Extended kalman filter for estimation of parameters in nonlinear state-space models of biochemical networks.

It is system dynamics that determines the function of cells, tissues and organisms. To develop mathematical models and estimate their parameters are an essential issue for studying dynamic behaviors of biological systems which include metabolic networks, genetic regulatory networks and signal transduction pathways, under perturbation of external stimuli. In general, biological dynamic systems are partially observed. Therefore, a natural way to model dynamic biological systems is to employ nonlinear state-space equations. Although statistical methods for parameter estimation of linear models in biological dynamic systems have been developed intensively in the recent years, the estimation of both states and parameters of nonlinear dynamic systems remains a challenging task. In this report, we apply extended Kalman Filter (EKF) to the estimation of both states and parameters of nonlinear state-space models. To evaluate the performance of the EKF for parameter estimation, we apply the EKF to a simulation dataset and two real datasets: JAK-STAT signal transduction pathway and Ras/Raf/MEK/ERK signaling transduction pathways datasets. The preliminary results show that EKF can accurately estimate the parameters and predict states in nonlinear state-space equations for modeling dynamic biochemical networks.

Climatology of Vb cyclones, physical mechanisms and their impact on extreme precipitation over Central Europe

Cyclones, which develop over the western Mediterranean and move northeastward are a major source of extreme weather and known to be responsible for heavy precipitation over the northern side of the Alpine range and Central Europe. As the relevant processes triggering these so-called Vb events and their impact on extreme precipitation are not yet fully understood, this study focuses on gaining insight into the dynamics of past events. For this, a cyclone detection and tracking tool is applied to the ERA-Interim reanalysis (1979–2013) to identify prominent Vb situations. Precipitation in the ERA-Interim and the E-OBS data sets is used to evaluate case-to-case precipitation amounts and to assess consistency between the two data sets. Both data sets exhibit high variability in precipitation amounts among different Vb events. While only 23 % of all Vb events are associated with extreme precipitation, around 15 % of all extreme precipitation days (99 percentile) over the northern Alpine region and Central Europe are induced by Vb events, although Vb cyclones are rare events (2.3 per year). To obtain a better understanding of the variability within Vb events, the analysis of the 10 heaviest and lowest precipitation Vb events reveals noticeable differences in the state of the atmosphere. These differences are most pronounced in the geopotential height and potential vorticity field, indicating a much stronger cyclone for heavy precipitation events. The related differences in wind direction are responsible for the moisture transport around the Alps and the orographical lifting along the northern slopes of the Alps. These effects are the main reasons for a disastrous outcome of Vb events, and consequently are absent in the Vb events associated with low precipitation. Hence, our results point out that heavy precipitation related to Vb events is mainly related to large-scale dynamics rather than to thermodynamic processes.

Quantifying differences in land use emission estimates implied by definition discrepancies

The quantification of CO2 emissions from anthropogenic land use and land use change (eLUC) is essential to understand the drivers of the atmospheric CO2 increase and to inform climate change mitigation policy. Reported values in synthesis reports are commonly derived from different approaches (observation-driven bookkeeping and process-modelling) but recent work has emphasized that inconsistencies between methods may imply substantial differences in eLUC estimates. However, a consistent quantification is lacking and no concise modelling protocol for the separation of primary and secondary components of eLUC has been established. Here, we review differences of eLUC quantification methods and apply an Earth System Model (ESM) of Intermediate Complexity to quantify them. We find that the magnitude of effects due to merely conceptual differences between ESM and offline vegetation model-based quantifications is ~ 20 % for today. Under a future business-as-usual scenario, differences tend to increase further due to slowing land conversion rates and an increasing impact of altered environmental conditions on land-atmosphere fluxes. We establish how coupled Earth System Models may be applied to separate secondary component fluxes of eLUC arising from the replacement of potential C sinks/sources and the land use feedback and show that secondary fluxes derived from offline vegetation models are conceptually and quantitatively not identical to either, nor their sum. Therefore, we argue that synthesis studies should resort to the "least common denominator" of different methods, following the bookkeeping approach where only primary land use emissions are quantified under the assumption of constant environmental boundary conditions.

Retreat of top cliff of Kurungnakh Island, Lena Delta, Siberia, Russia, 2010-2014, with links to shapefiles

Thawing-induced cliff top retreat in permafrost landscapes is mainly due to thermo-erosion. Ground-ice-rich permafrost landscapes are specifically vulnerable to thermo-erosion and may show high degradation rates. Within the HGF Alliance Remote Sensing and the FP7 PAGE21 permafrost programs we investigated how SAR and optical remote sensing can contribute to the monitoring of erosion rates of ice-rich cliffs in Arctic Siberia (Lena Delta, Russia). We produced two different vector products: i) Intra-annual cliff top retreat based on TerraSAR-X (TSX) satellite data (2012-2014): High-temporal resolution time series of TSX satellite data allow the inter-annual and intra-annual monitoring of the upper cliff-line retreat also under bad weather conditions and continuous cloud coverage. This published SAR product contains the retreating upper cliff lines of a 1.5 km long part of eroding ice-rich coast of Kurungnakh Island in the central Lena Delta. The upper cliff line was mapped using a thresholding approach for images acquired in the years 2012, 2013 and 2014 for the months June (2013, 2014), July (2013, 2014), August (2012, 2013, 2014) and September (2013, 2014). The cliff top retreat vector product is called 'upper_cliff_TerraSAR-X'. While the 2014 cliff lines show a clear retreat of 2 to 3 m/month, the cliff top lines for 2012 and 2013 are not chronologically ordered. However, lines from the end of the season of a year are always close to the lines from the beginning of the next summer season, indicating low cliff retreat in winter. ii) 4-year cliff top retreat based on optical satellite data (2010-2014): Long-term cliff top retreat could be assessed with two high-spatial resolution optical satellite images (GeoEye-1, 2010-08-05 and Worldview-1, 2014-08-19). The cliff top retreat vector product is called 'upper_cliff_optical'. Results: The long-term cliff top retreat derived from optical satellite data are 35 m cliff retreat within 4 years. The higher-temporal resolution SAR data equivalently show long-term rates of 18 m within 2 years and nearly now degradation activities in winter but maximum erosion rates in summer months.The Intra-seasonal cliff top retreat lines from 2014 show a rate of 2 to 3 m per month.

Stable isotope record and lithic fragments distribution in sediments of MIS9-14 of the North Atlantic

Stable isotope and ice-rafted debris records from three core sites in the mid-latitude North Atlantic (IODP Site U1313, MD01-2446, MD03-2699) are combined with records of ODP Sites 1056/1058 and 980 to reconstruct hydrographic conditions during the middle Pleistocene spanning Marine Isotope Stages (MIS) 9-14 (300-540 ka). Core MD03-2699 is the first high-resolution mid-Brunhes record from the North Atlantic's eastern boundary upwelling system covering the complete MIS 11c interval and MIS 13. The array of sites reflect western and eastern basin boundary current as well as north to south transect sampling of subpolar and transitional water masses and allow the reconstruction of transport pathways in the upper limb of the North Atlantic's circulation. Hydrographic conditions in the surface and deep ocean during peak interglacial MIS 9 and 11 were similar among all the sites with relative stable conditions and confirm prolonged warmth during MIS 11c also for the mid-latitudes. Sea surface temperature (SST) reconstructions further reveal that in the mid-latitude North Atlantic MIS 11c is associated with two plateaus, the younger one of which is slightly warmer. Enhanced subsurface northward heat transport in the eastern boundary current system, especially during early MIS 11c, is denoted by the presence of tropical planktic foraminifer species and raises the question how strongly it impacted the Portuguese upwelling system. Deep water ventilation at the onset of MIS 11c significantly preceded surface water ventilation. Although MIS 13 was generally colder and more variable than the younger interglacials the surface water circulation scheme was the same. The greatest differences between the sites existed during the glacial inceptions and glacials. Then a north - south trending hydrographic front separated the nearshore and offshore waters off Portugal. While offshore waters originated from the North Atlantic Current as indicated by the similarities between the records of IODP Site U1313, ODP Site 980 and MD01-2446, nearshore waters as recorded in core MD03-2699 derived from the Azores Current and thus the subtropical gyre. Except for MIS 12, Azores Current influence seems to be related to eastern boundary system dynamics and not to changes in the Atlantic overturning circulation.

Inorganic carbon and geochemistry measurements from landfast sea ice in Resolute Passage, Nunavut, Canada, as part of the Arctic-ICE project, May - June 2010

We conducted a six-week investigation of the sea ice inorganic carbon system during the winter-spring transition in the Canadian Arctic Archipelago. Samples for the determination of sea ice geochemistry were collected in conjunction with physical and biological parameters as part of the 2010 Arctic-ICE (Arctic - Ice-Covered Ecosystem in a Rapidly Changing Environment) program, a sea ice-based process study in Resolute Passage, Nunavut. The goal of Arctic-ICE was to determine the physical-biological processes controlling the timing of primary production in Arctic landfast sea ice and to better understand the influence of these processes on the drawdown and release of climatically active gases. The field study was conducted from 1 May to 21 June, 2010.

Profiles of diatoms, pollen, XRD, XRF and organic composition of two sediment cores (PG2022 and PG2023) from Lake Kyutyunda in Yakutia, NE Siberia, Russia

Although the climate development over the Holocene in the Northern Hemisphere is well known, palaeolimnological climate reconstructions reveal spatiotemporal variability in northern Eurasia. Here we present a multi-proxy study from north-eastern Siberia combining sediment geochemistry, and diatom and pollen data from lake-sediment cores covering the last 38,000 cal. years. Our results show major changes in pyrite content and fragilarioid diatom species distributions, indicating prolonged seasonal lake-ice cover between ~13,500 and ~8,900 cal. years BP and possibly during the 8,200 cal. years BP cold event. A pollen-based climate reconstruction generated a mean July temperature of 17.8°C during the Holocene Thermal Maximum (HTM) between ~8,900 and ~4,500 cal. years BP. Naviculoid diatoms appear in the late Holocene indicating a shortening of the seasonal ice cover that continues today. Our results reveal a strong correlation between the applied terrestrial and aquatic indicators and natural seasonal climate dynamics in the Holocene. Planktonic diatoms show a strong response to changes in the lake ecosystem due to recent climate warming in the Anthropocene. We assess other palaeolimnological studies to infer the spatiotemporal pattern of the HTM and affirm that the timing of its onset, a difference of up to 3,000 years from north to south, can be well explained by climatic teleconnections. The westerlies brought cold air to this part of Siberia until the Laurentide ice-sheet vanished 7,000 years ago. The apparent delayed ending of the HTM in the central Siberian record can be ascribed to the exceedance of ecological thresholds trailing behind increases in winter temperatures and decreases in contrast in insolation between seasons during the mid to late Holocene as well as lacking differentiation between summer and winter trends in paleolimnological reconstructions.