Iowa State University

Abstract Let n observations Y 1, Y 2, ···, Y n be generated by the model Y t = pY t−1 + e t , where Y 0 is a fixed constant and {e t } t-1 n is a sequence of independent normal random variables with mean 0 and variance σ2. Properties of the regression estimator of p are obtained under the assumption that p = ±1. Representations for the limit distributions of the estimator of p and of the regression t test are derived. The estimator of p and the regression t test furnish methods of testing the hypothesis that p = 1.

Abstract A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed‐shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley & Sons, Inc.

Introduction Since its publication in 1985, the outstanding 1,800-page Comprehensive Grammar of the English Language, by Randolph Quirk, Sidney Greenbaum, Geoffrey Leech, and Jan Svartvik, has been the definitive description of the grammar of English and an in-. dispensable reference for any research in the analysis or generation of English that attempts serious coverage of the syntactic phenomena of the language. The new Longman Grammar of Spoken and Written English, by Douglas Biber, Stig Johansson, Geoffrey Leech, Susan Conrad, and Edward Finegan, is an important complement to the earlier work, extending and sometimes revising the descriptions of Quirk et al., by means of an extensive corpus analysis by the five authors and their research assistants. Now, the bookshelf of any researcher in English linguistics is incomplete without both volumes. Like Quirk et al. (hereafter CGEL), Biber and his colleagues attempt a detailed description of all the syntactic phenomena of English. But

Abstract. VEGAN adds vegetation analysis functions to the general‐purpose statistical program R. Both R and VEGAN can be downloaded for free. VEGAN implements several ordination methods, including Canonical Correspondence Analysis and Non‐metric Multidimensional Scaling, vector fitting of environmental variables, randomization tests, and various other analyses of vegetation data. It can be used for large data. Graphical output can be customized using the R language's extensive graphics capabilities. VEGAN is appropriate for routine and research use, if you are willing to learn some R.

Teaching by Principles: An Interactive Approach to Language Pedagogy, Third Edition, by H. Douglas Brown, is a widely acclaimed methodology text used in teacher education programs around the world. This user-friendly textbook offers a comprehensive survey of practical language teaching options, all firmly anchored in accepted principles of language learning and teaching. End-of-chapter exercises give readers opportunities to process material interactively. Suggested readings direct readers to important books and articles in the field.

This biennial Review summarizes much of particle physics. Using data from previous editions, plus 2658 new measurements from 644 papers, we list, evaluate, and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as Higgs bosons, heavy neutrinos, and supersymmetric particles. All the particle properties and search limits are listed in Summary Tables. We also give numerous tables, figures, formulae, and reviews of topics such as the Standard Model, particle detectors, probability, and statistics. Among the 112 reviews are many that are new or heavily revised including those on Heavy-Quark and Soft-Collinear Effective Theory, Neutrino Cross Section Measurements, Monte Carlo Event Generators, Lattice QCD, Heavy Quarkonium Spectroscopy, Top Quark, Dark Matter, ${V}_{\mathit{cb}}$ ${V}_{\mathit{ub}}$, Quantum Chromodynamics, High-Energy Collider Parameters, Astrophysical Constants, Cosmological Parameters, and Dark Matter.A booklet is available containing the Summary Tables and abbreviated versions of some of the other sections of this full Review. All tables, listings, and reviews (and errata) are also available on the Particle Data Group website: http://pdg.lbl.gov/.The 2012 edition of Review of Particle Physics is published for the Particle Data Group as article 010001 in volume 86 of Physical Review D.This edition should be cited as: J. Beringer et al. (Particle Data Group), Phys. Rev. D 86, 010001 (2012).

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

In this article I evaluated the psychometric properties of the UCLA Loneliness Scale (Version 3). Using data from prior studies of college students, nurses, teachers, and the elderly, analyses of the reliability, validity, and factor structure of this new version of the UCLA Loneliness Scale were conducted. Results indicated that the measure was highly reliable, both in terms of internal consistency (coefficient alpha ranging from .89 to .94) and test-retest reliability over a 1-year period (r = .73). Convergent validity for the scale was indicated by significant correlations with other measures of loneliness. Construct validity was supported by significant relations with measures of the adequacy of the individual's interpersonal relationships, and by correlations between loneliness and measures of health and well-being. Confirmatory factor analyses indicated that a model incorporating a global bipolar loneliness factor along with two method factor reflecting direction of item wording provided a very good fit to the data across samples. Implications of these results for future measurement research on loneliness are discussed.

PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties. Soybean (Glycine max) is an important commercial crop providing both protein and oil, and its symbiotic relationship to nitrogen-fixing bacteria makes it a profitable crop in rotation systems. Its genome has now been sequenced: it is the first legume and at 1.1 gigabases, the largest plant genome to be sequenced by whole-genome shotgun techniques. Soybean has a colourful genetic past; genome duplications occurred at 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. An accurate soybean genome sequence should accelerate the creation of improved soybean varieties. Soybean is an important crop plant, providing seed protein and oil and fixing atmospheric nitrogen through symbioses with soil-borne microorganisms. Using a whole-genome shotgun approach, its 1.1-gigabase genome is now sequenced and integrated with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly.

Wireless sensor networks consist of small nodes with sensing, computation, and wireless communications capabilities. Many routing, power management, and data dissemination protocols have been specifically designed for WSNs where energy awareness is an essential design issue. Routing protocols in WSNs might differ depending on the application and network architecture. In this article we present a survey of state-of-the-art routing techniques in WSNs. We first outline the design challenges for routing protocols in WSNs followed by a comprehensive survey of routing techniques. Overall, the routing techniques are classified into three categories based on the underlying network structure: flit, hierarchical, and location-based routing. Furthermore, these protocols can be classified into multipath-based, query-based, negotiation-based, QoS-based, and coherent-based depending on the protocol operation. We study the design trade-offs between energy and communication overhead savings in every routing paradigm. We also highlight the advantages and performance issues of each routing technique. The article concludes with possible future research areas.

A-Maize-ing Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112 ; see the cover) present the results of sequencing the B73 inbred maize line. The findings elucidate how maize became diploid after an ancestral doubling of its chromosomes and reveals transposable element movement and activity and recombination. Vielle-Calzada et al. (p. 1078 ) have sequenced the Palomero Toluqueño ( Palomero ) landrace, a highland popcorn from Mexico, which, when compared to the B73 line, reveals multiple loci impacted by domestication. Swanson-Wagner et al. (p. 1118 ) exploit possession of the genome to analyze expression differences occurring between lines. The identification of single nucleotide polymorphisms and copy number variations among lines was used by Gore et al. (p. 1115 ) to generate a Haplotype map of maize. While chromosomal diversity in maize is high, it is likely that recombination is the major force affecting the levels of heterozygosity in maize. The availability of the maize genome will help to guide future agricultural and biofuel applications (see the Perspective by Feuillet and Eversole ).

An extremely large magnetic entropy change has been discovered in $\mathrm{Gd}{}_{5}(\mathrm{Si}{}_{2}\mathrm{Ge}{}_{2})$ when subjected to a change in the magnetic field. It exceeds the reversible (with respect to an alternating magnetic field) magnetocaloric effect in any known magnetic material by at least a factor of 2, and it is due to a first order $[\mathrm{ferromagnetic}(\mathrm{I})\ensuremath{\leftrightarrow}\mathrm{ferromagnetic}(\mathrm{II})]$ phase transition at 276 K and its unique magnetic field dependence.

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

Author(s): Collaboration, The ATLAS; Aad, G; Abat, E; Abdallah, J; Abdelalim, AA; Abdesselam, A; Abdinov, O; Abi, BA; Abolins, M; Abramowicz, H; Acerbi, E; Acharya, BS; Achenbach, R; Ackers, M; Adams, DL; Adamyan, F; Addy, TN; Aderholz, M; Adorisio, C; Adragna, P; Aharrouche, M; Ahlen, SP; Ahles, F; Ahmad, A; Ahmed, H; Aielli, G; Åkesson, PF; Åkesson, TPA; Akimov, AV; Alam, SM; Albert, J; Albrand, S; Aleksa, M; Aleksandrov, IN; Aleppo, M; Alessandria, F; Alexa, C; Alexander, G; Alexopoulos, T; Alimonti, G; Aliyev, M; Allport, PP; Allwood-Spiers, SE; Aloisio, A; Alonso, J; Alves, R; Alviggi, MG; Amako, K; Amaral, P; Amaral, SP; Ambrosini, G; Ambrosio, G; Amelung, C; Ammosov, VV; Amorim, A; Amram, N; Anastopoulos, C; Anderson, B; Anderson, KJ; Anderssen, EC; Andreazza, A; Andrei, V; Andricek, L; Andrieux, M-L; Anduaga, XS; Anghinolfi, F; Antonaki, A; Antonelli, M; Antonelli, S; Apsimon, R; Arabidze, G; Aracena, I; Arai, Y; Arce, ATH; Archambault, JP; Arguin, J-F; Arik, E; Arik, M; Arms, KE; Armstrong, SR; Arnaud, M; Arnault, C; Artamonov, A; Asai, S; Ask, S

The model, Y ij = μ 1 + β 1 I j + δ ij , defines stability parameters that may be used to describe the performance of a variety over a series of environments. Y ij is the variety mean of the i th variety at the j th environment, µ 1 is the i th variety mean over all environments, β 1 is the regression coefficient that measures the response of the i th variety to varying environments, δ ij is the deviation from regression of the i th variety at the j th environment, and I j is the environmental index. The data from two single‐cross diallels and a set of 3‐way crosses were examined to see whether genetic differences could be detected. Genetic differences among lines were indicated for the regression of the lines on the environmental index with no evidence of nonadditive gene action. The estimates of the squared deviations from regression for many hybrids were near zero, whereas extremely large estimates were obtained for other hybrids.

Research on human aggression has progressed to a point at which a unifying framework is needed. Major domain-limited theories of aggression include cognitive neoassociation, social learning, social interaction, script, and excitation transfer theories. Using the general aggression model (GAM), this review posits cognition, affect, and arousal to mediate the effects of situational and personological variables on aggression. The review also organizes recent theories of the development and persistence of aggressive personality. Personality is conceptualized as a set of stable knowledge structures that individuals use to interpret events in their social world and to guide their behavior. In addition to organizing what is already known about human aggression, this review, using the GAM framework, also serves the heuristic function of suggesting what research is needed to fill in theoretical gaps and can be used to create and test interventions for reducing aggression.

The recent literature concerning the magnetocaloric effect (MCE) has been reviewed. The MCE properties have been compiled and correlations have been made comparing the behaviours of the different families of magnetic materials which exhibit large or unusual MCE values. These families include: the lanthanide (R) Laves phases (RM2, where M = Al, Co and Ni), Gd5(Si1−xGex)4, Mn(As1−xSbx), MnFe(P1−xAsx), La(Fe13−xSix) and their hydrides and the manganites (R1−xMxMnO3, where R = lanthanide and M = Ca, Sr and Ba). The potential for use of these materials in magnetic refrigeration is discussed, including a comparison with Gd as a near room temperature active magnetic regenerator material.

A simple and efficient randomized algorithm is presented for solving single-query path planning problems in high-dimensional configuration spaces. The method works by incrementally building two rapidly-exploring random trees (RRTs) rooted at the start and the goal configurations. The trees each explore space around them and also advance towards each other through, the use of a simple greedy heuristic. Although originally designed to plan motions for a human arm (modeled as a 7-DOF kinematic chain) for the automatic graphic animation of collision-free grasping and manipulation tasks, the algorithm has been successfully applied to a variety of path planning problems. Computed examples include generating collision-free motions for rigid objects in 2D and 3D, and collision-free manipulation motions for a 6-DOF PUMA arm in a 3D workspace. Some basic theoretical analysis is also presented.

SWAT (Soil and Water Assessment Tool) is a comprehensive, semi-distributed river basin model that requires a large number of input parameters, which complicates model parameterization and calibration. Several calibration techniques have been developed for SWAT, including manual calibration procedures and automated procedures using the shuffled complex evolution method and other common methods. In addition, SWAT-CUP was recently developed and provides a decision-making framework that incorporates a semi-automated approach (SUFI2) using both manual and automated calibration and incorporating sensitivity and uncertainty analysis. In SWAT-CUP, users can manually adjust parameters and ranges iteratively between autocalibration runs. Parameter sensitivity analysis helps focus the calibration and uncertainty analysis and is used to provide statistics for goodness-of-fit. The user interaction or manual component of the SWAT-CUP calibration forces the user to obtain a better understanding of the overall hydrologic processes (e.g., baseflow ratios, ET, sediment sources and sinks, crop yields, and nutrient balances) and of parameter sensitivity. It is important for future calibration developments to spatially account for hydrologic processes; improve model run time efficiency; include the impact of uncertainty in the conceptual model, model parameters, and measured variables used in calibration; and assist users in checking for model errors. When calibrating a physically based model like SWAT, it is important to remember that all model input parameters must be kept within a realistic uncertainty range and that no automatic procedure can substitute for actual physical knowledge of the watershed.