Express: a web-based technology to support human and computational experimentation

Experimental cognitive psychology has been greatly assisted by the development of general computer-based experiment presentation packages. Typically, however, such packages provide little support for running participants on different computers. It is left to the experimenter to ensure that group sizes are balanced between conditions and to merge data gathered on different computers once the experiment is complete. Equivalent issues arise in the evaluation of parameterized computational models, where it is frequently necessary to test a model's behavior over a range of parameter values (which amount to between-subjects factors) and where such testing can be speeded up significantly by the use of multiple processors. This article describes Express, a Web-based technology for coordinating "clients" (human participants or computational models) and collating client data. The technology provides an experiment design editor, client coordination facilities (e.g., automated randomized assignment of clients to groups so that group sizes are balanced), general data collation and tabulation facilities, a range of basic statistical functions (which are constrained by the specified experimental design), and facilities to export data to standard statistical packages (such as SPSS). We report case studies demonstrating the utility of Express in both human and computational experiments. Express may be freely downloaded from the Express Web site (http://express.psyc.bbk.ac.uk/)

Statistics of Lead Changes in Popularity-Driven Systems

We study statistical properties of the highest degree, or most popular, nodes in growing networks. We show that the number of lead changes increases logarithmically with network size N, independent of the details of the growth mechanism. The probability that the first node retains the lead approaches a finite constant for popularity-driven growth, and decays as N^{-phi}(ln N)^{-1/2}, with phi=0.08607..., for growth with no popularity bias.Comment: 4 pages, 4 figures, 2 column revtex format. Minor changes in response to referee comments. For publication in PR

The investigation of time dependent flame structure by ionization probes

Ionization probes were used to measure mean ionization current and frequency spectra, auto-correlations and cross-correlations in jet flames with variation in the initial Reynolds numbers and equivalence ratios. Special attention was paid to the transitional region between the burner exit plane and the plane of onset of turbulence

Detailed investigation of a vaporising fuel spray. Part 1: Experimental investigation of time averaged spray

A laser tomographic light scattering technique provides rapid and accurate high resolution measurements of droplet sizes, concentrations, and vaporization. Measurements using a computer interfaced thermocouple are presented and it is found that the potential exists for separating gas and liquid temperature measurements and diagnosing local spray density by in situ analysis of the response characteristics of the thermocouple. The thermocouple technique provides a convenient means for measuring mean gas velocity in both hot and cold two phase flows. The experimental spray is axisymmetric and has carefully controlled initial and boundary conditions. The flow is designed to give relatively insignificant transfer of momentum and mass from spray to air flow. The effects of (1) size-dependent droplet dispersion by the turbulence, (2) the initial spatial segregation of droplet sizes during atomization, and (3) the interaction between droplets and coherent large eddies are diagnosed

Redox regulation of type-I inositol trisphosphate receptors in intact mammalian cells.

A sensitization of inositol 1,4,5-trisphosphate receptor (IP3R)-mediated Ca2+ release is associated with oxidative stress in multiple cell types. These effects are thought to be mediated by alterations in the redox state of critical thiols in the IP3R, but this has not been directly demonstrated in intact cells. Here, we utilized a combination of gel-shift assays with MPEG-maleimides and LC-MS/MS to monitor the redox state of recombinant IP3R1 expressed in HEK293 cells. We found that under basal conditions, ∼5 of the 60 cysteines are oxidized in IP3R1. Cell treatment with 50 μm thimerosal altered gel shifts, indicating oxidation of ∼20 cysteines. By contrast, the shifts induced by 0.5 mm H2O2 or other oxidants were much smaller. Monitoring of biotin-maleimide attachment to IP3R1 by LC-MS/MS with 71% coverage of the receptor sequence revealed modification of two cytosolic (Cys-292 and Cys-1415) and two intraluminal cysteines (Cys-2496 and Cys-2533) under basal conditions. The thimerosal treatment modified an additional eleven cysteines, but only three (Cys-206, Cys-767, and Cys-1459) were consistently oxidized in multiple experiments. H2O2 also oxidized Cys-206 and additionally oxidized two residues not modified by thimerosal (Cys-214 and Cys-1397). Potentiation of IP3R channel function by oxidants was measured with cysteine variants transfected into a HEK293 IP3R triple-knockout cell line, indicating that the functionally relevant redox-sensitive cysteines are predominantly clustered within the N-terminal suppressor domain of IP3R. To our knowledge, this study is the first that has used proteomic methods to assess the redox state of individual thiols in IP3R in intact cells. © 2018 Joseph et al

Operative strategy for fistula-in-ano without division of the anal sphincter

We would like to thank Mr ER MacDonald for his contribution in data collection during the early years of the study. The material in this paper was presented as a poster at the annual meeting of the American Society of Colon and Rectal Surgeons held in Vancouver, Canada, May 2011.Peer reviewedPublisher PD

The simulation of action disorganisation in complex activities of daily living

Action selection in everyday goal-directed tasks of moderate complexity is known to be subject to breakdown following extensive frontal brain injury. A model of action selection in such tasks is presented and used to explore three hypotheses concerning the origins of action disorganisation: that it is a consequence of reduced top-down excitation within a hierarchical action schema network coupled with increased bottom-up triggering of schemas from environmental sources, that it is a more general disturbance of schema activation modelled by excessive noise in the schema network, and that it results from a general disturbance of the triggering of schemas by object representations. Results suggest that the action disorganisation syndrome is best accounted for by a general disturbance to schema activation, while altering the balance between top-down and bottom-up activation provides an account of a related disorder - utilisation behaviour. It is further suggested that ideational apraxia (which may result from lesions to left temporoparietal areas and which has similar behavioural consequences to action disorganisation syndrome on tasks of moderate complexity) is a consequence of a generalised disturbance of the triggering of schemas by object representations. Several predictions regarding differences between action disorganisation syndrome and ideational apraxia that follow from this interpretation are detailed

Who's afraid of the big bad wolf: a prospective paradigm to test Rachman's indirect pathways in children

Rachman's theory [The conditioning theory of fear insition: a critical examination. Behav. Res. Ther. 15 (1977) 375–387] of fear acquisition suggests that fears and phobias can be acquired through three pathways: direct conditioning, vicarious learning and information/instruction. Although retrospective studies have provided some evidence for these pathways in the development of phobias during childhood [see King, Gullone, & Ollendick, Etiology of childhood phobias: current status of Rachman's three pathway's theory. Behav. Res. Ther. 36 (1998) 297–309 for a review], these studies have relied on long-term past memories of adult phobics or their parents. The current study was aimed towards developing a paradigm in which the plausibility of Rachman's indirect pathways could be investigated prospectively. In Experiment 1, children aged between 7 and 9 were presented with two types of information about novel stimuli (two monsters): video information and verbal information in the form of a story. Fear-related beliefs about the monsters changed significantly as a result of verbal information but not video information. Having established an operational paradigm, Experiment 2 looked at whether the source of verbal information had an effect on changes in fear-beliefs. Using the same paradigm, information about the monsters was provided by either a teacher, an adult stranger or a peer, or no information was given. Again, verbal information significantly changed fear-beliefs, but only when the information came from an adult. The role of information in the acquisition of fear and maintenance of avoidant behaviour is discussed with reference to modern conditioning theories of fear acquisition

Critical and Near-Critical Branching Processes

Scale-free dynamics in physical and biological systems can arise from a variety of causes. Here, we explore a branching process which leads to such dynamics. We find conditions for the appearance of power laws and study quantitatively what happens to these power laws when such conditions are violated. From a branching process model, we predict the behavior of two systems which seem to exhibit near scale-free behavior--rank-frequency distributions of number of subtaxa in biology, and abundance distributions of genotypes in an artificial life system. In the light of these, we discuss distributions of avalanche sizes in the Bak-Tang-Wiesenfeld sandpile model.Comment: 9 pages LaTex with 10 PS figures. v.1 of this paper contains results from non-critical sandpile simulations that were excised from the published versio

Virus-induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana

Virus-induced gene silencing (VIGS) is an important forward and reverse genetics method for the study of gene function in many plant species, especially Nicotiana benthamiana. However, despite the widespread use of VIGS, a searchable database compiling the phenotypes observed with this method is lacking. Such a database would allow researchers to know the phenotype associated with the silencing of a large number of individual genes without experimentation. We have developed a VIGS phenomics and functional genomics database (VPGD) that has DNA sequence information derived from over 4,000 N. benthamiana VIGS clones along with the associated silencing phenotype for approximately 1,300 genes. The VPGD has a built-in BLAST search feature that provides silencing phenotype information of specific genes. In addition, a keyword-based search function could be used to find a specific phenotype of interest with the corresponding gene, including its Gene Ontology descriptions. Query gene sequences from other plant species that have not been used for VIGS can also be searched for their homologs and silencing phenotype in N. benthamiana. VPGD is useful for identifying gene function not only in N. benthamiana but also in related Solanaceae plants such as tomato and potato. The database is accessible at http://vigs.noble.org.Noble Research Institute and NSF IOS-102564