RapidHRV: an open-source toolbox for extracting heart rate and heart rate variability

Heart rate and heart rate variability have enabled insight into a myriad of psychophysiological phenomena. There is now an influx of research attempting using these metrics within both laboratory settings (typically derived through electrocardiography or pulse oximetry) and ecologically-rich contexts (via wearable photoplethysmography, i.e., smartwatches). However, these signals can be prone to artifacts and a low signal to noise ratio, which traditionally are detected and removed through visual inspection. Here, we developed an open-source Python package, RapidHRV, dedicated to the preprocessing, analysis, and visualization of heart rate and heart rate variability. Each of these modules can be executed with one line of code and includes automated cleaning. In simulated data, RapidHRV demonstrated excellent recovery of heart rate across most levels of noise (>=10 dB) and moderate-to-excellent recovery of heart rate variability even at relatively low signal to noise ratios (>=20 dB) and sampling rates (>=20 Hz). Validation in real datasets shows good-to-excellent recovery of heart rate and heart rate variability in electrocardiography and finger photoplethysmography recordings. Validation in wrist photoplethysmography demonstrated RapidHRV estimations were sensitive to heart rate and its variability under low motion conditions, but estimates were less stable under higher movement settings

238U/235U in calcite is more susceptible to carbonate diagenesis

The uranium isotopic composition (δ238U) of bulk marine calcium carbonates has been extensively explored as a promising paleoredox proxy to track the extent of global oceanic anoxia in deep time. Multiple studies have examined whether primary calcium carbonates can directly capture seawater δ238U and whether bulk measurements of recent and ancient carbonates preserve seawater U isotope signatures. Here we assess the role of diagenesis in altering δ238U signatures in carbonates sediments that have a primary calcitic mineralogy at the Paleocene-Eocene Thermal Maximum (PETM), an interval with rapid global warming and oceanic deoxygenation at ∼56 million years ago. Although primary abiotic and biogenic calcium carbonates (aragonite and calcite) can directly capture seawater δ238U with small offsets (1 ppm vs. <0.1 ppm), δ238U in calcite should be even more susceptible to diagenesis than that in aragonite. We find strong evidence of this effect in analysis of δ238U in PETM shallow-water carbonate sediments from Drilling Project (ODP) Hole 871C (Limalok Guyot, Pacific Ocean). Our results reveal large fluctuations in bulk carbonate δ238U from −0.69 to +0.71‰ around the PETM boundary but consistently heavier δ238U (between −0.14 and +0.47‰) than modern seawater outside of this interval. The significantly lighter δ238U values than modern seawater were interpreted to result from the operation of a Mn oxide shuttle. The heavier δ238U values are most likely caused by authigenic reductive accumulation of U(IV) in pore waters below the sediment-water interface. We found that carbonate δ238U values higher than modern seawater tend to increase with increasing U/Ca. This relationship is well-explained by an authigenic reductive accumulation model that simply assumes addition to primary calcite during diagenesis of calcitic cements containing isotopically heavier U(IV). Our work confirms expectations that δ238U in primary calcite is more susceptible to the amount of diagenetic cementation compared to primary aragonite, and that variations of δ238U in carbonate sediments with a primary calcitic mineralogy would more dominantly reflect the local redox state of depositional and early diagenetic environments. It is essential to identify the original carbonate mineralogy, the diagenetic history, and constrain the redox state of local deposition environments of sedimentary carbonate rocks when applying bulk carbonate δ238U as a global proxy for oceanic anoxia in deep time

The Size and Shape of Local Voids

We study the size and shape of low density regions in the local universe which we identify in the smoothed density field of the PSCz flux limited IRAS galaxy catalogue. After quantifying the systematic biases that enter in the detection of voids using our data set and method, we identify, using a smoothing length of 5 $h^{-1}$ Mpc, 14 voids within 80 $h^{-1}$ Mpc and using a smoothing length of 10 $h^{-1}$ Mpc, 8 voids within 130 $h^{-1}$ Mpc. We study the void size distribution and morphologies and find that there is roughly an equal number of prolate and oblate-like spheroidal voids. We compare the measured PSCz void shape and size distributions with those expected in six different CDM models and find that only the size distribution can discriminate between models. The models preferred by the PSCz data are those with intermediate values of $\sigma_{8} (\simeq 0.83)$, independent of cosmology.Comment: final version, Accepted in MNRA

Estimates of tropical bromoform emissions using an inversion method

Abstract. Bromine plays an important role in ozone chemistry in both the troposphere and stratosphere. When measured by mass, bromoform (CHBr3) is thought to be the largest organic source of bromine to the atmosphere. While seaweed and phytoplankton are known to be dominant sources, the size and the geographical distribution of CHBr3 emissions remains uncertain. Particularly little is known about emissions from the Maritime Continent, which have usually been assumed to be large, and which appear to be especially likely to reach the stratosphere. In this study we aim to reduce this uncertainty by combining the first multi-annual set of CHBr3 measurements from this region, and an inversion process, to investigate systematically the distribution and magnitude of CHBr3 emissions. The novelty of our approach lies in the application of the inversion method to CHBr3. We find that local measurements of a short-lived gas like CHBr3 can be used to constrain emissions from only a relatively small, sub-regional domain. We then obtain detailed estimates of CHBr3 emissions within this area, which appear to be relatively insensitive to the assumptions inherent in the inversion process. We extrapolate this information to produce estimated emissions for the entire tropics (defined as 20° S–20° N) of 225 Gg CHBr3 yr−1. The ocean in the area we base our extrapolations upon is typically somewhat shallower, and more biologically productive, than the tropical average. Despite this, our tropical estimate is lower than most other recent studies, and suggests that CHBr3 emissions in the coastline-rich Maritime Continent may not be stronger than emissions in other parts of the tropics. M. Ashfold thanks the Natural Environment Research Council (NERC) for a research studentship, and is grateful for support through the ERC ACCI project (project number 267760). N. Harris is supported by a NERC Advanced Research Fellowship. This work was supported through the EU SHIVA project, through the NERC OP3 project, and NERC grants NE/F020341/1 and NE/J006246/1. We also acknowledge the Department of Energy and Climate Change for their support in the development of InTEM (contract GA0201). For field site support we thank S.-M. Phang, A. A. Samah and M. S. M. Nadzir of Universiti Malaya, S. Ong and H. E. Ung of Global Satria, Maznorizan Mohamad, L. K. Peng and S. E. Yong of the Malaysian Meteorological Department, the Sabah Foundation, the Danum Valley Field Centre and the Royal Society. This paper constitutes publication no. 613 of the Royal Society South East Asia Rainforest Research Programme.This is the final published version. It first appeared at http://www.atmos-chem-phys.net/14/979/2014/acp-14-979-2014.html

Rapid transport of East Asian pollution to the deep tropics

Abstract. Anthropogenic emissions from East Asia have increased over recent decades, and under the prevailing westerly winds, these increases have led to changes in atmospheric composition as far afield as North America. Here we show that, during Northern Hemisphere (NH) winter, pollution originating in East Asia also directly affects atmospheric composition in the deep tropics. We present observations of marked intra-seasonal variability in the anthropogenic tracer perchloroethene (C2Cl4) collected at two locations in Borneo during the NH winter of 2008/09. We use the NAME trajectory model to show that the observed enhancements in C2Cl4 mixing ratio are caused by rapid meridional transport, in the form of "cold surges", from the relatively polluted East Asian land mass. In these events air masses can move across &gt; 30° of latitude in 4 days. We then present data from the Monitoring Atmospheric Composition and Climate reanalysis which suggests that air masses high in C2Cl4 may also contain levels of the pollutants carbon monoxide and ozone that are approximately double the typical "background" levels in Borneo. Convection in Southeast Asia can be enhanced by cold surges, and further trajectory calculations indicate that the polluted air masses can subsequently be lifted to the tropical upper troposphere. This suggests a potentially important connection between mid-latitude pollution sources and the very low stratosphere. This work was supported by a NERC consortium grant to the OP3 team, by NCAS, by the European Commission through the SCOUT-O3 project (505390-GOCECF2004), though the ERC ACCI project, Project No 267760, and by NERC western Pacific grant number NE/F020341/1 and NERC CAST grant number NE/J006246/1. M. J. Ashfold thanks NERC for a research studentship. A. D. Robinson acknowledges NERC for their support through small grant project NE/D008085/1. N. R. P. Harris is supported by a NERC Advanced Research Fellowship. We thank the Sabah Foundation, Danum Valley Field Centre and the Royal Society (Glen Reynolds) for field site support. This is paper number X of the Royal Society’s South East Asian Rainforest Research Programme. We are grateful for use of data provided by the MACC-II project, funded by the European Union under the 7th Framework Programme. We also acknowledge use of the NAME atmospheric dispersion model and associated NWP meteorological data sets made available to us by the Met O ce. We acknowledge the significant storage resources and analysis facilities made available to us on JASMIN by STFC CEDA along with the corresponding support teams.This is the published version. It first appeared at: http://www.atmos-chem-phys-discuss.net/14/30705/2014/acpd-14-30705-2014.html

Wait times for breast cancer care

Measurement of care time intervals is complex, being influenced by many factors. The definition of the care interval monitored can also bias the detection of changes in waits. The implications of using different care interval definitions to report wait times and identify delays in care provision were examined using a retrospective chart review of 637 women with surgically treated breast cancer who were referred to a cancer centre between September 1999 and 2000 or September 2003 and 2004. Overall waits between detection and adjuvant treatment increased by 12 days over the two periods, but their exact location and cause(s) could not be determined at such a low-resolution interval. At higher resolutions of care intervals, reporting the comprehensive sequence of care events, the prolongation was mainly associated with delayed access to surgery (4 days) and delivery of adjuvant chemotherapy (4 days). The latter went unnoticed when waits were reported at intermediate (referral to adjuvant treatment) and low (detection to adjuvant treatment) resolutions. Disease stage and type of first adjuvant treatment consistently and significantly influenced the length of waits. Comprehensive monitoring of the entire care path is essential to effectively prioritize interventions, assess their outcomes and optimise access to cancer care