Radio Frequency Plasma Discharge Lamps for Use as Stable Calibration Light Sources

Stable high radiance in visible and near-ultraviolet wavelengths is desirable for radiometric calibration sources. In this work, newly available electrodeless radio-frequency (RF) driven plasma light sources were combined with research grade, low-noise power supplies and coupled to an integrating sphere to produce a uniform radiance source. The stock light sources consist of a 28 VDC power supply, RF driver, and a resonant RF cavity. The RF cavity includes a small bulb with a fill gas that is ionized by the electric field and emits light. This assembly is known as the emitter. The RF driver supplies a source of RF energy to the emitter. In commercial form, embedded electronics within the RF driver perform a continual optimization routine to maximize energy transfer to the emitter. This optimization routine continually varies the light output sinusoidally by approximately 2% over a several-second period. Modifying to eliminate this optimization eliminates the sinusoidal variation but allows the output to slowly drift over time. This drift can be minimized by allowing sufficient warm-up time to achieve thermal equilibrium. It was also found that supplying the RF driver with a low-noise source of DC electrical power improves the stability of the lamp output. Finally, coupling the light into an integrating sphere reduces the effect of spatial fluctuations, and decreases noise at the output port of the sphere

Deriving simple predictions from complex models to support environmental decision-making

Recent decades have seen great advances in ecological modelling and computing power, enabling ecologists to build increasingly detailed models to more accurately represent ecological systems. To better inform environmental decision-making, it is important that the predictions of these models are expressed in simple ways that are straightforward for stakeholders to comprehend and use. One way to achieve this is to predict threshold values for environmental perturbations (e.g. climate change, habitat modification, food loss, sea level rise) associated with negative impacts on individuals, populations, communities or ecosystems. These thresholds can be used by stakeholders to inform management and policy. In this paper we demonstrate how this approach can use individual-based models of birds, their prey and habitats, to provide the evidence-base for coastal bird conservation and shellfishery management. In particular, we show how such models can be used to identify threshold values for perturbations of food abundance that can impact negatively on bird populations. We highlight how environmental thresholds could be used more widely to inform management of species and habitats under environmental change

Identification of a BRCA2-Specific modifier locus at 6p24 related to breast cancer risk

Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80-0.90, P = 3.9×10−8). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associat

The structure and spectroscopy of neutron-rich nuclei

Our knowledge of the structure and spectroscopy of neutron-rich nuclei has greatly increased due to two important developments in nuclear physics: the construction of large $\gamma$-ray arrays to investigate prompt $\gamma$-rays from fission and deep-inelastic reactions; and the availability of radioactive nuclei from fragmentation and spallation reactions. In this review examples will be given of the advances that have been made in our understanding of the properties of neutron-rich nuclei. The examples are necessarily selective, given the limitations of space and time