Role-similarity based functional prediction in networked systems: Application to the yeast proteome

We propose a general method to predict functions of vertices where: 1. The wiring of the network is somehow related to the vertex functionality. 2. A fraction of the vertices are functionally classified. The method is influenced by role-similarity measures of social network analysis. The two versions of our prediction scheme is tested on model networks were the functions of the vertices are designed to match their network surroundings. We also apply these methods to the proteome of the yeast Saccharomyces cerevisiae and find the results compatible with more specialized methods

Sub-Zero Alteration in an Isotopically Heavy Brine Preserved in a Pristine H Chondrite Xenolith

Introduction: Brecciated H chondrites host a variety of xenoliths, including unshocked, phyllo- silicate-rich carbonaceous chondrites (CCs). The brecciated H chondrite Zag (H3-6) is one of two chondrites to host macroscopic (1 - 5mm), xenolithic crystals of halite (NaCl) with aqueous fluid inclusions and organics. A ~1cm CC xenolith in Zag (Zag clast) has mineralogy similar to CI chondrites, but it has a unique bulk oxygen isotopic composition among all meteorites ((exp 17)O = 1.49 0.04 , (exp 18)O = 22.38 0.17 ). The Zag clast encloses halite in its matrix, linking the coarse, matrix halite and the xenolith to the same parent object, suggested to be hydrovolcanically active. Its bulk C and N contents are the highest among chondrites and bulk (exp 15)N is similar to CR chondrites and Bells. Insoluble organic material (IOM) in the Zag clast has D and (exp 15)N hotspots, also similar to CR chondrites and Bells (C2-ung.). We provide further isotopic characterization of the Zag clast to constrain the formation temperature and origin of its primary and secondary components

Clasts in the CM2 carbonaceous chondrite Lonewolf Nunataks 94101: evidence for aqueous alteration prior to complex mixing

Clasts in the CM2 carbonaceous chondrite Lonewolf Nunataks (LON) 94101 have been characterized using scanning and transmission electron microscopy and electron microprobe analysis to determine their degrees of aqueous alteration, and the timing of alteration relative to incorporation of clasts into the host. The provenance of the clasts, and the mechanism by which they were incorporated and mixed with their host material are also considered. Results show that at least five distinct types of clasts occur in LON 94101, of which four have been aqueously altered to various degrees and one is largely anhydrous. The fact that they have had different alteration histories implies that the main part of aqueous activity occurred prior to the mixing and assimilation of the clasts with their host. Further, the presence of such a variety of clasts suggests complex mixing in a dynamic environment involving material from various sources. Two of the clasts, one containing approximately 46 vol% carbonate and the other featuring crystals of pyrrhotite up to approximately 1 mm in size, are examples of unusual lithologies and indicate concentration of chemical elements in discrete areas of the parent body(ies), possibly by flow of aqueous solutions

Al-Mg systematics of CAIs, POI, and ferromagnesian chondrules from Ningqiang

We have made aluminum-magnesium isotopic measurements on 4 melilite-bearing calcium-aluminum-rich inclusions (CAIs), 1 plagioclase-olivine inclusion (POI), and 2 ferromagnesian chondrules from the Ningqiang carbonaceous chondrite. All of the CAIs measured contain clear evidence for radiogenic ^(26)Mg^* from the decay of ^(26)Al (τ = 1.05 Ma). Although the low Al/Mg ratios of the melilites introduce large uncertainties, the inferred initial ^(26)Al/^(27)Al ratios for the CAIs are generally consistent with the value of 5 x 10^(−5). There is clear evidence of ^(26)Al^* in one POI and two chondrules, but with considerable uncertainties in the value of (^(26)Al/^(27)Al)0. The (^(26)Al/^(27)Al)_0 ratios for the POI and the chondrules are 0.3–0.6 x 10^(−5), roughly an order of magnitude lower than the canonical value. Ningqiang shows very little evidence of metamorphism as a bulk object and the (^(26)Al/^(27)Al)_0 ratios in its refractory inclusions and chondrules are consistent with those found in other unmetamorphosed chondrites of several different classes. Our observations and those of other workers support the view that ^(26)Al was widely and approximately homogeneously distributed throughout the condensed matter of the solar system. The difference in (^(26)Al/^(27)Al)0 between CAIs and less refractory materials seems reasonably interpreted in terms of a ∼2 million year delay between the formation of CAIs and the onset of formation of less refractory objects. The POI shows clear differences in ^(25)Mg/^(24)Mg between its constituent spinels and olivine, which confirms that they are partially reprocessed material from different sources that were rapidly quenched

Life in soil by the actinorhizal root nodule endophyte Frankia

Frankia is a genus of soil actinomycetes famous for its ability to form N2-fixing root nodule symbioses with actinorhizal plants. Although Frankia strains diplay a high diversity in terms of ecological niches in soil, current knowledge about Frankia is dominated by its life as an endophyte in root nodules. Increased use of molecular methods has refined and expanded insights into endophyte-host specificities and Frankia phylogeny. This review has focus on Frankia as a soil organism, including its part of microbial consortia, and how to study Frankia in soil. We highlight the use of nodulation tests and molecular methods to reveal population size and genetic diversity of Frankia in soil and discuss how autoregulation of nodulation and interactions with other soil microorganisms may influence the results. A comprehensive record of published interactions between Frankia and other soil microbes is summarized

The solar oxygen-isotopic composition: Predictions and implications for solar nebula processes

The outer layers of the Sun are thought to preserve the average isotopic and chemical composition of the solar system. The solar O-isotopic composition is essentially unmeasured, though models based on variations in meteoritic materials yield several predictions. These predictions are reviewed and possible variations on these predictions are explored. In particular, the two-component mixing model of Clayton and Mayeda (1984) (slightly revised here) predicts solar compositions to lie along an extension of the calcium-aluminum-rich inclusion (CAI) ^(16)O line between (δ^(18)O, δ^(17)O) = (16.4, 11.4)%0 and (12.3, 7.5)%0. Consideration of data from ordinary chondrites suggests that the range of predicted solar composition should extend to slightly lower δ^(18)O values. The predicted solar composition is critically sensitive to the solid/gas ratio in the meteorite-forming region, which is often considered to be significantly enriched over solar composition. A factor of two solid/gas enrichment raises the predicted solar (δ^(18)O, δ^(17)O) values along an extension of the CAI ^(16)O line to (33, 28)%0. The model is also sensitive to the nebular O gas phase. If conversion of most of the gaseous O from CO to H_2O occurred at relatively low temperatures and was incomplete at the time of CM aqueous alteration, the predicted nebular gas composition (and hence the solar composition) would be isotopically heavier along a slope 1/2 line. The likelihood of having a single solid nebular O component is discussed. A distribution of initial solid compositions along the CAI ^(16)O line (rather than simply as an end-member) would not significantly change the predictions above in at least one scenario. Even considering these variations within the mixing model, the predicted range of solar compositions is distinct from that expected if the meteoritic variations are due to non-mass-dependent fractionation. Thus, a measurement of the solar O composition to a precision of several permil would clearly distinguish between these theories and should clarify a number of other important issues regarding solar system formation

Isotopes of H, N, and O in H Chondrite Xenoliths

Brecciated H chrondites host a variety of xenoliths, including unshocked, phyllosilate-rich carbonaceous chondrites (CCs) [1-2]. The brecciated H chondrite Zag (H3-6) is one of two chondrites to host macroscopic (1 - 5mm), xenolithic crystals of halite (NaCl) with aqueous fluid inclusions and organics [3-4]. A ~1cm CC xenolith in Zag (Zag clast) also encloses halite in its matrix, linking the halite and the xenolith to the same parent object. The Zag clast has mineralogy similar to CI chondrites, but it has a unique bulk oxygen isotopic composition among all meteorites (17O = 1.49 0.04 , 18O = 22.38 0.17 ) and is therefore derived from a uniquely sampled parent object [5-6]. Organics have high bulk D and 15N values with isotopic "hotspots" similar to organics in CR chondrites and Bells (C2-ung.) [6-7]. Bulk 15N is also similar to CRs and Bells [7]. We provide further isotopic characterization of the Zag clast to constrain the formation temperature and origin of its primary and secondary components

Control of near-infrared supercontinuum bandwidth by adjusting pump pulse duration

We experimentally and numerically investigated the impact of input pump pulse duration on the near-infrared bandwidth of supercontinuum generation in a photonic crystal fiber. We continuously stretched the temporal duration of the input pump laser (centered at 1030 nm) pulses from 500 fs up to 10 ps, while keeping fixed the pump peak power. We observed that the long-wavelength edge of the supercontinuum spectrum is increased by 200 nm as the pump pulse duration grows from 500 fs to 10 ps. We provide a quantitative fit of the experimental results by means of numerical simulations. Moreover, we have explained the observed spectral broadening enhancement induced by pump pulse energy by developing an approximate yet fully analytical model for soliton energy exchange through a series of collisions in the presence of stimulated Raman scattering