Open-source development experiences in scientific software: the HANDE quantum Monte Carlo project

The HANDE quantum Monte Carlo project offers accessible stochastic algorithms for general use for scientists in the field of quantum chemistry. HANDE is an ambitious and general high-performance code developed by a geographically-dispersed team with a variety of backgrounds in computational science. In the course of preparing a public, open-source release, we have taken this opportunity to step back and look at what we have done and what we hope to do in the future. We pay particular attention to development processes, the approach taken to train students joining the project, and how a flat hierarchical structure aids communicationComment: 6 pages. Submission to WSSSPE

Letter from Eiler Freece

Letter concerning qualifications for a position at the Utah Agricultural College, including references

Claw-free t-perfect graphs can be recognised in polynomial time

A graph is called t-perfect if its stable set polytope is defined by non-negativity, edge and odd-cycle inequalities. We show that it can be decided in polynomial time whether a given claw-free graph is t-perfect

The molecular genetic analysis of the expanding pachyonychia congenita case collection

BACKGROUND: Pachyonychia congenita (PC) is a rare autosomal dominant keratinizing disorder characterized by severe, painful, palmoplantar keratoderma and nail dystrophy, often accompanied by oral leucokeratosis, cysts and follicular keratosis. It is caused by mutations in one of five keratin genes: KRT6A, KRT6B, KRT6C, KRT16 or KRT17. OBJECTIVES: To identify mutations in 84 new families with a clinical diagnosis of PC, recruited by the International Pachyonychia Congenita Research Registry during the last few years. METHODS: Genomic DNA isolated from saliva or peripheral blood leucocytes was amplified using primers specific for the PC-associated keratin genes and polymerase chain reaction products were directly sequenced. RESULTS: Mutations were identified in 84 families in the PC-associated keratin genes, comprising 46 distinct keratin mutations. Fourteen were previously unreported mutations, bringing the total number of different keratin mutations associated with PC to 105. CONCLUSIONS: By identifying mutations in KRT6A, KRT6B, KRT6C, KRT16 or KRT17, this study has confirmed, at the molecular level, the clinical diagnosis of PC in these families

The effectiveness of SPARX, a computerised self help intervention for adolescents seeking help for depression: randomised controlled non-inferiority trial

Objective To evaluate whether a new computerised cognitive behavioural therapy intervention (SPARX, Smart, Positive, Active, Realistic, X-factor thoughts) could reduce depressive symptoms in help seeking adolescents as much or more than treatment as usual

Pubertal timing and breast density in young women: a prospective cohort study.

BACKGROUND:Earlier age at onset of pubertal events and longer intervals between them (tempo) have been associated with increased breast cancer risk. It is unknown whether the timing and tempo of puberty are associated with adult breast density, which could mediate the increased risk. METHODS:From 1988 to 1997, girls participating in the Dietary Intervention Study in Children (DISC) were clinically assessed annually between ages 8 and 17 years for Tanner stages of breast development (thelarche) and pubic hair (pubarche), and onset of menses (menarche) was self-reported. In 2006-2008, 182 participants then aged 25-29 years had their percent dense breast volume (%DBV) measured by magnetic resonance imaging. Multivariable, linear mixed-effects regression models adjusted for reproductive factors, demographics, and body size were used to evaluate associations of age and tempo of puberty events with %DBV. RESULTS:The mean (standard deviation) and range of %DBV were 27.6 (20.5) and 0.2-86.1. Age at thelarche was negatively associated with %DBV (p trend = 0.04), while pubertal tempo between thelarche and menarche was positively associated with %DBV (p trend = 0.007). %DBV was 40% higher in women whose thelarche-to-menarche tempo was 2.9 years or longer (geometric mean (95%CI) = 21.8% (18.2-26.2%)) compared to women whose thelarche-to-menarche tempo was less than 1.6 years (geometric mean (95%CI) = 15.6% (13.9-17.5%)). CONCLUSIONS:Our results suggest that a slower pubertal tempo, i.e., greater number of months between thelarche and menarche, is associated with higher percent breast density in young women. Future research should examine whether breast density mediates the association between slower tempo and increased breast cancer risk

Implications of albedo changes following afforestation on the benefits of forests as carbon sinks

Increased carbon storage with afforestation leads to a decrease in atmospheric carbon dioxide concentration and thus decreases radiative forcing and cools the Earth. However, afforestation also changes the reflective properties of the surface vegetation from more reflective pasture to relatively less reflective forest cover. This increase in radiation absorption by the forest constitutes an increase in radiative forcing, with a warming effect. The net effect of decreased albedo and carbon storage on radiative forcing depends on the relative magnitude of these two opposing processes. <br></br> We used data from an intensively studied site in New Zealand's Central North Island that has long-term, ground-based measurements of albedo over the full short-wave spectrum from a developing <i>Pinus radiata</i> forest. Data from this site were supplemented with satellite-derived albedo estimates from New Zealand pastures. The albedo of a well-established forest was measured as 13 % and pasture albedo as 20 %. We used these data to calculate the direct radiative forcing effect of changing albedo as the forest grew. <br></br> We calculated the radiative forcing resulting from the removal of carbon from the atmosphere as a decrease in radiative forcing of −104 GJ tC<sup>−1</sup> yr<sup>−1</sup>. We also showed that the observed change in albedo constituted a direct radiative forcing of 2759 GJ ha<sup>−1</sup> yr<sup>−1</sup>. Thus, following afforestation, 26.5 tC ha<sup>−1</sup> needs to be stored in a growing forest to balance the increase in radiative forcing resulting from the observed albedo change. Measurements of tree biomass and albedo were used to estimate the net change in radiative forcing as the newly planted forest grew. Albedo and carbon-storage effects were of similar magnitude for the first four to five years after tree planting, but as the stand grew older, the carbon storage effect increasingly dominated. Averaged over the whole length of the rotation, the changes in albedo negated the benefits from increased carbon storage by 17–24 %

Design, development and verification of the 30 and 44 GHz front-end modules for the Planck Low Frequency Instrument

We give a description of the design, construction and testing of the 30 and 44 GHz Front End Modules (FEMs) for the Low Frequency Instrument (LFI) of the Planck mission to be launched in 2009. The scientific requirements of the mission determine the performance parameters to be met by the FEMs, including their linear polarization characteristics. The FEM design is that of a differential pseudo-correlation radiometer in which the signal from the sky is compared with a 4-K blackbody load. The Low Noise Amplifier (LNA) at the heart of the FEM is based on indium phosphide High Electron Mobility Transistors (HEMTs). The radiometer incorporates a novel phase-switch design which gives excellent amplitude and phase match across the band. The noise temperature requirements are met within the measurement errors at the two frequencies. For the most sensitive LNAs, the noise temperature at the band centre is 3 and 5 times the quantum limit at 30 and 44 GHz respectively. For some of the FEMs, the noise temperature is still falling as the ambient temperature is reduced to 20 K. Stability tests of the FEMs, including a measurement of the 1/f knee frequency, also meet mission requirements. The 30 and 44 GHz FEMs have met or bettered the mission requirements in all critical aspects. The most sensitive LNAs have reached new limits of noise temperature for HEMTs at their band centres. The FEMs have well-defined linear polarization characteristcs.Comment: 39 pages, 33 figures (33 EPS files), 12 tables. Planck LFI technical papers published by JINST: http://www.iop.org/EJ/journal/-page=extra.proc5/1748-022