Supplanting crystallography or supplementing microscopy? A combined approach to the study of an enveloped virus

The recent advances in the resolution obtained by single-particle reconstructions from cryo-electron microscopy (cryo-EM) have led to an increase in studies that combine X-ray crystallographic results with those of electron microscopy (EM). Here, such a combination is described in the determination of the structure of an enveloped animal virus, Semliki Forest virus, at 9 Å resolution. The issues of model bias in determination of the structure, the definition of resolution in a single-particle reconstruction, the effect of the correction of the contrast-transfer function on the structure determined and the use of a high-resolution structure of a subunit in the interpretation of the structure of the complex are addressed

The initial conditions of stellar protocluster formation. II. A catalogue of starless and protostellar clumps embedded in IRDCs in the Galactic longitude range 15<l<55

We present a catalogue of starless and protostellar clumps associated with infrared dark clouds (IRDCs) in a 40 degrees wide region of the inner Galactic Plane (b<1). We have extracted the far-infrared (FIR) counterparts of 3493 IRDCs with known distance in the Galactic longitude range 15<l<55 and searched for the young clumps using Hi-GAL, the survey of the Galactic Plane carried out with the Herschel satellite. Each clump is identified as a compact source detected at 160, 250 and 350 mum. The clumps have been classified as protostellar or starless, based on their emission (or lack of emission) at 70 mum. We identify 1723 clumps, 1056 (61%) of which are protostellar and 667 (39%) starless. These clumps are found within 764 different IRDCs, 375 (49%) of which are only associated with protostellar clumps, 178 (23%) only with starless clumps, and 211 (28%) with both categories of clumps. The clumps have a median mass of 250 M_sun and range up to >10^4$ M_sun in mass and up to 10^5 L_sun in luminosity. The mass-radius distribution shows that almost 30% of the starless clumps identified in this survey could form high-mass stars, however these massive clumps are confined in only ~4% of the IRDCs. Assuming a minimum mass surface density threshold for the formation of high-mass stars, the comparison of the numbers of massive starless clumps and those already containing embedded sources suggests an upper limit lifetime for the starless phase of 10^5 years for clumps with a mass M>500 M_sun.Comment: accepted for publication in MNRAS. Online catalogues available soon, please contact the authors if intereste

Artificial atmosphere control system

Two-gas control system has been developed which uses existing hardware. Three systems are used for control, monitoring, and safety backup. Pure oxygen will be supplied to maintain safe pressure level should something go wrong

Deer reduce habitat quality for a woodland songbird: evidence from settlement patterns, demographic parameters, and body condition.

Understanding avian responses to ungulate-induced habitat modification is important because deer populations are increasing across much of temperate Europe and North America. Our experimental study examined whether habitat quality for Blackcaps (Sylvia atricapilla) in young woodland in eastern England was affected by deer, by comparing Blackcap behavior, abundance, and condition between paired plots (half of each pair protected from deer). The vegetation in each pair of plots was the same age. The Blackcap is an ideal model species for testing effects of deer on avian habitat quality because it is dependent on dense understory vegetation and is abundant throughout much of Europe. We compared timing of settlement, abundance, age structure (second-year vs. after-second-year), and phenotypic quality (measured as a body condition index, body mass divided by tarsus length) between experimental and control plots. We used point counts to examine Blackcap distribution, and standardized mist netting to collect demographic and biometric data. Incidence of singing Blackcaps was higher in nonbrowsed than in browsed plots, and singing males were recorded in nonbrowsed plots earlier in the season, indicating earlier and preferential territory establishment. Most Blackcaps, both males and females, were captured in vegetation prior to canopy closure (2–4 years of regrowth). Body condition was superior for male Blackcaps captured in nonbrowsed plots; for second-year males this was most marked in vegetation prior to canopy closure. We conclude that deer browsing in young woodland can alter habitat quality for understory-dependent species, with potential consequences for individual fitness and population productivity beyond the more obvious effects on population density

The genealogy of judgement: towards a deep history of academic freedom

The classical conception of academic freedom associated with Wilhelm von Humboldt and the rise of the modern university has a quite specific cultural foundation that centres on the controversial mental faculty of 'judgement'. This article traces the roots of 'judgement' back to the Protestant Reformation, through its heyday as the signature feature of German idealism, and to its gradual loss of salience as both a philosophical and a psychological concept. This trajectory has been accompanied by a general shrinking in the scope of academic freedom from the promulgation of world-views to the offering of expert opinion

A Survey of Coronal Cavity Density Profiles

Coronal cavities are common features of the solar corona that appear as darkened regions at the base of coronal helmet streamers in coronagraph images. Their darkened appearance indicates that they are regions of lowered density embedded within the comparatively higher density helmet streamer. Despite interfering projection effects of the surrounding helmet streamer (which we refer to as the cavity rim), Fuller et al. have shown that under certain conditions it is possible to use a Van de Hulst inversion of white-light polarized brightness (pB) data to calculate the electron density of both the cavity and cavity rim plasma. In this article, we apply minor modifications to the methods of Fuller et al. in order to improve the accuracy and versatility of the inversion process, and use the new methods to calculate density profiles for both the cavity and cavity rim in 24 cavity systems. We also examine trends in cavity morphology and how departures from the model geometry affect our density calculations. The density calculations reveal that in all 24 cases the cavity plasma has a flatter density profile than the plasma of the cavity rim, meaning that the cavity has a larger density depletion at low altitudes than it does at high altitudes. We find that the mean cavity density is over four times greater than that of a coronal hole at an altitude of 1.2 R_☉ and that every cavity in the sample is over twice as dense as a coronal hole at this altitude. Furthermore, we find that different cavity systems near solar maximum span a greater range in density at 1.2 R_☉ than do cavity systems near solar minimum, with a slight trend toward higher densities for systems nearer to solar maximum. Finally, we found no significant correlation of cavity density properties with cavity height—indeed, cavities show remarkably similar density depletions—except for the two smallest cavities that show significantly greater depletion

On Characterizing the Data Access Complexity of Programs

Technology trends will cause data movement to account for the majority of energy expenditure and execution time on emerging computers. Therefore, computational complexity will no longer be a sufficient metric for comparing algorithms, and a fundamental characterization of data access complexity will be increasingly important. The problem of developing lower bounds for data access complexity has been modeled using the formalism of Hong & Kung's red/blue pebble game for computational directed acyclic graphs (CDAGs). However, previously developed approaches to lower bounds analysis for the red/blue pebble game are very limited in effectiveness when applied to CDAGs of real programs, with computations comprised of multiple sub-computations with differing DAG structure. We address this problem by developing an approach for effectively composing lower bounds based on graph decomposition. We also develop a static analysis algorithm to derive the asymptotic data-access lower bounds of programs, as a function of the problem size and cache size

Frequency shift of hyperfine transitions due to blackbody radiation

We have performed calculations of the size of the frequency shift induced by a static electric field on the clock transition frequencies of the hyperfine splitting in Yb+, Rb, Cs, Ba+, and Hg+. The calculations are used to find the frequency shifts due to blackbody radiation which are needed for accurate frequency measurements and improvements of the limits on variation of the fine structure constant, alpha. Our result for Cs (delta nu E^2=-2.26 times 10^{-10}Hz/(V/m)^2) is in good agreement with early measurements and ab initio calculations. We present arguments against recent claims that the actual value might be smaller. The difference (approx 10%) is due to the contribution of the continuum spectrum in the sum over intermediate states.Comment: Added discussion of Cs results and reference