Atmospheric dispersion and the implications for phase calibration

The success of any ALMA phase-calibration strategy, which incorporates phase transfer, depends on a good understanding of how the atmospheric path delay changes with frequency (e.g. Holdaway & Pardo 2001). We explore how the wet dispersive path delay varies for realistic atmospheric conditions at the ALMA site using the ATM transmission code. We find the wet dispersive path delay becomes a significant fraction (>5 per cent) of the non-dispersive delay for the high-frequency ALMA bands (>160 GHz, Bands 5 to 10). Additionally, the variation in dispersive path delay across ALMA's 4-GHz contiguous bandwidth is not significant except in Bands 9 and 10. The ratio of dispersive path delay to total column of water vapour does not vary significantly for typical amounts of water vapour, water vapour scale heights and ground pressures above Chajnantor. However, the temperature profile and particularly the ground-level temperature are more important. Given the likely constraints from ALMA's ancillary calibration devices, the uncertainty on the dispersive-path scaling will be around 2 per cent in the worst case and should contribute about 1 per cent overall to the wet path fluctuations at the highest frequencies.Comment: 13 pages, 10 figures, ALMA Memo 59

A submillimetre survey of the kinematics of the Perseus molecular cloud - III. Clump kinematics

We explore the kinematics of continuum clumps in the Perseus molecular cloud, derived from C18O J=3-2 data. Two populations are examined, identified using the automated algorithms CLFIND and GAUSSCLUMPS on existing SCUBA data. The clumps have supersonic linewidths with distributions which suggest the C18O line probes a lower-density 'envelope' rather than a dense inner core. Similar linewidth distributions for protostellar and starless clumps implies protostars do not have a significant impact on their immediate environment. The proximity to an active young stellar cluster seems to affect the linewidths: those in NGC1333 are greater than elsewhere. In IC348 the proximity to the old IR cluster has little influence, with the linewidths being the smallest of all. A virial analysis suggests that the clumps are bound and close to equipartition. In particular, the starless clumps occupy the same parameter space as the protostars, suggesting they are true stellar precursors and will go on to form stars. We also search for ordered C18O velocity gradients across the face of each core, usually interpreted as rotation. We note a correlation between the directions of the identified gradients and outflows across protostars, indicating we may not have a purely rotational signature. The fitted gradients are larger than found in previous work, probably as a result of the higher resolution of our data and/or outflow contamination. These gradients, if interpreted solely in terms of rotation, suggest that rotation is not dynamically significant. Furthermore, derived specific angular momenta are smaller than observed in previous studies, centred around j~0.001 km/s pc, which indicates we have identified lower levels of rotation, or that the C18O J=3-2 line probes conditions significantly denser and/or colder than n~10^5 per cc and T~10 K.Comment: 20 pages, 20 figures, accepted for publication by MNRAS. Supplementary, on-line only material available from http://www.mrao.cam.ac.uk/~eic22/Papers/CR10b_suppmaterial.pd

The properties of SCUBA cores in the Perseus molecular cloud: the bias of clump-finding algorithms

We present a new analysis of the properties of star-forming cores in the Perseus molecular cloud, identified in SCUBA 850 micron data. Our goal is to determine which core properties can be robustly identified and which depend on the extraction technique. Four regions in the cloud are examined: NGC1333, IC348/HH211, L1448 and L1455. We identify clumps of dust emission using two popular automated algorithms, CLFIND and GAUSSCLUMPS, finding 85 and 122 clumps in total respectively. Some trends are true for both populations: clumps become increasingly elongated over time and are consistent with constant surface brightness objects, with an average brightness ~4 to 10 times larger than the surrounding molecular cloud; the clump mass distribution (CMD) resembles the stellar intial mass function, with a slope alpha = -2.0+/-0.1 for CLFIND and alpha = -3.15+/-0.08 for GAUSSCLUMPS, which straddle the Salpeter value. The mass at which the slope shallows (similar for both algorithms at M~6 Msun) implies a star-forming efficiency of between 10 and 20 per cent. Other trends reported elsewhere depend on the clump-finding technique: we find protostellar clumps are both smaller (for GAUSSCLUMPS) and larger (for CLFIND) than their starless counterparts; the functional form, best-fitting to the CMD, is different for the two algorithms. The GAUSSCLUMPS CMD is best-fitted with a log-normal distribution, whereas a broken power law is best for CLFIND; the reported lack of massive starless cores in previous studies can be seen in the CLFIND but not the GAUSSCLUMPS data. Our approach highlights similarities and differences between the clump populations, illustrating the caution that must be exercised when comparing results from different studies and interpreting the properties of continuum cores.Comment: 19 pages, 17 figures, accepted for publication by MNRA

A submillimetre survey of the kinematics of the Perseus molecular cloud: I. data

We present submillimetre observations of the J = 3-2 rotational transition of 12CO, 13CO and C18O across over 600 sq arcmin of the Perseus molecular cloud, undertaken with HARP, a new array spectrograph on the James Clerk Maxwell Telescope. The data encompass four regions of the cloud, containing the largest clusters of dust continuum condensations: NGC 1333, IC348, L1448 and L1455. A new procedure to remove striping artefacts from the raw HARP data is introduced. We compare the maps to those of the dust continuum emission mapped with SCUBA (Hatchell et al. 2005) and the positions of starless and protostellar cores (Hatchell et al. 2007a). No straightforward correlation is found between the masses of each region derived from the HARP CO and SCUBA data, underlining the care that must be exercised when comparing masses of the same object derived from different tracers. From the 13CO/C18O line ratio the relative abundance of the two species ([13CO]/[C18O] ~ 7) and their opacities (typically tau is 0.02-0.22 and 0.15-1.52 for the C18O and 13CO gas respectively) are calculated. C18O is optically thin nearly everywhere, increasing in opacity towards star-forming cores but not beyond tau(C18O)~0.9. Assuming the 12CO gas is optically thick we compute its excitation temperature (around 8-30 K), which has little correlation with estimates of the dust temperature.Comment: 20 pages, 15 figures, accepted for publication by MNRA

AMI Large Array radio continuum observations of Spitzer c2d small clouds and cores

We perform deep 1.8 cm radio continuum imaging towards thirteen protostellar regions selected from the Spitzer c2d small clouds and cores programme at high resolution (25") in order to detect and quantify the cm-wave emission from deeply embedded young protostars. Within these regions we detect fifteen compact radio sources which we identify as radio protostars including two probable new detections. The sample is in general of low bolometric luminosity and contains several of the newly detected VeLLO sources. We determine the 1.8 cm radio luminosity to bolometric luminosity correlation, L_rad -L_bol, for the sample and discuss the nature of the radio emission in terms of the available sources of ionized gas. We also investigate the L_rad-L_IR correlation and suggest that radio flux density may be used as a proxy for the internal luminosity of low luminosity protostars.Comment: submitted MNRA

Natural climate solutions for the United States

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Science Advances 4 (2018): eaat1869, doi:10.1126/sciadv.aat1869.Limiting climate warming to <2°C requires increased mitigation efforts, including land stewardship, whose potential in the United States is poorly understood. We quantified the potential of natural climate solutions (NCS)—21 conservation, restoration, and improved land management interventions on natural and agricultural lands—to increase carbon storage and avoid greenhouse gas emissions in the United States. We found a maximum potential of 1.2 (0.9 to 1.6) Pg CO2e year−1, the equivalent of 21% of current net annual emissions of the United States. At current carbon market prices (USD 10 per Mg CO2e), 299 Tg CO2e year−1 could be achieved. NCS would also provide air and water filtration, flood control, soil health, wildlife habitat, and climate resilience benefits.This study was made possible by funding from the Doris Duke Charitable Foundation. C.A.W. and H.G. acknowledge financial support from NASA’s Carbon Monitoring System program (NNH14ZDA001N-CMS) under award NNX14AR39G. S.D.B. acknowledges support from the DOE’s Office of Biological and Environmental Research Program under the award DE-SC0014416. J.W.F. acknowledges financial support from the Florida Coastal Everglades Long-Term Ecological Research program under National Science Foundation grant no. DEB-1237517

Placental uptake and metabolism of 25(OH)vitamin D determine its activity within the fetoplacental unit

Pregnancy 25-hydroxyvitamin D [25(OH)D] concentrations are associated with maternal and fetal health outcomes. Using physiological human placental perfusion and villous explants, we investigate the role of the placenta in regulating the relationships between maternal 25(OH)D and fetal physiology. We demonstrate active placental uptake of 25(OH)D3 by endocytosis, placental metabolism of 25(OH)D3 into 24,25-dihydroxyvitamin D3 and active 1,25-dihydroxyvitamin D [1,25(OH)2D3], with subsequent release of these metabolites into both the maternal and fetal circulations. Active placental transport of 25(OH)D3 and synthesis of 1,25(OH)2D3 demonstrate that fetal supply is dependent on placental function rather than simply the availability of maternal 25(OH)D3. We demonstrate that 25(OH)D3 exposure induces rapid effects on the placental transcriptome and proteome. These map to multiple pathways central to placental function and thereby fetal development, independent of vitamin D transfer. Our data suggest that the underlying epigenetic landscape helps dictate the transcriptional response to vitamin D treatment. This is the first quantitative study demonstrating vitamin D transfer and metabolism by the human placenta, with widespread effects on the placenta itself. These data demonstrate a complex interplay between vitamin D and the placenta and will inform future interventions using vitamin D to support fetal development and maternal adaptations to pregnancy.</jats:p

Proceedings of the third international molecular pathological epidemiology (MPE) meeting

Molecular pathological epidemiology (MPE) is a transdisciplinary and relatively new scientific discipline that integrates theory, methods and resources from epidemiology, pathology, biostatistics, bioinformatics and computational biology. The underlying objective of MPE research is to better understand the etiology and progression of complex and heterogeneous human diseases with the goal of informing prevention and treatment efforts in population health and clinical medicine. Although MPE research has been commonly applied to investigating breast, lung, and colorectal cancers, its methodology can be used to study most diseases. Recent successes in MPE studies include: 1) the development of new statistical methods to address etiologic heterogeneity; 2) the enhancement of causal inference; 3) the identification of previously unknown exposure-subtype disease associations; and 4) better understanding of the role of lifestyle/behavioral factors on modifying prognosis according to disease subtype. Central challenges to MPE include the relative lack of transdisciplinary experts, educational programs, and forums to discuss issues related to the advancement of the field. To address these challenges, highlight recent successes in the field, and identify new opportunities, a series of MPE meetings have been held at the Dana-Farber Cancer Institute in Boston, MA. Herein, we share the proceedings of the Third International MPE Meeting, held in May 2016 and attended by 150 scientists from 17 countries. Special topics included integration of MPE with immunology and health disparity research. This meeting series will continue to provide an impetus to foster further transdisciplinary integration of divergent scientific fields

Evaluation of polygenic risk scores for breast and ovarian cancer risk prediction in BRCA1 and BRCA2 mutation carriers

Background: Genome-wide association studies (GWAS) have identified 94 common single-nucleotide polymorphisms (SNPs) associated with breast cancer (BC) risk and 18 associated with ovarian cancer (OC) risk. Several of these are also associated with risk of BC or OC for women who carry a pathogenic mutation in the high-risk BC and OC genes BRCA1 or BRCA2. The combined effects of these variants on BC or OC risk for BRCA1 and BRCA2 mutation carriers have not yet been assessed while their clinical management could benefit from improved personalized risk estimates. Methods: We constructed polygenic risk scores (PRS) using BC and OC susceptibility SNPs identified through population-based GWAS: for BC (overall, estrogen receptor [ER]-positive, and ER-negative) and for OC. Using data from 15 252 female BRCA1 and 8211 BRCA2 carriers, the association of each PRS with BC or OC risk was evaluated using a weighted cohort approach, with time to diagnosis as the outcome and estimation of the hazard ratios (HRs) per standard deviation increase in the PRS. Results: The PRS for ER-negative BC displayed the strongest association with BC risk in BRCA1 carriers (HR = 1.27, 95% confidence interval [CI] = 1.23 to 1.31, P = 8.2 x 10(53)). In BRCA2 carriers, the strongest association with BC risk was seen for the overall BC PRS (HR = 1.22, 95% CI = 1.17 to 1.28, P = 7.2 x 10(-20)). The OC PRS was strongly associated with OC risk for both BRCA1 and BRCA2 carriers. These translate to differences in absolute risks (more than 10% in each case) between the top and bottom deciles of the PRS distribution; for example, the OC risk was 6% by age 80 years for BRCA2 carriers at the 10th percentile of the OC PRS compared with 19% risk for those at the 90th percentile of PRS. Conclusions: BC and OC PRS are predictive of cancer risk in BRCA1 and BRCA2 carriers. Incorporation of the PRS into risk prediction models has promise to better inform decisions on cancer risk management

Study protocol: Comparison of different risk prediction modelling approaches for COVID-19 related death using the OpenSAFELY platform

On March 11th 2020, the World Health Organization characterised COVID-19 as a pandemic. Responses to containing the spread of the virus have relied heavily on policies involving restricting contact between people. Evolving policies regarding shielding and individual choices about restricting social contact will rely heavily on perceived risk of poor outcomes from COVID-19. In order to make informed decisions, both individual and collective, good predictive models are required.   For outcomes related to an infectious disease, the performance of any risk prediction model will depend heavily on the underlying prevalence of infection in the population of interest. Incorporating measures of how this changes over time may result in important improvements in prediction model performance.  This protocol reports details of a planned study to explore the extent to which incorporating time-varying measures of infection burden over time improves the quality of risk prediction models for COVID-19 death in a large population of adult patients in England. To achieve this aim, we will compare the performance of different modelling approaches to risk prediction, including static cohort approaches typically used in chronic disease settings and landmarking approaches incorporating time-varying measures of infection prevalence and policy change, using COVID-19 related deaths data linked to longitudinal primary care electronic health records data within the OpenSAFELY secure analytics platform.</ns4:p