students enrolled in teacher training courses of both public and private universities of Sao Paulo, as well as to analyze it in relation to demographic variables. Data was collected through a Likert scale. Intrinsic motivation was predominant in the sample and significant relationships emerged between participants' type of motivation to learn and demographic variables. Educational implications and directions for further research are presented.
Operationalization of conceptual imagery for BCIs

We present a Brain Computer Interface (BCI) system in an asynchronous setting that allows classifying objects in their semantic categories (e.g. a hammer is a tool). For training, we use visual cues that are representative of the concepts (e.g. a hammer image for the concept of hammer). We evaluate the system in an offline synchronous setting and in an online asynchronous setting. We consider two scenarios: the first one, where concepts are in close semantic families (10 subjects) and the second where concepts are from distinctly different categories (10 subjects). We find that both have classification accuracies of 70% and above, although more distant conceptual categories lead to 5% more in classification accuracy.
Reconfiguration of the Achene and Receptacle Metabolic Networks during Strawberry Fruit Development1[C][W]

The anatomy of strawberry (Fragaria × ananassa) fruit, in which the achene is found on the outer part of the fruit, makes it an excellent species for studying the regulation of fruit development. It can provide a model for the cross talk between primary and secondary metabolism, whose role is of pivotal importance in the process. By combining gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry with the aim of addressing the metabolic regulation underlying fruit seed development, we simultaneously analyzed the composition of primary and secondary metabolites, separately, in achene and receptacle during fruit ripening of strawberry cultivar Herut. The results from these analyses suggest that changes in primary and secondary metabolism reflect organ and developmental specificities. For instance, the receptacle was characterized by increases in sugars and their direct derivatives, while the achene was characterized by a major decrease in the levels of carbon- and nitrogen-rich compounds, with the exception of storage-related metabolites (e.g. raffinose). Furthermore, the receptacle, and to a lesser extent the achene, exhibited dynamic fluctuations in the levels and nature of secondary metabolites across the ripening process. In the receptacle, proanthocyanidins and flavonol derivatives characterized mainly early developmental stages, while anthocyanins were abundant in the mature red stage; in the achene, ellagitannin and flavonoids were abundant during early and late development, respectively. Correlation-based network analysis suggested that metabolism is substantially coordinated during early development in either organ. Nonetheless, a higher degree of connectivity within and between metabolic pathways was measured in the achenes. The data are discussed within the context of current models both of the interaction of primary and secondary metabolism and of the metabolic interaction between the different plant organs.
Educational administration, policy, and reform : research and measurement

About the Authors. Editors' Comments, Wayne K. Hoy and Cecil G. Miskel. Reform Refractions: Organizational Perspectives On Standards-Based Reform, Jane Coggshall. Local Anchors Versus State Levers In State-Led School Reform: Identifying The Community Around Public Schools, John Sipple. District Central Office-Community Partnerships: From Contracts To Collaboration To Control, Meredith I. Honig. Communities Of Practice And Teacher Quality, Susan M. Printy and Helen M. Marks. Estimating the Effects of Academic Departments on Organic Design in High Schools: A Crossed-Multilevel Analysis, Sang-Jin Kang, Brian Rowan, and Stephen W. Raudenbush. Implementing Teacher Evaluation Systems: How Principals Make Sense Of Complex Artifacts To Shape Local Instructional Practice, Richard Halverson, Carolyn Kelley, and Steven Kimball. We Must Model How We Teach: Learning To Lead With Compelling Models Of Professional Development, Ellen Goldring and Nancy Vye. Putting Tab A Into Slot B: A Reliable Method For Identifying Subsystem Advocacy Coalitions, Thomas V. Shepley. Social Capital in Education: Taking Stock of Concept and Measure, Patrick B. Forsyth and Curt M. Adams. An Exploratory Analysis Of Faculty Trust In Higher Education, Alan R. Shoho and Page A. Smith. Theoretical And Empirical Foundations Of Mindful Schools, Wayne K. Hoy, Charles Quincey Gage, III, and C. John Tarter The Outsider-Within: Toward A Socially Critical Theory Of Leadership, Khaula Murtadha and Colleen L. Larson.
Robust and adaptive backstepping control for nonlinear systems using RBF neural networks

In this paper, two different backstepping neural network (NN) control approaches are presented for a class of affine nonlinear systems in the strict-feedback form with unknown nonlinearities. By a special design scheme, the controller singularity problem is avoided perfectly in both approaches. Furthermore, the closed loop signals are guaranteed to be semiglobally uniformly ultimately bounded and the outputs of the system are proved to converge to a small neighborhood of the desired trajectory. The control performances of the closed-loop systems can be shaped as desired by suitably choosing the design parameters. Simulation results obtained demonstrate the effectiveness of the approaches proposed. The differences observed between the inputs of the two controllers are analyzed briefly.
Nutrient regimes control phytoplankton ecophysiology in the South Atlantic

Fast Repetition Rate fluorometry (FRRf) measurements of phytoplankton photophysiology from an acrossbasin South Atlantic cruise (as part of the GEOTRACES programme) characterised two dominant ecophysiological regimes which were interpreted on the basis of nutrient limitation. South of the South Subtropical Convergence (SSTC) in the northern sub-Antarctic sector of the Antarctic Circumpolar Current (ACC) in the Eastern Atlantic Basin, waters are characterised by elevated chlorophyll concentrations, a dominance by larger phytoplankton cells, and low apparent photochemical efficiency (Fv / Fm). Shipboard 24 h iron (Fe) addition incubation experiments confirmed that Fe stress was primarily responsible for the low Fv / Fm, with Fe addition to these waters, either within the artificial bottle additions or naturally occurring downstream enrichment from Gough Island, significantly increasing Fv / Fm values. To the north of the SSTC at the southern boundary of the South Atlantic Gyre, phytoplankton are characterised by high values of Fv / Fm which, coupled with the low macronutrient concentrations and increased presence of picocyanobacteria, are interpreted as conditions of Fe replete, balanced macronutrient-limited growth. Spatial correlation was found between Fv / Fm and Fe:nitrate ratios, supporting the suggestion that the relative supply ratios of these two nutrients can control patterns of limitation and consequently the ecophysiology of phytoplankton in subtropical gyre and ACC regimes.
Cleavage of S-Ribosyl-l-Homocysteine by Extracts from Escherichia coli

Duerre, John A. (University of North Dakota, Grand Forks), and Chris H. Miller. Cleavage of S-ribosyl-l-homocysteine by extracts from Escherichia coli. J. Bacteriol. 91:1210–1217. 1966. —Cell-free extracts prepared from Escherichia coli catalyze the cleavage of the thioether linkage of S-ribosylhomocysteine. One of the products has been identified as homocysteine by paper chromatography of the N-ethyl-maleimide derivative and can be measured directly in reaction mixtures by sulfhydryl reagents. The other compound has been tentatively identified as ribose by column chromatography. Free sulfhydryl groups were also detected with use of S-adenosylhomocysteine as substrate; however, enzymatic cleavage of the glycosidic linkage of this compound appears to be required prior to cleavage of the thioether linkage. Homocysteine formed from either substrate could be converted readily to methionine, provided the necessary cofactors were added. Some of the properties of the ribosylhomocysteinase are discussed.
Polarization of Chemokine Receptors to the Leading Edge during Lymphocyte Chemotaxis

Leukocyte migration in response to cell attractant gradients or chemotaxis is a key phenomenon both in cell movement and in the inflammatory response. Chemokines are quite likely to be the key molecules directing migration of leukocytes that involve cell polarization with generation of specialized cell compartments. The precise mechanism of leukocyte chemoattraction is not known, however. In this study, we demonstrate that the CC chemokine receptors CCR2 and CCR5, but not cytokine receptors such as interleukin (IL)-2Rα, IL-2Rβ, tumor necrosis factor receptor 1, or transforming growth factor βR, are redistributed to a pole in T cells that are migrating in response to chemokines. Immunofluorescence and confocal microscopy studies show that the chemokine receptors concentrate at the leading edge of the cell on the flattened cell-substratum contact area, induced specifically by the signals that trigger cell polarization. The redistribution of chemokine receptors is blocked by pertussis toxin and is dependent on cell adhesion through integrin receptors, which mediate cell migration. Chemokine receptor expression on the leading edge of migrating polarized lymphocytes appears to act as a sensor mechanism for the directed migration of leukocytes through a chemoattractant gradient.
Inferring itineraries of containerized cargo through the application of Conditional Random Fields

This paper proposes a method to infer the itinerary of cargo transported in shipping containers based on a large, heterogeneous and noisy dataset of Container Status Messages. Such itinerary information can be used to improve the risk analysis performed by authorities in their effort to secure the global trade and fight frauds. Our method, based on conditional random fields, is able not only to partition the original noisy dataset into appropriate sequences describing distinct shipments of containerized cargo but also to identify the messages that describe the various stages of the transportation. The experiments performed suggest that conditional random fields provide a high accuracy for this sequential pattern mining problem.
NBER WORKING PAPER SERIES ESTIMATION OF DYNAMIC DISCRETE CHOICE MODELS IN CONTINUOUS TIME WITH AN APPLICATION TO RETAIL COMPETITION

This paper develops a dynamic model of retail competition and uses it to study the impact of the expansion of a new national competitor on the structure of urban markets. In order to accommodate substantial heterogeneity (both observed and unobserved) across agents and markets, the paper first develops a general framework for estimating and solving dynamic discrete choice models in continuous time that is computationally light and readily applicable to dynamic games. In the proposed framework, players face a standard dynamic discrete choice problem at decision times that occur stochastically. The resulting stochastic-sequential structure naturally admits the use of CCP methods for estimation and makes it possible to compute counterfactual simulations for relatively high-dimensional games. The model and method are applied to the retail grocery industry, into which Wal-Mart began rapidly expanding in the early 1990s, eventually attaining a dominant position. We find that Wal-Mart’s expansion into groceries came mostly at the expense of the large incumbent supermarket chains, rather than the single-store outlets that bore the brunt of its earlier conquest of the broader general merchandise sector. Instead, we find that independent grocers actually thrive when Wal-Mart enters, leading to an overall reduction in market concentration. These competitive effects are strongest in larger markets and those into which Wal-Mart expanded most rapidly, suggesting a diminishing role of scale and a greater emphasis on differentiation in this previously mature industry. Peter Arcidiacono Department of Economics 201A Social Sciences Building Duke University Durham, NC 27708 and NBER psarcidi@econ.duke.edu Patrick Bayer Department of Economics Duke University 213 Social Sciences Durham, NC 27708 and NBER patrick.bayer@duke.edu Jason R. Blevins Department of Economics Ohio State University Columbus, OH blevins.141@osu.edu Paul B. Ellickson Simon School of Business Administration University of Rochester Rochester, NY 14627 Email: paul.ellickson@simon.rochester. edu paul.ellickson@simon.rochester. edu
MHD Simulation of Resonant Magnetic Perturbations

Resonant magnetic perturbations (RMP) have been found effe ctive in suppressing ELMs in the DIII-D experiment [1, 2] Simulations with the M3D code indicate that plasma rotation has an essential effect on the RMP. When rotation is below a thresho ld, the RMP magnetic field is amplified above the vacuum field, and acquires a helical structure. The magnetic field is stochastic in the outer part of the plasma, causing temperature and density loss. At higher rotation speed, the stochastic layer is thinner. The temperature is similar to the initial n on rotating unperturbed state. Rotation and the screened RMP cause a density loss which extends into the p lasma core.
Use of Doehlert design for optimizing the digestion of beans for multi-element determination by inductively coupled plasma optical emission spectrometry

design. The factor block temperature was found to be the most important parameter and Doehlert designs were applied in order to determine the optimum conditions. Decomposition conditions were attained using 3.5 mL of concentrated HNO 3 and lasts 45 min. The accuracy of the results was demonstrated using one certified reference material (spinach leaves NIST 1570a) and comparison with recommended official method. A paired t-test showed a good agreement for all analytes at 95% confidence values.
Disruption of vascular endothelial homeostasis by tobacco smoke—impact on atherosclerosis

The World Health Organization (WHO) predicts that by 2020 tobacco will become the largest single health problem worldwide and will cause an estimated 8.4 million deaths annually (http://www5.who.int/tobacco/). Although the impact of smoking on human health is well defined from the medical point of view, surprisingly little is known about the mechanisms by which tobacco smoke mediates its disastrous effects. Here, we demonstrate that tobacco smoke dramatically changes vascular endothelial cell and tissue morphology, leading to a loss of endothelial barrier function within minutes. Long‐term exposure of endothelial cells to tobacco smoke extracts induces necrosis that may trigger a pro‐inflammatory status of the vessel wall. Pre‐incubation of the extracts without cells for 6 h at 37°C led to a complete loss of activity. Further, the endothelium could be rescued by changing to fresh medium even at times when the extracts had lost their activity. Finally, we show that N‐acetyl cysteine and statins inhibit the adverse tobacco smoke effects.
Studies on the time course of apparent diffusion coefficient and signal intensities on T2- and diffusion-weighted MR Imaging in acute cerebral ischemic stroke

The time course of changes in apparent diffusion coefficient (ADC) and signal intensity on diffusion-weighted magnetic resonance imaging (DW MR) imaging in acute ischemic stroke is a very dynamic event. There is an initial reduction in ADCs with no change on T2-W imaging but signal intensity increase on T2-weighted takes place about 6–12 hours after onset of stroke. As necrosis begins to set in, there is a gradual reversal of ADC change, and around 3–10 days post-onset, ADC pseudonormalizes. Twenty-four patients of acute stroke underwent diffusion MR imaging in addition to conventional T1W, T2W, and Fluid Attenuated Inversion Recovery (FLAIR) sequence performed within 12 hours, at 30 days, and at 90 days. The mean signal intensity at b = 0 s/mm2 and at b = 1000 s/mm2 were significantly higher than control values for all time periods. The ratio of signal intensity at b = 0 (rSI b=0) significantly increased from 1.63 ± 0.20 in the acute stage to 2.19 ± 0.24 in the chronic stage (P < 0.001). The ratio of signal intensity on DWI (r SIDWI) decreased from 2.54 ± 0.46 to 1.54 ± 0.22. The mean ADC in the lesion was found to be 41% lower than the mean ADC in the contralateral hemisphere . Linear regression analysis between rADC and log hours showed that pseudonormalization occurred at 6.61 days (P < 0.001). We conclude that the above information could be useful in the management of very early stroke.