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Throughout this book, you will use the WinBUGS (Lunn et al., 2000, 2009) software to work your way through the exercises. Although it is possible to do the exercises using the graphical user interface provided by the WinBUGS package, you can also use the Matlab or R programs to interact with WinBUGS. In this chapter, we start by working through a concrete example using just WinBUGS. This provides an introduction to the WinBUGS interface, and the basic theoretical and practical components involved in Bayesian graphical model analysis. Completing the example will also quickly convince you that you do not want to rely on WinBUGS as your primary means for handling and analyzing data. It is not especially easy to use as a graphical user interface, and does not have all of the data management and visualization features needed for research. Instead, we encourage you to choose either Matlab or R as your primary research computing environment, and use WinBUGS as an “add-on” that does the computational sampling part of analyses. Some WinBUGS interface capabilities will remain useful, especially in the exploratory stages of research. But either Matlab or R will be primary. Matlab and R code for every example in this book, as well as the scripts that implement the models in WinBUGS, are all available at www.bayesmodels.com. This chapter first does a concrete example in WinBUGS, then re-works it in both Matlab and R. You should pay particular attention to the section that features your preferred research software.

We have developed a method for detecting a transgene and its protein product in maize endosperm that allows the kernel to be germinated after analysis. This technique could be highly useful for several monocots and dicots. Our method involves first sampling the endosperm with a hand-held rotary grinder so that the embryo is preserved and capable of germination. This tissue is then serially extracted, first with SDS-PAGE sample buffer to extract proteins, then with an aqueous buffer to extract DNA. The product of the transgene can be detected in the first extract by SDS-PAGE with visualization by total protein staining or immuno-blot detection. The second extract can be purified and used as template DNA in PCR reactions to detect the transgene. This method is particularly useful for screening transgenic kernels in breeding experiments and testing for gene silencing in kernels.

A cultivated oat linkage map was developed using a recombinant inbred population of 136 F6:7lines from the cross 'Ogle' × 'TAM O-301'. A total of 441 marker loci, including 355 restriction fragment length polymorphism (RFLP) markers, 40 amplified fragment length polymorphisms (AFLPs), 22 random amplified polymorphic DNAs (RAPDs), 7 sequence-tagged sites (STSs), 1 simple sequence repeat (SSR), 12 isozyme loci, and 4 discrete morphological traits, was mapped. Fifteen loci remained unlinked, and 426 loci produced 34 linkage groups (with 2–43 loci each) spanning 2049 cM of the oat genome (from 4.2 to 174.0 cM per group). Comparisons with other Avena maps revealed 35 genome regions syntenic between hexaploid maps and 16–34 regions conserved between diploid and hexaploid maps. Those portions of hexaploid oat maps that could be compared were completely conserved. Considerable conservation of diploid genome regions on the hexaploid map also was observed (89–95%); however, at the whole-chromosome level, colinearity was much lower. Comparisons among linkage groups, both within and among Avena mapping populations, revealed several putative homoeologous linkage group sets as well as some linkage groups composed of segments from different homoeologous groups. The relationships between many Avena linkage groups remain uncertain, however, due to incomplete coverage by comparative markers and to complications introduced by genomic duplications and rearrangements.Key words: Avena, linkage map, comparative mapping, homoeology.

The number of days from seedling emergence to flowering (DTF) is a major consideration in sunflower breeding programs. This is a complex trait determined by the genotype, environmental conditions and interactions. Photoperiod and temperature have major effects on DTF and could be important sources of genotype× environment interaction. The objectives of this study were to locate quantitative trait loci (QTLs) associated with growing degree days (GDD) to flowering and photoperiod (PP) response in an elite sunflower population. Two hundred and thirty five F2-generation plants and their F2:3 and F2:4 progenies of a single-cross population of two divergent inbred lines were evaluated in six environments (locations, years and sowing dates) with photoperiods known to elicit a PP response between the inbred lines. Detection of QTLs was facilitated with a genetic linkage map of 205 RFLP loci and composite interval mapping. The 205 restriction fragment length polymorphism (RFLP) loci covered 1380 cM and were arranged in 17 linkage groups, which is the haploid number of chromosomes in this species. The average interval size was 5.9 cM. Six QTLs in linkage groups A, B, F, I, J and L were associated with GDD to flowering and accounted for 76% of the genotypic variation in the mean environment. QTLs in linkage groups A and B accounted for 72% of the genetic variation. QTL×environment (QTL×E) interactions were highly significant for linkage groups A, B, F and J (P

Additive clustering provides a conceptually simple and potentially powerful approach to modeling the similarity relationships between stimuli. The ability of additive clustering models to accommodate similarity data, however, typically arises through the incorporation of large numbers of parameterized clusters. Accordingly, for the purposes of both model generation and model comparison, it is necessary to develop quantitative evaluative measures of additive clustering models that take into account both data-fit and complexity. Using a previously developed probabilistic formulation of additive clustering, the Bayesian Information Criterion is proposed for this role, and its application demonstrated. Limitations inherent in this approach, including the assumption that model complexity is equivalent to cluster cardinality, are discussed. These limitations are addressed by applying the Laplacian approximation of a marginal probability density, from which a measure of cluster structure complexity is derived. Using this measure, a preliminary investigation is made of the various properties of cluster structures that affect additive clustering model complexity. Among other things, these investigations show that, for a fixed number of clusters, a model with a strictly nested cluster structure is the least complicated, while a model with a partitioning cluster structure is the most complicated. Copyright 2001 Academic Press.

Multidimensional scaling models of stimulus domains are widely used as a representational basis for cognitive modeling. These representations associate stimuli with points in a coordinate space that has some predetermined number of dimensions. Although the choice of dimensionality can significantly influence cognitive modeling, it is often made on the basis of unsatisfactory heuristics. To address this problem, a Bayesian approach to dimensionality determination, based on the Bayesian Information Criterion (BIC), is developed using a probabilistic formulation of multidimensional scaling. The BIC approach formalizes the trade-off between data-fit and model complexity implicit in the problem of dimensionality determination and allows for the explicit introduction of information regarding data precision. Monte Carlo simulations are presented that indicate, by using this approach, the determined dimensionality is likely to be accurate if either a significant number of stimuli are considered or a reasonable estimate of precision is available. The approach is demonstrated using an established data set involving the judged pairwise similarities between a set of geometric stimuli. Copyright 2001 Academic Press.

DNA markers were used to identify quantitative trait loci (QTLs) for plant height, ear height, and three flowering traits in hybrid progeny of two generations (F2:3, F6:8) of lines from a Mo17×H99 maize population. For both generations, testcross (TC) progeny were developed by crossing the lines to three inbred testers (B91, A632, B73). The hybrid progeny from the two generations were evaluated at the same locations but in different years as per an early generation testing program. QTLs were identified within each TC population and for mean testcross (MTC) performance. Overall, more QTLs were detected in the F6:8 than the F2:3 generation. Totalled over all five traits, 41 (B91) to 69% (B73) of the QTLs for tester effects and 67% of the QTLs for MTC detected in the F2:3 generation were verified in the F6:8 generation. Although differences in relative rank of the QTL effects across generations were observed, especially for the flowering traits, parental contributions were nearly always consistent. Several (8–11) QTLs were identified with effects for all three tester populations and for all traits except the anthesis-silk interval, which had only two such regions. Over all five traits, previous evaluations in this population identified 26 QTLs with consistent effects for two (F2:3, F6:8) inbred-progeny evaluations, and 20 (77%) were also associated with MTC in at least one of the generations evaluated herein. In all instances of common inbred and TC QTLs, parental contributions were the same.

In their reply, Lecoutre and Killeen (2010) argue for a random effects version of prep, in which the observed effect from one experiment is used to predict the probability that an effect from a different but related experiment will have the same sign. They present a figure giving the impression that this version of prep accurately predicts the probability of replication. We show that their results are incorrect and conceptually limited, even when corrected. We then present a meaningful evaluation of the random effects prep as a predictor and find that, as with the fixed effects prep, it performs very poorly.

We introduce the special issue on formal models of semantic concepts. After outlining the research questions that motivated the issue, we summarize the rich set of data provided by the Leuven Natural Concepts Database, and provide an overview of the seven research articles in the special issue. Each of these articles applies a formal modeling approach to one or more parts of the database, attempting to further our understanding of how people represent and use semantic concepts.

With 2 tables Abstract Foxtail mosaic virus (FoMV) has been reported to have a broad range of hosts, including millet, sorghum, barley, and maize. FoMV-H93, a new strain of FoMV which was isolated from sorghum in 1993, was used to inoculate the Intermated B73 × Mo17 (IBM) syn4 population for quantitative trait loci/locus (QTL) analysis. The parents of the IBM population, B73 and Mo17, are susceptible and resistant, respectively, to this virus isolate. A panel of 94 recombinant inbred lines was used as the mapping population in our study. Eight different QTL responsible for resistance at three different stages on chromosomes 1, 2, 3, 5 and 7 were detected. The QTL provide new resources in both maize and closely related crops such as sorghum for breeding resistant plants.

Rapidly urbanizing regions present watershed managers with a range of challenges, especially when drinking water sources and their watersheds are located within the margins of urban and suburban expansion. These challenges can be acute in those developing countries where land-use regulations and environmental protection laws are inadequate or poorly applied, the latter often a result of the lack of defined institutional responsibilities and coordination. The Los Laureles reservoir and Guacerique watershed that supply 30 percent of Tegucigalpa's drinking water provide a powerful case study of the kinds of natural resource pressures that may lead to water quality and reliability deterioration as urban growth continues. Sedimentation, high turbidity, and high pathogen counts have accompanied decisions to locate projects such as the construction of a major ring-road/highway expansion, military bases and hospitals, and a 10,000 unit public worker housing complex in the watershed. These problems have b...

The number of days from seedling emergence to flowering (DTF) is a major consideration in sunflower (Helianthus annuus L.) breeding because the maximum yield of the crop can only be achieved if the cultivars are phenologically adapted to the production environment. Identification of genetic factors that affect flowering could create opportunities for improved breeding methods and for more fundamental investigations of this important trait and its interactions with the environment. The objectives of this study were to locate quantitative trait loci (QTL) for DTF in an elite sunflower population evaluated in four environments. Two hundred thirty-five F2-generation plants and their F3 progeny of a single-cross population of two divergent inbred lines were evaluated in four environments (Fargo, ND and Venado Tuerto, Daireaux, and Balcarce in Argentina). Detection of QTL was facilitated with a genetic linkage map of 205 loci defined by restriction fragment length polymorphism (RFLP) and composite interval mapping. Five QTL of five linkage groups accounted for 89% of the genetic variation for DTF. Gene action was additive at four QTL and dominant at the other locus. Three QTL were detected in all environments and generations. The parental effects and the relative magnitudes of the genetic effects of those QTL were consistent across generations and environments. Fil: Leon, A. J.. Zeneca Semillas; Argentina Fil: Andrade, Fernando Héctor. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina Fil: Lee, M.. Iowa State University; Estados Unidos

Most complex quantitative traits in maize (Zea mays L.), especially grain yield, display low correlations between the trait values observed in inbred and hybrid progeny. Comparisons of quantitative trait loci (QTL) controlling inbred per se and hybrid performance are needed to understand the underlying genetic factors, and to determine the utility of QTL detected in the two progeny types. DNA markers were used to identify QTL for grain yield and grain moisture in hybrid progeny of F 2:3 and F 6:8 lines from a Mo17xH99 population. For both generations, testcross progeny were developed by crossing the lines to three inbred testers (B91, A632, B73). Each testcross population was evaluated in field trials with two replications in eight environments. The testcross progeny from the two generations were evaluated at the same locations but in different years. QTL were identified within each testcross population and for mean testcross (MTC) performance. Individual tester QTL effects were not consistent in rank or detection across generations; however, parental contributions were consistent. MTC effects were more consistent across generations with most of the QTL with large effects being detected across generations. QTL detected with only one tester were not necessarily detected for the other two testers, especially for grain yield, but parental contributions were consistent when QTL were detected in a region for more than one tester. The QTL for grain yield identified in this population for inbred and hybrid progeny show only partial correspondence, indicating that marker-assisted selection programs would need to identify and incorporate QTL for both progeny types.

DNA markers are being increasingly utilized in cultivar development, quality control of seed production, measurement of genetic diversity for conservation management, varietal identity, and to assist in maintenance of intellectual property protection (IPP). The use of simple sequence repeats (SSRs) for variety profiling can provide high discrimination, with excellent reproducibility at less cost than for restriction fragment length polymorphisms (RFLPs). The objective of this study was to evaluate the potential utility of SSR technology for applications in research, product development, seed production, and genetic resource conservation management for sorghum. Fifty genetically diverse elite sorghum [Sorghum bicolor (L.) Moench] inbreds were used to compare the discrimination abilities of 15 SSR primers with 104 RFLPs and to compare the associations among lines revealed by these molecular data and by pedigrees. RFLP data allowed all lines to be uniquely identified; two lines could not be distinguished by the SSR data. The mean polymorphism information content (PIC) values were 0.62 (RFLPs) and 0.58 (SSRs). Correlations for pairwise molecular profile distances with pedigree distances among the maintainer female (B) lines were 0.52 and 0.53 for RFLP and SSR data, respectively; data for the male parental restorer (R) lines were 0.41 and 0.47. This set of SSRs could be used to help genetic conservation management and to support IPP. Data from additional SSRs that collectively cover more of the genome will be required for applications to assist in breeding.

This is the second of two papers comparing connectionist and traditional stochastic latency mechanisms with respect to their ability to account for simple judgments. In the first, we reviewed evidence for a self-regulating accumulator module for two- and three-category discrimination. In this paper, we examine established neural network models that have been applied to predicting response time measures, and discuss their representational and adaptational limitations. We go on to describe and evaluate the network implementation of a Parallel Adaptive Generalized Accumulator Network (PAGAN), based on the interconnection of a number of self-regulating, generalized accumulator modules. The enhancement of PAGAN through the incorporation of distributed connectionist representation is briefly discussed.

The effects of breeding on allele frequency changes at 82 restriction fragment length polymorphism (RFLP) loci were examined in two maize (Zea mays L.) populations undergoing reciprocal recurrent selection, Iowa Stiff Stalk Synthetic and Iowa Corn Borer Synthetic #1. After 12 cycles of selection, approximately 30% of the alleles were extinct and 10% near fixation in each population. A test of selective neutrality identified several loci in each population whose allele frequency changes cannot be explained by genetic drift; interpopulation mean expected heterozygosity increased for that subset of 28 loci but not for the remaining 54 loci. Mean expected heterozygosity within the two subpopulations decreased 39%, while the between-population component of genetic variation increased from 0.5% to 33.4% of the total. Effective population size is a key parameter for discerning allele frequency changes due to genetic drift versus those resulting from selection and genetic hitchhiking. Empirical estimates of effective population size for each population were within the range predicted by the breeding method.

Release of an estimated 150,000 gallons of 1,2-dichloroethane (EDC) from a buried pipeline into a ditch and surrounding soil resulted in shallow subsurface contamination of a Gulf Coast site. Short-term remediation included removal of EDC DNAPL (dense nonaqueous phase liquid) by dredging and vacuuming the ditch, and by dredging the river where the ditch discharged. EDC saturation in shallow impacted sediments located beneath the ditch was at or below residual saturation and these sediments were therefore left in place. The ditch was lined, backfilled, and capped. Long-term remediation includes EDC DNAPL recovery and hydraulic containment from the shallow zone with long-term monitoring of the shallow, intermediate, and deep aquifers. Ground water, DNAPL, and dissolved phase models were used to guide field investigations and the selection of an effective remedial action strategy. The DNAPL modeling was conducted for a two-dimensional vertical cross section of the site, and included the three aquifers separated by two aquitards with microfractures. These aquitards were modeled using a dual porosity approach. Matrix and fracture properties of the aquitards used for DNAPL modeling were determined from small-scale laboratory properties. These properties were consistent with effective hydraulic conductivity determined from ground water flow modeling. A sensitivity analysis demonstratedmore » that the vertical migration of EDC was attenuated by dissolution of EDC into the matrix of the upper aquitard. When the organic/water entry pressure of the aquitard matrix, or the solubility of EDC were decreased to unrealistically low values, EDC DNAPL accumulated in the aquifer below the upper aquitard. EDC DNAPL did not reach the regional (deepest) aquifer in any of the cases modeled. The limited extent of vertical EDC migration predicted is supported by ground water monitoring conducted over the four years since the spill.« less

A release of 1,2-dichloroethane, also known as ethylene dichloride (EDC), resulted in shallow subsurface free-phase contamination of a Gulf Coast site in the southern US. The site stratigraphy consists primarily of a low permeability, surficial peat, silt, and clay zone underlain by fractured clay; a confined 12 m deep sand ground water flow zone; a confined 21 m deep fine sand zone of limited ground water flow, followed by a deep aquitard. The Gumbo clay and sandy clay aquitard below the release area overlies and protects the 61 m deep Upper Chicot Aquifer, which is a confined regional aquifer. An ongoing recovery and hydraulic containment program from the primary impacted and laterally and vertically restricted shallow 40-foot sand zone has effectively recovered dense nonaqueous phase liquid (DNAPL) and contained dissolved phase EDC. Natural attenuation of EDC was demonstrated through (1) a laboratory microcosm study substantiating the ability of the native microbial population in the deeper aquifer to degrade EDC under anaerobic environmental conditions found at the site, (2) field investigations showing reductions in EDC concentrations over time in many of the wells on site, and (3) an evaluation of the ground water for EDC and its degradation products and othermore » geochemical parameters such as dissolved oxygen, redox potential, and pH. Degradation products of EDC found in the field investigations included 2-chloroethanol, ethanol, ethene, and ethane. Dissolved EDC concentrations in selected wells between the first recorded samples and the fourth quarter of 1997 ranged from greater than 4% to 99% reductions. First-order exponential decay half-lives ranged from 0.21 to 4.2 years for wells showing decreases in EDC concentrations over time. Elevated methane concentrators indicated carbon dioxide to be the major terminal electron acceptor.« less

Additive clustering provides a conceptually simple similarity model which is, nevertheless, capable of accommodating arbitrary similarity structures. The discrete nature of the clusters, coupled with the general flexibility of the model, however, means that the derivation of additive clustering models from given similarity data is difficult. After reviewing a number of previously developed algorithms, a new two stage algorithm for generating additive cluster models is developed. In the first stage, an extraction process generates a manageable number of candidate clusters which, in the second stage, are subject to a regularization process. The number of clusters included in the derived model is controlled by a parameter specifying the target level of variance to be accounted for by the final model. Several applications of the proposed algorithm are presented, including three involving previously examined data sets that facilitate an evaluation of performance relative to several other algorithms. It is argued that the proposed algorithm exhibits comparable performance in relation to these previous algorithms, and has the advantage of being developed within a framework that potentially allows the optimization of the tradeoff between goodness-of-fit and model parsimony.

This study identified and purified specific isoamylase- and pullulanase-type starch-debranching enzymes (DBEs) present in developing maize (Zea mays L.) endosperm. The cDNA clone Zpu1 was isolated based on its homology with a rice (Oryza sativaL.) cDNA coding for a pullulanase-type DBE. Comparison of the protein product, ZPU1, with 18 other DBEs identified motifs common to both isoamylase- and pullulanase-type enzymes, as well as class-specific sequence blocks. Hybridization of Zpu1 to genomic DNA defined a single-copy gene, zpu1, located on chromosome 2. Zpu1 mRNA was abundant in endosperm throughout starch biosynthesis, but was not detected in the leaf or the root. Anti-ZPU1 antiserum specifically recognized the approximately 100-kD ZPU1 protein in developing endosperm, but not in leaves. Pullulanase- and isoamylase-type DBEs were purified from extracts of developing maize kernels. The pullulanase-type activity was identified as ZPU1 and the isoamylase-type activity as SU1. Mutations of thesugary1 (su1) gene are known to cause deficiencies of SU1 isoamylase and a pullulanase-type DBE. ZPU1 activity, protein level, and electrophoretic mobility were altered insu1-mutant kernels, indicating that it is the affected pullulanase-type DBE. The Zpu1 transcript levels were equivalent in nonmutant and su1-mutant kernels, suggesting that coordinated regulation of ZPU1 and SU1 occurs posttranscriptionally.

The common neural network modeling practice of representing the elements of a task domain in terms of a set of features lacks justification if the features are derived through some form of ad hoc preabstraction. By examining a featural similarity model related to established multidimensional scaling techniques, a neural network is developed that generates features from similarity data and attaches weights to these features. The network performs a constrained search of a continuous solution space to determine the features and uses a previously developed regularization technique to minimize the number of features it derives. The network is demonstrated on artificial data, from which it recovers known features and weights, and on two real data sets involving the similarity of a set of geometric shapes and the abstract conceptual similarities of the 10 Arabic numerals. On the basis of these results, the relationship between the multidimensional scaling approach adopted by the network and an alternative additive clustering approach to feature extraction is discussed.

The Halstead-Reitan Trail Making Test (TMT) is one of the most widely used neuropsychological instruments for the assessment of brain damage. Despite its usefulness, however, the TMT has two major disadvantages. It has not been constructed in a principled manner that would facilitate systematic investigation, and there is no established procedure for generating equivalent, but stochastically different, test forms. The reason is that the generation of self-avoiding TMT pathways resembles the finding of near-optimal solutions to the Euclidean Traveling Salesman Problem (TSP) and constitutes a computational problem that is NP-complete. This article describes a practical approach to the problem of generating stochastically different test forms. This approach employs anelastic net neural network to generate TMT forms based on self-avoiding, near-optimal paths, and closed circuits. The usefulness and limitations of this solution are discussed briefly in relation to alternative and complementary problems and procedures.

Grain yield is the primary trait of interest in maize (Zea mays L.) breeding programs, but its evaluation is complicated by genetic heterogeneity, a complex biological basis, and genotype × environment interactions. Genetic mapping studies of grain yield and yield components, with common sets of DNA marker loci and different populations evaluated across a range of environments, might identify regions of the genome associated with more or less consistent effects in different genetic and environmental contexts. Our objective was to evaluate the consistency of quantitative trait loci (QTL) detection for grain yield and four yield components in maize across stress and nonstress environments. One hundred eighty-five F 6:7 lines from a cross between inbred lines Mo17 and H99 were evaluated in two climatically diverse years at the same location. The stress environment was characterized by cool, wet conditions and a 56% reduction in grain yield relative to the nonstress environment. Over all five traits, 59 QTL were detected in at least one of the two environments with 10 being detected in both environments. Thirty-two (54%) of the QTL were detected in the mean environment, and an additional eight QTL were detected in the mean that were not detected in either of the individual environments. Comparison of the F 6:7 mean environment QTL with the mean environment (same location, different years) results from the F 2:3 generation of the same population revealed 13 of 40 QTL detected in the F 2:3 were verified in the F 6:7 generation. Little evidence of cross-over type QTL interactions was observed, and QTL × environment interactions seem to be in the form of change in magnitude of effects.

This is the first of two papers comparing connectionist and traditional stochastic latency mechanisms with respect to their ability to account for simple judgments. In this paper, we show how the need to account for additional features of judgment has led to the formulation of progressively more sophisticated models. One of these, a self-regulating, generalized accumulator process, is treated in detail, and its simulated performance across a sample of tasks is described. Since an adaptive decision module of this kind possesses all the ingredients of intelligent behavior, it is eminently suited as a basic computing element in more complex networks.

Although ocular lymphoproliferative diseases may be rarely encountered by dermatopathologists, the frequency may increase particularly as more and more subspecialties rely on dermatopathology services. Emerging data suggest that there are some similarities between ocular and cutaneous lymphoproliferative diseases with respect to their clinical behavior, prognosis, and cytogenetics. In this case report, a patient with ocular follicle center lymphoma who subsequently developed ocular reactive lymphoid hyperplasia is presented with an accompanying review of the literature on the subjects. The encounter of both follicular center lymphoma and reactive lymphoid hyperplasia in the same patient provides a rare opportunity to compare and contrast the clinical, histological, and immunohistochemical findings of the respective lymphoproliferative diseases situated at opposite ends of the spectrum.

We develop a cognitive modeling approach, motivated by classic theories of knowledge representation and judgment from psychology, for combining people's rankings of items. The model makes simple assumptions about how individual differences in knowledge lead to observed ranking data in behavioral tasks. We implement the cognitive model as a Bayesian graphical model, and use computational sampling to infer an aggregate ranking and measures of the individual expertise. Applications of the model to 23 data sets, dealing with general knowledge and prediction tasks, show that the model performs well in producing an aggregate ranking that is often close to the ground truth and, as in the "wisdom of the crowd" effect, usually performs better than most of individuals. We also present some evidence that the model outperforms the traditional statistical Borda count method, and that the model is able to infer people's relative expertise surprisingly well without knowing the ground truth. We discuss the advantages of the cognitive modeling approach to combining ranking data, and in wisdom of the crowd research generally, as well as highlighting a number of potential directions for future model development. © 2014 Lee et al.

We study how people terminate their search for information when making decisions in a changing environment. In 3 experiments, differing in the cost of search, participants made a sequence of 2-alternative decisions, based on the information provided by binary cues they could search. Whether limited or extensive search was required to maintain accurate decisions changed across the course of the experiment, but was not indicated to participants. We find large individual differences but that, in general, the extent of search is changed in response to environmental change, and is not necessarily triggered by a reduction in accuracy. We then examine the ability of 4 models to account for individual participant behavior, using a generalization measure that tests model predictions. Two of the models use reinforcement learning, and differ in whether they use error or both error and effort signals to control how many cues are searched. The other 2 models use sequential sampling processes, and differ in the regulatory mechanisms they use to adjust the decision thresholds that control the extent of search. We find that error-based reinforcement learning is usually an inadequate account of behavior, especially when search is costly. We also find evidence in the model predictions for the use of confidence as a regulatory variable. This provides an alternative theoretical approach to balancing error and effort, and highlights the possibility of hierarchical regulatory mechanisms that lead to delayed and abrupt changes in the extent of search.

The application of connectionist learning procedures to the development of psychological internal representations requires a constraining theory of mental structure. The psychological space construct is advanced for this role and, consequently, a connectionist network which learns the multi-dimensionally scaled representations of a set of stimuli is developed. The model assumes that the function relating similarity to distance in psychological space is an exponential decay function, operates under the family of Minkowskian metrics and is able to determine the appropriate dimensionality of the psychological spaces it derives. The model is demonstrated on both separable and integral stimuli, and the validity of its application of gradient descent optimization principles over the city-block metric is examined. Several modelling extensions are discussed, including means by which the model might learn more general psychophysical mappings, and be able to derive internally the measures of psychological similarit...

Objectives: To determine long-term results of patients who underwent primary ligament repair and delayed reconstruction for lateral ligament instability. Design: Retrospective. Setting: Outpatient clinic. Patients/Participants: Patients who had undergone acute repair or delayed reconstruction at this institution between 1958 and 1977, excluding patients who were deceased or who could not be located. Intervention: Forty-eight patients (fifty-three ankles) underwent twenty-two primary ligament repairs and thirty-one delayed reconstruction operations. Main Outcome Measurements: Clinical results graded with clinical scale and radiologic results based on stress radiographs and plain film radiographs. Results: At an average of twenty years after operation (range 12 to 33 years), patients were satisfied with forty-nine ankles, satisfied with reservations with two ankles, and dissatisfied with two ankles. Clinical results after repair were excellent in twenty ankles, good in one, fair in none, and poor in one. After reconstruction, the results were excellent in twenty-one ankles, good in six, fair in one, and poor in three. In the primary repair group, the mean talar tilt with stress testing improved from 20.7 ± 10.7 degrees before operation to 2.8 ± 3.0 degrees after operation. In the reconstruction group, the mean talar tilt improved from 20.7 ± 8.4 degrees before operation to 2.8 ± 3.5 degrees after operation. Conclusions: Clinical and radiologic results were similar in the repair and reconstruction groups. The majority of severe (Grade III) ankle sprains may be treated nonoperatively, but if residual instability occurs, late reconstruction should achieve satisfactory results.

Stress radiography was performed on 21 patients with unilateral posterior cruciate ligament tears: 10 com plete and 11 partial. An 89-N posterior load was ap plied to the proximal tibia and a lateral radiograph was taken of each knee in 70° of flexion. The relative amount of sagittal translation (involved minus nonin volved) was determined at both the medial and lateral tibial plateaus from the radiographic films. Arthrometric (KT-1000 arthrometer) and posterior drawer tests were also performed. The mean relative posterior translation averaged 12.2 ± 3.7 mm for knees with complete tears. Arthrometer testing of the same knees showed 7.6 ± 2.5 mm of increased translation, and posterior drawer testing showed 9.2 ± 3.3 mm of increased dropback. Stress radiographic results were statistically similar to the electrogoniometric measurements in ca daveric knees. In knees with a partially torn posterior cruciate ligament, mean relative translation measured on stress radiographs was 5.6 ± 1.5 mm, which was significantly different from that for knees with complete ruptures. The arthrometer and posterior drawer test data were not significantly different for knees with com plete and partial tears. Stress radiography is superior to both the arthrometer and clinical posterior drawer testing for determining posterior cruciate ligament sta tus. Eight millimeters or more of increased posterior translation on stress radiographs is indicative of com plete rupture.

Oat (Avena sativa L.) genotypes differ in their patterns of growth and development in response to vernalization (cold temperatures applied to germinating seeds). Genomic regions controlling vernalization response in heading date, plant height, and tiller number were mapped in a recombinant inbred (RI) population derived from the cross of oat cultivars 'Kanota' (vernalization-responsive) and 'Ogle' (vernalization-insensitive). Seventy-one F6-derived RI lines were subjected to vernalization and no-vernalization treatments, and then grown in growth chambers. A genetic linkage map of 561 (primarily RFLP) loci was used to identify quantitative trait loci (QTLs) affecting the traits in vernalized and non-vernalized plants. Nine to 16 linkage groups and unlinked loci were associated with each trait assessed herein. Individual loci explained up to 37% of the phenotypic variation. Three to five significant loci were included in multiple locus linear models which explained up to 66% of phenotypic variation for each trait. One to 14 interactions between loci were found for each trait. The interactions explained up to 30% of the phenotypic variation not accounted for by the main effects of loci involved in the interactions. Inclusion of epistatic interactions tended to improve the fit of multiple locus models. As much as 83% of phenotypic variation was explained by multiple locus models including epistasis. Numerous epistatic interactions involving at least one locus with no significant main effect were detected.

The utility of restriction fragment length polymorphisms (RFLPs) in mapping quantitative trait loci (QTL) has been established in elite maize (Zea mays L.) populations, hut the ability to consistently detect QTL in diverse environments has not been assessed. QTL mapping studies conducted in diverse environments could be a means of locating genes which respond to stress conditions and could provide further understanding of some types of genotype × environment interaction. Our objectives were to investigate the ability to detect QTL for flowering and plant stature traits in two diverse environments and to assess the genetic relationship of QTL for correlated traits. A single-cross of elite inbreds Mo17 and H99 was used to produce a population of 150 F₂:₃ lines. Traits were measured on replicated progeny grown in two climatically diverse years at the same location, in which one year was an average environment, and the other year was a stress environment. QTL determinations were made in each environment and the mean of the two environments by using a linkage map of 111 loci. About 50% of all QTL were detected in both environments. The location and parental contribution of these QTL were consistent, hut their effects varied in size. More QTL were identified in the stress environment for anthesis and silk emergence, but the other traits had equivalent numbers of QTL detected in each environment. All QTL identified in the nonstress environment and all QTL identified in the stress environment were also detected in the mean environment. Correlations between traits were generally reflected in the similarity of locations and parental contributions of QTL for these traits. The exception was anthesis and anthesis-to-silking interval, which had QTL in common but very poor correlation. The locus of a probe for an1, a plant height mutant, was most closely associated with the QTL having the largest effect on plant height. This finding contributes to the supposition that quantitatively and qualitatively inherited traits share a common set of loci with alleles of varying magnitude of effects. Journal Paper no. J-16059 of the Iowa Agric. and Home Economics Exp. Stn. Project 3134.

The utility of restriction fragment length polymorphisms (RFLPs) in detecting quantitative trait loci (QTL) in maize (Zea mays L.) populations has been established. Conflicting results have been reported on the ability to consistently detect the same QTL across environments. Grain yield is considered to be highly polygenic and strongly influenced by the environment. QTL mapping studies conducted in contrasting environments might increase our understanding genotype x environment interactions and improve selection response in maize breeding. Our objectives were to compare the QTL for grain yield and yield components detected in two diverse environments in an elite, adapted maize population and to investigate the relationship among the genetic factors controlling these traits. A population of 150 F 2:3 lines was produced from the cross of elite inbreds Mo17 and H99. The lines per se were evaluated for 2 yr at the same location. The first year had relatively average growing conditions, but the second year with cool, wet growing conditions provided a stress environment. Grain yield and yield components were measured on replicated progeny each year. By using a linkage map of 111 loci, QTL determinations were made in the two environments and in the mean of the two environments. About 50% of all QTL detected across environments were detected in both environments. These QTL were consistent in the magnitude of their effects and parental contribution. Determinations of QTL in the mean of the two environments were most informative in that 74% of all QTL and 82% of the QTL detected in each of the individual environments were identified in the mean environment. Most QTL identified regions associated with two or more yield components in a manner consistent with correlations among traits and parents phenotypes.

This study was conducted to compare maize quantitative trait loci (QTL) detection for grain yield and yield components in F2∶3 and F6∶7 recombinant inbred (RI) lines from the same population. One hundred and eighty-six F6∶7 RIs from a Mo17×H99 population were grown in a replicated field experiment and analyzed at 101 loci detected by restriction fragment length polymorphisms (RFLPs). Single-factor analysis of variance was conducted for each locus-trait combination to identify QTL. For grain yield, 6 QTL were detected accounting for 22% of the phenotypic variation. A total of 63 QTL were identified for the seven grain yield components with alleles from both parents contributing to increased trait values. Several genetic regions were associated with more than one trait, indicating possible linked and/or pleiotropic effects. In a comparison with 150 F2∶3 lines from the same population, the same genetic regions and parental effects were detected across generations despite being evaluated under diverse environmental conditions. Some of the QTL detected in the F2∶3 seem to be dissected into multiple, linked QTL in the F6∶7 generation, indicating better genetic resolution for QTL detection with RIs. Also, genetic effects at QTL are smaller in the F6∶7 generation for all traits.

The scale-invariant memory, perception, and learning (SIMPLE) model developed by Brown, Neath, and Chater (2007) formalizes the theoretical idea that scale invariance is an important organizing principle across numerous cognitive domains and has made an influential contribution to the literature dealing with modeling human memory. In the context of free recall data, however, there is a previously unreported conceptual error in the specification of the SIMPLE model. We show that the error matters not only in theory but also in practice by reapplying the corrected SIMPLE model to the benchmark data reported by Murdock (1962). The corrected model makes different predictions about serial position curves, shows better fit to the Murdock (1962) data, and infers different parameters that require substantively different psychological interpretation.

In most decision-making situations, there is a plethora of information potentially available to people. Deciding what information to gather and what to ignore is no small feat. How do decision makers determine in what sequence to collect information and when to stop? In two experiments, we administered a version of the German cities task developed by Gigerenzer and Goldstein (1996), in which participants had to decide which of two cities had the larger population. Decision makers were not provided with the names of the cities, but they were able to collect different kinds of cues for both response alternatives (e.g., “Does this city have a university?”) before making a decision. Our experiments differed in whether participants were free to determine the number of cues they examined. We demonstrate that a novel model, using hierarchical latent mixtures and Bayesian inference (Lee & Newell, 2011) provides a more complete description of the data from both experiments than simple conventional strategies, such as the take–the–best or the Weighted Additive heuristics.

A detailed linkage map of Helianthus annuus was constructed based on segregation at 234 RFLP loci, detected by 213 probes, in an F2 population of 289 individuals (derived from a cross between the inbred lines HA89 and ZENB8). The genetic markers covered 1380 centiMorgans (cM) of the sunflower genome and were aranged in 17 linkage groups, corresponding to the haploid number of chromosomes in this species. One locus was found to be unlinked. Although the average interval size was 5.9 cM, there were a number of regions larger than 20 cM that were devoid of markers. Genotypic classes at 23 loci deviated significantly from the expected ratios (1∶2∶1 or 3∶1), all showing a reduction in the ZENB8 homozygous class. The majority of these loci were found to map to four regions on linkage groups G, L and P.

A molecular linkage map of cultivated oat composed of 561 loci has been developed using 71 recombinant inbred lines from a cross between Avena byzantina cv. Kanota and A. sativa cv. Ogle. The loci are mainly restriction fragment length polymorphisms detected by oat cDNA clones from leaf, endosperm, and root tissue, as well as by barley leaf cDNA clones. The loci form 38 linkage groups ranging in size from 0.0 to 122.1 cM (mean, 39 cM) and consist of 2–51 loci each (mean, 14). Twenty-nine loci remain unlinked. The current map size is 1482 cM and the total size, on the basis of the number of unlinked loci, is estimated to be 2932.0 cM. This indicates that this map covers at least 50% of the cultivated oat genome. Comparisons with an A-genome diploid oat map and between linkage groups exhibiting homoeology to each other indicate that several major chromosomal rearrangements exist in cultivated oat. This map provides a tool for marker-assisted selection, quantitative trait loci analyses, and studies of genome organization in oat.Key words: Avena, restriction fragment length polymorphism, linkage map, polyploidy, genome evolution.

Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16 h, 18°C/8 h) and optimum temperature (28°C/24 h) between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM) were umc1303 (265.1 cM) on chromosome 4, umc1 (246.4 cM) on chromosome 5, umc62 (459.1 cM) on chromosome 6, bnl14.28a (477.4 cM) on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org). Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.