SoFiA: a flexible source finder for 3D spectral line data

We introduce SoFiA, a flexible software application for the detection and parameterization of sources in 3D spectral-line datasets. SoFiA combines for the first time in a single piece of software a set of new source-finding and parameterization algorithms developed on the way to future HI surveys with ASKAP (WALLABY, DINGO) and APERTIF. It is designed to enable the general use of these new algorithms by the community on a broad range of datasets. The key advantages of SoFiA are the ability to: search for line emission on multiple scales to detect 3D sources in a complete and reliable way, taking into account noise level variations and the presence of artefacts in a data cube; estimate the reliability of individual detections; look for signal in arbitrarily large data cubes using a catalogue of 3D coordinates as a prior; provide a wide range of source parameters and output products which facilitate further analysis by the user. We highlight the modularity of SoFiA, which makes it a flexible package allowing users to select and apply only the algorithms useful for their data and science questions. This modularity makes it also possible to easily expand SoFiA in order to include additional methods as they become available. The full SoFiA distribution, including a dedicated graphical user interface, is publicly available for download.Comment: MNRAS, accepted. SoFiA is registered at the Astrophysics Source Code Library with ID ascl:1412.001. Download SoFiA at https://github.com/SoFiA-Admin/SoFi

Middepth circulation of the eastern tropical South Pacific and its link to the oxygen minimum zone

There is an incomplete description of the mid-depth circulation and its link to the oxygen minimum zone (OMZ) in the eastern tropical South Pacific. Subsurface currents of the OMZ in the eastern tropical South Pacific are investigated with a focus at 400 m depth, close to the core of the OMZ, using several Acoustic Doppler Current Profiler sections recorded in January and February 2009. Five profiling floats with oxygen sensors were deployed along 85°50’W in February 2009 with a drift depth at 400 m. Their spreading paths are compared with the model flow field from a 1/10° Tropical Pacific model (TROPAC01) and the Simple Ocean Data Assimilation (SODA) model. Overall the mean currents in the eastern tropical South Pacific are weak so that eddy variability influences the flow and ultimately feed oxygen-poor water to the OMZ. The center of the OMZ is a stagnant area so that floats stay much longer in this region and can even reverse direction. In one case of one float deployed at 8°S returned to the same location after 15 month. On the northern side of the OMZ in the equatorial current system, floats move rapidly to the west. Most current bands reported for the near surface layer exist also in the depth range of the OMZ. A schematic circulation flow field for the OMZ core depth is derived which shows the northern part of the South Pacific subtropical gyre south of the OMZ and the complicated zonal equatorial flow field north of the OMZ

Antiinflammatory Therapy with Canakinumab for Atherosclerotic Disease

Background: Experimental and clinical data suggest that reducing inflammation without affecting lipid levels may reduce the risk of cardiovascular disease. Yet, the inflammatory hypothesis of atherothrombosis has remained unproved. Methods: We conducted a randomized, double-blind trial of canakinumab, a therapeutic monoclonal antibody targeting interleukin-1β, involving 10,061 patients with previous myocardial infarction and a high-sensitivity C-reactive protein level of 2 mg or more per liter. The trial compared three doses of canakinumab (50 mg, 150 mg, and 300 mg, administered subcutaneously every 3 months) with placebo. The primary efficacy end point was nonfatal myocardial infarction, nonfatal stroke, or cardiovascular death. RESULTS: At 48 months, the median reduction from baseline in the high-sensitivity C-reactive protein level was 26 percentage points greater in the group that received the 50-mg dose of canakinumab, 37 percentage points greater in the 150-mg group, and 41 percentage points greater in the 300-mg group than in the placebo group. Canakinumab did not reduce lipid levels from baseline. At a median follow-up of 3.7 years, the incidence rate for the primary end point was 4.50 events per 100 person-years in the placebo group, 4.11 events per 100 person-years in the 50-mg group, 3.86 events per 100 person-years in the 150-mg group, and 3.90 events per 100 person-years in the 300-mg group. The hazard ratios as compared with placebo were as follows: in the 50-mg group, 0.93 (95% confidence interval [CI], 0.80 to 1.07; P = 0.30); in the 150-mg group, 0.85 (95% CI, 0.74 to 0.98; P = 0.021); and in the 300-mg group, 0.86 (95% CI, 0.75 to 0.99; P = 0.031). The 150-mg dose, but not the other doses, met the prespecified multiplicity-adjusted threshold for statistical significance for the primary end point and the secondary end point that additionally included hospitalization for unstable angina that led to urgent revascularization (hazard ratio vs. placebo, 0.83; 95% CI, 0.73 to 0.95; P = 0.005). Canakinumab was associated with a higher incidence of fatal infection than was placebo. There was no significant difference in all-cause mortality (hazard ratio for all canakinumab doses vs. placebo, 0.94; 95% CI, 0.83 to 1.06; P = 0.31). Conclusions: Antiinflammatory therapy targeting the interleukin-1β innate immunity pathway with canakinumab at a dose of 150 mg every 3 months led to a significantly lower rate of recurrent cardiovascular events than placebo, independent of lipid-level lowering. (Funded by Novartis; CANTOS ClinicalTrials.gov number, NCT01327846.

Towards a more reliable historical reanalysis: improvements for version 3 of the Twentieth Century Reanalysis system

Historical reanalyses that span more than a century are needed for a wide range of studies, from understanding large‐scale climate trends to diagnosing the impacts of individual historical extreme weather events. The Twentieth Century Reanalysis (20CR) Project is an effort to fill this need. It is supported by the National Oceanic and Atmospheric Administration (NOAA), the Cooperative Institute for Research in Environmental Sciences (CIRES), and the U.S. Department of Energy (DOE), and is facilitated by collaboration with the international Atmospheric Circulation Reconstructions over the Earth initiative. 20CR is the first ensemble of sub‐daily global atmospheric conditions spanning over 100 years. This provides a best estimate of the weather at any given place and time as well as an estimate of its confidence and uncertainty. While extremely useful, version 2c of this dataset (20CRv2c) has several significant issues, including inaccurate estimates of confidence and a global sea level pressure bias in the mid‐19th century. These and other issues can reduce its effectiveness for studies at many spatial and temporal scales. Therefore, the 20CR system underwent a series of developments to generate a significant new version of the reanalysis. The version 3 system (NOAA‐CIRES‐DOE 20CRv3) uses upgraded data assimilation methods including an adaptive inflation algorithm; has a newer, higher‐resolution forecast model that specifies dry air mass; and assimilates a larger set of pressure observations. These changes have improved the ensemble‐based estimates of confidence, removed spin‐up effects in the precipitation fields, and diminished the sea‐level pressure bias. Other improvements include more accurate representations of storm intensity, smaller errors, and large‐scale reductions in model bias. The 20CRv3 system is comprehensively reviewed, focusing on the aspects that have ameliorated issues in 20CRv2c. Despite the many improvements, some challenges remain, including a systematic bias in tropical precipitation and time‐varying biases in southern high‐latitude pressure fields

25th annual computational neuroscience meeting: CNS-2016

The same neuron may play different functional roles in the neural circuits to which it belongs. For example, neurons in the Tritonia pedal ganglia may participate in variable phases of the swim motor rhythms [1]. While such neuronal functional variability is likely to play a major role the delivery of the functionality of neural systems, it is difficult to study it in most nervous systems. We work on the pyloric rhythm network of the crustacean stomatogastric ganglion (STG) [2]. Typically network models of the STG treat neurons of the same functional type as a single model neuron (e.g. PD neurons), assuming the same conductance parameters for these neurons and implying their synchronous firing [3, 4]. However, simultaneous recording of PD neurons shows differences between the timings of spikes of these neurons. This may indicate functional variability of these neurons. Here we modelled separately the two PD neurons of the STG in a multi-neuron model of the pyloric network. Our neuron models comply with known correlations between conductance parameters of ionic currents. Our results reproduce the experimental finding of increasing spike time distance between spikes originating from the two model PD neurons during their synchronised burst phase. The PD neuron with the larger calcium conductance generates its spikes before the other PD neuron. Larger potassium conductance values in the follower neuron imply longer delays between spikes, see Fig. 17.Neuromodulators change the conductance parameters of neurons and maintain the ratios of these parameters [5]. Our results show that such changes may shift the individual contribution of two PD neurons to the PD-phase of the pyloric rhythm altering their functionality within this rhythm. Our work paves the way towards an accessible experimental and computational framework for the analysis of the mechanisms and impact of functional variability of neurons within the neural circuits to which they belong

Modelling human choices: MADeM and decision‑making

Research supported by FAPESP 2015/50122-0 and DFG-GRTK 1740/2. RP and AR are also part of the Research, Innovation and Dissemination Center for Neuromathematics FAPESP grant (2013/07699-0). RP is supported by a FAPESP scholarship (2013/25667-8). ACR is partially supported by a CNPq fellowship (grant 306251/2014-0)

Historical changes in El Niño and La Niña characteristics in an ocean reanalysis

International audienceThe variation of El Niño Southern Oscillation (ENSO) events from the mid-nineteenth century until the beginning of the twenty-first century is explored using an ocean reanalysis. A comparison of the reanalysis with three sea surface temperature reconstructions shows that the timing of events is similar in all four products, however there are important differences in the strength and location of events. The difference between the reconstructions is sometimes larger than the difference between the reanalysis and a given reconstruction. These differences are larger in the first half of the record, a period for which there are relatively sparse observations. The reanalysis is used to explore decadal variability and trends in the frequency, duration, and propagation direction of ENSO events. There is considerable decadal variability of these ENSO characteristics with the time between events ranging from several months to ten years and the duration of ENSO varying from 5 to 27 months. As has been previously shown for the strength and location of ENSO there is little overall trend in the characteristics. Having a three dimensional representation of the ocean from the reanalysis allows exploration of subsurface changes during ENSO. An analysis of subsurface anomalies shows that during ENSO events the subsurface anomalies are highly correlated with the strength of surface anomalies over the 140 year period. Overall, there is no evidence that there are changes in the strength, frequency, duration, location or direction of propagation of El Niño and La Niña anomalies caused by global warming during the period from 1871 to 2008

ENSO diversity in observations

ENSO (El Niño-Southern Oscillation) is characterized by interannual sea surface temperature (SST) variations in the eastern-to-central equatorial Pacific. In the composite ENSO event portrayed by Rasmusson and Carpenter (1982) SST anomalies develop along the coast of South America before propagating westward along the equator. However, it has become clear that there are events in which anomalies develop and remain near the International Dateline in the central equatorial Pacific. In fact, most of the El Niño events in the 21st Century (the 2002/03, 2004/05, and 2009/10 events) have had their largest SST anomaly in the western Pacific (Yu and Kim 2013). An example of an ENSO event in the east (1997) and an ENSO event in the west (2009) are shown in Figure 1. The fact that warming is observed sometimes in the east Pacific (EP), sometimes in the central Pacific (CP), and sometime simultaneously in both eastern and central Pacific (e.g., the 2006-07 event; Figure 1) has led to the suggestion that there are two types of events that represent physically distinct phenomena (Larkin and Harrison 2005; Yu and Kao 2007; Ashok et al. 2007; Guan and Nigam 2008; Kao and Yu 2009; Kug et al. 2009). There are also studies that further separate the two types of ENSO into more sub-types (Wang and Wang 2013). An alternative interpretation is that ENSO normally occurs in the central Pacific, with events sometimes displaced to the east and sometimes displaced to the wes