The salt dependence of DNA recognition by NF-kappaB p50 : a detailed kinetic analysis of the effects on affinityand specificity

The binding kinetics of NF-kappaB p50 to the Ig-kappaB site and to a DNA duplex with no specific binding site were determined under varying conditions of potassium chloride concentration using a surface plasmonresonance biosensor. Association and dissociation rate constants were measured enabling calculation of the dissociation constants. Under previously established high affinity buffer conditions, the k a for both sequences was in the order of 10(7) M-1s-1whilst the k d values varied 600-fold in a sequence-dependent manner between 10(-1) and 10(-4 )s-1, suggesting that the selectivity of p50 for different sequences is mediated primarily through sequence-dependent dissociation rates. The calculated K D value for the Ig-kappaB sequence was 16 pM, whilst the K D for the non-specific sequence was 9.9 nM. As the ionic strength increased to levels which are closer to that of the cellular environment, the binding of p50 to the non-specific sequence was abolished whilst the specific affinity dropped to nanomolar levels. From these results, a mechanism is proposed in which p50 binds specific sequences with high affinity whilst binding non-specific sequences weakly enough to allow efficient searching of the DNA.

Don't think but look : a Gestalt interactionist approach to legal thinking

We propose here a new approach to legal thinking that is based on principles of Gestalt perception. Using a Gestalt view of perception, which sees perception as the process of building a conceptual representation of the given stimulus, we articulate legal thinking as the process of building a representation for the given facts of a case. We propose a model in which top-down and bottom-up processes interact together to build arguments (or representations) in legal thinking. We discuss some implications of our approach, especially with respect to modeling precedential reasoning and creativity in legal thinking.

A meshfree-based local Galerkin method with condensation of degree of freedom for elastic dynamic analysis

Condensation technique of degree of freedom is first proposed to improve the computational efficiency of meshfree method with Galerkin weak form for elastic dynamic analysis. In the present method, scattered nodes without connectivity are divided into several subsets by cells with arbitrary shape. Local discrete equation is established over each cell by using moving Kriging interpolation, in which the nodes that located in the cell are used for approximation. Then local discrete equations can be simplified by condensation of degree of freedom, which transfers equations of inner nodes to equations of boundary nodes based on cells. The global dynamic system equations are obtained by assembling all local discrete equations and are solved by using the standard implicit Newmark’s time integration scheme. In the scheme of present method, the calculation of each cell is carried out by meshfree method, and local search is implemented in interpolation. Numerical examples show that the present method has high computational efficiency and good accuracy in solving elastic dynamic problems.

Designing intelligent litigation support tools : The IKBALS perspective

In the legal domain, it is rare to find solutions to problems by simply applying algorithms or invoking deductive rules in some knowledge‐based program. Instead, expert practitioners often supplement domain‐specific knowledge with field experience. This type of expertise is often applied in the form of an analogy. This research proposes to combine both reasoning with precedents and reasoning with statutes and regulations in a way that will enhance the statutory interpretation task. This is being attempted through the integration of database and expert system technologies. Case‐based reasoning is being used to model legal precedents while rule‐based reasoning modules are being used to model the legislation and other types of causal knowledge. It is hoped to generalise these findings and to develop a formal methodology for integrating case‐based databases with rule‐based expert systems in the legal domain.

Chalcophile element geochemistry of the Boggy Plain Zoned Pluton, southeastern Australia : a S-saturated barren compositionally diverse magma

The behavior of the platinum group elements (PGE) and Re in felsic magmas is poorly understood due to scarcity of data. We report the concentrations of Ni, Cu, Re, and PGE in the compositionally diverse Boggy Plain zoned pluton (BPZP), which shows a variation of rock type from gabbro through granodiorite and granite to aplite with a SiO2 range from 52 to 74 wt %. In addition, major silicate and oxide minerals were analyzed for Ni, Cu, and Re, and a systematic sulfide study was carried out to investigate the role of silicate, oxide, and sulfide minerals on chalcophile element geochemistry of the BPZP. Mass balance calculation shows that the whole rock Cu budget hosted by silicate and oxide minerals is <13 wt % and that Cu is dominantly located in sulfide phases, whereas most of the whole rock Ni budget (>70 wt %) is held in major silicate and oxide minerals. Rhenium is dominantly hosted by magnetite and ilmenite. Ovoid-shaped sulfide blebs occur at the boundary between pyroxene phenocrysts and neighboring interstitial phases or within interstitial minerals in the gabbro and the granodiorite. The blebs are composed of pyrrhotite, pyrite, chalcopyrite, and S-bearing Fe-oxide, which contain total trace metals (Co, Ni, Cu, Ag, Pb) up to ~16 wt %. The mineral assemblage, occurrence, shape, and composition of the sulfide blebs are a typical of magmatic sulfide. PGE concentrations in the BPZP vary by more than two orders of magnitude from gabbro (2.7–7.8 ppb Pd, 0.025–0.116 ppb Ir) to aplite (0.05 ppb Pd, 0.001 ppb Ir). Nickel, Cu, Re, and PGE concentrations are positively correlated with MgO in all the rock types although there is a clear discontinuity between the granodiorite and the granite in the trends for Ni, Rh, and Ir when plotted against MgO. Cu/Pd values gradually increase from 6,100 to 52,600 as the MgO content decreases. The sulfide petrology and chalcophile element geochemistry of the BPZP show that sulfide saturation occurred in the late gabbroic stage of magma differentiation. Segregation and distribution of these sulfide blebs controlled Cu and PGE variations within the BPZP rocks although the magma of each rock type may have experienced a different magma evolution history in terms of crustal assimilation and crystal fractionation. The sulfide melt locked in the cumulate rocks must have sequestered a significant portion of the chalcophile elements, which restricted the availability of these metals to magmatic-hydrothermal ore fluids. Therefore, we suggest that the roof rocks that overlay the BPZP were not prospective for magmatic-hydrothermal Cu, Au, or Cu–Au deposits.

Development of a dose assessment tool for the auditing of radiotherapy treatment dosimetric quality

The reporting and auditing of patient dose is an important component of radiotherapy quality assurance. The manual extraction of dose-volume metrics is time consuming and undesirable when auditing the dosimetric quality of a large cohort of patient plans. A dose assessment application was written to overcome this, allowing the calculation of various dose-volume metrics for large numbers of plans exported from treatment planning systems. This application expanded on the DICOM-handling functionality of the MCDTK software suite. The software extracts dose values in the volume of interest by using a ray casting point-in-polygon algorithm, where the polygons have been defined by the contours in the RTSTRUCT file...

CTCombine : rotating and combining CT data with an accurate detector model to simulate radiotherapy portal imaging at non-zero beam angles

Established Monte Carlo user codes BEAMnrc and DOSXYZnrc permit the accurate and straightforward simulation of radiotherapy experiments and treatments delivered from multiple beam angles. However, when an electronic portal imaging detector (EPID) is included in these simulations, treatment delivery from non-zero beam angles becomes problematic. This study introduces CTCombine, a purpose-built code for rotating selected CT data volumes, converting CT numbers to mass densities, combining the results with model EPIDs and writing output in a form which can easily be read and used by the dose calculation code DOSXYZnrc...

Polarized infrared absorption spectrum of matrix-isolated methylperoxyl radicals, CH3OO (X)over-tilde 2A ''

We have used a tandem pair of supersonic nozzles to produce clean samples of CH3OO radicals in cryogenic matrices. One hyperthermal nozzle decomposes azomethane (CH3NNCH3) to generate intense pulses of CH3 radicals, While the second nozzle alternately fires a burst Of O-2/Ar at the 20 K matrix. The CH3/O-2/20 K argon radical sandwich acts to produce target methylperoxyl radicals: CH3 + O-2 --> CH3OO. The absorption spectra of the radicals are monitored with a Fourier transform infrared spectrometer. We report 10 of the 12 fundamental infrared bands of the methylperoxyl radical CH3OO, (X) over tilde (2)A", in an argon matrix at 20 K. The experimental frequencies (cm(-1)) and polarizations follow: the a' modes are 3032, 2957, 1448, 1410, 1180, 1109, 90, 492, while the a" modes are 3024 and 1434. We cannot detect the asymmetric CH3 rocking mode, nu(11), nor the torsion, nu(12). The infrared spectra of (CH3OO)-O-18-O-18, (CH3OO)-C-13, and CD3OO have been measured as well in order to determine the isotopic shifts. The experimental frequencies, {nu}, for the methylperoxyl radicals are compared to harmonic frequencies, {omega}, resulting from a UB3LYP/6-311G(d,p) electronic structure calculation. Linear dichroism spectra were measured with photooriented radical samples in order to establish the experimental polarizations of most vibrational bands. The methylperoxyl radical matrix frequencies listed above are within +/-2% of the gas-phase vibrational frequencies. A final set of vibrational frequencies for the H radical, are recommended. See also http://ellison.colorado.edu/methylperoxyl.

Calculate excess mortality during heatwaves using Hilbert-Huang transform algorithm

Background Heatwaves could cause the population excess death numbers to be ranged from tens to thousands within a couple of weeks in a local area. An excess mortality due to a special event (e.g., a heatwave or an epidemic outbreak) is estimated by subtracting the mortality figure under ‘normal’ conditions from the historical daily mortality records. The calculation of the excess mortality is a scientific challenge because of the stochastic temporal pattern of the daily mortality data which is characterised by (a) the long-term changing mean levels (i.e., non-stationarity); (b) the non-linear temperature-mortality association. The Hilbert-Huang Transform (HHT) algorithm is a novel method originally developed for analysing the non-linear and non-stationary time series data in the field of signal processing, however, it has not been applied in public health research. This paper aimed to demonstrate the applicability and strength of the HHT algorithm in analysing health data. Methods Special R functions were developed to implement the HHT algorithm to decompose the daily mortality time series into trend and non-trend components in terms of the underlying physical mechanism. The excess mortality is calculated directly from the resulting non-trend component series. Results The Brisbane (Queensland, Australia) and the Chicago (United States) daily mortality time series data were utilized for calculating the excess mortality associated with heatwaves. The HHT algorithm estimated 62 excess deaths related to the February 2004 Brisbane heatwave. To calculate the excess mortality associated with the July 1995 Chicago heatwave, the HHT algorithm needed to handle the mode mixing issue. The HHT algorithm estimated 510 excess deaths for the 1995 Chicago heatwave event. To exemplify potential applications, the HHT decomposition results were used as the input data for a subsequent regression analysis, using the Brisbane data, to investigate the association between excess mortality and different risk factors. Conclusions The HHT algorithm is a novel and powerful analytical tool in time series data analysis. It has a real potential to have a wide range of applications in public health research because of its ability to decompose a nonlinear and non-stationary time series into trend and non-trend components consistently and efficiently.

Bike share's impact on car use : evidence from the United States, Great Britain, and Australia

There are currently more than 700 cities operating bike share programs. Purported benefits of bike share include flexible mobility, physical activity, reduced congestion, emissions and fuel use. Implicit or explicit in the calculation of program benefits are assumptions regarding the modes of travel replaced by bike share journeys. This paper examines the degree to which car trips are replaced by bike share, through an examination of survey and trip data from bike share programs in Melbourne, Brisbane, Washington, D.C., London, and Minneapolis/St. Paul. A secondary and unique component of this analysis examines motor vehicle support services required for bike share fleet rebalancing and maintenance. These two components are then combined to estimate bike share’s overall contribution to changes in vehicle kilometers traveled. The results indicate an estimated reduction in motor vehicle use due to bike share of approx. 90,000 km per annum in Melbourne and Minneapolis/St. Paul and 243,291 km for Washington, D.C. London’s bike share program however recorded an additional 766,341 km in motor vehicle use. This was largely due to a low car mode substitution rate and substantial truck use for rebalancing of bicycles. As bike share programs mature, evaluation of their effectiveness in reducing car use may become increasingly important. Researchers can adapt the analytical approach proposed in this paper to assist in the evaluation of current and future bike share programs.

A comparison of stability and bifurcation criteria for inflated spherical elastic shells

The nonlinear stability analysis introduced by Chen and Haughton [1] is employed to study the full nonlinear stability of the non-homogeneous spherically symmetric deformation of an elastic thick-walled sphere. The shell is composed of an arbitrary homogeneous, incompressible elastic material. The stability criterion ultimately requires the solution of a third-order nonlinear ordinary differential equation. Numerical calculations performed for a wide variety of well-known incompressible materials are then compared with existing bifurcation results and are found to be identical. Further analysis and comparison between stability and bifurcation are conducted for the case of thin shells and we prove by direct calculation that the two criteria are identical for all modes and all materials.

Demonstration of nonlinear absorption in Au semi-continuous film by electrical measurement

We have demonstrated the nonlinear absorption at 532 nm wavelength in an Au semi-continuous film (SF) resulting from smearing of the Fermi distribution and diffusion of conduction electrons into the substrate. The Au SF was irradiated by a pulsed laser with 8 ns pulse width at 532 nm in near resonance with the interband transition of the Au. We determined the temperature increase in the SF for different intensities by electrical measurement. We calculated the temperature increase by using a 1D heat transport equation; comparing the results of the calculation with measured values for the temperature increase, revealed the nonlinear absorption in the Au SF. We employed this deviation from linear behaviour to determine the nonlinear absorption coefficient.

Electron/ion energy loss to discharge walls revised : a case study in low-temperature, thermally nonequilibrium plasmas

Reliable calculations of the electron/ion energy losses in low-pressure thermally nonequilibrium low-temperature plasmas are indispensable for predictive modeling related to numerous applications of such discharges. The commonly used simplified approaches to calculation of electron/ion energy losses to the chamber walls use a number of simplifying assumptions that often do not account for the details of the prevailing electron energy distribution function (EEDF) and overestimate the contributions of the electron losses to the walls. By direct measurements of the EEDF and careful calculation of contributions of the plasma electrons in low-pressure inductively coupled plasmas, it is shown that the actual losses of kinetic energy of the electrons and ions strongly depend on the EEDF. It is revealed that the overestimates of the total electron/ion energy losses to the walls caused by improper assumptions about the prevailing EEDF and about the ability of the electrons to pass through the repulsive potential of the wall may lead to significant overestimates that are typically in the range between 9 and 32%. These results are particularly important for the development of power-saving strategies for operation of low-temperature, low-pressure gas discharges in diverse applications that require reasonably low power densities. © 2008 American Institute of Physics.

Bistability and hysteresis in inductively coupled plasmas

The transition between the two stable operation regimes (E and H discharge modes) in inductively coupled argon plasmas has been studied experimentally and theoretically. Analogy with other physical phenomena exhibiting hysteresis has been drawn. Analysis of power balance, electromagnetic field, plasma parameters, densities of the excited states, and optical emission spectra shows that the hysteresis may be due to nonlinearities associated with step-wise ionization through excited states of the argon atoms.

Drosophila 3′ UTRs are more complex than protein-coding sequences

The 3′ UTRs of eukaryotic genes participate in a variety of post-transcriptional (and some transcriptional) regulatory interactions. Some of these interactions are well characterised, but an undetermined number remain to be discovered. While some regulatory sequences in 3′ UTRs may be conserved over long evolutionary time scales, others may have only ephemeral functional significance as regulatory profiles respond to changing selective pressures. Here we propose a sensitive segmentation methodology for investigating patterns of composition and conservation in 3′ UTRs based on comparison of closely related species. We describe encodings of pairwise and three-way alignments integrating information about conservation, GC content and transition/transversion ratios and apply the method to three closely related Drosophila species: D. melanogaster, D. simulans and D. yakuba. Incorporating multiple data types greatly increased the number of segment classes identified compared to similar methods based on conservation or GC content alone. We propose that the number of segments and number of types of segment identified by the method can be used as proxies for functional complexity. Our main finding is that the number of segments and segment classes identified in 3′ UTRs is greater than in the same length of protein-coding sequence, suggesting greater functional complexity in 3′ UTRs. There is thus a need for sustained and extensive efforts by bioinformaticians to delineate functional elements in this important genomic fraction. C code, data and results are available upon request.