Rotating Resonator-Oscillator Experiments to Test Lorentz Invariance in Electrodynamics

In this work we outline the two most commonly used test theories (RMS and SME) for testing Local Lorentz Invariance (LLI) of the photon. Then we develop the general framework of applying these test theories to resonator experiments with an emphasis on rotating experiments in the laboratory. We compare the inherent sensitivity factors of common experiments and propose some new configurations. Finally we apply the test theories to the rotating cryogenic experiment at the University of Western Australia, which recently set new limits in both the RMS and SME frameworks [hep-ph/0506074].Comment: Submitted to Lecture Notes in Physics, 36 pages, minor modifications, updated list of reference

Variable response of nirK and nirS containing denitrifier communities to long term pH manipulation and cultivation

Denitrification is a key process responsible for the majority of soil nitrous oxide (N2O) emissions but the influences of pH and cultivation on the soil denitrifier community remain poorly understood. We hypothesised that the abundance and community structure of the total bacterial community and bacterial denitrifiers would be pH sensitive and that nirK and nirS containing denitrifiers would differ in their responses to change in pH and cultivation. We investigated the effect of long-term pH adjusted soils (ranging from pH 4.2 to pH 6.6) under different lengths of grass cultivation (one, two and three years of ley grass) on the general bacterial and denitrifier functional communities using 16S rRNA, nirK and nirS genes as markers. Denitrifier abundance increased with pH, and at pH below 4.7 there was a greater loss in nirS abundance per unit drop in pH than soils above this threshold pH. All community structures responded to changes in soil pH whilst cultivation only influenced the community structure of nirK. These differences in denitrifier responses highlight the importance of considering both nirK and nirS gene markers for estimating denitrifier activity. Identifying such thresholds in response of the microbial community to changes in pH is essential to understanding impacts of management or environmental change

Effect of model root exudate on denitrifier community dynamics and activity at different water-filled pore space levels in a fertilised soil

Although a “rhizosphere effect” on denitrification rates has been established, a clear understanding of the effects of exudate addition on denitrifier community dynamics remains elusive. A microcosm experiment was designed to explore the interaction between exudate addition and soil moisture on community dynamics and denitrification rates. Artificial root exudate at 5 different carbon concentrations was added daily to soil microcosms at contrasting target WFPS (50, 70 and 90%). After a 7-day period, total denitrification and N2O emission rates were measured and community dynamics assessed using molecular methods. The response of denitrifier genes to exudate addition was different, with nirS and nosZ-I showing a stronger effect than nirK and nosZ-II. Distinct community structures were observed for nirS and nosZ-I at 90% target WFPS when compared to 50% and 70%. NirS denitrifier population size showed a ca. 5-fold increase in gene copy number at 90% WFPS when exudate was added at the highest C input. Significant total denitrification and N2O emission rates were observed only at 90% WFPS, which increased with C input. Our study improves the understanding of the complex interaction between microbial communities, the abiotic environment and process rates which can inform management practices aimed at increasing complete denitrification and controlling greenhouse gas production from agriculture

Effects of Chromium(VI) and Chromium(III) on Desulfovibrio vulgaris Cells

Desulfovibrio vulgaris ATCC 29579 is a well studied sulfate reducer that has known capabilities of reducing heavy metals and radionuclides, like chromium and uranium. Cultures grown in a defined medium (i.e. LS4D) had a lag period of approximately 40 h when exposed to 50 μMof Cr(VI). Substrate analysis revealed that although chromium is reduced within the first 5 h, growth does not resume for another 35 h. During this time, small amounts of lactate are still utilized but the reduction of sulfate does not occur. Sulfate reduction occurs concurrently with the accumulation of acetate approximately 40 h after inoculation, when growth resumes. Similar amounts of hydrogen are produced during this time compared to hydrogen production by cells not exposed to Cr(VI); therefore an accumulation of hydrogen cannot account for the utilization of lactate. There is a significant decrease in the carbohydrate to protein ratio at approximately 25 h, and this result indicated that lactate is not converted to glycogen. Most probable number analysis indicated that cell viability decreased steadily after inoculation and reached approximately 6 x 104 cells/ml 20 h post-chromium exposure. Regeneration of reducing conditions during chromium exposure does not induce growth and in fact may make the growth conditions even more unfavorable. This result suggested that an increase in Eh was not solely responsible for the decline in viability. Cell pellets collected 10 h after chromium-exposure were unable to resume growth when suspended into fresh medium. Supernatants from these pellets were able to support cell growth upon re- inoculation. D. vulgaris cells treated with a non-dose dependent addition of ascorbate at the same time of Cr(VI) addition did not enter a lag period. Ascorbate added 3 h post-Cr(VI) exposure did not prevent the growth lag. These results indicated that Desulfovibrio utilized lactate to reduce Cr(VI) without the reduction of sulfate, that the decline in cell viability and cell growth was most likely a consequence of Cr(III), and that an organic ligand could protect D. vulgaris cells from Cr(III) toxicity. Lactate consumption decoupled from sulfate reduction in the presence of Cr(VI) could provide organic carbon for organo- Cr(III) complexes

Measuring the vulnerability of Scottish soils to a changing climate

The second Scottish Climate Change Adaptation Programme (SCCAP) identifies soil health as a priority research area to support sustainable soil management and ecosystem services. This follows concerns over a perceived lack of data or gaps in understanding that have been raised in both independent assessments of the first SCCAP by the Committee on Climate Change. The aim of this study is to summarise previous work on Scottish soils, explore existing datasets, and identify those metrics which could support the monitoring of Scotland’s soil health and measure the vulnerability of Scottish soils to climate change in future

Heterogeneity of luminal breast cancer characterised by immunohistochemical expression of basal markers

Background: Luminal A breast cancer defined as hormone receptor positive and human epidermal growth factor receptor 2 (HER2) negative is known to be heterogeneous. Previous study showed that luminal A tumours with the expression of basal markers ((cytokeratin (CK) 5 or CK5/6) or epidermal growth factor receptor (EGFR)) were associated with poorer prognosis compared with those that stained negative for basal markers. Prompted by this study, we assessed whether tumour characteristics and risk factors differed by basal marker status within luminal A tumours. Methods: We pooled 5040 luminal A cases defined by immunohistochemistry (4490 basal-negative ((CK5 (or CK5/6))− and EGFR−) and 550 basal-positive ((CK5 (or CK5/6+)) or EGFR+)) from eight studies participating in the Breast Cancer Association Consortium. Case–case comparison was performed using unconditional logistic regression. Results: Tumour characteristics and risk factors did not vary significantly by the expression of basal markers, although results suggested that basal-positive luminal tumours tended to be smaller and node negative, and were more common in women with a positive family history and lower body mass index. Conclusions: Most established breast cancer risk factors were similar in basal-positive and basal-negative luminal A tumours. The non-significant but suggestive differences in tumour features and family history warrant further investigations

Hypertensive conditions of pregnancy, preterm birth, and premenopausal breast cancer risk: a premenopausal breast cancer collaborative group analysis

Purpose: Women with preeclampsia are more likely to deliver preterm. Reports of inverse associations between preeclampsia and breast cancer risk, and positive associations between preterm birth and breast cancer risk are difficult to reconcile. We investigated the co-occurrence of preeclampsia/gestational hypertension with preterm birth and breast cancer risk using data from the Premenopausal Breast Cancer Collaborative Group. Methods: Across 6 cohorts, 3096 premenopausal breast cancers were diagnosed among 184,866 parous women. We estimated multivariable hazard ratios (HR) and 95% confidence intervals (CI) for premenopausal breast cancer risk using Cox proportional hazards regression. Results: Overall, preterm birth was not associated (HR 1.02, 95% CI 0.92, 1.14), and preeclampsia was inversely associated (HR 0.86, 95% CI 0.76, 0.99), with premenopausal breast cancer risk. In stratified analyses using data from 3 cohorts, preterm birth associations with breast cancer risk were modified by hypertensive conditions in first pregnancies (P-interaction = 0.09). Preterm birth was positively associated with premenopausal breast cancer in strata of women with preeclampsia or gestational hypertension (HR 1.52, 95% CI: 1.06, 2.18), but not among women with normotensive pregnancy (HR = 1.09, 95% CI: 0.93, 1.28). When stratified by preterm birth, the inverse association with preeclampsia was more apparent, but not statistically different (P-interaction = 0.2), among women who did not deliver preterm (HR = 0.82, 95% CI 0.68, 1.00) than those who did (HR = 1.07, 95% CI 0.73, 1.56). Conclusion: Findings support an overall inverse association of preeclampsia history with premenopausal breast cancer risk. Estimates for preterm birth and breast cancer may vary according to other conditions of pregnancy

Protocol for a nested case-control study design for omics investigations in the Environmental Determinants of Islet Autoimmunity cohort

Background: The Environmental Determinants of Islet Autoimmunity (ENDIA) pregnancy-birth cohort investigates the developmental origins of type 1 diabetes (T1D), with recruitment between 2013 and 2019. ENDIA is the first study in the world with comprehensive data and biospecimen collection during pregnancy, at birth and through childhood from at-risk children who have a first-degree relative with T1D. Environmental exposures are thought to drive the progression to clinical T1D, with pancreatic islet autoimmunity (IA) developing in genetically susceptible individuals. The exposures and key molecular mechanisms driving this progression are unknown. Persistent IA is the primary outcome of ENDIA; defined as a positive antibody for at least one of IAA, GAD, ZnT8 or IA2 on two consecutive occasions and signifies high risk of clinical T1D.Method: A nested case-control (NCC) study design with 54 cases and 161 matched controls aims to investigate associations between persistent IA and longitudinal omics exposures in ENDIA. The NCC study will analyse samples obtained from ENDIA children who have either developed persistent IA or progressed to clinical T1D (cases) and matched control children at risk of developing persistent IA. Control children were matched on sex and age, with all four autoantibodies absent within a defined window of the case's onset date. Cases seroconverted at a median of 1.37 years (IQR 0.95, 2.56). Longitudinal omics data generated from approximately 16,000 samples of different biospecimen types, will enable evaluation of changes from pregnancy through childhood.Conclusions: This paper describes the ENDIA NCC study, omics platform design considerations and planned univariate and multivariate analyses for its longitudinal data. Methodologies for multivariate omics analysis with longitudinal data are discovery-focused and data driven. There is currently no single multivariate method tailored specifically for the longitudinal omics data that the ENDIA NCC study will generate and therefore omics analysis results will require either cross validation or independent validation.KEY MESSAGESThe ENDIA nested case-control study will utilize longitudinal omics data on approximately 16,000 samples from 190 unique children at risk of type 1 diabetes (T1D), including 54 who have developed islet autoimmunity (IA), followed during pregnancy, at birth and during early childhood, enabling the developmental origins of T1D to be explored.Helena Oakey ... Lynne C. Giles ... Rebecca L. Thomson ... Pat Ashwood ... Emma J. Knight ... Simon C. Barry ... Kelly McGorm ... Jennifer J. Couper ... Megan A. S. Penno ... the ENDIA Study Group ... et al

PHIP - a novel candidate breast cancer susceptibility locus on 6q14.1

Most non-BRCA1/2 breast cancer families have no identified genetic cause. We used linkage and haplotype analyses in familial and sporadic breast cancer cases to identify a susceptibility locus on chromosome 6q. Two independent genome-wide linkage analysis studies suggested a 3 Mb locus on chromosome 6q and two unrelated Swedish families with a LOD > 2 together seemed to share a haplotype in 6q14.1. We hypothesized that this region harbored a rare high-risk founder allele contributing to breast cancer in these two families. Sequencing of DNA and RNA from the two families did not detect any pathogenic mutations. Finally, 29 SNPs in the region were analyzed in 44,214 cases and 43,532 controls from BCAC, and the original haplotypes in the two families were suggested as low-risk alleles for European and Swedish women specifically. There was also some support for one additional independent moderate-risk allele in Swedish familial samples. The results were consistent with our previous findings in familial breast cancer and supported a breast cancer susceptibility locus at 6q14.1 around the PHIP gene.Peer reviewe

Materializing digital collecting: an extended view of digital materiality

If digital objects are abundant and ubiquitous, why should consumers pay for, much less collect them? The qualities of digital code present numerous challenges for collecting, yet digital collecting can and does occur. We explore the role of companies in constructing digital consumption objects that encourage and support collecting behaviours, identifying material configuration techniques that materialise these objects as elusive and authentic. Such techniques, we argue, may facilitate those pleasures of collecting otherwise absent in the digital realm. We extend theories of collecting by highlighting the role of objects and the companies that construct them in materialising digital collecting. More broadly, we extend theories of digital materiality by highlighting processes of digital material configuration that occur in the pre-objectification phase of materialisation, acknowledging the role of marketing and design in shaping the qualities exhibited by digital consumption objects and consequently related consumption behaviours and experiences