How to change the oligomeric state of a circular protein assembly: switch from 11-subunit to 12-subunit TRAP suggests a general mechanism

Many critical cellular functions are performed by multisubunit circular protein oligomers whose internal geometry has evolved to meet functional requirements. The subunit number is arguably the most critical parameter of a circular protein assembly, affecting the internal and external diameters of the assembly and often impacting on the protein's function. Although accurate structural information has been obtained for several circular proteins, a lack of accurate information on alternative oligomeric states has prevented engineering such transitions. In this study we used the bacterial transcription regulator TRAP as a model system to investigate the features that define the oligomeric state of a circular protein and to question how the subunit number could be manipulated.We find that while Bacillus subtilis and Bacillus stearothermophilus TRAP form 11-subunit oligomers, the Bacillus halodurans TRAP exclusively forms 12-subunit assemblies. Significantly, the two states of TRAP are related by a simple rigid body rotation of individual subunits around inter-subunit axes. We tested if such a rotation could be induced by insertion or deletion mutations at the subunit interface. Using wild type 11-subunit TRAP, we demonstrate that removal of five C-terminal residues at the outer side of the inter-subunit axis or extension of an amino acid side chain at the opposite, inner side, increased the subunit number from 11 to 12. Our findings are supported by crystal structures of TRAP oligomers and by native mass spectrometry data.The subunit number of the TRAP oligomer can be manipulated by introducing deletion or addition mutations at the subunit interface. An analysis of available and emerging structural data on alternative oligomeric states indicates that the same principles may also apply to the subunit number of other circular assemblies suggesting that the deletion/addition approach could be used generally to engineer transitions between different oligomeric states

Absence of evidence is not evidence of absence:On the limited use of regression discontinuity analysis in higher education

When higher education students are assessed multiple times, teachers need to consider how these assessments can be combined into a single pass or fail decision. A common question that arises is whether students should be allowed to take a resit. Previous research has found little to no clear learning benefits of resits and therefore suggested they might not be advantangeous as they are costly for both students and institutions. However, we conducted a simulation study that shows such a conclusion to be presumptuous. Absence of evidence is not evidence of absence; our results illustrate that if a resit effect were to exist, the analysis used in these studies (i.e. regression discontinuity analysis; RDA) lacked the power to detect such an effect. Power of RDA was only sufficient under extremely implausible conditions (i.e. large sample, large effect size, high correlation between examinations). To adequately compare the effect of assessment policies, researchers are recommended to use other methods than RDA

Roughness-induced critical phenomena in a turbulent flow

I present empirical evidence that turbulent flows are closely analogous to critical phenomena, from a reanalysis of friction factor measurements in rough pipes. The data collapse found here corresponds to Widom scaling near critical points, and implies that a full understanding of turbulence requires explicit accounting for boundary roughness

Improving Predictions for Helium Emission Lines

We have combined the detailed He I recombination model of Smits with the collisional transitions of Sawey & Berrington in order to produce new accurate helium emissivities that include the effects of collisional excitation from both the 2 (3)S and 2 (1) S levels. We present a grid of emissivities for a range of temperature and densities along with analytical fits and error estimates. Fits accurate to within 1% are given for the emissivities of the brightest lines over a restricted range for estimates of primordial helium abundance. We characterize the analysis uncertainties associated with uncertainties in temperature, density, fitting functions, and input atomic data. We estimate that atomic data uncertainties alone may limit abundance estimates to an accuracy of 1.5%; systematic errors may be greater than this. This analysis uncertainty must be incorporated when attempting to make high accuracy estimates of the helium abundance. For example, in recent determinations of the primordial helium abundance, uncertainties in the input atomic data have been neglected.Comment: ApJ, accepte

Gravitational wave astronomy of single sources with a pulsar timing array

Abbreviated: We investigate the potential of detecting the gravitational wave from individual binary black hole systems using pulsar timing arrays (PTAs) and calculate the accuracy for determining the GW properties. This is done in a consistent analysis, which at the same time accounts for the measurement of the pulsar distances via the timing parallax. We find that, at low redshift, a PTA is able to detect the nano-Hertz GW from super massive black hole binary systems with masses of \sim10^8 - 10^{10}\,M_{\sun} less than $\sim10^5$\,years before the final merger, and those with less than $\sim10^3 - 10^4$ years before merger may allow us to detect the evolution of binaries. We derive an analytical expression to describe the accuracy of a pulsar distance measurement via timing parallax. We consider five years of bi-weekly observations at a precision of 15\,ns for close-by ($\sim 0.5 - 1$\,kpc) pulsars. Timing twenty pulsars would allow us to detect a GW source with an amplitude larger than $5\times 10^{-17}$. We calculate the corresponding GW and binary orbital parameters and their measurement precision. The accuracy of measuring the binary orbital inclination angle, the sky position, and the GW frequency are calculated as functions of the GW amplitude. We note that the "pulsar term", which is commonly regarded as noise, is essential for obtaining an accurate measurement for the GW source location. We also show that utilizing the information encoded in the GW signal passing the Earth also increases the accuracy of pulsar distance measurements. If the gravitational wave is strong enough, one can achieve sub-parsec distance measurements for nearby pulsars with distance less than $\sim 0.5 - 1$\,kpc.Comment: 16 pages, 5 figure,, accepted by MNRA

Carbon nanotube-based sensor and method for detection of crack growth in a structure

A sensor has a plurality of carbon nanotube (CNT)-based conductors operatively positioned on a substrate. The conductors are arranged side-by-side, such as in a substantially parallel relationship to one another. At least one pair of spaced-apart electrodes is coupled to opposing ends of the conductors. A portion of each of the conductors spanning between each pair of electrodes comprises a plurality of carbon nanotubes arranged end-to-end and substantially aligned along an axis. Because a direct correlation exists between the resistance of a carbon nanotube and its strain, changes experienced by the portion of the structure to which the sensor is coupled induce a corresponding change in the electrical properties of the conductors, thereby enabling detection of crack growth in the structure

Size of the Vela Pulsar's Radio Emission Region: 500 km

We use interstellar scattering of the Vela pulsar to determine the size of its emission region. From interferometric phase variations on short baselines, we find that radio-wave scattering broadens the source by 3.4+/-0.3 milliarcseconds along the major axis at position angle 81+/-3 degrees. The ratio of minor axis to major axis is 0.51+/-0.03. Comparison of angular and temporal broadening indicates that the scattering material lies in the Vela-X supernova remnant surrounding the pulsar. From the modulation of the pulsar's scintillation on very short baselines, we infer a size of 500 km for the pulsar's emission region. We suggest that radio-wave refraction within the pulsar's magnetosphere may plausibly explain this size.Comment: 14 pages, includes 2 figures. Also available at: http://charm.physics.ucsb.edu:80/people/cgwinn/cgwinn_group/cgwinn_group.htm

Pulsars with the Australian Square Kilometre Array Pathfinder

The Australian Square Kilometre Array Pathfinder (ASKAP) is a 36-element array with a 30-square-degree field of view being built at the proposed SKA site in Western Australia. We are conducting a Design Study for pulsar observations with ASKAP, planning both timing and search observations. We provide an overview of the ASKAP telescope and an update on pulsar-related progress.Comment: To appear in proceedings of "Radio Pulsars: An astrophysical key to unlock the secrets of the Universe

Clinical practice of language fMRI in epilepsy centers: a European survey and conclusions by the ESNR Epilepsy Working Group

Purpose: To assess current clinical practices throughout Europe with respect to acquisition, implementation, evaluation, and interpretation of language functional MRI (fMRI) in epilepsy patients. Methods: An online survey was emailed to all European Society of Neuroradiology members (n = 1662), known associates (n = 6400), and 64 members of European Epilepsy network. The questionnaire featured 40 individual items on demographic data, clinical practice and indications, fMRI paradigms, radiological workflow, data post-processing protocol, and reporting. Results: A total of 49 non-duplicate entries from European centers were received from 20 countries. Of these, 73.5% were board-certified neuroradiologists and 69.4% had an in-house epilepsy surgery program. Seventy-one percent of centers performed fewer than five scans per month for epilepsy. The most frequently used paradigms were phonemic verbal fluency (47.7%) and audi