Predicting Combinatorial Binding of Transcription Factors to Regulatory Elements in the Human Genome by Association Rule Mining

Cis-acting transcriptional regulatory elements in mammalian genomes typically contain specific combinations of binding sites for various transcription factors. Although some cisregulatory elements have been well studied, the combinations of transcription factors that regulate normal expression levels for the vast majority of the 20,000 genes in the human genome are unknown. We hypothesized that it should be possible to discover transcription factor combinations that regulate gene expression in concert by identifying over-represented combinations of sequence motifs that occur together in the genome. In order to detect combinations of transcription factor binding motifs, we developed a data mining approach based on the use of association rules, which are typically used in market basket analysis. We scored each segment of the genome for the presence or absence of each of 83 transcription factor binding motifs, then used association rule mining algorithms to mine this dataset, thus identifying frequently occurring pairs of distinct motifs within a segment. Results: Support for most pairs of transcription factor binding motifs was highly correlated across different chromosomes although pair significance varied. Known true positive motif pairs showed higher association rule support, confidence, and significance than background. Our subsets of high-confidence, high-significance mined pairs of transcription factors showed enrichment for co-citation in PubMed abstracts relative to all pairs, and the predicted associations were often readily verifiable in the literature. Conclusion: Functional elements in the genome where transcription factors bind to regulate expression in a combinatorial manner are more likely to be predicted by identifying statistically and biologically significant combinations of transcription factor binding motifs than by simply scanning the genome for the occurrence of binding sites for a single transcription factor.NIAAA Alcohol Training GrantNational Science FoundationCellular and Molecular Biolog

Preliminary calibration of a generic scramjet combustor

The results of a preliminary investigation of the combustion of hydrogen fuel at hypersonic flow conditions are provided. The tests were performed in a generic, constant-area combustor model with test gas supplied by a free-piston-driven reflected-shock tunnel. Static pressure measurements along the combustor wall indicated that burning did occur for combustor inlet conditions of P(static) approximately equal to 19kPa, T(static) approximately equal to 1080 K, and U approximately equal to 3630 m/s with a fuel equivalence ratio approximately equal to 0.9. These inlet conditions were obtained by operating the tunnel with stagnation enthalpy approximately equal to 8.1 MJ/kg, stagnation pressure approximately equal to 52 MPa, and a contoured nozzle with a nominal exit Mach number of 5.5

Using schedulers to test probabilistic distributed systems

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s00165-012-0244-5. Copyright © 2012, British Computer Society.Formal methods are one of the most important approaches to increasing the confidence in the correctness of software systems. A formal specification can be used as an oracle in testing since one can determine whether an observed behaviour is allowed by the specification. This is an important feature of formal testing: behaviours of the system observed in testing are compared with the specification and ideally this comparison is automated. In this paper we study a formal testing framework to deal with systems that interact with their environment at physically distributed interfaces, called ports, and where choices between different possibilities are probabilistically quantified. Building on previous work, we introduce two families of schedulers to resolve nondeterministic choices among different actions of the system. The first type of schedulers, which we call global schedulers, resolves nondeterministic choices by representing the environment as a single global scheduler. The second type, which we call localised schedulers, models the environment as a set of schedulers with there being one scheduler for each port. We formally define the application of schedulers to systems and provide and study different implementation relations in this setting

The kinetics of surfactant desorption at the air–solution interface

The kinetics of desorption of the anionic surfactant sodium dodecylbenzene sulfonate at the air–solution interface have been studied using neutron reflectivity (NR). The experimental arrangement incorporates a novel flow cell in which the subphase can be exchanged (diluted) using a laminar flow whilst the surface region remains unaltered. The kinetics of the desorption is relatively slow and occurs over many tens of minutes compared with the dilution timescale of approximately 10–30 minutes. A detailed mathematical model, in which the rate of the desorption is determined by transport through a near-surface diffusion layer into a diluted bulk solution below, is developed and provides a good description of the timedependent adsorption data.\ud \ud A key parameter of the model is the ratio of the depth of the diffusion layer, Hc , to the depth of the fluid, Hf, and we find that this is related to the reduced Péclet number, Pe*, for the system, via Hc/Hf, = C/Pe* 1/ 2 . Although from a highly idealised experimental arrangement, the results provide an important insight into the ‘rinse mechanism’, which is applicable to a wide variety of domestic and industrial circumstances

Shock tunnel studies of scramjet phenomena

Commissioning of the new T4 shock tunnel at the University of Queensland implied that it was no longer necessary to focus the work of the research group about an annual test series conducted in the T3 shock tunnel in Canberra. Therefore, it has been possible to organize a group for work to proceed along lines such that particular personnel are associated with particular project areas. The format of this report consists of a series of reports on specific project areas, with a brief general introduction commenting on each report. The introduction is structured by project areas, with the title of the relevant report stated under the project area heading. The reports themselves follow in the order of the project area headings

Shock tunnel studies of scramjet phenomena, supplement 5

A series of reports are presented on SCRAMjet studies, shock tunnel studies, and expansion tube studies. The SCRAMjet studies include: (1) Investigation of a Supersonic Combustion Layer; (2) Wall Injected SCRAMjet Experiments; (3) Supersonic Combustion with Transvers, Circular, Wall Jets; (4) Dissociated Test Gas Effects on SCRAMjet Combustors; (5) Use of Silane as a Fuel Additive for Hypersonic Thrust Production, (6) Pressure-length Correlations in Supersonic Combustion; (7) Hot Hydrogen Injection Technique for Shock Tunnels; (8) Heat Release - Wave Interaction Phenomena in Hypersonic Flows; (9) A Study of the Wave Drag in Hypersonic SCRAMjets; (10) Parametric Study of Thrust Production in the Two Dimensional SCRAMjet; (11) The Design of a Mass Spectrometer for use in Hypersonic Impulse Facilities; and (12) Development of a Skin Friction Gauge for use in an Impulse Facility. The shock tunnel studies include: (1) Hypervelocity flow in Axisymmetric Nozzles; (2) Shock Tunnel Development; and (3) Real Gas Efects in Hypervelocity Flows over an Inclined Cone. The expansion tube studies include: (1) Investigation of Flow Characteristics in TQ Expansion Tube; and (2) Disturbances in the Driver Gas of a Shock Tube

Identification of the slow E3 transition 136mCs -> 136Cs with conversion electrons

We performed at ISOLDE the spectroscopy of the decay of the 8- isomer in 136Cs by and conversion-electron detection. For the first time the excitation energy of the isomer and the multipolarity of its decay have been measured. The half-life of the isomeric state was remeasured to T1/2 = 17.5(2) s. This isomer decays via a very slow 518 keV E3 transition to the ground state. In addition to this, a much weaker decay branch via a 413 keV M4 and a subsequent 105 keV E2 transition has been found. Thus we have found a new level at 105 keV with spin 4+ between the isomeric and the ground state. The results are discussed in comparison to shell model calculations.Comment: Phys. Rev. C accepted for publicatio

Free-space quantum key distribution

A working free-space quantum key distribution (QKD) system has been developed and tested over a 205-m indoor optical path at Los Alamos National Laboratory under fluorescent lighting conditions. Results show that free-space QKD can provide secure real-time key distribution between parties who have a need to communicate secretly.Comment: 5 pages, 2 figures, 2 tables. To be published in Physical review A on or about 1 April 199

The Pan-STARRS1 Photometric System

The Pan-STARRS1 survey is collecting multi-epoch, multi-color observations of the sky north of declination -30 deg to unprecedented depths. These data are being photometrically and astrometrically calibrated and will serve as a reference for many other purposes. In this paper we present our determination of the Pan-STARRS photometric system: gp1, rp1, ip1, zp1, yp1, and wp1. The Pan-STARRS photometric system is fundamentally based on the HST Calspec spectrophotometric observations, which in turn are fundamentally based on models of white dwarf atmospheres. We define the Pan-STARRS magnitude system, and describe in detail our measurement of the system passbands, including both the instrumental sensitivity and atmospheric transmission functions. Byproducts, including transformations to other photometric systems, galactic extinction, and stellar locus are also provided. We close with a discussion of remaining systematic errors.Comment: 39 pages, 9 figures, machine readable table of bandpasses, accepted for publication in Ap