Astrophysically robust systematics removal using variational inference: application to the first month of Kepler data

Space-based transit search missions such as Kepler are collecting large numbers of stellar light curves of unprecedented photometric precision and time coverage. However, before this scientific goldmine can be exploited fully, the data must be cleaned of instrumental artefacts. We present a new method to correct common-mode systematics in large ensembles of very high precision light curves. It is based on a Bayesian linear basis model and uses shrinkage priors for robustness, variational inference for speed, and a de-noising step based on empirical mode decomposition to prevent the introduction of spurious noise into the corrected light curves. After demonstrating the performance of our method on a synthetic dataset, we apply it to the first month of Kepler data. We compare the results, which are publicly available, to the output of the Kepler pipeline's pre-search data conditioning, and show that the two generally give similar results, but the light curves corrected using our approach have lower scatter, on average, on both long and short timescales. We finish by discussing some limitations of our method and outlining some avenues for further development. The trend-corrected data produced by our approach are publicly available.Comment: 15 pages, 13 figures, accepted for publication in MNRA

Towards the Green-Griffiths-Lang conjecture

The Green-Griffiths-Lang conjecture stipulates that for every projective variety X of general type over C, there exists a proper algebraic subvariety of X containing all non constant entire curves f : C $\rightarrow$ X. Using the formalism of directed varieties, we prove here that this assertion holds true in case X satisfies a strong general type condition that is related to a certain jet-semistability property of the tangent bundle TX . We then give a sufficient criterion for the Kobayashi hyperbolicity of an arbitrary directed variety (X,V). This work is dedicated to the memory of Professor Salah Baouendi.Comment: version 2 has been expanded and improved (15 pages

Recombinase polymerase amplification for fast, selective, DNA‐based detection of faecal indicator Escherichia coli

The bacterium Escherichia coli is commonly associated with the presence of faecal contamination in environmental samples, and is therefore subject to statutory surveillance. This is normally done using a culture‐based methodology, which can be slow and laborious. Nucleic acid amplification for the detection of E. coli DNA sequences is a significantly more rapid approach, suited for applications in the field such as a point of sample analysis, and to provide an early warning of contamination. An existing, high integrity qPCR method to detect the E. coli ybbW gene, which requires almost an hour to detect low quantities of the target, was compared with a novel, isothermal RPA method, targeting the same sequence but achieving the result within a few minutes. The RPA technique demonstrated equivalent inclusivity and selectivity, and was able to detect DNA extracted from 100% of 99 E. coli strains, and exclude 100% of 30 non‐target bacterial species. The limit of detection of the RPA assay was at least 100 target sequence copies. The high speed, and simple, isothermal amplification chemistry may indicate that RPA is a more suitable methodology for on‐site E. coli monitoring than an existing qPCR technique

The regulation of copper stress response genes in the Polychaete Nereis diversicolor during prolonged extreme copper contamination

Polychaetes are frequented in toxicological studies, one reason being that some members occupy shallow burrows in sediments and are maximally exposed to the contaminants that accumulate within them. We have been studying one population of the polychaete Nereis (Hediste) diversicolor exhibiting inheritable tolerance to extreme copper contamination in estuarine sediment. Using transcriptome sequencing data we have identified a suite of genes with putative roles in metal detoxification and tolerance, and measured their regulation. Copper tolerant individuals display significantly different gene expression profiles compared to animals from a nearby population living without remarkable copper levels. Gene transcripts encoding principle copper homeostasis proteins including membrane copper ion transporters, copper ion chaperones and putative metallothionein-like proteins were significantly more abundant in tolerant animals occupying contaminated sediment. In contrast, those encoding antioxidants and cellular repair pathways were unchanged. Nontolerant animals living in contaminated sediment showed no difference in copper homeostasis-related gene expression but did have significantly elevated levels of mRNAs encoding Glutathione Peroxidase enzymes. This study represents the first use of functional genomics to investigate the copper tolerance trait in this species and provides insight into the mechanism used by these individuals to survive and flourish in conditions which are lethal to their conspecifics

The Social Construction of Infertility

Health and illness are not objective states but socially constructed categories. We focus here on infertility, a phenomenon that has shifted from being seen as a private problem of couples to being seen as a medical condition. Studying infertility provides an ideal vantage point from which to study such features of health care as inter-societal and cross-cultural disparities in health care, the relationship between identity and health, gender roles, and social and cultural variations in the process of medicalization. Infertility is stratified, both globally and within Western societies. Access to care is extremely limited for many women in developing societies and also for marginalized women in some highly industrialized societies. We also discuss the ways in which responses to infertility are influenced by the process of self-definition. The experience of infertility is profoundly shaped by varying degrees of pronatalism and patriarchy. In advanced industrial societies, where voluntary childfree status is acknowledged, many women experience infertility as a “secret stigma”; in other cultures, where motherhood is normative for all women, infertility may be impossible to hide. In the West, acceptance of the medical model is virtually hegemonic, but in other societies medical interpretations of infertility coexist with traditional interpretations

Monitoring young associations and open clusters with Kepler in two-wheel mode

We outline a proposal to use the Kepler spacecraft in two-wheel mode to monitor a handful of young associations and open clusters, for a few weeks each. Judging from the experience of similar projects using ground-based telescopes and the CoRoT spacecraft, this program would transform our understanding of early stellar evolution through the study of pulsations, rotation, activity, the detection and characterisation of eclipsing binaries, and the possible detection of transiting exoplanets. Importantly, Kepler's wide field-of-view would enable key spatially extended, nearby regions to be monitored in their entirety for the first time, and the proposed observations would exploit unique synergies with the GAIA ESO spectroscopic survey and, in the longer term, the GAIA mission itself. We also outline possible strategies for optimising the photometric performance of Kepler in two-wheel mode by modelling pixel sensitivity variations and other systematics.Comment: 10 pages, 6 figures, white paper submitted in response to NASA call for community input for alternative science investigations for the Kepler spacecraf

Effective algebraic degeneracy

We prove that any nonconstant entire holomorphic curve from the complex line C into a projective algebraic hypersurface X = X^n in P^{n+1}(C) of arbitrary dimension n (at least 2) must be algebraically degenerate provided X is generic if its degree d = deg(X) satisfies the effective lower bound: d larger than or equal to n^{{(n+1)}^{n+5}}