University of Illinois Urbana-Champaign

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

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The Agrobacterium vacuum infiltration method has made it possible to transform Arabidopsis thaliana without plant tissue culture or regeneration. In the present study, this method was evaluated and a substantially modified transformation method was developed. The labor-intensive vacuum infiltration process was eliminated in favor of simple dipping of developing floral tissues into a solution containing Agrobacterium tumefaciens, 5% sucrose and 500 microliters per litre of surfactant Silwet L-77. Sucrose and surfactant were critical to the success of the floral dip method. Plants inoculated when numerous immature floral buds and few siliques were present produced transformed progeny at the highest rate. Plant tissue culture media, the hormone benzylamino purine and pH adjustment were unnecessary, and Agrobacterium could be applied to plants at a range of cell densities. Repeated application of Agrobacterium improved transformation rates and overall yield of transformants approximately twofold. Covering plants for 1 day to retain humidity after inoculation also raised transformation rates twofold. Multiple ecotypes were transformable by this method. The modified method should facilitate high-throughput transformation of Arabidopsis for efforts such as T-DNA gene tagging, positional cloning, or attempts at targeted gene replacement.

Four software designers present a catalog of simple and succinct solutions to commonly occurring design problems, using Smalltalk and C++ in example code. These 23 patterns allow designers to create more flexible, elegant, and ultimately reusable designs without having to rediscover the design solutions themselves. The authors begin by describing what patterns are and how they can help you design object-oriented software. They go on to systematically name, explain, evaluate, and catalog recurring designs in object-oriented systems.--From publisher description.

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

Social network analysis is used widely in the social and behavioral sciences, as well as in economics, marketing, and industrial engineering. The social network perspective focuses on relationships among social entities and is an important addition to standard social and behavioral research, which is primarily concerned with attributes of the social units. Social Network Analysis: Methods and Applications reviews and discusses methods for the analysis of social networks with a focus on applications of these methods to many substantive examples. It is a reference book that can be used by those who want a comprehensive review of network methods, or by researchers who have gathered network data and want to find the most appropriate method by which to analyze it. It is also intended for use as a textbook as it is the first book to provide comprehensive coverage of the methodology and applications of the field.

Introduction An Intensive Study of Case Study Research Methods The Unique Case Research Questions The Nature of Qualitative Research Data Gathering Analysis and Interpretation Case Researcher Roles Triangulation Writing the Report Reflections Harper School

The past decade has seen many advances in physical layer wireless communication theory and their implementation in wireless systems. This textbook takes a unified view of the fundamentals of wireless communication and explains the web of concepts underpinning these advances at a level accessible to an audience with a basic background in probability and digital communication. Topics covered include MIMO (multi-input, multi-output) communication, space-time coding, opportunistic communication, OFDM and CDMA. The concepts are illustrated using many examples from real wireless systems such as GSM, IS-95 (CDMA), IS-856 (1 x EV-DO), Flash OFDM and UWB (ultra-wideband). Particular emphasis is placed on the interplay between concepts and their implementation in real systems. An abundant supply of exercises and figures reinforce the material in the text. This book is intended for use on graduate courses in electrical and computer engineering and will also be of great interest to practising engineers.

A theory of superconductivity is presented, based on the fact that the interaction between electrons resulting from virtual exchange of phonons is attractive when the energy difference between the electrons states involved is less than the phonon energy, $\ensuremath{\hbar}\ensuremath{\omega}$. It is favorable to form a superconducting phase when this attractive interaction dominates the repulsive screened Coulomb interaction. The normal phase is described by the Bloch individual-particle model. The ground state of a superconductor, formed from a linear combination of normal state configurations in which electrons are virtually excited in pairs of opposite spin and momentum, is lower in energy than the normal state by amount proportional to an average ${(\ensuremath{\hbar}\ensuremath{\omega})}^{2}$, consistent with the isotope effect. A mutually orthogonal set of excited states in one-to-one correspondence with those of the normal phase is obtained by specifying occupation of certain Bloch states and by using the rest to form a linear combination of virtual pair configurations. The theory yields a second-order phase transition and a Meissner effect in the form suggested by Pippard. Calculated values of specific heats and penetration depths and their temperature variation are in good agreement with experiment. There is an energy gap for individual-particle excitations which decreases from about $3.5k{T}_{c}$ at $T=0\ifmmode^\circ\else\textdegree\fi{}$K to zero at ${T}_{c}$. Tables of matrix elements of single-particle operators between the excited-state superconducting wave functions, useful for perturbation expansions and calculations of transition probabilities, are given.

BACKGROUND: The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. DESCRIPTION: We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12-24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. CONCLUSION: By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.

Abstract: SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

W. Wilson's (1967) review of the area of subjective well-being (SWB) advanced several conclusions regarding those who report high levels of A number of his conclusions have been overturned: youth and modest aspirations no longer are seen as prerequisites of SWB. E. Diener's (1984) review placed greater emphasis on theories that stressed psychological factors. In the current article, the authors review current evidence for Wilson's conclusions and discuss modern theories of SWB that stress dispositional influences, adaptation, goals, and coping strategies. The next steps in the evolution of the field are to comprehend the interaction of psychological factors with life circumstances in producing SWB, to understand the causal pathways leading to happiness, understand the processes underlying adaptation to events, and develop theories that explain why certain variables differentially influence the different components of SWB (life satisfaction, pleasant affect, and unpleasant affect). In 1967, Warner Wilson presented a broad review of subjective well-being (SWB) research entitled, Correlates of Avowed Happiness. Based on the limited data available at that time, Wilson concluded that the happy person is a young, healthy, welleducated, well-paid, extroverted, optimistic, worry-free, religious, married person with high self-esteem, job morale, modest aspirations, of either sex and of a wide range of intelligence (p. 294). In the three decades since Wilson's review, investigations into SWB have evolved. Although researchers now know a great deal more about the correlates of SWB, they are less interested in simply describing the demographic characteristics that correlate with it. Instead, they focus their effort on understanding the processes that underlie happiness. This trend represents a greater recognition of the central role played by people's goals, coping efforts, and dispositions. In this article, we review research on several major theoretical approaches to well-being and then indicate how these theories clarify the findings on demographic correlates of SWB. Throughout the review we suggest four directions that researchers should pursue in the decades ahead. These are by no means the only questions left to answer, but we believe they are the most interesting issues left to resolve. First, the causal direction of the correlates of happiness must be examined through more sophisticated methodologies. Although the causal priority of demographic factors such as marriage and income is intuitively appealing, it is by no means certain. Second, researchers must focus greater attention on the interaction between internal factors (such as personality traits) and external circumstances. As we shall see, demographic factors have surprisingly small effects on SWB, but these effects may depend on the personalities of those individuals being studied. Thus, future research must take Person X Situation interactions into account. Third, researchers must strive to understand the processes underlying adaptation. Considerable adaptation to both good and bad circumstances often occurs, yet the processes responsible for these effects are poorly understood. Research that examines how habituation, coping strategies, and changing goals influence adaptation will shed much light on the processes responsible for SWB. Finally, theories must be refined to make specific predictions about how input variables differentially influence the components of SWB. In the past, many researchers have treated SWB as a monolithic entity, but it is now clear that there are separable components that exhibit unique patterns of relations with different variables. In each section of this article we discuss progress and opportunities in these four areas.

Construct Validity in Psychological TestsVALIDATION of psychological tests has not yet been adequately concep• tua1ized, as the APA Committee on Psychological Tests learned when it undertook to specify what qualities should be investigated before a test is published.In order to make coherent recommendations the Committee found it necessary to distinguish four types of validity, established by different types of research and requiring different interpre• tation.The chief innovation in the Committee's report was the term constmct validity.*This idea was first formulated hy a subcommittee {Meehl and R. C. Cballman) studying how proposed recommendations would apply to projective techniques, and later modified and clarified by the entire Committee {Bordin, Challman, Conrad, Humphreys, Super, and the present writers).The statements agreed upon by tbe Committee (and by committees of two other associations) were published in the Technical Recommendations ( 59).The present interpretation of construct validity is not "official" and deals with some areas in which the Committee would probably not be unanimous.The present writers are solely responsible for this attempt to explain the concept and elaborate its implications.Identification of construct validity was not an isolated development.Writers on validity during the preceding decade had shown a great deal of dissatisfaction with conventional notions of validity, and intro• dnced new terms and ideas, hut the resulting aggregation of types of * Referred to in a preliminary report ( 58) as cougruent validity.

Here, this paper presents cosmological results based on full-mission Planck observations of temperature and polarization anisotropies of the cosmic microwave background (CMB) radiation. Our results are in very good agreement with the 2013 analysis of the Planck nominal-mission temperature data, but with increased precision. The temperature and polarization power spectra are consistent with the standard spatially-flat 6-parameter ΛCDM cosmology with a power-law spectrum of adiabatic scalar perturbations (denoted “base ΛCDM” in this paper). From the Planck temperature data combined with Planck lensing, for this cosmology we find a Hubble constant, H₀ = (67.8 ± 0.9) km s^-1Mpc^-1, a matter density parameter Ω_m = 0.308 ± 0.012, and a tilted scalar spectral index with n_s = 0.968 ± 0.006, consistent with the 2013 analysis. Note that in this abstract we quote 68% confidence limits on measured parameters and 95% upper limits on other parameters. We present the first results of polarization measurements with the Low Frequency Instrument at large angular scales. Combined with the Planck temperature and lensing data, these measurements give a reionization optical depth of τ = 0.066 ± 0.016, corresponding to a reionization redshift of z_re= 8.8$+1.7\atop{-1.4}$. These results are consistent with those from WMAP polarization measurements cleaned for dust emission using 353-GHz polarization maps from the High Frequency Instrument. We find no evidence for any departure from base ΛCDM in the neutrino sector of the theory; for example, combining Planck observations with other astrophysical data we find N_eff = 3.15 ± 0.23 for the effective number of relativistic degrees of freedom, consistent with the value N_eff = 3.046 of the Standard Model of particle physics. The sum of neutrino masses is constrained to Σ m_ν < 0.23 eV. The spatial curvature of our Universe is found to be very close to zero, with | Ω_K | < 0.005. Adding a tensor component as a single-parameter extension to base ΛCDM we find an upper limit on the tensor-to-scalar ratio of r_0.002< 0.11, consistent with the Planck 2013 results and consistent with the B-mode polarization constraints from a joint analysis of BICEP2, Keck Array, and Planck (BKP) data. Adding the BKP B-mode data to our analysis leads to a tighter constraint of r_0.002 < 0.09 and disfavours inflationarymodels with a V(φ) ∝ φ² potential. The addition of Planck polarization data leads to strong constraints on deviations from a purely adiabatic spectrum of fluctuations. We find no evidence for any contribution from isocurvature perturbations or from cosmic defects. Combining Planck data with other astrophysical data, including Type Ia supernovae, the equation of state of dark energy is constrained to w = -1.006 ± 0.045, consistent with the expected value for a cosmological constant. The standard big bang nucleosynthesis predictions for the helium and deuterium abundances for the best-fit Planck base ΛCDM cosmology are in excellent agreement with observations. We also constraints on annihilating dark matter and on possible deviations from the standard recombination history. In neither case do we find no evidence for new physics. The Planck results for base ΛCDM are in good agreement with baryon acoustic oscillation data and with the JLA sample of Type Ia supernovae. However, as in the 2013 analysis, the amplitude of the fluctuation spectrum is found to be higher than inferred from some analyses of rich cluster counts and weak gravitational lensing. We show that these tensions cannot easily be resolved with simple modifications of the base ΛCDM cosmology. Finally, apart from these tensions, the base ΛCDM cosmology provides an excellent description of the Planck CMB observations and many other astrophysical data sets.

Starts with a brief review of the history and the application areas considered in the literature. The author then proceeds with introductory modeling examples, behavioral and structural properties, three methods of analysis, subclasses of Petri nets and their analysis. In particular, one section is devoted to marked graphs, the concurrent system model most amenable to analysis. Introductory discussions on stochastic nets with their application to performance modeling, and on high-level nets with their application to logic programming, are provided. Also included are recent results on reachability criteria. Suggestions are provided for further reading on many subject areas of Petri nets.&gt;

On August 17, 2017 at 12∶41:04 UTC the Advanced LIGO and Advanced Virgo gravitational-wave detectors made their first observation of a binary neutron star inspiral. The signal, GW170817, was detected with a combined signal-to-noise ratio of 32.4 and a false-alarm-rate estimate of less than one per 8.0×10^{4} years. We infer the component masses of the binary to be between 0.86 and 2.26 M_{⊙}, in agreement with masses of known neutron stars. Restricting the component spins to the range inferred in binary neutron stars, we find the component masses to be in the range 1.17-1.60 M_{⊙}, with the total mass of the system 2.74_{-0.01}^{+0.04}M_{⊙}. The source was localized within a sky region of 28 deg^{2} (90% probability) and had a luminosity distance of 40_{-14}^{+8} Mpc, the closest and most precisely localized gravitational-wave signal yet. The association with the γ-ray burst GRB 170817A, detected by Fermi-GBM 1.7 s after the coalescence, corroborates the hypothesis of a neutron star merger and provides the first direct evidence of a link between these mergers and short γ-ray bursts. Subsequent identification of transient counterparts across the electromagnetic spectrum in the same location further supports the interpretation of this event as a neutron star merger. This unprecedented joint gravitational and electromagnetic observation provides insight into astrophysics, dense matter, gravitation, and cosmology.

We consider the problem of automatically recognizing human faces from frontal views with varying expression and illumination, as well as occlusion and disguise. We cast the recognition problem as one of classifying among multiple linear regression models and argue that new theory from sparse signal representation offers the key to addressing this problem. Based on a sparse representation computed by l{1}-minimization, we propose a general classification algorithm for (image-based) object recognition. This new framework provides new insights into two crucial issues in face recognition: feature extraction and robustness to occlusion. For feature extraction, we show that if sparsity in the recognition problem is properly harnessed, the choice of features is no longer critical. What is critical, however, is whether the number of features is sufficiently large and whether the sparse representation is correctly computed. Unconventional features such as downsampled images and random projections perform just as well as conventional features such as Eigenfaces and Laplacianfaces, as long as the dimension of the feature space surpasses certain threshold, predicted by the theory of sparse representation. This framework can handle errors due to occlusion and corruption uniformly by exploiting the fact that these errors are often sparse with respect to the standard (pixel) basis. The theory of sparse representation helps predict how much occlusion the recognition algorithm can handle and how to choose the training images to maximize robustness to occlusion. We conduct extensive experiments on publicly available databases to verify the efficacy of the proposed algorithm and corroborate the above claims.

Part One: Introduction Part Two: Focusing and Bounding the Collection of Data Part Three: Analysis During Data Collection Part Four: Within-Site Analysis Part Five: Cross-Site Analysis Part Six: Matrix Displays: Some General Suggestions Part Seven: Drawing and Verifying Conclusions Part Eight: Concluding Remarks

When n identical randomly located nodes, each capable of transmitting at W bits per second and using a fixed range, form a wireless network, the throughput /spl lambda/(n) obtainable by each node for a randomly chosen destination is /spl Theta/(W//spl radic/(nlogn)) bits per second under a noninterference protocol. If the nodes are optimally placed in a disk of unit area, traffic patterns are optimally assigned, and each transmission's range is optimally chosen, the bit-distance product that can be transported by the network per second is /spl Theta/(W/spl radic/An) bit-meters per second. Thus even under optimal circumstances, the throughput is only /spl Theta/(W//spl radic/n) bits per second for each node for a destination nonvanishingly far away. Similar results also hold under an alternate physical model where a required signal-to-interference ratio is specified for successful receptions. Fundamentally, it is the need for every node all over the domain to share whatever portion of the channel it is utilizing with nodes in its local neighborhood that is the reason for the constriction in capacity. Splitting the channel into several subchannels does not change any of the results. Some implications may be worth considering by designers. Since the throughput furnished to each user diminishes to zero as the number of users is increased, perhaps networks connecting smaller numbers of users, or featuring connections mostly with nearby neighbors, may be more likely to be find acceptance.

The problem of multiprogram scheduling on a single processor is studied from the viewpoint of the characteristics peculiar to the program functions that need guaranteed service. It is shown that an optimum fixed priority scheduler possesses an upper bound to processor utilization which may be as low as 70 percent for large task sets. It is also shown that full processor utilization can be achieved by dynamically assigning priorities on the basis of their current deadlines. A combination of these two scheduling techniques is also discussed.