A comparison of theoretical line intensity ratios for Ni XII with extreme ultraviolet observations from the JET tokamak

Recent R-matrix calculations of electron impact excitation rates in Ni XII are used to derive the emission line ratios R1 = I (154.17 Å)/I (152.15 Å), R2 = I (152.95 Å)/I (152.15 Å) and R3 = I (160.55 Å)/I (152.15 Å). This is the first time (to our knowledge) that theoretical emission line ratios have been calculated for this ion. The ratios are found to be insensitive to changes in the adopted electron density (Ne) when Ne >= 5 × 10^11 cm−3, typical of laboratory plasmas. However, they do vary with electron temperature (Te), with for example R1 and R3 changing by factors of 1.3 and 1.8, respectively, between Te = 10^5 and 10^6 K. A comparison of the theoretical line ratios with measurements from the Joint European Torus (JET) tokamak reveals very good agreement between theory and observation for R1, with an average discrepancy of only 7%. Agreement between the calculated and experimental ratios for R2 and R3 is less satisfactory, with average differences of 30 and 33%, respectively. These probably arise from errors in the JET instrument calibration curve. However, the discrepancies are smaller than the uncertainties in the R2 and R3 measurements. Our results, in particular for R1, provide experimental support for the accuracy of the Ni XII line ratio calculations, and hence for the atomic data adopted in their derivation

HIV-infected sex workers with beneficial HLA-variants are potential hubs for selection of HIV-1 recombinants that may affect disease progression

Cytotoxic T lymphocyte (CTL) responses against the HIV Gag protein are associated with lowering viremia; however, immune control is undermined by viral escape mutations. The rapid viral mutation rate is a key factor, but recombination may also contribute. We hypothesized that CTL responses drive the outgrowth of unique intra-patient HIV-recombinants (URFs) and examined gag sequences from a Kenyan sex worker cohort. We determined whether patients with HLA variants associated with effective CTL responses (beneficial HLA variants) were more likely to carry URFs and, if so, examined whether they progressed more rapidly than patients with beneficial HLA-variants who did not carry URFs. Women with beneficial HLA-variants (12/52) were more likely to carry URFs than those without beneficial HLA variants (3/61) (p < 0.0055; odds ratio = 5.7). Beneficial HLA variants were primarily found in slow/standard progressors in the URF group, whereas they predominated in long-term non-progressors/survivors in the remaining cohort (p = 0.0377). The URFs may sometimes spread and become circulating recombinant forms (CRFs) of HIV and local CRF fragments were over-represented in the URF sequences (p < 0.0001). Collectively, our results suggest that CTL-responses associated with beneficial HLA variants likely drive the outgrowth of URFs that might reduce the positive effect of these CTL responses on disease progression

The HPC next door: enabling research outcomes using QCIF HPC facilities

The paper begins with a background of the problem, a description of the research projects requiring use of HPC, followed by the problems with accessing the HPC resources required, and an account of the approach taken to solve the problem. A description of the solutions is provided, followed by a discussion on the research outcomes and a reflection on lessons learnt

The Mineralogical Record of Oxygen Fugacity Variation and Alteration in Northwest Africa 8159: Evidence for Interaction Between a Mantle Derived Martian Basalt and a Crustal Component(s)

A prominent geochemical feature of basaltic magmatism on Mars is the large range in initial Sr isotopic ratios (approx. 0.702 - 0.724) and initial epsilon-Nd values (approx. -10 to greater than +50). Within this range, the shergottites fall into three discreet subgroups. These subgroups have distinct bulk rock REE patterns, mineral chemistries (i.e. phosphate REE patterns, Ni, Co, V in olivine), oxygen fugacity of crystallization, and stable isotopes, such as O. In contrast, nakhlites and chassignites have depleted epsilon-Nd values (greater than or equal to +15), have REE patterns that are light REE enriched, and appear to have crystallized near the FMQ buffer. The characteristics of these various martian basalts have been linked to different reservoirs in the martian crust and mantle, and their interactions during the petrogenesis of these magmas. These observations pose interesting interpretive challenges to our understanding of the conditions of the martian mantle (e.g. oxygen fugacity) and the interaction of mantle derived magmas with the martian crust and surface. Martian meteorite NWA 8159 is a unique fine-grained augite basalt derived from a highly depleted mantle source as reflected in its initial epsilon-Nd value, contains a pronounced light REE depleted pattern, and crystallized presumably under very oxidizing conditions. Although considerably older than both shergottites and nahklites, it has been petrogenetically linked to both styles of martian magmatism. These unique characteristics of NWA 8159 may provide an additional perspective for deciphering the petrogenesis of martian basalts and the nature of the crust of Mars

Graphs for which the least eigenvalue is minimal, II

We continue our investigation of graphs G for which the least eigenvalue ?(G) is minimal among the connected graphs of prescribed order and size. We provide structural details of the bipartite graphs that arise, and study the behaviour of ?(G) as the size increases while the order remains constant. The non-bipartite graphs that arise were investigated in a previous paper [F.K. Bell, D. Cvetkovic', P. Rowlinson, S.K. Simic', Graphs for which the least eigenvalue is minimal, I, Linear Algebra Appl. (2008), doi: 10.1016/j.laa.2008.02.032]; here we distinguish the cases of bipartite and non-bipartite graphs in terms of size. Erratum is published in: Richard A Brualdi, 'From the Editor-in-Chief', Linear Algebra Applications, 432(1) pp.1-6, 01/2010 &nbsp

A catalogue of the Chandra Deep Field South with multi-colour classification and photometric redshifts from COMBO-17

We present the COMBO-17 object catalogue of the Chandra Deep Field South for public use, covering a field which is 31.5' x 30' in size. This catalogue lists astrometry, photometry in 17 passbands from 350 to 930 nm, and ground-based morphological data for 63,501 objects. The catalogue also contains multi-colour classification into the categories 'Star', 'Galaxy' and 'Quasar' as well as photometric redshifts. We include restframe luminosities in Johnson, SDSS and Bessell passbands and estimated errors. The redshifts are most reliable at R<24, where the sample contains approximately 100 quasars, 1000 stars and 10000 galaxies. We use nearly 1000 spectroscopically identified objects in conjunction with detailed simulations to characterize the performance of COMBO-17. We show that the selection of quasars, more generally type-1 AGN, is nearly complete and minimally contaminated at z=[0.5,5] for luminosities above M_B=-21.7. Their photometric redshifts are accurate to roughly 5000 km/sec. Galaxy redshifts are accurate to 1% in dz/(1+z) at R<21. They degrade in quality for progressively fainter galaxies, reaching accuracies of 2% for galaxies with R~222 and of 10% for galaxies with R>24. The selection of stars is complete to R~23, and deeper for M stars. We also present an updated discussion of our classification technique with maps of survey completeness, and discuss possible failures of the statistical classification in the faint regime at R>24.Comment: submitted to Astronomy & Astrophysics, public data set available at http://www.mpia.de/COMBO/combo_index.htm

Science and Ideology in Economic, Political, and Social Thought

This paper has two sources: One is my own research in three broad areas: business cycles, economic measurement and social choice. In all of these fields I attempted to apply the basic precepts of the scientific method as it is understood in the natural sciences. I found that my effort at using natural science methods in economics was met with little understanding and often considerable hostility. I found economics to be driven less by common sense and empirical evidence, then by various ideologies that exhibited either a political or a methodological bias, or both. This brings me to the second source: Several books have appeared recently that describe in historical terms the ideological forces that have shaped either the direct areas in which I worked, or a broader background. These books taught me that the ideological forces in the social sciences are even stronger than I imagined on the basis of my own experiences. The scientific method is the antipode to ideology. I feel that the scientific work that I have done on specific, long standing and fundamental problems in economics and political science have given me additional insights into the destructive role of ideology beyond the history of thought orientation of the works I will be discussing

Financial considerations in the conduct of multi-centre randomised controlled trials: evidence from a qualitative study.

National Coordinating Centre for Research Methodology; Medical Research Council, UK Department of Health; Chief Scientist OfficeNot peer reviewedPublisher PD

Optimization of sequence alignment for simple sequence repeat regions

Abstract Background Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs) mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs). SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic phylogenic relationship.</p