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The Optical Spectrograph and Infra-Red Imager System (OSIRIS) and the Atmospheric Chemistry Experiment (ACE) have been taking measurements from space since 2001 and 2003, respectively. This paper presents intercomparisons between ozone and NO2 measured by the ACE and OSIRIS satellite instruments and by ground-based instruments at the Polar Environment Atmospheric Research Laboratory (PEARL), which is located at Eureka, Canada (80° N, 86° W) and is operated by the Canadian Network for the Detection of Atmospheric Change (CANDAC). The ground-based instruments included in this study are four zenith-sky differential optical absorption spectroscopy (DOAS) instruments, one Bruker Fourier transform infrared spectrometer (FTIR) and four Brewer spectrophotometers. Ozone total columns measured by the DOAS instruments were retrieved using new Network for the Detection of Atmospheric Composition Change (NDACC) guidelines and agree to within 3.2%. The DOAS ozone columns agree with the Brewer spectrophotometers with mean relative differences that are smaller than 1.5%. This suggests that for these instruments the new NDACC data guidelines were successful in producing a homogenous and accurate ozone dataset at 80° N. Satellite 14–52 km ozone and 17–40 km NO2 partial columns within 500 km of PEARL were calculated for ACE-FTS Version 2.2 (v2.2) plus updates, ACE-FTS v3.0, ACE-MAESTRO (Measurements of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation) v1.2 and OSIRIS SaskMART v5.0x ozone and Optimal Estimation v3.0 NO2 data products. The new ACE-FTS v3.0 and the validated ACE-FTS v2.2 partial columns are nearly identical, with mean relative differences of 0.0 ± 0.2% and −0.2 ± 0.1% for v2.2 minus v3.0 ozone and NO2, respectively. Ozone columns were constructed from 14–52 km satellite and 0–14 km ozonesonde partial columns and compared with the ground-based total column measurements. The satellite-plus-sonde measurements agree with the ground-based ozone total columns with mean relative differences of 0.1–7.3%. For NO2, partial columns from 17 km upward were scaled to noon using a photochemical model. Mean relative differences between OSIRIS, ACE-FTS and ground-based NO2 measurements do not exceed 20%. ACE-MAESTRO measures more NO2 than the other instruments, with mean relative differences of 25–52%. Seasonal variation in the differences between NO2 partial columns is observed, suggesting that there are systematic errors in the measurements and/or the photochemical model corrections. For ozone spring-time measurements, additional coincidence criteria based on stratospheric temperature and the location of the polar vortex were found to improve agreement between some of the instruments. For ACE-FTS v2.2 minus Bruker FTIR, the 2007–2009 spring-time mean relative difference improved from −5.0 ± 0.4% to −3.1 ± 0.8% with the dynamical selection criteria. This was the largest improvement, likely because both instruments measure direct sunlight and therefore have well-characterized lines-of-sight compared with scattered sunlight measurements. For NO2, the addition of a ±1° latitude coincidence criterion improved spring-time intercomparison results, likely due to the sharp latitudinal gradient of NO2 during polar sunrise. The differences between satellite and ground-based measurements do not show any obvious trends over the missions, indicating that both the ACE and OSIRIS instruments continue to perform well.

The genetic component of Alzheimer’s disease (AD) has been mainly assessed using Genome Wide Association Studies (GWAS), which do not capture the risk contributed by rare variants. Here, we compared the gene-based burden of rare damaging variants in exome sequencing data from 32,558 individuals —16,036 AD cases and 16,522 controls— in a two-stage analysis. Next to known genes TREM2, SORL1 and ABCA7, we observed a significant association of rare, predicted damaging variants in ATP8B4 and ABCA1 with AD risk, and a suggestive signal in ADAM10. Next to these genes, the rare variant burden in RIN3, CLU, ZCWPW1 and ACE highlighted these genes as potential driver genes in AD-GWAS loci. Rare damaging variants in these genes, and in particular loss-of-function variants, have a large effect on AD-risk, and they are enriched in early onset AD cases. The newly identified AD-associated genes provide additional evidence for a major role for APP-processing, Aβ-aggregation, lipid metabolism and microglial function in AD.

Bias correction of climate variables is a standard practice in climate change impact (CCI) studies. Various methodologies have been developed within the framework of quantile mapping. However, it is well known that quantile mapping may significantly modify the long-term statistics due to the time dependency of the temperature bias. Here, a method to overcome this issue without compromising the day-to-day correction statistics is presented. The methodology separates the modeled temperature signal into a normalized and a residual component relative to the modeled reference period climatology, in order to adjust the biases only for the former and preserve the signal of the later. The results show that this method allows for the preservation of the originally modeled long-term signal in the mean, the standard deviation and higher and lower percentiles of temperature. To illustrate the improvements, the methodology is tested on daily time series obtained from five Euro CORDEX regional climate models (RCMs).

Enhanced release of alkalinity from the seafloor, principally driven by anaerobic degradation of organic matter under low-oxygen conditions and associated secondary redox reactions, can increase the carbon dioxide (CO2) buffering capacity of seawater and therefore oceanic CO2 uptake. The Baltic Sea has undergone severe changes in oxygenation state and total alkalinity (TA) over the past decades. The link between these concurrent changes has not yet been investigated in detail. A recent system-wide TA budget constructed for the past 50 years using BALTSEM, a coupled physical–biogeochemical model for the whole Baltic Sea area revealed an unknown TA source. Here we use BALTSEM in combination with observational data and one-dimensional reactive-transport modeling of sedimentary processes in the Fårö Deep, a deep Baltic Sea basin, to test whether sulfate (SO42-) reduction coupled to iron (Fe) sulfide burial can explain the missing TA source in the Baltic Proper. We calculated that this burial can account for up to 26 % of the missing source in this basin, with the remaining TA possibly originating from unknown river inputs or submarine groundwater discharge. We also show that temporal variability in the input of Fe to the sediments since the 1970s drives changes in sulfur (S) burial in the Fårö Deep, suggesting that Fe availability is the ultimate limiting factor for TA generation under anoxic conditions. The implementation of projected climate change and two nutrient load scenarios for the 21st century in BALTSEM shows that reducing nutrient loads will improve deep water oxygen conditions, but at the expense of lower surface water TA concentrations, CO2 buffering capacities and faster acidification. When these changes additionally lead to a decrease in Fe inputs to the sediment of the deep basins, anaerobic TA generation will be reduced even further, thus exacerbating acidification. This work highlights that Fe dynamics plays a key role in the release of TA from sediments where Fe sulfide formation is limited by Fe availability, as exemplified by the Baltic Sea. Moreover, it demonstrates that burial of Fe sulfides should be included in TA budgets of low-oxygen basins.

The mid-Pliocene is a valuable time interval for investigating equilibrium climate at current atmospheric CO2 concentrations because atmospheric CO2 concentrations are thought to have been comparable to the current day and yet the climate and distribution of ecosystems were quite different. One intriguing, but not fully understood, feature of the early to mid-Pliocene climate is the amplified Arctic temperature response and its impact on Arctic ecosystems. Only the most recent models appear to correctly estimate the degree of warming in the Pliocene Arctic and validation of the currently proposed feedbacks is limited by scarce terrestrial records of climate and environment. Here we reconstruct the summer temperature and fire regime from a subfossil fen-peat deposit on west–central Ellesmere Island, Canada, that has been chronologically constrained using cosmogenic nuclide burial dating to 3.9+1.5/-0.5 Ma. The estimate for average mean summer temperature is 15.4±0.8 ∘C using specific bacterial membrane lipids, i.e., branched glycerol dialkyl glycerol tetraethers. This is above the proposed threshold that predicts a substantial increase in wildfire in the modern high latitudes. Macro-charcoal was present in all samples from this Pliocene section with notably higher charcoal concentration in the upper part of the sequence. This change in charcoal was synchronous with a change in vegetation that included an increase in abundance of fire-promoting Pinus and Picea. Paleo-vegetation reconstructions are consistent with warm summer temperatures, relatively low summer precipitation and an incidence of fire comparable to fire-adapted boreal forests of North America and central Siberia. To our knowledge, this site provides the northernmost evidence of fire during the Pliocene. It suggests that ecosystem productivity was greater than in the present day, providing fuel for wildfires, and that the climate was conducive to the ignition of fire during this period. The results reveal that interactions between paleo-vegetation and paleoclimate were mediated by fire in the High Arctic during the Pliocene, even though CO2 concentrations were similar to modern values.

Global climate model (GCM) outputs feature systematic biases that render them unsuitable for direct use by impact models, especially for hydrological studies. To deal with this issue, many bias correction techniques have been developed to adjust the modelled variables against observations, focusing mainly on precipitation and temperature. However, most state-of-the-art hydrological models require more forcing variables, in addition to precipitation and temperature, such as radiation, humidity, air pressure, and wind speed. The biases in these additional variables can hinder hydrological simulations, but the effect of the bias of each variable is unexplored. Here we examine the effect of GCM biases on historical runoff simulations for each forcing variable individually, using the JULES land surface model set up at the global scale. Based on the quantified effect, we assess which variables should be included in bias correction procedures. To this end, a partial correction bias assessment experiment is conducted, to test the effect of the biases of six climate variables from a set of three GCMs. The effect of the bias of each climate variable individually is quantified by comparing the changes in simulated runoff that correspond to the bias of each tested variable. A methodology for the classification of the effect of biases in four effect categories (ECs), based on the magnitude and sensitivity of runoff changes, is developed and applied. Our results show that, while globally the largest changes in modelled runoff are caused by precipitation and temperature biases, there are regions where runoff is substantially affected by and/or more sensitive to radiation and humidity. Global maps of bias ECs reveal the regions mostly affected by the bias of each variable. Based on our findings, for global-scale applications, bias correction of radiation and humidity, in addition to that of precipitation and temperature, is advised. Finer spatial-scale information is also provided, to suggest bias correction of variables beyond precipitation and temperature for regional studies.

Improving measurements of water vapour in the upper troposphere and lower stratosphere (UTLS) is a priority for the atmospheric science community. In this work, UTLS water vapour profiles derived from Atmospheric Chemistry Experiment (ACE) satellite measurements are assessed with coincident ground-based measurements taken at a high Arctic observatory at Eureka, Nunavut, Canada. Additional comparisons to satellite measurements taken by the Atmospheric Infrared Sounder (AIRS), Michelson Interferometer for Passive Atmospheric Sounding (MIPAS), Microwave Limb Sounder (MLS), Scanning Imaging Absorption Spectrometer for Atmospheric CHartography (SCIAMACHY), and Tropospheric Emission Spectrometer (TES) are included to put the ACE Fourier transform spectrometer (ACE-FTS) and ACE Measurement of Aerosol Extinction in the Stratosphere and Troposphere Retrieved by Occultation (ACE-MAESTRO) results in context. Measurements of water vapour profiles at Eureka are made using a Bruker 125HR solar absorption Fourier transform infrared spectrometer at the Polar Environment Atmospheric Research Laboratory (PEARL) and radiosondes launched from the Eureka Weather Station. Radiosonde measurements used in this study were processed with software developed by the Global Climate Observing System (GCOS) Reference Upper-Air Network (GRUAN) to account for known biases and calculate uncertainties in a well-documented and consistent manner. ACE-FTS measurements were within 11 ppmv (parts per million by volume; 13 %) of 125HR measurements between 6 and 14 km. Between 8 and 14 km ACE-FTS profiles showed a small wet bias of approximately 8 % relative to the 125HR. ACE-FTS water vapour profiles had mean differences of 13 ppmv (32 %) or better when compared to coincident radiosonde profiles at altitudes between 6 and 14 km; mean differences were within 6 ppmv (12 %) between 7 and 11 km. ACE-MAESTRO profiles showed a small dry bias relative to the 125HR of approximately 7 % between 6 and 9 km and 10 % between 10 and 14 km. ACE-MAESTRO profiles agreed within 30 ppmv (36 %) of the radiosondes between 7 and 14 km. ACE-FTS and ACE-MAESTRO comparison results show closer agreement with the radiosondes and PEARL 125HR overall than other satellite datasets – except for AIRS. Close agreement was observed between AIRS and the 125HR and radiosonde measurements, with mean differences within 5 % and correlation coefficients above 0.83 in the troposphere between 1 and 7 km. Comparisons to MLS at altitudes around 10 km showed a dry bias, e.g. mean differences between MLS and radiosondes were −25.6 %. SCIAMACHY comparisons were very limited due to minimal overlap between the vertical extent of the measurements. TES had no temporal overlap with the radiosonde dataset used in this study. Comparisons between TES and the 125HR showed a wet bias of approximately 25 % in the UTLS and mean differences within 14 % below 5 km.

During the last decade, several limb sounding satellites have measured the global sodium (Na) number densities in the mesosphere and lower thermosphere (MLT). Datasets are now available from Global Ozone Monitoring by Occultation of Stars (GOMOS), the SCanning Imaging Absorption spectroMeter for Atmospheric CHartography (SCIAMACHY) (both on Envisat) and the Optical Spectrograph and InfraRed Imager System (OSIRIS) (on Odin). Furthermore, global model simulations of the Na layer in the MLT simulated by the Whole Atmosphere Community Climate Model, including the Na species (WACCM-Na), are available. In this paper, we compare these global datasets.The observed and simulated monthly averages of Na vertical column densities agree reasonably well with each other. They show a clear seasonal cycle with a summer minimum most pronounced at the poles. They also show signs of a semi-annual oscillation in the equatorial region. The vertical column densities vary from 0. 5 × 109 to 7 × 109 cm−2 near the poles and from 3 × 109 to 4 × 109 cm−2 at the Equator. The phase of the seasonal cycle and semi-annual oscillation shows small differences between the Na amounts retrieved from different instruments. The full width at half maximum of the profiles is 10 to 16 km for most latitudes, but significantly smaller in the polar summer. The centroid altitudes of the measured sodium profiles range from 89 to 95 km, whereas the model shows on average 2 to 4 km lower centroid altitudes. This may be explained by the mesopause being 3 km lower in the WACCM simulations than in measurements. Despite this global 2–4 km shift, the model captures well the latitudinal and temporal variations. The variation of the WACCM dataset during the year at different latitudes is similar to the one of the measurements. Furthermore, the differences between the measured profiles with different instruments and therefore different local times (LTs) are also present in the model-simulated profiles. This capturing of latitudinal and temporal variations is also found for the vertical column densities and profile widths.

Salmonella Typhimurium ST313 causes invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa, targeting susceptible HIV + , malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered the S. Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of the Salmonella expression compendium SalComD23580: bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl . We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.

Streamflow in south-central Chile (SCC, ∼ 37–42∘ S) is vital for agriculture, forestry production, hydroelectricity, and human consumption. Recent drought episodes have generated hydrological deficits with damaging effects on these activities. This region is projected to undergo major reductions in water availability, concomitant with projected increases in water demand. However, the lack of long-term records hampers the development of accurate estimations of natural variability and trends. In order to provide more information on long-term streamflow variability and trends in SCC, here we report findings of an analysis of instrumental records and a tree-ring reconstruction of the summer streamflow of the Río Imperial (∼ 37∘ 40′ S–38∘ 50′ S). This is the first reconstruction in Chile targeted at this season. Results from the instrumental streamflow record (∼ 1940 onwards) indicated that the hydrological regime is fundamentally pluvial with a small snowmelt contribution during spring, and evidenced a decreasing trend, both for the summer and the full annual record. The reconstruction showed that streamflow below the average characterized the post-1980 period, with more frequent, but not more intense, drought episodes. We additionally found that the recent positive phase of the Southern Annular Mode has significantly influenced streamflow. These findings agree with previous studies, suggesting a robust regional signal and a shift to a new hydrological scenario. In this paper, we also discuss implications of these results for water managers and stakeholders; we provide rationale and examples that support the need for the incorporation of tree-ring reconstructions into water resources management.