Energy deposition by heavy ions: Additivity of kinetic and potential energy contributions in hillock formation on CaF2

The formation of nano-hillocks on CaF2 crystal surfaces by individual ion impact has been studied using medium energy (3 and 5 MeV) highly charged ions (Xe19+ to Xe30+) as well as swift (kinetic energies between 12 and 58 MeV) heavy ions. For very slow highly charged ions the appearance of hillocks is known to be linked to a threshold in potential energy while for swift heavy ions a minimum electronic energy loss is necessary. With our results we bridge the gap between these two extreme cases and demonstrate, that with increasing energy deposition via electronic energy loss the potential energy threshold for hillock production can be substantially lowered. Surprisingly, both mechanisms of energy deposition in the target surface seem to contribute in an additive way, as demonstrated when plotting the results in a phase diagram. We show that the inelastic thermal spike model, originally developed to describe such material modifications for swift heavy ions, can be extended to case where kinetic and potential energies are deposited into the surface.Comment: 12 pages, 4 figure

Iptycene-Derived Pyridazines and Phthalazines

The synthesis of new heterocyclic oligo(phenylene) analogues based on soluble, nonaggregating 1,2-diazines is reported. Improved palladium-catalyzed reductive coupling methods were developed to allow for the preparation of large quantities of iptycene-derived bipyridazines and biphthalazines, and the controlled synthesis of well-defined oligomers up to sexipyridazine. Crystallographic, spectroscopic, and computational evidence indicate that in these analogues, hindrance at the ortho position is relaxed relative to poly(phenylenes). The resulting building blocks are promising for incorporation in conjugated electronics materials, and as new iptycene-derived ligands for transition metals

Creation of multiple nanodots by single ions

In the challenging search for tools that are able to modify surfaces on the nanometer scale, heavy ions with energies of several 10 MeV are becoming more and more attractive. In contrast to slow ions where nuclear stopping is important and the energy is dissipated into a large volume in the crystal, in the high energy regime the stopping is due to electronic excitations only. Because of the extremely local (< 1 nm) energy deposition with densities of up to 10E19 W/cm^2, nanoscaled hillocks can be created under normal incidence. Usually, each nanodot is due to the impact of a single ion and the dots are randomly distributed. We demonstrate that multiple periodically spaced dots separated by a few 10 nanometers can be created by a single ion if the sample is irradiated under grazing angles of incidence. By varying this angle the number of dots can be controlled.Comment: 12 pages, 6 figure

Neurobehavioral Function in School-Age Children Exposed to Manganese in Drinking Water

Background: Manganese neurotoxicity is well documented in individuals occupationally exposed to airborne particulates, but few data are available on risks from drinking-water exposure. Objective: We examined associations of exposure from concentrations of manganese in water and hair with memory, attention, motor function, and parent- and teacher-reported hyperactive behaviors. Methods: We recruited 375 children and measured manganese in home tap water (MnW) and hair (MnH). We estimated manganese intake from water ingestion. Using structural equation modeling, we estimated associations between neurobehavioral functions and MnH, MnW, and manganese intake from water. We evaluated exposure–response relationships using generalized additive models. Results: After adjusting for potential confounders, a 1-SD increase in log10 MnH was associated with a significant difference of –24% (95% CI: –36, –12%) SD in memory and –25% (95% CI: –41, –9%) SD in attention. The relations between log10 MnH and poorer memory and attention were linear. A 1-SD increase in log10 MnW was associated with a significant difference of –14% (95% CI: –24, –4%) SD in memory, and this relation was nonlinear, with a steeper decline in performance at MnW > 100 μg/L. A 1-SD increase in log10 manganese intake from water was associated with a significant difference of –11% (95% CI: –21, –0.4%) SD in motor function. The relation between log10 manganese intake and poorer motor function was linear. There was no significant association between manganese exposure and hyperactivity. Conclusion: Exposure to manganese in water was associated with poorer neurobehavioral performances in children, even at low levels commonly encountered in North America. Citation: Oulhote Y, Mergler D, Barbeau B, Bellinger DC, Bouffard T, Brodeur ME, Saint-Amour D, Legrand M, Sauvé S, Bouchard MF. 2014. Neurobehavioral function in school-age children exposed to manganese in drinking water. Environ Health Perspect 122:1343–1350; http://dx.doi.org/10.1289/ehp.130791

Possible Triplet Electron Pairing and an Anisotropic Spin Susceptibility in Organic Superconductors (TMTSF)_2 X

We argue that (TMTSF)_2 PF_6 compound under pressure is likely a triplet superconductor with a vector order parameter d(k) \equiv (d_a(k) \neq 0, d_c(k) = ?, d_{b'}(k) = 0); |d_a(k)| > |d_c(k)|. It corresponds to an anisotropic spin susceptibility at T=0: \chi_{b'} = \chi_0, \chi_a \ll \chi_0, where \chi_0 is its value in a metallic phase. [The spin quantization axis, z, is parallel to a so-called b'-axis]. We show that the suggested order parameter explains why the upper critical field along the b'-axis exceeds all paramagnetic limiting fields, including that for a nonuniform superconducting state, whereas the upper critical field along the a-axis (a \perp b') is limited by the Pauli paramagnetic effects [I. J. Lee, M. J. Naughton, G. M. Danner and P. M. Chaikin, Phys. Rev. Lett. 78, 3555 (1997)]. The triplet order parameter is in agreement with the recent Knight shift measurements by I. J. Lee et al. as well as with the early results on a destruction of superconductivity by nonmagnetic impurities and on the absence of the Hebel-Slichter peak in the NMR relaxation rate.Comment: 4 pages, 1 eps figur

Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome

<p>Abstract</p> <p>Background</p> <p>With a whole genome duplication event and wealth of biological data, salmonids are excellent model organisms for studying evolutionary processes, fates of duplicated genes and genetic and physiological processes associated with complex behavioral phenotypes. It is surprising therefore, that no salmonid genome has been sequenced. Atlantic salmon (<it>Salmo salar</it>) is a good representative salmonid for sequencing given its importance in aquaculture and the genomic resources available. However, the size and complexity of the genome combined with the lack of a sequenced reference genome from a closely related fish makes assembly challenging. Given the cost and time limitations of Sanger sequencing as well as recent improvements to next generation sequencing technologies, we examined the feasibility of using the Genome Sequencer (GS) FLX pyrosequencing system to obtain the sequence of a salmonid genome. Eight pooled BACs belonging to a minimum tiling path covering ~1 Mb of the Atlantic salmon genome were sequenced by GS FLX shotgun and Long Paired End sequencing and compared with a ninth BAC sequenced by Sanger sequencing of a shotgun library.</p> <p>Results</p> <p>An initial assembly using only GS FLX shotgun sequences (average read length 248.5 bp) with ~30× coverage allowed gene identification, but was incomplete even when 126 Sanger-generated BAC-end sequences (~0.09× coverage) were incorporated. The addition of paired end sequencing reads (additional ~26× coverage) produced a final assembly comprising 175 contigs assembled into four scaffolds with 171 gaps. Sanger sequencing of the ninth BAC (~10.5× coverage) produced nine contigs and two scaffolds. The number of scaffolds produced by the GS FLX assembly was comparable to Sanger-generated sequencing; however, the number of gaps was much higher in the GS FLX assembly.</p> <p>Conclusion</p> <p>These results represent the first use of GS FLX paired end reads for <it>de novo </it>sequence assembly. Our data demonstrated that this improved the GS FLX assemblies; however, with respect to <it>de novo </it>sequencing of complex genomes, the GS FLX technology is limited to gene mining and establishing a set of ordered sequence contigs. Currently, for a salmonid reference sequence, it appears that a substantial portion of sequencing should be done using Sanger technology.</p

Lateral diffusivity coefficients from the dynamics of a SF6 patch in a coastal environment

The dispersion of a patch of the tracer sulfur hexafluoride (SF6) is used to assess the lateral diffusivity in the coastal waters of the western part of the Gulf of Lion (GoL), northwestern Mediterranean Sea, during the Latex10 experiment (September 2010). Immediately after the release, the spreading of the patch is associated with a strong decrease of the SF6 concentrations due to the gas exchange from the ocean to the atmosphere. This has been accurately quantified, evidencing the impact of the strong wind conditions during the first days of this campaign. Few days after the release, as the atmospheric loss of SF6 decreased, lateral diffusivity coefficient at spatial scales of 10 km has been computed using two approaches. First, the evolution of the patch with time was combined with a diffusion-strain model to obtain estimates of the strain rate (γ = 2.5 10- 6 s- 1) and of the lateral diffusivity coefficient (Kh = 23.2 m2s− 1). Second, a steady state model was applied, showing Kh values similar to the previous method after a period of adjustment between 2 and 4.5 days. This implies that after such period, our computation of Kh becomes insensitive to the inclusion of further straining of the patch. Analysis of sea surface temperature satellite imagery shows the presence of a strong front in the study area. The front clearly affected the dynamics within the region and thus the temporal evolution of the patch. Our results are consistent with previous studies in open ocean and demonstrate the success and feasibility of those methods also under small-scale, rapidly-evolving dynamics typical of coastal environments

Midgap edge states and pairing symmetry of quasi-one-dimensional organic superconductors

The singlet s-, d- and triplet p-wave pairing symmetries in quasi-one-dimensional organic superconductors can be experimentally discriminated by probing the Andreev bound states at the sample edges. These states have the energy in the middle of the superconducting gap and manifest themselves as a zero-bias peak in tunneling conductance into the corresponding edge. Their existence is related to the sign change of the pairing potential around the Fermi surface. We present an exact self-consistent solution of the edge problem showing the presence of the midgap states for p_x-wave superconductivity. The spins of the edge state respond paramagnetically to a magnetic field parallel to the vector d that characterizes triplet pairing.Comment: 6 pages, 4 figures. V.2: New section on spin response is added and references are updated. V.3: Final version accepted to PRB. Typos are corrected and important note is added in proof

Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates

<p>Abstract</p> <p>Background</p> <p>The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing') remains tedious, labor-intensive, and expensive. As a result, the vast majority of vertebrate genome sequences generated to date remain at a draft stage.</p> <p>Results</p> <p>To date, our genome sequencing efforts have focused on comparative studies of targeted genomic regions, requiring sequence finishing of large blocks of orthologous sequence (average size 0.5-2 Mb) from various subsets of 75 vertebrates. This experience has provided a unique opportunity to compare the relative effort required to finish shotgun-generated genome sequence assemblies from different species, which we report here. Importantly, we found that the sequence assemblies generated for the same orthologous regions from various vertebrates show substantial variation with respect to misassemblies and, in particular, the frequency and characteristics of sequence gaps. As a consequence, the work required to finish different species' sequences varied greatly. Application of the same standardized methods for finishing provided a novel opportunity to "assay" characteristics of genome sequences among many vertebrate species. It is important to note that many of the problems we have encountered during sequence finishing reflect unique architectural features of a particular vertebrate's genome, which in some cases may have important functional and/or evolutionary implications. Finally, based on our analyses, we have been able to improve our procedures to overcome some of these problems and to increase the overall efficiency of the sequence-finishing process, although significant challenges still remain.</p> <p>Conclusion</p> <p>Our findings have important implications for the eventual finishing of the draft whole-genome sequences that have now been generated for a large number of vertebrates.</p