ALBERT

Description: The evaluation of potential landslides in mountain areas is a very complex process. Currently, event understanding is scarce due to information limitations. Identifying the whole chain of events is not a straightforward task, and the impacts of mass-wasting processes depend on the conditions downstream of the origin. In this paper, we present an example that illustrates the complexities in the evaluation of the chain of events that may lead to a natural disaster. On 16 December 2017, a landslide occurred in the Yelcho mountain range (southern Chile). In that event, 7 million m3 of rocks and soil fell on the Yelcho glacier, depositing 2 million m3 on the glacier terminal, and the rest continued downstream, triggering a mudflow that hit Villa Santa Lucía in Chilean Patagonia and killing 22 people. The complex event was anticipated in the region by the National Geological and Mining Survey (Sernageomin in Spanish). However, the effects of the terrain characteristics along the run-out area were more significant than anticipated. In this work, we evaluate the conditions that enabled the mudflow that hit Villa Santa Lucía. We used the information generated by Sernageomin's professionals after the mudflow. We carried out geotechnical tests to characterize the soil. We simulated the mudflow using two hydrodynamic programs (r.avaflow and Flo-2D) that can handle the rheology of the water–soil mixture. Our results indicate that the soil is classified as volcanic pumices. This type of soil can be susceptible to the collapse of the structure when subjected to shearing (molding), flowing as a viscous liquid. From the numerical modeling, we concluded that r.avaflow performs better than Flo-2D. The mudflow was satisfactorily simulated using a water content in the mixture ranging from 30 % to 40 %, which would have required a source of about 3 million m3 of water. Coupling the simulations and the soil tests that we performed, we estimated that in the area scoured by the mudflow, there were probably around 2 800 000 m3 of water within the soil. Therefore, the conditions of the valley were crucial to enhancing the impacts of the landslide. This result is relevant because it highlights the importance of evaluating the complete chain of events to map hazards. We suggest that in future hazard mapping, geotechnical studies in combination with hydrodynamic simulation should be included, in particular when human lives are at risk.

Description: Evapotranspiration (ET) from tropical forests serves as a critical moisture source for regional and global climate cycles. However, the magnitude, seasonality, and interannual variability of ET in the Congo Basin remain poorly constrained due to a scarcity of direct observations, despite the Congo being the second-largest river basin in the world and containing a vast region of tropical forest. In this study, we applied a water balance model to an array of remotely sensed and in situ datasets to produce monthly, basin-wide ET estimates spanning April 2002 to November 2016. Data sources include water storage changes estimated from the Gravity Recovery and Climate Experiment (GRACE) satellites, in situ measurements of river discharge, and precipitation from several remotely sensed and gauge-based sources. An optimal precipitation dataset was determined as a weighted average of interpolated data by Nicholson et al. (2018), Climate Hazards InfraRed Precipitation with Station data version 2 (CHIRPS2) , and the Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks–Climate Data Record product (PERSIANN-CDR), with the relative weights based on the error magnitudes of each dataset as determined by triple collocation. The resulting water-balance-derived ET (ETwb) features a long-term average that is consistent with previous studies (117.2±3.5 cm yr−1) but displays greater seasonal and interannual variability than seven global ET products. The seasonal cycle of ETwb generally tracks that of precipitation over the basin, with the exception that ETwb is greater in March–April–May (MAM) than in the relatively wetter September–October–November (SON) periods. This pattern appears to be driven by seasonal variations in the diffuse photosynthetically active radiation (PAR) fraction, net radiation (Rn), and soil water availability. From 2002 to 2016, Rn, PAR, and vapor-pressure deficit (VPD) all increased significantly within the Congo Basin; however, no corresponding trend occurred in ETwb. We hypothesize that the stability of ETwb over the study period despite sunnier and less humid conditions may be due to increasing atmospheric CO2 concentrations that offset the impacts of rising VPD and irradiance on stomatal water use efficiency (WUE).

Description: Optimum management of irrigated crops in regions with shallow saline groundwater requires a careful balance between application of irrigation water and upward movement of salinity from the groundwater. Few field-validated surrogate models are available to aid in the management of irrigation water under shallow groundwater conditions. The objective of this research is to develop a model that can aid in the management using a minimum of input data that are field validated. In this paper a 2-year field experiment was carried out in the Hetao irrigation district in Inner Mongolia, China, and a physically based integrated surrogate model for arid irrigated areas with shallow groundwater was developed and validated with the collected field data. The integrated model that links crop growth with available water and salinity in the vadose zone is called Evaluation of the Performance of Irrigated Crops and Soils (EPICS). EPICS recognizes that field capacity is reached when the matric potential is equal to the height above the groundwater table and thus not by a limiting hydraulic conductivity. In the field experiment, soil moisture contents and soil salt conductivity at five depths in the top 100 cm, groundwater depth, crop height, and leaf area index were measured in 2017 and 2018. The field results were used for calibration and validation of EPICS. Simulated and observed data fitted generally well during both calibration and validation. The EPICS model that can predict crop growth, soil water, groundwater depth, and soil salinity can aid in optimizing water management in irrigation districts with shallow aquifers.

Description: In the framework of the EU Copernicus programme, the European Centre for Medium-Range Weather Forecasts (ECMWF) on behalf of the Joint Research Centre (JRC) is forecasting daily fire weather indices using its medium-range ensemble prediction system. The use of weather forecasts in place of local observations can extend early warnings by up to 1–2 weeks, allowing for greater proactive coordination of resource-sharing and mobilization within and across countries. Using 1 year of pre-operational service in 2017 and the Fire Weather Index (FWI), here we assess the capability of the system globally and analyse in detail three major events in Chile, Portugal and California. The analysis shows that the skill provided by the ensemble forecast system extends to more than 10 d when compared to the use of mean climate, making a case for extending the forecast range to the sub-seasonal to seasonal timescale. However, accurate FWI prediction does not translate into accuracy in the forecast of fire activity globally. Indeed, when all fires detected in 2017 are considered, including agricultural- and human-induced burning, high FWI values only occur in 50 % of the cases and are limited to the Boreal regions. Nevertheless for very large events which were driven by weather conditions, FWI forecasts provide advance warning that could be instrumental in setting up management and containment strategies.

Description: In the past decades, severe heat waves have frequently occurred in many parts of the world. These conspicuous heat waves exerted terrible influences on human health, society, the economy, agriculture, the ecosystem and so on. Based on observed daily temperatures in China, an integrated index of heat waves and extreme-temperature days was established involving the frequency, duration, intensity and scale of these events across large cities in China. Heat waves and extreme-temperature days showed an increasing trend in most regions except northwest China from 1955 to 2014. After the late 1980s, the increasing trend was more obvious than the decades before. The cities in the middle and lower reaches of the Yangtze River were threatened by the most serious heat events in the past 60 years, especially Chongqing and Changsha. Due to the subtropical monsoon climate and special terrain, Chongqing experienced the most heat events in a long period of time. In particular, there was obvious fluctuation of hot years in 31 cities, which did not continuously rise with global warming; 21 cities mainly located in the eastern and southern regions of China had an obvious rising trend; eight cities had a clear declining trend which was mainly distributed in the western and northern regions of China; and there were no extreme-temperature days in Kunming and Lhasa in the past 60 years. The study revealed an obvious differentiation of heat events for 31 cities under climate change; heat threat in most cities is increasing but declining or remaining unchanged in the other cities. The trend is likely to intensify with global warming.

Description: The total Antarctic sea ice extent (SIE) experiences a distinct annual cycle, peaking in September and reaching its minimum in February. In this paper we propose a mathematical and statistical decomposition of this temporal variation in SIE. Each component is interpretable and, when combined, gives a complete picture of the variation in the sea ice. We consider timescales varying from the instantaneous and not previously defined to the multi-decadal curvilinear trend, the longest. Because our representation is daily, these timescales of variability give precise information about the timing and rates of advance and retreat of the ice and may be used to diagnose physical contributors to variability in the sea ice. We define a number of annual cycles each capturing different components of variation, especially the yearly amplitude and phase that are major contributors to SIE variation. Using daily sea ice concentration data, we show that our proposed invariant annual cycle explains 29 % more of the variation in daily SIE than the traditional method. The proposed annual cycle that incorporates amplitude and phase variation explains 77 % more variation than the traditional method. The variation in phase explains more of the variability in SIE than the amplitude. Using our methodology, we show that the anomalous decay of sea ice in 2016 was associated largely with a change of phase rather than amplitude. We show that the long term trend in Antarctic sea ice extent is strongly curvilinear and the reported positive linear trend is small and dependent strongly on a positive trend that began around 2011 and continued until 2016.

Description: The invasion of aquifer microbial communities by aboveground microorganisms, a phenomenon known as community coalescence, is likely to be exacerbated in groundwaters fed by stormwater infiltration systems (SISs). Here, the incidence of this increased connectivity with upslope soils and impermeabilized surfaces was assessed through a meta-analysis of 16S rRNA gene libraries. Specifically, DNA sequences encoding 16S rRNA V5-V6 regions from free-living and attached aquifer bacteria (i.e., water and biofilm samples) were analysed upstream and downstream of a SIS and compared with those from bacterial communities from watershed runoffs and surface sediments from the SIS detention and infiltration basins. Significant bacterial transfers were inferred by the SourceTracker Bayesian approach, with 23 % to 57 % of the aquifer bacterial biofilms being composed of taxa from aboveground sediments and urban runoffs. Sediments from the detention basin were found more significant contributors of taxa involved in the buildup of these biofilms than soils from the infiltration basin. Inferred taxa among the coalesced biofilm community were predicted to be high in hydrocarbon degraders such as Sphingobium and Nocardia. The 16S rRNA-based bacterial community structure of the downstream-SIS aquifer waters showed lower coalescence with aboveground taxa (8 % to 38 %) than those of biofilms and higher numbers of taxa predicted to be involved in the N and S cycles. A DNA marker named tpm enabled the tracking of bacterial species from 24 genera including Pseudomonas, Aeromonas and Xanthomonas, among these communities. Several tpm sequence types were found to be shared between the aboveground and aquifer samples. Reads related to Pseudomonas were allocated to 50 species, of which 16 were found in the aquifer samples. Several of these aquifer species were found to be involved in denitrification but also hydrocarbon degradation (P. aeruginosa, P. putida and P. fluorescens). Some tpm sequence types allocated to P. umsongensis and P. chengduensis were found to be enriched among the tpm-harbouring bacteria, respectively, of the aquifer biofilms and waters. Reads related to Aeromonas were allocated to 11 species, but only those from A. caviae were recovered aboveground and in the aquifer samples. Some tpm sequence types of the X. axonopodis phytopathogen  were recorded in higher proportions among the tpm-harbouring bacteria of the aquifer waters than in the aboveground samples. A significant coalescence of microbial communities from an urban watershed with those of an aquifer was thus observed, and recent aquifer biofilms were found to be significantly colonized by runoff-opportunistic taxa able to use urban C sources from aboveground compartments.

Description: Landfast sea ice (fast ice) attached to Antarctic (near-)coastal elements is a critical component of the local physical and ecological systems. Through its direct coupling with the atmosphere and ocean, fast-ice properties are also a potential indicator of processes related to a changing climate. However, in situ fast-ice observations in Antarctica are extremely sparse because of logistical challenges and harsh environmental conditions. Since 2010, a monitoring program observing the seasonal evolution of fast ice in Atka Bay has been conducted as part of the Antarctic Fast Ice Network (AFIN). The bay is located on the northeastern edge of Ekström Ice Shelf in the eastern Weddell Sea, close to the German wintering station Neumayer III. A number of sampling sites have been regularly revisited each year between annual ice formation and breakup to obtain a continuous record of sea-ice and sub-ice platelet-layer thickness, as well as snow depth and freeboard across the bay. Here, we present the time series of these measurements over the last 9 years. Combining them with observations from the nearby Neumayer III meteorological observatory as well as auxiliary satellite images enables us to relate the seasonal and interannual fast-ice cycle to the factors that influence their evolution. On average, the annual consolidated fast-ice thickness at the end of the growth season is about 2 m, with a loose platelet layer of 4 m thickness beneath and 0.70 m thick snow on top. Results highlight the predominately seasonal character of the fast-ice regime in Atka Bay without a significant interannual trend in any of the observed variables over the 9-year observation period. Also, no changes are evident when comparing with sporadic measurements in the 1980s and 1990s. It is shown that strong easterly winds in the area govern the year-round snow distribution and also trigger the breakup of fast ice in the bay during summer months. Due to the substantial snow accumulation on the fast ice, a characteristic feature is frequent negative freeboard, associated flooding of the snow–ice interface, and a likely subsequent snow ice formation. The buoyant platelet layer beneath negates the snow weight to some extent, but snow thermodynamics is identified as the main driver of the energy and mass budgets for the fast-ice cover in Atka Bay. The new knowledge of the seasonal and interannual variability of fast-ice properties from the present study helps to improve our understanding of interactions between atmosphere, fast ice, ocean, and ice shelves in one of the key regions of Antarctica and calls for intensified multidisciplinary studies in this region.

Description: Storm tides are a major hazard for the German North Sea coasts. For coastal protection and economic activities, planning information on the probability and magnitude of extreme storm tides and their possible future changes is important. This study focuses on the most extreme events and examines whether they could have become more severe under slightly different conditions while still remaining within physical plausibility. In the face of a limited number of observational data on very severe events, an extensive set of model data is used to extract most extreme storm tide events for locations in the German Bight, in particular Borkum and the Ems estuary. The data set includes water levels and respective atmospheric conditions from a hindcast and future climate realizations without sea level rise describing today's and possible future conditions. A number of very severe events with water levels exceeding those measured near Borkum since 1906 are identified in the data set. A possible further amplification of the highest events is investigated by simulating these events for the North Sea with different phase lags between the astronomical tide given at the open model boundaries and the wind forcing. It is found that superposition of spring tide conditions, different timing of the astronomical high water and atmospheric conditions during the highest storm event would cause an enhancement of the highest water level up to about 50 cm. The water levels of the two highest events from the data set are used to analyse the effects in the Ems estuary using a high-resolution model of the German Bight. Additionally, the influences of an extreme river runoff and of sea level rise are studied. The extreme river runoff of 1200 m3 s−1 increases the highest water levels by several decimetres in the narrow upstream part of the Ems estuary. This effect diminishes downstream. The sea level rise increases the water level in the downstream part of the Ems estuary by the amount applied at the model boundary to the North Sea. In the upstream part, its influence on the water level decreases. This study may serve as a first step towards an impact assessment for severe storm tides and towards implications for coastal zone management in times of climate change.

Description: Submarine groundwater discharge (SGD) is an important gateway for nutrients and pollutants from land to sea. While understanding SGD is crucial for managing nearshore ecosystems and coastal freshwater reserves, studying this discharge is complicated by its occurrence at the limit between land and sea, a dynamic environment. This practical difficulty is exacerbated by the significant spatial and temporal variability. Therefore, to capture the magnitude of SGD, a variety of techniques and measurements, applied over multiple periods, is needed. Here, we combine several geophysical methods to detect zones of fresh submarine groundwater discharge (FSGD) in the intertidal zone, upper beach, dunes, and shallow coastal area. Both terrestrial electrical-resistivity tomography (ERT; roll-along) and marine continuous resistivity profiling (CRP) are used from the shallow continental shelf up to the dunes and combined with frequency domain electromagnetic (FDEM) mapping in the intertidal zone. In particular, we apply an estimation of robust apparent electrical conductivity (rECa) from FDEM data to provide reliable lateral and vertical discrimination of FSGD zones. The study area is a very dynamic environment along the North Sea, characterized by semi-diurnal tides between 3 and 5 m. CRP is usually applied in calmer conditions, but we prove that such surveys are possible and provide additional information to primarily land-bound ERT surveying. The 2D inversion models created from ERT and CRP data clearly indicate the presence of FSGD on the lower beach or below the low-water line. This discharge originates from a potable freshwater lens below the dunes and flows underneath a thick saltwater lens, present from the dunes to the lower sandy beach, which is fully observed with ERT. Freshwater outflow intensity has increased since 1980, due to a decrease of groundwater pumping in the dunes. FDEM mapping at two different times reveals discharge at the same locations, clearly displays the lateral variation of the zone of discharge, and suggests that FSGD is stronger at the end of winter compared to the beginning of autumn. ERT, CRP, and FDEM are complementary tools in the investigation of SGD. They provide a high-resolution 3D image of the saltwater and freshwater distribution in the phreatic coastal aquifer over a relatively large area, both off- and onshore.

Description: The Copernicus Polar Ice and Snow Topography Altimeter (CRISTAL) mission is one of six high-priority candidate missions (HPCMs) under consideration by the European Commission to enlarge the Copernicus Space Component. Together, the high-priority candidate missions fill gaps in the measurement capability of the existing Copernicus Space Component to address emerging and urgent user requirements in relation to monitoring anthropogenic CO2 emissions, polar environments, and land surfaces. The ambition is to enlarge the Copernicus Space Component with the high-priority candidate missions in the mid-2020s to provide enhanced continuity of services in synergy with the next generation of the existing Copernicus Sentinel missions. CRISTAL will carry a dual-frequency synthetic-aperture radar altimeter as its primary payload for measuring surface height and a passive microwave radiometer to support atmospheric corrections and surface-type classification. The altimeter will have interferometric capabilities at Ku-band for improved ground resolution and a second (non-interferometric) Ka-band frequency to provide information on snow layer properties. This paper outlines the user consultations that have supported expansion of the Copernicus Space Component to include the high-priority candidate missions, describes the primary and secondary objectives of the CRISTAL mission, identifies the key contributions the CRISTAL mission will make, and presents a concept – as far as it is already defined – for the mission payload.

Description: Für die Verortung der deutschen akademischen Humangeographie im Geflecht zwischen wissenschaftlicher Praxis, theoretischen Propositionen und Lehralltag war der Geographentag in Kiel im Jahre 1969 ein Meilenstein. Anlässlich der Erinnerung an den Ort und die Debatten vor 50 Jahren wurde wiederum Kiel im Jahre 2019 zu einem Ort der Reflektion. Der hier vorliegende Beitrag versucht in einer bewusst persönlich formulierten Art die Impulse, die von „Kiel 1969“ ausgingen, im universitären Alltag des Geographischen Institutes der TU München in den 1980er Jahren zu verorten und hierdurch gewissermaßen zu relativieren. Hierdurch entsteht ein differenziertes Bild von richtungsweisenden Veränderungen und verharrenden Strukturen, welche ineinander verwoben die damals überregional bekannte Münchener Sozialgeographie charakterisierten – und für die deutschsprachige Humangeographie über die speziell Münchner Zustände hinaus bezeichnend waren.

Description: Per capita arable land is decreasing due to the rapidly increasing population, and fresh water is becoming scarce and more expensive. Therefore, farmers should continue to use technology and innovative solutions to improve efficiency, save input costs, and optimise environmental resources (such as water). In the case study presented in this paper, the Global Navigation Satellite System interferometric reflectometry (GNSS-IR) technique was used to monitor soil moisture during 66 d, from 3 December 2018 to 6 February 2019, in the installations of the Cajamar Centre of Experiences, Paiporta, Valencia, Spain. Two main objectives were pursued. The first was the extension of the technique to a multi-constellation solution using GPS, GLONASS, and GALILEO satellites, and the second was to test whether mass-market sensors could be used for this technique. Both objectives were achieved. At the same time that the GNSS observations were made, soil samples taken at 5 cm depth were used for soil moisture determination to establish a reference data set. Based on a comparison with that reference data set, all GNSS solutions, including the three constellations and the two sensors (geodetic and mass market), were highly correlated, with a correlation coefficient between 0.7 and 0.85.

Description: Projecting the spatiotemporal changes in water resources under a no-analog future climate requires physically based integrated hydrologic models which simulate the transfer of water and energy across the earth's surface. These models show promise in the context of unprecedented climate extremes given their reliance on the underlying physics of the system as opposed to empirical relationships. However, these techniques are plagued by several sources of uncertainty, including the inaccuracy of input datasets such as meteorological forcing. These datasets, usually derived from climate models or satellite-based products, are typically only resolved on the order of tens to hundreds of kilometers, while hydrologic variables of interest (e.g., discharge and groundwater levels) require a resolution at much smaller scales. In this work, a high-resolution hydrologic model is forced with various resolutions of meteorological forcing (0.5 to 40.5 km) generated by a dynamical downscaling analysis from the regional climate model Weather Research and Forecasting (WRF). The Cosumnes watershed, which spans the Sierra Nevada and Central Valley interface of California (USA), exhibits semi-natural flow conditions due to its rare undammed river basin and is used here as a test bed to illustrate potential impacts of various resolutions of meteorological forcing on snow accumulation and snowmelt, surface runoff, infiltration, evapotranspiration, and groundwater levels. Results show that the errors in spatial distribution patterns impact land surface processes and can be delayed in time. Localized biases in groundwater levels can be as large as 5–10 m and 3 m in surface water. Most hydrologic variables reveal that biases are seasonally and spatially dependent, which can have serious implications for model calibration and ultimately water management decisions.

Description: Snow instability tests provide valuable information regarding the stability of the snowpack. Test results are key data used to prepare public avalanche forecasts. However, to include them into operational procedures, a quantitative interpretation scheme is needed. Whereas the interpretation of the rutschblock test (RB) is well established, a similar detailed classification for the extended column test (ECT) is lacking. Therefore, we develop a four-class stability interpretation scheme. Exploring a large data set of 1719 ECTs observed at 1226 sites, often performed together with a RB in the same snow pit, and corresponding slope stability information, we revisit the existing stability interpretations and suggest a more detailed classification. In addition, we consider the interpretation of cases when two ECTs were performed in the same snow pit. Our findings confirm previous research, namely that the crack propagation propensity is the most relevant ECT result and that the loading step required to initiate a crack is of secondary importance for stability assessment. The comparison with the RB showed that the ECT classifies slope stability less reliably than the RB. In some situations, performing a second ECT may be helpful when the first test did not indicate rather unstable or stable conditions. Finally, the data clearly show that false-unstable predictions of stability tests outnumber the correct-unstable predictions in an environment where overall unstable locations are rare.

Description: On 5 March 2019 12:00 UTC, an atmospheric river (AR) made landfall in Santa Barbara, CA, and lasted approximately 30 h. While ARs are typical winter storms in the area, the extraordinary number of lightning strikes observed near coastal Santa Barbara made this event unique. The Earth Networks Global Lightning Network (ENGLN) detected 8811 lightning flashes around southern California (30 to 37∘ N and 130 to 115∘ W) in 24 h, which is roughly 2500 times the climatological flash rate in this region. The AR-related thunderstorm resulted in approximately 23.18 mm accumulated precipitation in 30 h in Santa Barbara. This article examines synoptic and mesoscale features conducive to this electrifying AR event, characterizing its uniqueness in the context of previous March events that made landfall in the region. We show that this AR was characterized by an unusual deep moist layer extending from the low to mid-troposphere in an environment with potential instability and low-elevation freezing level. Despite the negligible convective available potential energy (CAPE) during the peak of the thunderstorm near Santa Barbara, the lifting of layers with high water vapor content in the AR via warm conveyor belt and orographic forcing in a convectively unstable atmosphere resulted in the formation of hail and enhanced electrification.

Description: Limited availability of ground measurements in the vast majority of river basins world-wide increases the value of alternative data sources such as satellite observations in hydrological modelling. This study investigates the potential of using remotely sensed river water levels, i.e. altimetry observations, from multiple satellite missions to identify parameter sets for a hydrological model in the semi-arid Luangwa River basin in Zambia. A distributed process-based rainfall–runoff model with sub-grid process heterogeneity was developed and run on a daily timescale for the time period 2002 to 2016. As a benchmark, feasible model parameter sets were identified using traditional model calibration with observed river discharge data. For the parameter identification using remote sensing, data from the Gravity Recovery and Climate Experiment (GRACE) were used in a first step to restrict the feasible parameter sets based on the seasonal fluctuations in total water storage. Next, three alternative ways of further restricting feasible model parameter sets using satellite altimetry time series from 18 different locations along the river were compared. In the calibrated benchmark case, daily river flows were reproduced relatively well with an optimum Nash–Sutcliffe efficiency of ENS,Q=0.78 (5/95th percentiles of all feasible solutions ENS,Q,5/95=0.61–0.75). When using only GRACE observations to restrict the parameter space, assuming no discharge observations are available, an optimum of ENS,Q=-1.4 (ENS,Q,5/95=-2.3–0.38) with respect to discharge was obtained. The direct use of altimetry-based river levels frequently led to overestimated flows and poorly identified feasible parameter sets (ENS,Q,5/95=-2.9–0.10). Similarly, converting modelled discharge into water levels using rating curves in the form of power relationships with two additional free calibration parameters per virtual station resulted in an overestimation of the discharge and poorly identified feasible parameter sets (ENS,Q,5/95=-2.6–0.25). However, accounting for river geometry proved to be highly effective. This included using river cross-section and gradient information extracted from global high-resolution terrain data available on Google Earth and applying the Strickler–Manning equation to convert modelled discharge into water levels. Many parameter sets identified with this method reproduced the hydrograph and multiple other signatures of discharge reasonably well, with an optimum of ENS,Q=0.60 (ENS,Q,5/95=-0.31–0.50). It was further shown that more accurate river cross-section data improved the water-level simulations, modelled rating curve, and discharge simulations during intermediate and low flows at the basin outlet where detailed on-site cross-section information was available. Also, increasing the number of virtual stations used for parameter selection in the calibration period considerably improved the model performance in a spatial split-sample validation. The results provide robust evidence that in the absence of directly observed discharge data for larger rivers in data-scarce regions, altimetry data from multiple virtual stations combined with GRACE observations have the potential to fill this gap when combined with readily available estimates of river geometry, thereby allowing a step towards more reliable hydrological modelling in poorly gauged or ungauged basins.

Description: The Maxwell elasto-brittle (MEB) rheology is implemented in the Eulerian finite-difference (FD) modeling framework commonly used in classical viscous-plastic (VP) models. The role of the damage parameterization, the cornerstone of the MEB rheology, in the formation and collapse of ice arches and ice bridges in a narrow channel is investigated. Ice bridge simulations are compared with observations to derive constraints on the mechanical properties of landfast sea ice. Results show that the overall dynamical behavior documented in previous MEB models is reproduced in the FD implementation, such as the localization of the damage in space and time and the propagation of ice fractures in space at very short timescales. In the simulations, an ice arch is easily formed downstream of the channel, sustaining an ice bridge upstream. The ice bridge collapses under a critical surface forcing that depends on the material cohesion. Typical ice arch conditions observed in the Arctic are best simulated using a material cohesion in the range of 5–10 kN m−2. Upstream of the channel, fracture lines along which convergence (ridging) takes place are oriented at an angle that depends on the angle of internal friction. Their orientation, however, deviates from the Mohr–Coulomb theory. The damage parameterization is found to cause instabilities at large compressive stresses, which prevents the production of longer-term simulations required for the formation of stable ice arches upstream of the channel between these lines of fracture. Based on these results, we propose that the stress correction scheme used in the damage parameterization be modified to remove numerical instabilities.

Description: Based on the discourse analysis of articles collected between 2010 and 2016 from the Süddeutsche Zeitung – a leading local and German national newspaper – my aim is to reconstruct the central conditions limiting or enabling the participation of those citizens in the public discourse who are generally constructed as „migrants“. Therefore, I analyse the central elements of the discourse around the subject migration/integration. My analysis is guided by the ‚postmigrant debate‘, in particular by the approaches of the ‚differential inclusion‘ of migrantised groups and their ‚struggles of migration‘ combining it with critical race debates. My aim is to outline the different discursive ways that allow migrantised citizens to participate in public meaning making, and the ways, they use to contest majoritarian views. My analysis reveals their critical reconsideration of the system of differentiated inclusion, which is organizing the majoritarian discourse and ‚migrants‘ everyday lives. While the journalistic strategy exemplified within the analysis is working in support of the ‚migrant's perspectives‘, it simultaneously acts to normalize majoritarian position contra migration.

Description: Cave microclimate and geochemical monitoring is vitally important for correct interpretations of proxy time series from speleothems with regard to past climatic and environmental dynamics. We present results of a comprehensive cave-monitoring programme in Waipuna Cave in the North Island of New Zealand, a region that is strongly influenced by the Southern Westerlies and the El Niño–Southern Oscillation (ENSO). This study aims to characterise the response of the Waipuna Cave hydrological system to atmospheric circulation dynamics in the southwestern Pacific region in order to assure the quality of ongoing palaeo-environmental reconstructions from this cave. Drip water from 10 drip sites was collected at roughly monthly intervals for a period of ca. 3 years for isotopic (δ18O, δD, d-excess parameter, δ17O, and 17Oexcess) and elemental (Mg∕Ca and Sr∕Ca) analysis. The monitoring included spot measurements of drip rates and cave air CO2 concentration. Cave air temperature and drip rates were also continuously recorded by automatic loggers. These datasets were compared to surface air temperature, rainfall, and potential evaporation from nearby meteorological stations to test the degree of signal transfer and expression of surface environmental conditions in Waipuna Cave hydrochemistry. Based on the drip response dynamics to rainfall and other characteristics, we identified three types of discharge associated with hydrological routing in Waipuna Cave: (i) type 1 – diffuse flow, (ii) type 2 – fracture flow, and (iii) type 3 – combined flow. Drip water isotopes do not reflect seasonal variability but show higher values during severe drought. Drip water δ18O values are characterised by small variability and reflect the mean isotopic signature of precipitation, testifying to rapid and thorough homogenisation in the epikarst. Mg∕Ca and Sr∕Ca ratios in drip waters are predominantly controlled by prior calcite precipitation (PCP). Prior calcite precipitation is strongest during austral summer (December–February), reflecting drier conditions and a lack of effective infiltration, and is weakest during the wet austral winter (July–September). The Sr∕Ca ratio is particularly sensitive to ENSO conditions due to the interplay of congruent or incongruent host rock dissolution, which manifests itself in lower Sr∕Ca in above-average warmer and wetter (La Niña-like) conditions. Our microclimatic observations at Waipuna Cave provide a valuable baseline for the rigorous interpretation of speleothem proxy records aiming at reconstructing the past expression of Pacific climate modes.

Description: A number of seaside communities in Troms, northern Norway, are vulnerable to sudden weather-induced access disruptions due to high-impact weather and dependency on one or few roads. In this paper we study changes in winter weather known to potentially cause access disruptions in Troms, for the present climate (1958–2017) and two future periods (2041–2070; 2071–2100). We focus on climate indices associated with snow avalanches and weather that may lead to for example slippery road conditions. In two focus areas, the most important results show larger snow amounts now compared to 50 years ago, and heavy snowfall has become more intense and frequent. This trend is expected to turn in the future, particularly at low elevations where snow cover during winter might become a rarity by 2100. Strong snow drift, due to a combination of snowfall and wind speed, has slightly increased in the two focus areas, but a strong decrease is expected in the future due to less snow. Events of heavy rain during winter are rather infrequent in the present winter climate of Troms, but we show that these events are likely to occur much more often in all regions in the future.

Description: The Antarctic ice sheet extent in the Weddell Sea embayment (WSE) during the Last Glacial Maximum (LGM; ca. 19–25 calibrated kiloyears before present, ka cal BP) and its subsequent retreat from the shelf are poorly constrained, with two conflicting scenarios being discussed. Today, the modern Brunt Ice Shelf, the last remaining ice shelf in the northeastern WSE, is only pinned at a single location and recent crevasse development may lead to its rapid disintegration in the near future. We investigated the seafloor morphology on the northeastern WSE shelf and discuss its implications, in combination with marine geological records, to create reconstructions of the past behaviour of this sector of the East Antarctic Ice Sheet (EAIS), including ice–seafloor interactions. Our data show that an ice stream flowed through Stancomb-Wills Trough and acted as the main conduit for EAIS drainage during the LGM in this sector. Post-LGM ice stream retreat occurred stepwise, with at least three documented grounding-line still-stands, and the trough had become free of grounded ice by ∼10.5 ka cal BP. In contrast, slow-flowing ice once covered the shelf in Brunt Basin and extended westwards toward McDonald Bank. During a later time period, only floating ice was present within Brunt Basin, but large “ice slabs” enclosed within the ice shelf occasionally ran aground at the eastern side of McDonald Bank, forming 10 unusual ramp-shaped seabed features. These ramps are the result of temporary ice shelf grounding events buttressing the ice further upstream. To the west of this area, Halley Trough very likely was free of grounded ice during the LGM, representing a potential refuge for benthic shelf fauna at this time.

Description: Expansion of the hydrologically connected area during rainfall events causes previously disconnected areas to contribute to streamflow. If these newly contributing areas have a different hydrochemical composition compared to the previously connected contributing areas, this may cause a change in stream water chemistry that cannot be explained by simple mixing of rainfall and baseflow. Changes in stormflow composition are, therefore, sometimes used to identify when transiently connected areas (or water sources) contribute to stormflow. We identified the dominant sources of streamflow for a steep 20 ha pre-Alpine headwater catchment in Switzerland and investigated the temporal changes in connectivity for four rainfall events based on stream water concentrations and groundwater level data. First, we compared the isotopic and chemical composition of stormflow at the catchment outlet to the composition of rainfall, groundwater and soil water. Three-component end-member mixing analyses indicated that groundwater dominated stormflow during all events, and that soil water fractions were minimal for three of the four events. However, the large variability in soil and groundwater composition compared to the temporal changes in stormflow composition inhibited the determination of the contributions from the different groundwater sources. Second, we estimated the concentrations of different solutes in stormflow based on the mixing fractions derived from two-component hydrograph separation using a conservative tracer (δ2H) and the measured concentrations of the solutes in baseflow and rainfall. The estimated concentrations differed from the measured stormflow concentrations for many solutes and samples. The deviations increased gradually with increasing streamflow for some solutes (e.g. iron and copper), suggesting increased contributions from riparian and hillslope groundwater with higher concentrations of these solutes and thus increased hydrological connectivity. The findings of this study show that solute concentrations partly reflect the gradual changes in hydrologic connectivity, and that it is important to quantify the variability in the composition of different source areas.

Description: In this study, the fine-scale responses of a stratified oligotrophic karstic lake (Kozjak Lake, Plitvice Lakes, Croatia; the lake fetch is 2.3 km, and the maximum depth is 46 m) to atmospheric forcing on the lake surface are investigated. Lake temperatures measured at a resolution of 2 min at 15 depths ranging from 0.2 to 43 m, which were observed during the 6 July–5 November 2018 period, were analyzed. The results show thermocline deepening from 10 m at the beginning of the observation period to 16 m at the end of the observation period, where the latter depth corresponds to approximately one-third of the lake depth. The pycnocline followed the same pattern, except that the deepening occurred throughout the entire period approximately 1 m above the thermocline. On average, thermocline deepening was 3–4 cm d−1, while the maximum deepening (12.5 cm d−1) coincided with the occurrence of internal seiches. Furthermore, the results indicate three different types of forcings on the lake surface; two of these forcings have diurnal periodicity – (1) continuous heat fluxes and (2) occasional periodic stronger winds – whereas forcing (3) corresponds to occasional nonperiodic stronger winds with steady along-basin directions. Continuous heat fluxes (1) produced forced diurnal oscillations in the lake temperature within the first 5 m of the lake throughout the entire observation period. Noncontinuous periodic stronger winds (2) resulted in occasional forced diurnal oscillations in the lake temperatures at depths from approximately 7 to 20 m. Occasional strong and steady along-basin winds (3) triggered both baroclinic internal seiches with a principal period of 8.0 h and barotropic surface seiches with a principal period of 9 min. Lake currents produced by the surface seiches under realistic-topography conditions generated baroclinic oscillations of the thermocline region (at depths from 9 to 17 m) with periods corresponding to the period of surface seiches (≈ 9 min), which, to the best of our knowledge, has not been reported in previous lake studies.

Description: Estimating greenhouse gas emissions from travel – a GIS-based study Geographica Helvetica, 70, 185-192, 2015 Author(s): S. Kuonen Conferences, meetings and congresses are an important part of today's economic and scientific world. But the environmental impact, especially from greenhouse gas emissions associated with travel, can be extensive. Anthropogenic greenhouse gas (GHG) emissions account for the warming of the atmosphere and oceans. This study draws on the need to quantify and reduce greenhouse gas emissions associated with travel activities and aims to give suggestions for organizers and participants on possible ways to reduce greenhouse gas emissions, demonstrated on the example of the European Geography Association (EGEA) Annual Congress 2013 in Wasilkow, Poland. The lack of a comprehensive methodology for the estimation of greenhouse gas emissions from travel led to an outline of a methodology that uses geographic information systems (GIS) to calculate travel distances. The calculation of travel distances in GIS is adapted from actual transportation infrastructure, derived from the open-source platform OpenStreetMap. The methodology also aims to assess the possibilities to reduce GHG emissions by choosing different means of transportation and a more central conference location. The results of the participants of the EGEA congress, who shared their travel data for this study, show that the total travel distance adds up to 238 000 km, with average travel distance of 2429 km per participant. The travel activities of the participants in the study result in total GHG emissions of 39 300 kg CO 2 -eq including both outward and return trip. On average a participant caused GHG emissions of 401 kg CO 2 -eq. In addition, the analysis of the travel data showed differences in travel behaviour depending on the distance between conference site and point of origin. The findings on travel behaviour have then been used to give an estimation of total greenhouse gas emissions from travel for all participants of the conference, which result in a total amount of 79 711 kg CO 2 -eq. The potential for reducing greenhouse gas emissions by substituting short flights with train rides and car rides with bus and train rides is limited. Only 6 % of greenhouse gas emissions could be saved by applying these measures. Further considerable savings could only be made by substituting longer flights (32.6 %) or choosing a more central conference location (26.3 %).

Description: Uncertainties in calculating precipitation climatology in East Asia Hydrology and Earth System Sciences Discussions, 12, 7765-7783, 2015 Author(s): J. Kim and S. K. Park This study examines the uncertainty in calculating the fundamental climatological characteristics of precipitation in the East Asia region from multiple fine-resolution gridded analysis datasets based on in-situ rain gauge observations. Five observation-based gridded precipitation datasets are used to derive the long-term means, standard deviations in lieu of interannual variability and linear trends over the 28-year period from 1980 to 2007. Both the annual and summer (June–July–August) mean precipitation is examined. The agreement amongst these precipitation datasets are examined using multiple metrics including the signal-to-noise ratio (SNR) defined as the ratio between long-term means and the corresponding standard deviations, and Taylor diagrams which allows examinations of the pattern correlation, the standard deviation, and the centered root mean square error. It is found that the five gauge-based precipitation analysis datasets agree well in the long-term mean and interannual variability in most of the East Asia region including eastern China, Manchuria, South Korea, and Japan, which are densely populated and have fairly high density observation networks. The regions of large inter-dataset variations include Tibetan Plateau, Mongolia, northern Indo-China, and North Korea. The regions of large uncertainties are typically lightly populated and are characterized by severe terrain and/or extreme high elevations. Unlike the long-term mean and interannual variability, agreements between datasets in the linear trend is weak, both for the annual and summer mean values. In most of the East Asia region, the SNR for the linear trend is below 0.5, i.e., the inter-dataset variability exceeds the multi-data ensemble mean. The uncertainty in the spatial distribution of long-term means among these datasets occurs both in the spatial pattern and variability, but the uncertainty for the interannual variability and time trend is much larger in the variability than in the pattern correlation. Thus, care must be taken in using long-term trends calculated from gridded precipitation analysis data for climate studies over the East Asia region.

Description: Qualitative soil moisture assessment in semi-arid Africa – the role of experience and training on inter-rater reliability Hydrology and Earth System Sciences, 19, 3505-3516, 2015 Author(s): M. Rinderer, H. C. Komakech, D. Müller, G. L. B. Wiesenberg, and J. Seibert Soil and water management is particularly relevant in semi-arid regions to enhance agricultural productivity. During periods of water scarcity, soil moisture differences are important indicators of the soil water deficit and are traditionally used for allocating water resources among farmers of a village community. Here we present a simple, inexpensive soil wetness classification scheme based on qualitative indicators which one can see or touch on the soil surface. It incorporates the local farmers' knowledge on the best soil moisture conditions for seeding and brick making in the semi-arid environment of the study site near Arusha, Tanzania. The scheme was tested twice in 2014 with farmers, students and experts (April: 40 persons, June: 25 persons) for inter-rater reliability, bias of individuals and functional relation between qualitative and quantitative soil moisture values. During the test in April farmers assigned the same wetness class in 46 % of all cases, while students and experts agreed on about 60 % of all cases. Students who had been trained in how to apply the method gained higher inter-rater reliability than their colleagues with only a basic introduction. When repeating the test in June, participants were given improved instructions, organized in small subgroups, which resulted in a higher inter-rater reliability among farmers. In 66 % of all classifications, farmers assigned the same wetness class and the spread of class assignments was smaller. This study demonstrates that a wetness classification scheme based on qualitative indicators is a robust tool and can be applied successfully regardless of experience in crop growing and education level when an in-depth introduction and training is provided. The use of a simple and clear layout of the assessment form is important for reliable wetness class assignments.

Description: Nonlinear effects of locally heterogeneous hydraulic conductivity fields on regional stream–aquifer exchanges Hydrology and Earth System Sciences Discussions, 12, 7727-7764, 2015 Author(s): J. Zhu, C. L. Winter, and Z. Wang Computational experiments are performed to evaluate the effects of locally heterogeneous conductivity fields on regional exchanges of water between stream and aquifer systems in the Middle Heihe River Basin (MHRB) of northwestern China. The effects are found to be nonlinear in the sense that simulated discharges from aquifers to streams are systematically lower than discharges produced by a base model parameterized with relatively coarse effective conductivity. A similar, but weaker, effect is observed for stream leakage. The study is organized around three hypotheses: (H1) small-scale spatial variations of conductivity significantly affect regional exchanges of water between streams and aquifers in river basins, (H2) aggregating small-scale heterogeneities into regional effective parameters systematically biases estimates of stream–aquifer exchanges, and (H3) the biases result from slow-paths in groundwater flow that emerge due to small-scale heterogeneities. The hypotheses are evaluated by comparing stream–aquifer fluxes produced by the base model to fluxes simulated using realizations of the MHRB characterized by local (grid-scale) heterogeneity. Levels of local heterogeneity are manipulated as control variables by adjusting coefficients of variation. All models are implemented using the MODFLOW simulation environment, and the PEST tool is used to calibrate effective conductivities defined over 16 zones within the MHRB. The effective parameters are also used as expected values to develop log-normally distributed conductivity ( K ) fields on local grid scales. Stream-aquifer exchanges are simulated with K fields at both scales and then compared. Results show that the effects of small-scale heterogeneities significantly influence exchanges with simulations based on local-scale heterogeneities always producing discharges that are less than those produced by the base model. Although aquifer heterogeneities are uncorrelated at local scales, they appear to induce coherent slow-paths in groundwater fluxes that in turn reduce aquifer–stream exchanges. Since surface water–groundwater exchanges are critical hydrologic processes in basin-scale water budgets, these results also have implications for water resources management.

Description: Near–surface air temperature and snow skin temperature comparison from CREST-SAFE station data with MODIS land surface temperature data Hydrology and Earth System Sciences Discussions, 12, 7665-7687, 2015 Author(s): C. L. Pérez Díaz, T. Lakhankar, P. Romanov, J. Muñoz, R. Khanbilvardi, and Y. Yu Land Surface Temperature (LST) is a key variable (commonly studied to understand the hydrological cycle) that helps drive the energy balance and water exchange between the Earth's surface and its atmosphere. One observable constituent of much importance in the land surface water balance model is snow. Snow cover plays a critical role in the regional to global scale hydrological cycle because rain-on-snow with warm air temperatures accelerates rapid snow-melt, which is responsible for the majority of the spring floods. Accurate information on near-surface air temperature ( T -air) and snow skin temperature ( T -skin) helps us comprehend the energy and water balances in the Earth's hydrological cycle. T -skin is critical in estimating latent and sensible heat fluxes over snow covered areas because incoming and outgoing radiation fluxes from the snow mass and the air temperature above make it different from the average snowpack temperature. This study investigates the correlation between MODerate resolution Imaging Spectroradiometer (MODIS) LST data and observed T -air and T -skin data from NOAA-CREST-Snow Analysis and Field Experiment (CREST-SAFE) for the winters of 2013 and 2014. LST satellite validation is imperative because high-latitude regions are significantly affected by climate warming and there is a need to aid existing meteorological station networks with the spatially continuous measurements provided by satellites. Results indicate that near-surface air temperature correlates better than snow skin temperature with MODIS LST data. Additional findings show that there is a negative trend demonstrating that the air minus snow skin temperature difference is inversely proportional to cloud cover. To a lesser extent, it will be examined whether the surface properties at the site are representative for the LST properties within the instrument field of view.

Description: Does drought alter hydrological functions in forest soils? An infiltration experiment Hydrology and Earth System Sciences Discussions, 12, 7689-7725, 2015 Author(s): K. F. Gimbel, H. Puhlmann, and M. Weiler The water cycle is expected to change in future and severely affect precipitation patterns across central Europe and in other parts of the world, leading to more frequent and severe droughts. Usually, it is assumed that system properties, like soil properties, remain stable and will not be affected by drought events. To study if this assumption is appropriate, we address the effects of drought on the infiltration behavior of forest soils using dye tracer experiments on six sites in three regions across Germany, which were forced into drought conditions. The sites cover clayey, loamy and sandy textured soils. In each region, we compared a deciduous and a coniferous forest stand to address differences between the main tree species. The results of the dye tracer experiments show clear evidence for changes in infiltration behavior at the sites. The infiltration changed at the clayey plots from regular and homogeneous flow to fast preferential flow. Similar behavior was observed at the loamy plots, where large areas in the upper layers remained dry, displaying signs of strong water repellency. This was confirmed by WDPT tests, which revealed, in all except one plot, moderate to severe water repellency. Water repellency was also accountable for the change of regular infiltration to fingered flow in the sandy soils. The results of this study suggest that the "drought-history" or generally the climatic conditions in the past of a soil are more important than the actual antecedent soil moisture status regarding hydrophobicity and infiltration behavior; and also, that drought effects on infiltration need to be considered in hydrological models to obtain realistic predictions concerning water quality and quantity in runoff and groundwater recharge.

Description: : As sequencing becomes cheaper and more widely available, there is a greater need to quickly and effectively analyze large-scale genomic data. While the functionality of AVIA v1.0, whose implementation was based on ANNOVAR, was comparable with other annotation web servers, AVIA v2.0 represents an enhanced web-based server that extends genomic annotations to cell-specific transcripts and protein-level functional annotations. With AVIA’s improved interface, users can better visualize their data, perform comprehensive searches and categorize both coding and non-coding variants. Availability and implementation : AVIA is freely available through the web at http://avia.abcc.ncifcrf.gov . Contact : Hue.Vuong@fnlcr.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : As new methods for multivariate analysis of genome wide association studies become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance-based method for meta-analysis, generalized to an n -dimensional setting. Availability and implementation: The R package MultiMeta can be downloaded from CRAN. Contact: dragana.vuckovic@burlo.trieste.it ; vi1@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Impact of model developments on present and future simulations of permafrost in a global land-surface model The Cryosphere, 9, 1505-1521, 2015 Author(s): S. E. Chadburn, E. J. Burke, R. L. H. Essery, J. Boike, M. Langer, M. Heikenfeld, P. M. Cox, and P. Friedlingstein There is a large amount of organic carbon stored in permafrost in the northern high latitudes, which may become vulnerable to microbial decomposition under future climate warming. In order to estimate this potential carbon–climate feedback it is necessary to correctly simulate the physical dynamics of permafrost within global Earth system models (ESMs) and to determine the rate at which it will thaw. Additional new processes within JULES, the land-surface scheme of the UK ESM (UKESM), include a representation of organic soils, moss and bedrock and a modification to the snow scheme; the sensitivity of permafrost to these new developments is investigated in this study. The impact of a higher vertical soil resolution and deeper soil column is also considered. Evaluation against a large group of sites shows the annual cycle of soil temperatures is approximately 25 % too large in the standard JULES version, but this error is corrected by the model improvements, in particular by deeper soil, organic soils, moss and the modified snow scheme. A comparison with active layer monitoring sites shows that the active layer is on average just over 1 m too deep in the standard model version, and this bias is reduced by 70 cm in the improved version. Increasing the soil vertical resolution allows the full range of active layer depths to be simulated; by contrast, with a poorly resolved soil at least 50 % of the permafrost area has a maximum thaw depth at the centre of the bottom soil layer. Thus all the model modifications are seen to improve the permafrost simulations. Historical permafrost area corresponds fairly well to observations in all simulations, covering an area between 14 and 19 million km 2 . Simulations under two future climate scenarios show a reduced sensitivity of permafrost degradation to temperature, with the near-surface permafrost loss per degree of warming reduced from 1.5 million km 2 °C −1 in the standard version of JULES to between 1.1 and 1.2 million km 2 °C −1 in the new model version. However, the near-surface permafrost area is still projected to approximately half by the end of the 21st century under the RCP8.5 scenario.

Description: Numerical simulations of the Cordilleran ice sheet through the last glacial cycle The Cryosphere Discussions, 9, 4147-4203, 2015 Author(s): J. Seguinot, I. Rogozhina, A. P. Stroeven, M. Margold, and J. Kleman Despite more than a century of geological observations, the Cordilleran ice sheet of North America remains poorly understood in terms of its former extent, volume and dynamics. Although geomorphological evidence is abundant, its complexity is such that whole ice-sheet reconstructions of advance and retreat patterns are lacking. Here we use a numerical ice sheet model calibrated against field-based evidence to attempt a quantitative reconstruction of the Cordilleran ice sheet history through the last glacial cycle. A series of simulations is driven by time-dependent temperature offsets from six proxy records located around the globe. Although this approach reveals large variations in model response to evolving climate forcing, all simulations produce two major glaciations during marine oxygen isotope stages 4 (61.9–56.5 ka) and 2 (23.2–16.8 ka). The timing of glaciation is better reproduced using temperature reconstructions from Greenland and Antarctic ice cores than from regional oceanic sediment cores. During most of the last glacial cycle, the modelled ice cover is discontinuous and restricted to high mountain areas. However, widespread precipitation over the Skeena Mountains favours the persistence of a central ice dome throughout the glacial cycle. It acts as a nucleation centre before the Last Glacial Maximum and hosts the last remains of Cordilleran ice until the middle Holocene (6.6–6.2 ka).

Description: Statistical detection and modeling of the over-dispersion of winter storm occurrence Natural Hazards and Earth System Science, 15, 1757-1761, 2015 Author(s): M. Raschke In this communication, I improve the detection and modeling of the over-dispersion of winter storm occurrence. For this purpose, the generalized Poisson distribution and the Bayesian information criterion are introduced; the latter is used for statistical model selection. Moreover, I replace the frequently used dispersion statistics by an over-dispersion parameter which does not depend on the considered return period of storm events. These models and methods are applied in order to properly detect the over-dispersion in winter storm data for Germany, carrying out a joint estimation of the distribution models for different samples.

Description: Impacts of beaver dams on hydrologic and temperature regimes in a mountain stream Hydrology and Earth System Sciences, 19, 3541-3556, 2015 Author(s): M. Majerova, B. T. Neilson, N. M. Schmadel, J. M. Wheaton, and C. J. Snow Beaver dams affect hydrologic processes, channel complexity, and stream temperature in part by inundating riparian areas, influencing groundwater–surface water interactions, and changing fluvial processes within stream systems. We explored the impacts of beaver dams on hydrologic and temperature regimes at different spatial and temporal scales within a mountain stream in northern Utah over a 3-year period spanning pre- and post-beaver colonization. Using continuous stream discharge, stream temperature, synoptic tracer experiments, and groundwater elevation measurements, we documented pre-beaver conditions in the first year of the study. In the second year, we captured the initial effects of three beaver dams, while the third year included the effects of ten dams. After beaver colonization, reach-scale (~ 750 m in length) discharge observations showed a shift from slightly losing to gaining. However, at the smaller sub-reach scale (ranging from 56 to 185 m in length), the discharge gains and losses increased in variability due to more complex flow pathways with beaver dams forcing overland flow, increasing surface and subsurface storage, and increasing groundwater elevations. At the reach scale, temperatures were found to increase by 0.38 °C (3.8 %), which in part is explained by a 230 % increase in mean reach residence time. At the smallest, beaver dam scale (including upstream ponded area, beaver dam structure, and immediate downstream section), there were notable increases in the thermal heterogeneity where warmer and cooler niches were created. Through the quantification of hydrologic and thermal changes at different spatial and temporal scales, we document increased variability during post-beaver colonization and highlight the need to understand the impacts of beaver dams on stream ecosystems and their potential role in stream restoration.

Description: Does the Budyko curve reflect a maximum power state of hydrological systems? A backward analysis Hydrology and Earth System Sciences Discussions, 12, 7821-7842, 2015 Author(s): M. Westhoff, E. Zehe, P. Archambeau, and B. Dewals Almost all catchments plot within a small envelope around the Budyko curve. This apparent behaviour suggests that organizing principles may play a role in the evolution of catchments. In this paper we applied the thermodynamic principle of maximum power as the organizing principle. In a top-down approach we derived mathematical formulations of the relation between relative wetness and gradients driving runoff and evaporation for a simple one-box model. We did this in such a way that when the conductances are optimized with the maximum power principle, the steady state behaviour of the model leads exactly to a point on the Budyko curve. Subsequently we derived gradients that, under constant forcing, resulted in a Budyko curve following the asymptotes closely. With these gradients we explored the sensitivity of dry spells and dynamics in actual evaporation. Despite the simplicity of the model, catchment observations compare reasonably well with the Budyko curves derived with dynamics in rainfall and evaporation. This indicates that the maximum power principle may be used (i) to derive the Budyko curve and (ii) to move away from the empiricism in free parameters present in many Budyko functions. Future work should focus on better representing the boundary conditions of real catchments and eventually adding more complexity to the model.

Description: Impacts of land use change and climate variations on annual inflow into Miyun Reservoir, Beijing, China Hydrology and Earth System Sciences Discussions, 12, 7785-7819, 2015 Author(s): J. K. Zheng, G. Sun, W. H. Li, X. X. Yu, C. Zhang, Y. B. Gong, and L. H. Tu Miyun reservoir, the only surface water source for Beijing city, has experienced water supply decline in recent decades. Previous studies suggest that both land use change and climate contributes the changes of water supply in this critical watershed. However, the specific causes of the decline in Miyun reservoir are debatable in a non-stationary climate in the past four decades. The central objective of this study was to quantify the separate and collective contributions of land use change and climate variability to the decreasing inflow into Miyun reservoir during 1961–2008. Different from previous studies, this work objectively identified breakpoints by analyzing the long-term historical hydrometeorology and land cover records. To effectively study the different impacts of the climate variation and land cover change during different sub-periods, annual water balance model (AWB), climate elasticity model (CEM), and rainfall–runoff model (RRM) were employed to conduct attribution analysis synthetically. We found a significant decrease in annual streamflow ( p 〈 0.01), a significant positive trend in annual potential evapotranspiration ( p 〈 0.01), and an insignificant negative trend in annual precipitation ( p 〉 0.1) during 1961–2008. Combined with historical records, we identified two breakpoints as in 1983 and 1999 for the period 1961–2008 by the sequential Mann–Kendall Test and Double Mass Curve. Climate variability alone did not explain the decrease in inflow to Miyun reservoir. Reduction of water yield was closely related to increase in evapotranspiration rates due to the expansion of forestlands and reduction in cropland and grassland, and was likely exacerbated by increased water consumption for domestic and industrial uses in the basin. Our study found that the contribution to the observed streamflow decline from land use change fell from 64–92 % during 1984–1999 to 36–58 % during 2000–2008, whereas the contribution from climate variation climbed from 8–36 % during the 1984–1999 to 42–64 % during 2000–2008. Model uncertainty analysis further demonstrated that climate warming played a dominant role in streamflow reduction in the 2000s. We conclude that future climate change and variability will further challenge the goal of water supply of Miyun reservoir to meet water demand. A comprehensive watershed management strategy needs to consider the climate variations besides vegetation management.

Description: Impacts on wave-driven harbour agitation due to climate change in Catalan ports Natural Hazards and Earth System Science, 15, 1695-1709, 2015 Author(s): J. P. Sierra, M. Casas-Prat, M. Virgili, C. Mösso, and A. Sánchez-Arcilla The objective of the present work is to analyse how changes in wave patterns due to the effect of climate change can affect harbour agitation (oscillations within the port due to wind waves). The study focuses on 13 harbours located on the Catalan coast (NW Mediterranean) using a methodology with general applicability. To obtain the patterns of agitation, a Boussinesq-type model is used, which is forced at the boundaries by present/future offshore wave conditions extracted from recently developed high-resolution wave projections in the NW Mediterranean. These wave projections were obtained with the SWAN model forced by present/future surface wind fields projected, respectively, by five different combinations of global and regional circulation models (GCMs and RCMs) for the A1B scenario. The results show a general slight reduction in the annual average agitation for most of the ports, except for the northernmost and southernmost areas of the region, where a slight increase is obtained. A seasonal analysis reveals that the tendency to decrease is accentuated in winter. However, the inter-model variability is large for both the winter and the annual analysis. Conversely, a general increase with a larger agreement among models is found during summer, which is the period with greater activity in most of the studied ports (marinas). A qualitative assessment of the factors of variability seems to indicate that the choice of GCM tends to affect the spatial pattern, whereas the choice of RCM induces a more homogeneous bias over the regional domain.

Description: Utilisation of CryoSat-2 SAR altimeter in operational ice charting The Cryosphere Discussions, 9, 4117-4145, 2015 Author(s): E. Rinne and M. Similä We present methods to utilise Cryosat-2 (CS-2) Synthetic Aperture (SAR) mode data in operational ice charting. We compare CS-2 data qualitatively to Synthetic Aperture Radar (SAR) mosaics over Barents and Kara seas. Furthermore, we compare the CS-2 to archived operational ice charts. We present distributions of four CS-2 waveform parameters for different ice types as presented in the ice charts. We go on to present an automatic classification method for CS-2 data which, after training with operational ice charts, is capable of determining open water from ice with a hit rate of 〉 90 %. The training data is dynamically updated every five days using the most recent 15 days CS-2 data and operative ice charts. This helps the adaption of the classifier to the evolving ice/snow conditions throughout winter. The classifier is also capable of detecting three different ice classes (thin and thick first year ice as well as old ice) with success rates good enough for the output to be usable to support operational ice charting. Finally, we present a near real time CS-2 product just plotting the waveform characteristics and conclude that even such a simple product is usable for some of the needs of ice charting.

Description: Relating seasonal dynamics of enhanced vegetation index to the recycling of water in two endorheic river basins in north-west China Hydrology and Earth System Sciences, 19, 3387-3403, 2015 Author(s): M. A. Matin and C. P.-A. Bourque This study associates the dynamics of enhanced vegetation index in lowland desert oases to the recycling of water in two endorheic (hydrologically closed) river basins in Gansu Province, north-west China, along a gradient of elevation zones and land cover types. Each river basin was subdivided into four elevation zones representative of (i) oasis plains and foothills, and (ii) low-, (iii) mid-, and (iv) high-mountain elevations. Comparison of monthly vegetation phenology with precipitation and snowmelt dynamics within the same basins over a 10-year period (2000–2009) suggested that the onset of the precipitation season (cumulative % precipitation 〉 7–8 %) in the mountains, typically in late April to early May, was triggered by the greening of vegetation and increased production of water vapour at the base of the mountains. Seasonal evolution of in-mountain precipitation correlated fairly well with the temporal variation in oasis-vegetation coverage and phenology characterised by monthly enhanced vegetation index, yielding coefficients of determination of 0.65 and 0.85 for the two basins. Convergent cross-mapping of related time series indicated bi-directional causality (feedback) between the two variables. Comparisons between same-zone monthly precipitation amounts and enhanced vegetation index provided weaker correlations. Start of the growing season in the oases was shown to coincide with favourable spring warming and discharge of meltwater from low- to mid-elevations of the Qilian Mountains (zones 1 and 2) in mid-to-late March. In terms of plant requirement for water, mid-seasonal development of oasis vegetation was seen to be controlled to a greater extent by the production of rain in the mountains. Comparison of water volumes associated with in-basin production of rainfall and snowmelt with that associated with evaporation seemed to suggest that about 90 % of the available liquid water (i.e. mostly in the form of direct rainfall and snowmelt in the mountains) was recycled locally.

Description: Investigating suspended sediment dynamics in contrasting agricultural catchments using ex situ turbidity-based suspended sediment monitoring Hydrology and Earth System Sciences, 19, 3349-3363, 2015 Author(s): S. C. Sherriff, J. S. Rowan, A. R. Melland, P. Jordan, O. Fenton, and D. Ó hUallacháin Soil erosion and suspended sediment (SS) pose risks to chemical and ecological water quality. Agricultural activities may accelerate erosional fluxes from bare, poached or compacted soils, and enhance connectivity through modified channels and artificial drainage networks. Storm-event fluxes dominate SS transport in agricultural catchments; therefore, high temporal-resolution monitoring approaches are required, but can be expensive and technically challenging. Here, the performance of in situ turbidity sensors, conventionally installed submerged at the river bankside, is compared with installations where river water is delivered to sensors ex situ, i.e. within instrument kiosks on the riverbank, at two experimental catchments (Grassland B and Arable B). The in situ and ex situ installations gave comparable results when calibrated against storm-period, depth-integrated SS data, with total loads at Grassland B estimated at 12 800 and 15 400 t, and 22 600 and 24 900 t at Arable B, respectively. The absence of spurious turbidity readings relating to bankside debris around the in situ sensor and its greater security make the ex situ sensor more robust. The ex situ approach was then used to characterise SS dynamics and fluxes in five intensively managed agricultural catchments in Ireland which feature a range of landscape characteristics and land use pressures. Average annual suspended sediment concentration (SSC) was below the Freshwater Fish Directive (78/659/EEC) guideline of 25 mg L −1 , and the continuous hourly record demonstrated that exceedance occurred less than 12 % of the observation year. Soil drainage class and proportion of arable land were key controls determining flux rates, but all catchments reported a high degree of inter-annual variability associated with variable precipitation patterns compared to the long-term average. Poorly drained soils had greater sensitivity to runoff and soil erosion, particularly in catchments with periods of bare soils. Well drained soils were less sensitive to erosion even on arable land; however, under extreme rainfall conditions, all bare soils remain a high sediment loss risk. Analysis of storm-period and seasonal dynamics (over the long term) using high-resolution monitoring would be beneficial to further explore the impact of landscape, climate and land use characteristics on SS export.

Description: Landscape heterogeneity drives contrasting concentration–discharge relationships in shale headwater catchments Hydrology and Earth System Sciences, 19, 3333-3347, 2015 Author(s): E. M. Herndon, A. L. Dere, P. L. Sullivan, D. Norris, B. Reynolds, and S. L. Brantley Solute concentrations in stream water vary with discharge in patterns that record complex feedbacks between hydrologic and biogeochemical processes. In a comparison of three shale-underlain headwater catchments located in Pennsylvania, USA (the forested Shale Hills Critical Zone Observatory), and Wales, UK (the peatland-dominated Upper Hafren and forest-dominated Upper Hore catchments in the Plynlimon forest), dissimilar concentration–discharge ( C – Q ) behaviors are best explained by contrasting landscape distributions of soil solution chemistry – especially dissolved organic carbon (DOC) – that have been established by patterns of vegetation and soil organic matter (SOM). Specifically, elements that are concentrated in organic-rich soils due to biotic cycling (Mn, Ca, K) or that form strong complexes with DOC (Fe, Al) are spatially heterogeneous in pore waters because organic matter is heterogeneously distributed across the catchments. These solutes exhibit non-chemostatic behavior in the streams, and solute concentrations either decrease (Shale Hills) or increase (Plynlimon) with increasing discharge. In contrast, solutes that are concentrated in soil minerals and form only weak complexes with DOC (Na, Mg, Si) are spatially homogeneous in pore waters across each catchment. These solutes are chemostatic in that their stream concentrations vary little with stream discharge, likely because these solutes are released quickly from exchange sites in the soils during rainfall events. Furthermore, concentration–discharge relationships of non-chemostatic solutes changed following tree harvest in the Upper Hore catchment in Plynlimon, while no changes were observed for chemostatic solutes, underscoring the role of vegetation in regulating the concentrations of certain elements in the stream. These results indicate that differences in the hydrologic connectivity of organic-rich soils to the stream drive differences in concentration behavior between catchments. As such, in catchments where SOM is dominantly in lowlands (e.g., Shale Hills), we infer that non-chemostatic elements associated with organic matter are released to the stream early during rainfall events, whereas in catchments where SOM is dominantly in uplands (e.g., Plynlimon), these non-chemostatic elements are released later during rainfall events. The distribution of SOM across the landscape is thus a key component for predictive models of solute transport in headwater catchments.

Description: Future changes in flash flood frequency and intensity of the Tha Di River (Thailand) based on rainfall–runoff modeling and advanced delta change scaling Hydrology and Earth System Sciences Discussions, 12, 7327-7352, 2015 Author(s): S. Hilgert, A. Wagner, and S. Fuchs As a consequence of climate change, extreme and flood-causing precipitation events are expected to increase in magnitude and frequency, especially in today's high-precipitation areas. During the north-east monsoon seasons, Nakhon Si Thammarat in southern Thailand is flash-flooded every 2.22 years on average. This study investigates frequency and intensity of harmful discharges of the Tha Di River regarding the IPCC emission scenarios A2 and B2. The regional climate model (RCM) PRECIS was transformed using the advanced delta change (ADC) method. The hydrologic response model HBV-Light was calibrated to the catchment and supplied with ADC-scaled daily precipitation and temperature data for 2010–2089. Under the A2 (B2) scenario, the flood threshold exceedance frequency on average increases by 133 % (decreases by 10 %), average flood intensity increases by 3 % (decreases by 2 %) and the annual top five discharge peaks intensities increase by 46 % (decrease by 5 %). Yearly precipitation sums increase by 30 % (10 %) towards the end of the century. The A2 scenario predicts a precipitation increase during the rainy season, which intensifies flood events; while increases projected exclusively for the dry season are not expected to cause floods. Retention volume demand of past events was calculated to be up to 12 × 10 6 m 3 . Flood risks are staying at high levels under the B2 scenario or increase dramatically under the A2 scenario. Results show that the RCM scaling process is inflicted with systematic biases but is crucial to investigate small, mountainous catchments. Improvement of scaling techniques should therefore accompany the development towards high-resolution climate models.

Description: A pan-African medium-range ensemble flood forecast system Hydrology and Earth System Sciences, 19, 3365-3385, 2015 Author(s): V. Thiemig, B. Bisselink, F. Pappenberger, and J. Thielen The African Flood Forecasting System (AFFS) is a probabilistic flood forecast system for medium- to large-scale African river basins, with lead times of up to 15 days. The key components are the hydrological model LISFLOOD, the African GIS database, the meteorological ensemble predictions by the ECMWF (European Centre for Medium-Ranged Weather Forecasts) and critical hydrological thresholds. In this paper, the predictive capability is investigated in a hindcast mode, by reproducing hydrological predictions for the year 2003 when important floods were observed. Results were verified by ground measurements of 36 sub-catchments as well as by reports of various flood archives. Results showed that AFFS detected around 70 % of the reported flood events correctly. In particular, the system showed good performance in predicting riverine flood events of long duration (〉 1 week) and large affected areas (〉 10 000 km 2 ) well in advance, whereas AFFS showed limitations for small-scale and short duration flood events. The case study for the flood event in March 2003 in the Sabi Basin (Zimbabwe) illustrated the good performance of AFFS in forecasting timing and severity of the floods, gave an example of the clear and concise output products, and showed that the system is capable of producing flood warnings even in ungauged river basins. Hence, from a technical perspective, AFFS shows a large potential as an operational pan-African flood forecasting system, although issues related to the practical implication will still need to be investigated.

Description: A comprehensive filtering scheme for high-resolution estimation of the water balance components from high-precision lysimeters Hydrology and Earth System Sciences, 19, 3405-3418, 2015 Author(s): M. Hannes, U. Wollschläger, F. Schrader, W. Durner, S. Gebler, T. Pütz, J. Fank, G. von Unold, and H.-J. Vogel Large weighing lysimeters are currently the most precise method to directly measure all components of the terrestrial water balance in parallel via the built-in weighing system. As lysimeters are exposed to several external forces such as management practices or wind influencing the weighing data, the calculated fluxes of precipitation and evapotranspiration can be altered considerably without having applied appropriate corrections to the raw data. Therefore, adequate filtering schemes for obtaining most accurate estimates of the water balance components are required. In this study, we use data from the TERENO (TERrestrial ENvironmental Observatories) SoilCan research site in Bad Lauchstädt to develop a comprehensive filtering procedure for high-precision lysimeter data, which is designed to deal with various kinds of possible errors starting from the elimination of large disturbances in the raw data resulting e.g., from management practices all the way to the reduction of noise caused e.g., by moderate wind. Furthermore, we analyze the influence of averaging times and thresholds required by some of the filtering steps on the calculated water balance and investigate the ability of two adaptive filtering methods (the adaptive window and adaptive threshold filter (AWAT filter; Peters et al., 2014), and a new synchro filter applicable to the data from a set of several lysimeters) to further reduce the filtering error. Finally, we take advantage of the data sets of all 18 lysimeters running in parallel at the Bad Lauchstädt site to evaluate the performance and accuracy of the proposed filtering scheme. For the tested time interval of 2 months, we show that the estimation of the water balance with high temporal resolution and good accuracy is possible. The filtering code can be downloaded from the journal website as Supplement to this publication.

Description: Assimilation of Antarctic velocity observations provides evidence for uncharted pinning points The Cryosphere, 9, 1427-1443, 2015 Author(s): J. J. Fürst, G. Durand, F. Gillet-Chaulet, N. Merino, L. Tavard, J. Mouginot, N. Gourmelen, and O. Gagliardini In ice flow modelling, the use of control methods to assimilate the dynamic and geometric state of an ice body has become common practice. These methods have primarily focussed on inverting for one of the two least known properties in glaciology, namely the basal friction coefficient or the ice viscosity parameter. Here, we present an approach to infer both properties simultaneously for the whole of the Antarctic ice sheet. After the assimilation, the root-mean-square deviation between modelled and observed surface velocities attains 8.7 m a −1 for the entire domain, with a slightly higher value of 14.0 m a −1 for the ice shelves. An exception in terms of the velocity mismatch is the Thwaites Glacier Ice Shelf, where the RMS value is almost 70 m a −1 . The reason is that the underlying Bedmap2 geometry ignores the presence of an ice rise, which exerts major control on the dynamics of the eastern part of the ice shelf. On these grounds, we suggest an approach to account for pinning points not included in Bedmap2 by locally allowing an optimisation of basal friction during the inversion. In this way, the velocity mismatch on the ice shelf of Thwaites Glacier is more than halved. A characteristic velocity mismatch pattern emerges for unaccounted pinning points close to the marine shelf front. This pattern is exploited to manually identify seven uncharted features around Antarctica that exert significant resistance to the shelf flow. Potential pinning points are detected on Fimbul, West, Shackleton, Nickerson and Venable ice shelves. As pinning points can provide substantial resistance to shelf flow, with considerable consequences if they became ungrounded in the future, the model community is in need of detailed bathymetry there. Our data assimilation points to some of these dynamically important features not present in Bedmap2 and implicitly quantifies their relevance.

Description: Long-term coastal-polynya dynamics in the Southern Weddell Sea from MODIS thermal-infrared imagery The Cryosphere Discussions, 9, 3959-3993, 2015 Author(s): S. Paul, S. Willmes, and G. Heinemann Based upon high-resolution thermal-infrared Moderate-Resolution Imaging Spectroradiometer (MODIS) satellite imagery in combination with ERA-Interim atmospheric reanalysis data, we derived long-term polynya parameters such as polynya area, thin-ice thickness distribution and ice-production rates from daily cloud-cover corrected thin-ice thickness composites. Our study is based on a thirteen year investigation period (2002–2014) for the austral winter (1 April to 30 September) in the Antarctic Southern Weddell Sea. The focus lies on coastal polynyas which are important hot spots for new-ice formation, bottom-water formation and heat/moisture release into the atmosphere. MODIS has the capability to resolve even very narrow coastal polynyas. Its major disadvantage is the sensor limitation due to cloud cover. We make use of a newly developed and adapted spatial feature reconstruction scheme to account for cloud-covered areas. We find the sea-ice areas in front of Ronne and Brunt Ice Shelf to be the most active with an annual average polynya area of 3018 ± 1298 and 3516 ± 1420 km 2 as well as an accumulated volume ice production of 31 ± 13 and 31 ± 12 km 3 , respectively. For the remaining four regions, estimates amount to 421 ± 294 km 2 and 4 ± 3 km 3 (Antarctic Peninsula), 1148 ± 432 km 2 and 12 ± 5 km 3 (Iceberg A23A), 901 ± 703 km 2 and 10 ± 8 km 3 (Filchner Ice Shelf) as well as 499 ± 277 km 2 and 5 ± 2 km 3 (Coats Land). Our findings are discussed in comparison to recent studies based on coupled sea-ice/ocean models and passive-microwave satellite imagery, each investigating different parts of the Southern Weddell Sea.

Description: Climatic controls and climate proxy potential of Lewis Glacier, Mt Kenya The Cryosphere Discussions, 9, 3887-3924, 2015 Author(s): R. Prinz, L. I. Nicholson, T. Mölg, W. Gurgiser, and G. Kaser The Lewis Glacier on Mt Kenya is one of the best studied tropical glaciers and has experienced considerable retreat since a maximum extent in the late 19th century (L19). From distributed mass and energy balance modelling, this study evaluates the current sensitivity of the surface mass and energy balance to climatic drivers, explores climate conditions under which the L19 maximum extent might have sustained, and discusses the potential for using the glacier retreat to quantify climate change. Multiyear meteorological measurements at 4828 m provide data for input, optimization and evaluation of a spatially distributed glacier mass balance model to quantify the exchanges of energy and mass at the glacier–atmosphere interface. Currently the glacier loses mass due to the imbalance between insufficient accumulation and enhanced melt, because radiative energy gains cannot be compensated by turbulent energy sinks. Exchanging model input data with synthetic climate scenarios, which were sampled from the meteorological measurements and account for coupled climatic variable perturbations, reveal that the current mass balance is most sensitive to changes in atmospheric moisture (via its impact on solid precipitation, cloudiness and surface albedo). Positive mass balances result from scenarios with an increase of annual (seasonal) accumulation of 30 % (100 %), compared to values observed today, without significant changes in air temperature required. Scenarios with lower air temperatures are drier and associated with lower accumulation and increased net radiation due to reduced cloudiness and albedo. If the scenarios currently producing positive mass balances are applied to the L19 extent, negative mass balances are the result, meaning that the conditions required to sustain the glacier in its L19 extent are not reflected in today's observations. Alternatively, a balanced mass budget for the L19 extent can be explained by changing model parameters that imply a distinctly different coupling between the glacier's local surface-air layer and its surrounding boundary-layer. This result underlines the difficulty of deriving paleoclimates for larger glacier extents on the basis of modern measurements of small glaciers.

Description: Towards predictive data-driven simulations of wildfire spread – Part II: Ensemble Kalman Filter for the state estimation of a front-tracking simulator of wildfire spread Natural Hazards and Earth System Science, 15, 1721-1739, 2015 Author(s): M. C. Rochoux, C. Emery, S. Ricci, B. Cuenot, and A. Trouvé This paper is the second part in a series of two articles, which aims at presenting a data-driven modeling strategy for forecasting wildfire spread scenarios based on the assimilation of the observed fire front location and on the sequential correction of model parameters or model state. This model relies on an estimation of the local rate of fire spread (ROS) as a function of environmental conditions based on Rothermel's semi-empirical formulation, in order to propagate the fire front with an Eulerian front-tracking simulator. In Part I, a data assimilation (DA) system based on an ensemble Kalman filter (EnKF) was implemented to provide a spatially uniform correction of biomass fuel and wind parameters and thereby, produce an improved forecast of the wildfire behavior (addressing uncertainties in the input parameters of the ROS model only). In Part II, the objective of the EnKF algorithm is to sequentially update the two-dimensional coordinates of the markers along the discretized fire front, in order to provide a spatially distributed correction of the fire front location and thereby, a more reliable initial condition for further model time-integration (addressing all sources of uncertainties in the ROS model). The resulting prototype data-driven wildfire spread simulator is first evaluated in a series of verification tests using synthetically generated observations; tests include representative cases with spatially varying biomass properties and temporally varying wind conditions. In order to properly account for uncertainties during the EnKF update step and to accurately represent error correlations along the fireline, it is shown that members of the EnKF ensemble must be generated through variations in estimates of the fire's initial location as well as through variations in the parameters of the ROS model. The performance of the prototype simulator based on state estimation (SE) or parameter estimation (PE) is then evaluated by comparison with data taken from a reduced-scale controlled grassland fire experiment. Results indicate that data-driven simulations are capable of correcting inaccurate predictions of the fire front location and of subsequently providing an optimized forecast of the wildfire behavior at future lead times. The complementary benefits of both PE and SE approaches, in terms of analysis and forecast performance, are also emphasized. In particular, it is found that the size of the assimilation window must be specified adequately with the persistence of the model initial condition and/or with the temporal and spatial variability of the environmental conditions in order to track sudden changes in wildfire behavior. The present prototype data-driven forecast system is still at an early stage of development. In this regard, this preliminary investigation provides valuable information on how to combine observations with a fire spread model in an efficient way, as well as guidelines to design the future system evolution in order to meet the operational requirements of wildfire spread monitoring.

Description: Multiscale evaluation of the standardized precipitation index as a groundwater drought indicator Hydrology and Earth System Sciences Discussions, 12, 7405-7436, 2015 Author(s): R. Kumar, J. L. Musuuza, A. F. Van Loon, A. J. Teuling, R. Barthel, J. Ten Broek, J. Mai, L. Samaniego, and S. Attinger The lack of comprehensive groundwater observations at regional and global scales has promoted the use of alternative proxies and indices to quantify and predict groundwater droughts. Among them, the Standardized Precipitation Index (SPI) is commonly used to characterize droughts in different compartments of the hydro-meteorological system. In this study, we explore the suitability of the SPI to characterize local and regional scale groundwater droughts using observations at more than 2000 groundwater wells in geologically different areas in Germany and the Netherlands. A multiscale evaluation of the SPI is performed using the station data and their corresponding 0.5° gridded estimates to analyze the local and regional behavior of groundwater droughts, respectively. The standardized anomalies in the groundwater heads (SGI) were correlated against SPIs obtained using different accumulation periods. The accumulation periods to achieve maximum correlation exhibited high spatial variability (ranges 3 to 36 months) at both scales, leading to the conclusion that an a priori selection of the accumulation period (for computing the SPI) would result in inadequate characterization of groundwater droughts. The application of the uniform accumulation periods over the entire domain significantly reduced the correlation between SPI and SGI (≈ 21–66 %) indicating the limited applicability of SPI as a proxy for groundwater droughts even at long accumulation times. Furthermore, the low scores of the hit rate (0.3–0.6) and high false alarm ratio (0.4–0.7) at the majority of the wells and grid cells demonstrated the low reliability of groundwater drought predictions using the SPI. The findings of this study highlight the pitfalls of using the SPI as a groundwater drought indicator at both local and regional scales, and stress the need for more groundwater observations and accounting for regional hydrogeological characteristics in groundwater drought monitoring.

Description: Comparing the Ensemble and Extended Kalman Filters for in situ soil moisture assimilation with contrasting soil conditions Hydrology and Earth System Sciences Discussions, 12, 7353-7403, 2015 Author(s): D. Fairbairn, A. L. Barbu, J.-F. Mahfouf, J.-C. Calvet, and E. Gelati Two data assimilation methods are compared for their ability to produce a deterministic soil moisture analysis on the Météo-France land surface model: (i) SEKF, a Simplified Extended Kalman Filter, which uses a climatological background-error covariance, (ii) EnSRF, the Ensemble Square Root Filter, which uses an ensemble background-error covariance and approximates random forcing errors stochastically. The accuracy of the deterministic analysis is measured on 12 sites with in situ observations and various soil textures in Southwest France (SMOSMANIA network). In the experiments with real observations, the two methods perform similarly and improve on the open loop. Both methods suffer from incorrect linear assumptions which are particularly degrading to the analysis during water-stressed conditions: the EnSRF by a dry bias and the SEKF by an over-sensitivity of the model Jacobian between the surface and the root zone layers. These problems are less severe for sandy soils than clay soils because sandy soils are less sensitive to perturbations in the initial conditions. A simple bias correction technique is tested on the EnSRF. Although this reduces the bias, it also suppresses the ensemble spread, which degrades the analysis performance. However, the EnSRF flow-dependent background-error covariance evidently captures seasonal variability in the soil moisture errors and should exploit planned improvements in the model physics. Synthetic experiments demonstrate that when there is only a random component in the precipitation forcing errors, the correct stochastic representation of these errors enables the EnSRF to perform better than the SEKF. But in the real experiments the same rainfall error specification does not improve the EnSRF analysis. It is likely that the actual rainfall errors are underestimated and that other sources of errors could limit the usefulness of this information. More comprehensive ways of representing the rainfall errors are suggested, which might improve the EnSRF performance.

Description: Huntington's disease (HD) is a hereditary neurodegenerative disorder characterized by brain atrophy particularly in striatum leading to personality changes, chorea and dementia. Glycogen synthase kinase-3 (GSK-3) is a serine/threonine kinase in the crossroad of many signaling pathways that is highly pleiotropic as it phosphorylates more than hundred substrates including structural, metabolic, and signaling proteins. Increased GSK-3 activity is believed to contribute to the pathogenesis of neurodegenerative diseases like Alzheimer's disease and GSK-3 inhibitors have been postulated as therapeutic agents for neurodegeneration. Regarding HD, GSK-3 inhibitors have shown beneficial effects in cell and invertebrate animal models but no evident efficacy in mouse models. Intriguingly, those studies were performed without interrogating GSK-3 level and activity in HD brain. Here we aim to explore the level and also the enzymatic activity of GSK-3 in the striatum and other less affected brain regions of HD patients and of the R6/1 mouse model to then elucidate the possible contribution of its alteration to HD pathogenesis by genetic manipulation in mice. We report a dramatic decrease in GSK-3 levels and activity in striatum and cortex of HD patients with similar results in the mouse model. Correction of the GSK-3 deficit in HD mice, by combining with transgenic mice with conditional GSK-3 expression, resulted in amelioration of their brain atrophy and behavioral motor and learning deficits. Thus, our results demonstrate that decreased brain GSK-3 contributes to HD neurological phenotype and open new therapeutic opportunities based on increasing GSK-3 activity or attenuating the harmful consequences of its decrease.

Description: Spinocerebellar ataxia type 6 (SCA6) is dominantly inherited neurodegenerative disease, caused by an expansion of CAG repeat encoding a polyglutamine (PolyQ) tract in the Ca v 2.1 voltage-gated calcium channel. Its key pathological features include selective degeneration of the cerebellar Purkinje cells (PCs), a common target for PolyQ-induced toxicity in various SCAs. Mutant Ca v 2.1 confers toxicity primarily through a toxic gain-of-function mechanism; however, its molecular basis remains elusive. Here, we studied the cerebellar gene expression patterns of young Sca6 -MPI 118Q/118Q knockin (KI) mice, which expressed mutant Ca v 2.1 from an endogenous locus and recapitulated many phenotypic features of human SCA6. Transcriptional signatures in the MPI 118Q/118Q mice were distinct from those in the Sca1 154Q/2Q mice, a faithful SCA1 KI mouse model. Temporal expression profiles of the candidate genes revealed that the up-regulation of genes associated with microglial activation was initiated before PC degeneration and was augmented as the disease progressed. Histological analysis of the MPI 118Q/118Q cerebellum showed the predominance of M1-like pro-inflammatory microglia and it was concomitant with elevated expression levels of tumor necrosis factor, interleukin-6, Toll-like receptor (TLR) 2 and 7. Genetic ablation of MyD88, a major adaptor protein conveying TLR signaling, altered expression patterns of M1/M2 microglial phenotypic markers in the MPI 118Q/118Q cerebellum. More importantly, it ameliorated PC loss and partially rescued motor impairments in the early disease phase. These results suggest that early neuroinflammatory response may play an important role in the pathogenesis of SCA6 and its modulation could pave the way for slowing the disease progression during the early stage of the disease.

Description: Morphological dynamics of an englacial channel Hydrology and Earth System Sciences Discussions, 12, 7615-7664, 2015 Author(s): G. Vatne and T. D. L. Irvine-Fynn Despite an interest in the hydraulic functioning of supraglacial and englacial channels over the last four decades, the processes and forms of such ice-bounded streams have remained poorly documented. Recent glaciological research has demonstrated the potential significance of so-called "cut and closure" streams, where englacial or subglacial flowpaths are created from the long-term incision of supraglacial channels. These flowpaths are reported to exhibit step-pool morphology, comprising knickpoints and/or knickzones, albeit exaggerated in dimensions in comparison to their supraglacial channel counterparts. However, little is known of the development of such channels' morphology. Here, we examine the spatial organization of step-pools and the upstream migration of steps, many of which form knickzones, with repeated surveys over a 10 year period in an englacial conduit in cold-based Austre Brøggerbreen, Svalbard. The observations show upstream knickpoint recession to be the dominant process for channel evolution. This is paralleled by an increase in average step height and conduit gradient over time. Characteristic channel reach types and step-riser forms are consistently observed in each of the morphological surveys reported. We suggest that the formation of steps has a hydrodynamic origin, where step-pool geometry is more efficient for energy dissipation than meanders, and that the englacial channel system is one in rapid transition rather than in dynamic equilibrium. The evolution and recession of knickzones reported here result in the formation of a 37 m moulin, suggesting over time the englacial channel may evolve towards a stable end-point characterised by a singular vertical descent to the local hydraulic base level. In light of this, our observations highlight the need to further examine the adjustment processes in cut-and-closure channels to better understand their coupling to supraglacial meltwater sources and role and potential significance in cold-based glacier hydrology and ice dynamics.

Description: Scenario based approach for multiple source Tsunami Hazard assessment for Sines, Portugal Natural Hazards and Earth System Sciences Discussions, 3, 4663-4693, 2015 Author(s): M. Wronna, R. Omira, and M. A. Baptista In this paper, we present a scenario-based approach for tsunami hazard assessment for the city and harbour of Sines – Portugal, one of the test-sites of project ASTARTE. Sines holds one of the most important deep-water ports which contains oil-bearing, petrochemical, liquid bulk, coal and container terminals. The port and its industrial infrastructures are facing the ocean southwest towards the main seismogenic sources. This work considers two different seismic zones: the Southwest Iberian Margin and the Gloria Fault. Within these two regions, we selected a total of six scenarios to assess the tsunami impact at the test site. The tsunami simulations are computed using NSWING a Non-linear Shallow Water Model With Nested Grids. In this study, the static effect of tides is analysed for three different tidal stages MLLW (mean lower low water), MSL (mean sea level) and MHHW (mean higher high water). For each scenario, inundation is described by maximum values of wave height, flow depth, drawback, runup and inundation distance. Synthetic waveforms are computed at virtual tide gauges at specific locations outside and inside the harbour. The final results describe the impact at Sines test site considering the single scenarios at mean sea level, the aggregate scenario and the influence of the tide on the aggregate scenario. The results confirm the composite of Horseshoe and Marques Pombal fault as the worst case scenario. It governs the aggregate scenario with about 60 % and inundates an area of 3.5 km 2 .

Description: Motivation: Stem cell differentiation is largely guided by master transcriptional regulators, but it also depends on the expression of other types of genes, such as cell cycle genes, signaling genes, metabolic genes, trafficking genes, etc. Traditional approaches to understanding gene expression patterns across multiple conditions, such as principal components analysis or K-means clustering, can group cell types based on gene expression, but they do so without knowledge of the differentiation hierarchy. Hierarchical clustering can organize cell types into a tree, but in general this tree is different from the differentiation hierarchy itself. Methods: Given the differentiation hierarchy and gene expression data at each node, we construct a weighted Euclidean distance metric such that the minimum spanning tree with respect to that metric is precisely the given differentiation hierarchy. We provide a set of linear constraints that are provably sufficient for the desired construction and a linear programming approach to identify sparse sets of weights, effectively identifying genes that are most relevant for discriminating different parts of the tree. Results: We apply our method to microarray gene expression data describing 38 cell types in the hematopoiesis hierarchy, constructing a weighted Euclidean metric that uses just 175 genes. However, we find that there are many alternative sets of weights that satisfy the linear constraints. Thus, in the style of random-forest training, we also construct metrics based on random subsets of the genes and compare them to the metric of 175 genes. We then report on the selected genes and their biological functions. Our approach offers a new way to identify genes that may have important roles in stem cell differentiation. Contact: tperkins@ohri.ca Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Principal component analysis (PCA) is a basic tool often used in bioinformatics for visualization and dimension reduction. However, it is known that PCA may not consistently estimate the true direction of maximal variability in high-dimensional, low sample size settings, which are typical for molecular data. Assuming that the underlying signal is sparse, i.e. that only a fraction of features contribute to a principal component (PC), this estimation consistency can be retained. Most existing sparse PCA methods use L1-penalization, i.e. the lasso , to perform feature selection. But, the lasso is known to lack variable selection consistency in high dimensions and therefore a subsequent interpretation of selected features can give misleading results. Results: We present S4VDPCA, a sparse PCA method that incorporates a subsampling approach, namely stability selection. S4VDPCA can consistently select the truly relevant variables contributing to a sparse PC while also consistently estimate the direction of maximal variability. The performance of the S4VDPCA is assessed in a simulation study and compared to other PCA approaches, as well as to a hypothetical oracle PCA that ‘knows’ the truly relevant features in advance and thus finds optimal, unbiased sparse PCs. S4VDPCA is computationally efficient and performs best in simulations regarding parameter estimation consistency and feature selection consistency. Furthermore, S4VDPCA is applied to a publicly available gene expression data set of medulloblastoma brain tumors. Features contributing to the first two estimated sparse PCs represent genes significantly over-represented in pathways typically deregulated between molecular subgroups of medulloblastoma. Availability and implementation: Software is available at https://github.com/mwsill/s4vdpca . Contact: m.sill@dkfz.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. Comparative structural studies of biological molecules provide useful insight into their biological relationships. However, most computational tools are designed for protein structure, and despite their importance, there is no currently available tool for comparing glycan structures in a sequence order- and size-independent manner. Results: A novel method, GS-align, is developed for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition. The optimal alignment is then determined by the maximum structural similarity score, GS-score, which is size-independent. Benchmark tests against the Protein Data Bank (PDB) N -linked glycan library and PDB homologous/non-homologous N -glycoprotein sets indicate that GS-align is a robust computational tool to align glycan structures and quantify their structural similarity. GS-align is also applied to template-based glycan structure prediction and monosaccharide substitution matrix generation to illustrate its utility. Availability and implementation: http://www.glycanstructure.org/gsalign . Contact: wonpil@ku.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Impedance-based technologies are advancing methods for measuring proliferation of adherent cell cultures non-invasively and in real time. The analysis of the resulting data has so far been hampered by inappropriate computational methods and the lack of systematic data to evaluate the characteristics of the assay. Results: We used a commercially available system for impedance-based growth measurement (xCELLigence) and compared the reported cell index with data from microscopy. We found that the measured signal correlates linearly with the cell number throughout the time of an experiment with sufficient accuracy in subconfluent cell cultures. The resulting growth curves for various colon cancer cells could be well described with the empirical Richards growth model, which allows for extracting quantitative parameters (such as characteristic cycle times). We found that frequently used readouts like the cell index at a specific time or the area under the growth curve cannot be used to faithfully characterize growth inhibition. We propose to calculate the average growth rate of selected time intervals to accurately estimate time-dependent IC50 values of drugs from growth curves. Contact: nils.bluethgen@charite.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: The impact of near-surface soil moisture assimilation at subseasonal, seasonal, and inter-annual time scales Hydrology and Earth System Sciences Discussions, 12, 7971-8004, 2015 Author(s): C. Draper and R. Reichle Nine years of Advanced Microwave Scanning Radiometer – Earth Observing System (AMSR-E) soil moisture retrievals are assimilated into the Catchment land surface model at four locations in the US. The assimilation is evaluated using the unbiased Mean Square Error (ubMSE) relative to watershed-scale in situ observations, with the ubMSE separated into contributions from the subseasonal (SM short ), mean seasonal (SM seas ) and inter-annual (SM long ) soil moisture dynamics. For near-surface soil moisture, the average ubMSE for Catchment without assimilation was (1.8 × 10 −3 m 3 m −3 ) 2 , of which 19 % was in SM long , 26 % in SM seas , and 55 % in SM short . The AMSR-E assimilation significantly reduced the total ubMSE at every site, with an average reduction of 33 %. Of this ubMSE reduction, 37 % occurred in SM long , 24 % in SM seas , and 38 % in SM short . For root-zone soil moisture, in situ observations were available at one site only, and the near-surface and root-zone results were very similar at this site. These results suggest that, in addition to the well-reported improvements in SM short , assimilating a sufficiently long soil moisture data record can also improve the model representation of important long term events, such as droughts. The improved agreement between the modeled and in situ SM seas is harder to interpret, given that mean seasonal cycle errors are systematic, and systematic errors are not typically targeted by (bias-blind) data assimilation. Finally, the use of one year subsets of the AMSR-E and Catchment soil moisture for estimating the observation-bias correction (rescaling) parameters is investigated. It is concluded that when only one year of data is available, the associated uncertainty in the rescaling parameters should not greatly reduce the average benefit gained from data assimilation, but locally and in extreme years there is a risk of increased errors.

Description: Century-scale simulations of the response of the West Antarctic Ice Sheet to a warming climate The Cryosphere, 9, 1579-1600, 2015 Author(s): S. L. Cornford, D. F. Martin, A. J. Payne, E. G. Ng, A. M. Le Brocq, R. M. Gladstone, T. L. Edwards, S. R. Shannon, C. Agosta, M. R. van den Broeke, H. H. Hellmer, G. Krinner, S. R. M. Ligtenberg, R. Timmermann, and D. G. Vaughan We use the BISICLES adaptive mesh ice sheet model to carry out one, two, and three century simulations of the fast-flowing ice streams of the West Antarctic Ice Sheet, deploying sub-kilometer resolution around the grounding line since coarser resolution results in substantial underestimation of the response. Each of the simulations begins with a geometry and velocity close to present-day observations, and evolves according to variation in meteoric ice accumulation rates and oceanic ice shelf melt rates. Future changes in accumulation and melt rates range from no change, through anomalies computed by atmosphere and ocean models driven by the E1 and A1B emissions scenarios, to spatially uniform melt rate anomalies that remove most of the ice shelves over a few centuries. We find that variation in the resulting ice dynamics is dominated by the choice of initial conditions and ice shelf melt rate and mesh resolution, although ice accumulation affects the net change in volume above flotation to a similar degree. Given sufficient melt rates, we compute grounding line retreat over hundreds of kilometers in every major ice stream, but the ocean models do not predict such melt rates outside of the Amundsen Sea Embayment until after 2100. Within the Amundsen Sea Embayment the largest single source of variability is the onset of sustained retreat in Thwaites Glacier, which can triple the rate of eustatic sea level rise.

Description: A method for predicting the factor of safety of an infinite slope based on the depth ratio of the wetting front induced by rainfall infiltration Natural Hazards and Earth System Science, 15, 1835-1849, 2015 Author(s): B.-G. Chae, J.-H. Lee, H.-J. Park, and J. Choi Most landslides in Korea are classified as shallow landslides with an average depth of less than 2 m. These shallow landslides are associated with the advance of a wetting front in the unsaturated soil due to rainfall infiltration, which results in an increase in water content and a reduction in the matric suction in the soil. Therefore, this study presents a modified equation of infinite slope stability analysis based on the concept of the saturation depth ratio to analyze the slope stability change associated with the rainfall on a slope. A rainfall infiltration test in unsaturated soil was performed using a column to develop an understanding of the effect of the saturation depth ratio following rainfall infiltration. The results indicated that the rainfall infiltration velocity due to the increase in rainfall in the soil layer was faster when the rainfall intensity increased. In addition, the rainfall infiltration velocity tends to decrease with increases in the unit weight of soil. The proposed model was applied to assess its feasibility and to develop a regional landslide susceptibility map using a geographic information system (GIS). For that purpose, spatial databases for input parameters were constructed and landslide locations were obtained. In order to validate the proposed approach, the results of the proposed approach were compared with the landslide inventory using a ROC (receiver operating characteristics) graph. In addition, the results of the proposed approach were compared with the previous approach used: a steady-state hydrological model. Consequently, the approach proposed in this study displayed satisfactory performance in classifying landslide susceptibility and showed better performance than the steady-state approach.

Description: Regional trends and controlling factors of fatal landslides in Latin America and the Caribbean Natural Hazards and Earth System Science, 15, 1821-1833, 2015 Author(s): S. A. Sepúlveda and D. N. Petley A new data set of landslides that caused loss of life in Latin America and the Caribbean in the 10-year period from 2004 and 2013 inclusive has been compiled, providing new insight into the impact of landslides in this key part of the world. This data set indicates that in the 10-year period a total of 11 631 people lost their lives across the region in 611 landslides. The geographical distribution of the landslides is highly heterogeneous, with areas of high incidence in parts of the Caribbean (most notably Haiti), Central America, Colombia, and southeast Brazil. There is significant interannual variation in the number of landslides, with the El Niño/La Niña cycle emerging as a key control. Our analysis suggests that on a continental scale the mapped factors that best explain the observed distribution are topography, annual precipitation and population density. On a national basis we have compared the occurrence of fatality-inducing landslide occurrence with the production of locally authored research articles, demonstrating that there is a landslide research deficit in Latin America and the Caribbean. Understanding better the mechanisms, distribution causes and triggers of landslides in Latin America and the Caribbean must be an essential first step towards managing the hazard.

Description: It has been hypothesised that positive associations between age and levels of oxidative stress-generated damage to DNA may be related to an age-dependent decline in DNA repair activity. The objective of this study was to investigate the association between age and repair activity of oxidatively damaged DNA in peripheral blood mononuclear cells (PBMCs). We isolated PBMCs from subjects aged 18–83 years, as part of a health survey of the Danish population that focussed on lifestyle factors. The level of DNA repair activity was measured as incisions on potassium bromate-damaged DNA by the comet assay. There was an inverse association between age and DNA repair activity with a 0.65% decline in activity per year from age 18 to 83 (95% confidence interval: 0.16–1.14% per year). Univariate regression analysis also indicated inverse associations between DNA repair activity and waist-hip ratio ( P 〈 0.05) and plasma concentrations of glycosylated hemoglobin ( P = 0.07). However, multivariate regression analysis only showed an inverse association between age and DNA repair activity ( P 〈 0.05), indicating that the decline in repair activity was not mediated by metabolic risk factors. In summary, the results show an inverse association between age and DNA repair activity of oxidatively damaged DNA.

Description: A numerical study of the early stages of a tropical cyclogenesis in relation to the MJO Natural Hazards and Earth System Sciences Discussions, 3, 4919-4935, 2015 Author(s): J. Guerbette, M. Plu, C. Barthe, and J.-F. Mahfouf The role of an active phase of the Madden–Julian Oscillation (MJO) on the evolution of a mesoscale convective systems (MCS) leading to a tropical depression is investigated in the South-West Indian Ocean during the Dynamics of the Madden–Julian Oscillation (DYNAMO) field experiment, with a numerical limited-area atmospheric model. A mesoscale vortex is followed in the low-troposphere from the initiation of the active MJO phase. It is shown that the interaction of the vortex with the Equatorial jet associated with the MJO plays an important role on the vortex development. As the vortex encounters the southern part of the low-level jet, it undergoes intensification that is explained by the barotropic conversion of kinetic energy from the low-level jet to the vortex.

Description: Exposure to traffic-related particulate matter (PM) has been associated with increased risk of lung disease, cancer and cardiovascular disease especially in elderly and overweight subjects. The proposed mechanisms involve intracellular production of reactive oxygen species (ROS), inflammation and oxidation-induced DNA damage studied mainly in young normal-weight subjects. We performed a controlled cross-over, randomised, single-blinded, repeated-measure study where 60 healthy subjects (25 males and 35 females) with age 55–83 years and body mass index above 25kg/m 2 were exposed for 5h to either particle-filtered or sham-filtered air from a busy street with number of concentrations and PM 2.5 levels of 1800/cm 3 versus 23 000/cm 3 and 3 µg/m 3 versus 24 µg/m 3 , respectively. Peripheral blood mononuclear cells (PBMCs) were collected and assayed for production of ROS with and without ex vivo exposure to nanosized carbon black as well as expression of genes related to inflammation ( chemokine (C-C motif) ligand 2 , interleukin-8 and tumour necrosis factor ), oxidative stress response ( heme oxygenase (decycling)-1 ) and DNA repair ( oxoguanine DNA glycosylase ). DNA strand breaks and oxidised purines were assayed by the alkaline comet assay. No statistically significant differences were found for any biomarker immediately after exposure to PM from urban street air although strand breaks and oxidised purines combined were significantly associated with the particle number concentration during exposure. In conclusion, 5h of controlled exposure to PM from urban traffic did not change the gene expression related to inflammation, oxidative stress or DNA repair, ROS production or oxidatively damaged DNA in PBMCs from elderly overweight human subjects.

Description: Ionising radiation causes free radical–mediated damage in cellular DNA. This damage is manifested as chromosomal aberrations and micronuclei (MN) in proliferating cells. Sesamol, present in sesame seeds, has the potential to scavenge free radicals; therefore, it can reduce radiation-induced cytogenetic damage in cells. The aim of this study was to investigate the radioprotective potential of sesamol in bone marrow cells of mice and related haematopoietic system against radiation-induced genotoxicity. A comparative study with melatonin was designed for assessing the radioprotective potential of sesamol. C57BL/6 mice were administered intraperitoneally with either sesamol or melatonin (10 and 20mg/kg body weight) 30min prior to 2-Gy whole-body irradiation (WBI) and sacrificed after 24h. Total chromosomal aberrations (TCA), MN and cell cycle analyses were performed using bone marrow cells. The comet assay was performed on bone marrow cells, splenocytes and lymphocytes. Blood was drawn to study haematological parameters. Prophylactic doses of sesamol (10 and 20mg/kg) in irradiated mice reduced TCA and micronucleated polychromatic erythrocyte frequency in bone marrow cells by 57% and 50%, respectively, in comparison with radiation-only groups. Sesamol-reduced radiation-induced apoptosis and facilitated cell proliferation. In the comet assay, sesamol (20mg/kg) treatment reduced radiation-induced comets (% DNA in tail) compared with radiation only ( P 〈 0.05). Sesamol also increased granulocyte populations in peripheral blood similar to melatonin. Overall, the radioprotective efficacy of sesamol was found to be similar to that of melatonin. Sesamol treatment also showed recovery of relative spleen weight at 24h of WBI. The results strongly suggest the radioprotective efficacy of sesamol in the haematopoietic system of mice.

Description: Individualized treatment rules recommend treatments on the basis of individual patient characteristics. A high-quality treatment rule can produce better patient outcomes, lower costs and less treatment burden. If a treatment rule learned from data is to be used to inform clinical practice or provide scientific insight, it is crucial that it be interpretable; clinicians may be unwilling to implement models they do not understand, and black-box models may not be useful for guiding future research. The canonical example of an interpretable prediction model is a decision tree. We propose a method for estimating an optimal individualized treatment rule within the class of rules that are representable as decision trees. The class of rules we consider is interpretable but expressive. A novel feature of this problem is that the learning task is unsupervised, as the optimal treatment for each patient is unknown and must be estimated. The proposed method applies to both categorical and continuous treatments and produces favourable marginal mean outcomes in simulation experiments. We illustrate it using data from a study of major depressive disorder.

Description: Sufficient dimension reduction in regression aims to reduce the predictor dimension by replacing the original predictors with some set of linear combinations of them without loss of information. Numerous dimension reduction methods have been developed based on this paradigm. However, little effort has been devoted to diagnostic studies within the context of dimension reduction. In this paper we introduce methods to check goodness-of-fit for a given dimension reduction subspace. The key idea is to extend the so-called distance correlation to measure the conditional dependence relationship between the covariates and the response given a reduction subspace. Our methods require minimal assumptions, which are usually much less restrictive than the conditions needed to justify the original methods. Asymptotic properties of the test statistic are studied. Numerical examples demonstrate the effectiveness of the proposed approach.

Description: We propose a geometric framework to assess sensitivity of Bayesian procedures to modelling assumptions based on the nonparametric Fisher–Rao metric. While the framework is general, the focus of this article is on assessing local and global robustness in Bayesian procedures with respect to perturbations of the likelihood and prior, and on the identification of influential observations. The approach is based on a square-root representation of densities, which enables analytical computation of geodesic paths and distances, facilitating the definition of naturally calibrated local and global discrepancy measures. An important feature of our approach is the definition of a geometric $\epsilon$ -contamination class of sampling distributions and priors via intrinsic analysis on the space of probability density functions. We demonstrate the applicability of our framework to generalized mixed-effects models and to directional and shape data.

Description: With the discovery of an increasing number of causal genes for complex human disorders, it is crucial to assess the genetic risk of disease onset for individuals who are carriers of these causal mutations and to compare the distribution of the age-at-onset for such individuals with the distribution for noncarriers. In many genetic epidemiological studies that aim to estimate causal gene effect on disease, the age-at-onset of disease is subject to censoring. In addition, the mutation carrier or noncarrier status of some individuals may be unknown, due to the high cost of in-person ascertainment by collecting DNA samples or because of the death of older individuals. Instead, the probability of such individuals’ mutation status can be obtained from various other sources. When mutation status is missing, the available data take the form of censored mixture data. Recently, various methods have been proposed for risk estimation using such data, but none is efficient for estimating a nonparametric distribution. We propose a fully efficient sieve maximum likelihood estimation method, in which we estimate the logarithm of the hazard ratio between genetic mutation groups using B-splines, while applying nonparametric maximum likelihood estimation to the reference baseline hazard function. Our estimator can be calculated via an expectation-maximization algorithm which is much faster than existing methods. We show that our estimator is consistent and semiparametrically efficient and establish its asymptotic distribution. Simulation studies demonstrate the superior performance of the proposed method, which is used to estimate the distribution of the age-at-onset of Parkinson's disease for carriers of mutations in the leucine-rich repeat kinase 2, LRRK2, gene.

Description: Smoothing splines provide flexible nonparametric regression estimators. However, the high computational cost of smoothing splines for large datasets has hindered their wide application. In this article, we develop a new method, named adaptive basis sampling, for efficient computation of smoothing splines in super-large samples. Except for the univariate case where the Reinsch algorithm is applicable, a smoothing spline for a regression problem with sample size n can be expressed as a linear combination of n basis functions and its computational complexity is generally O ( n 3 ). We achieve a more scalable computation in the multivariate case by evaluating the smoothing spline using a smaller set of basis functions, obtained by an adaptive sampling scheme that uses values of the response variable. Our asymptotic analysis shows that smoothing splines computed via adaptive basis sampling converge to the true function at the same rate as full basis smoothing splines. Using simulation studies and a large-scale deep earth core-mantle boundary imaging study, we show that the proposed method outperforms a sampling method that does not use the values of response variables.

Description: We propose tests for nonlinear serial dependence in time series under the null hypothesis of general linear dependence, in contrast to the more widely studied null hypothesis of independence. The approach is based on combining an entropy dependence metric, which possesses many desirable properties and is used as a test statistic, with a suitable extension of surrogate data methods, a class of Monte Carlo distribution-free tests for nonlinearity, and a smoothed sieve bootstrap scheme. We show how, in the same way as the autocorrelation function is used for linear models, our tests can in principle be employed to detect the lags at which a significant nonlinear relationship is present. We prove the asymptotic validity of the proposed procedures and the corresponding inferences. The small-sample performance of the tests in terms of power and size is assessed through a simulation study. Applications to real datasets of different kinds are also presented.

Description: Contamination caused by outliers is inevitable in data analysis, and robust statistical methods are often needed. In this paper we develop a new approach for robust data analysis on the basis of scoring rules. A scoring rule is a discrepancy measure to assess the quality of probabilistic forecasts. We propose a simple method of estimating not only parameters in the statistical model but also the contamination ratio, i.e., the ratio of outliers. The outliers are detected based on the estimated contamination ratio. For this purpose, we use scoring rules with extended statistical models called unnormalized models. Regression problems are also considered. We study complex heterogeneous contamination wherein the contamination ratio in a response variable may depend on covariate variables, and propose a simple method to estimate a robust regression function and expected contamination ratio. Simulation studies demonstrate the effectiveness of our method.

Description: The sample covariance matrix, which is well known to be highly nonrobust, plays a central role in many classical multivariate statistical methods. A popular way of making such multivariate methods more robust is to replace the sample covariance matrix with some robust scatter matrix. The aim of this paper is to point out that multivariate methods often require that certain properties of the covariance matrix hold also for the robust scatter matrix in order for the corresponding robust plug-in method to be a valid approach, but that not all scatter matrices possess the desired properties. Plug-in methods for independent components analysis, observational regression and graphical modelling are considered in more detail. For each case, it is shown that replacing the sample covariance matrix with a symmetrized robust scatter matrix yields a valid robust multivariate procedure.

Description: So-called big data are likely to have complex structure, in particular implying that estimates of precision obtained by applying standard statistical procedures are likely to be misleading, even if the point estimates of parameters themselves may be reasonably satisfactory. While this possibility is best explored in the context of each special case, here we outline a fairly general representation of the accretion of error in large systems and explore the possible implications for the estimation of regression coefficients. The discussion raises issues broadly parallel to the distinction between short-range and long-range dependence in time series theory.

Description: This paper extends the classical two-regime threshold autoregressive model by introducing hysteresis to its regime-switching structure, which leads to a new model: the hysteretic autoregressive model. The proposed model enjoys the piecewise linear structure of a threshold model but has a more flexible regime switching mechanism. A sufficient condition is given for geometric ergodicity. Conditional least squares estimation is discussed, and the asymptotic distributions of its estimators and information criteria for model selection are derived. Simulation results and an example support the model.

Description: This paper points out an error in Davidov and Iliopoulos's ( Biometrika 100 , 778–80) proof of convergence of an iterative algorithm for the proportional likelihood ratio model. It is shown that the iterative algorithm increases the likelihood in each iteration and converges under mild additional conditions when the odds ratio function is bounded.

Description: Retrieving the paleoclimatic signal from the deeper part of the EPICA Dome C ice core The Cryosphere, 9, 1633-1648, 2015 Author(s): J.-L. Tison, M. de Angelis, G. Littot, E. Wolff, H. Fischer, M. Hansson, M. Bigler, R. Udisti, A. Wegner, J. Jouzel, B. Stenni, S. Johnsen, V. Masson-Delmotte, A. Landais, V. Lipenkov, L. Loulergue, J.-M. Barnola, J.-R. Petit, B. Delmonte, G. Dreyfus, D. Dahl-Jensen, G. Durand, B. Bereiter, A. Schilt, R. Spahni, K. Pol, R. Lorrain, R. Souchez, and D. Samyn An important share of paleoclimatic information is buried within the lowermost layers of deep ice cores. Because improving our records further back in time is one of the main challenges in the near future, it is essential to judge how deep these records remain unaltered, since the proximity of the bedrock is likely to interfere both with the recorded temporal sequence and the ice properties. In this paper, we present a multiparametric study (δD-δ 18 O ice , δ 18 O atm , total air content, CO 2 , CH 4 , N 2 O, dust, high-resolution chemistry, ice texture) of the bottom 60 m of the EPICA (European Project for Ice Coring in Antarctica) Dome C ice core from central Antarctica. These bottom layers were subdivided into two distinct facies: the lower 12 m showing visible solid inclusions (basal dispersed ice facies) and the upper 48 m, which we will refer to as the "basal clean ice facies". Some of the data are consistent with a pristine paleoclimatic signal, others show clear anomalies. It is demonstrated that neither large-scale bottom refreezing of subglacial water, nor mixing (be it internal or with a local basal end term from a previous/initial ice sheet configuration) can explain the observed bottom-ice properties. We focus on the high-resolution chemical profiles and on the available remote sensing data on the subglacial topography of the site to propose a mechanism by which relative stretching of the bottom-ice sheet layers is made possible, due to the progressively confining effect of subglacial valley sides. This stress field change, combined with bottom-ice temperature close to the pressure melting point, induces accelerated migration recrystallization, which results in spatial chemical sorting of the impurities, depending on their state (dissolved vs. solid) and if they are involved or not in salt formation. This chemical sorting effect is responsible for the progressive build-up of the visible solid aggregates that therefore mainly originate "from within", and not from incorporation processes of debris from the ice sheet's substrate. We further discuss how the proposed mechanism is compatible with the other ice properties described. We conclude that the paleoclimatic signal is only marginally affected in terms of global ice properties at the bottom of EPICA Dome C, but that the timescale was considerably distorted by mechanical stretching of MIS20 due to the increasing influence of the subglacial topography, a process that might have started well above the bottom ice. A clear paleoclimatic signal can therefore not be inferred from the deeper part of the EPICA Dome C ice core. Our work suggests that the existence of a flat monotonic ice–bedrock interface, extending for several times the ice thickness, would be a crucial factor in choosing a future "oldest ice" drilling location in Antarctica.

Description: Impact of debris cover on glacier ablation and atmosphere–glacier feedbacks in the Karakoram The Cryosphere, 9, 1617-1632, 2015 Author(s): E. Collier, F. Maussion, L. I. Nicholson, T. Mölg, W. W. Immerzeel, and A. B. G. Bush The Karakoram range of the Hindu-Kush Himalaya is characterized by both extensive glaciation and a widespread prevalence of surficial debris cover on the glaciers. Surface debris exerts a strong control on glacier surface-energy and mass fluxes and, by modifying surface boundary conditions, has the potential to alter atmosphere–glacier feedbacks. To date, the influence of debris on Karakoram glaciers has only been directly assessed by a small number of glaciological measurements over short periods. Here, we include supraglacial debris in a high-resolution, interactively coupled atmosphere–glacier modeling system. To investigate glaciological and meteorological changes that arise due to the presence of debris, we perform two simulations using the coupled model from 1 May to 1 October 2004: one that treats all glacier surfaces as debris-free and one that introduces a simplified specification for the debris thickness. The basin-averaged impact of debris is a reduction in ablation of ~ 14 %, although the difference exceeds 5 m w.e. on the lowest-altitude glacier tongues. The relatively modest reduction in basin-mean mass loss results in part from non-negligible sub-debris melt rates under thicker covers and from compensating increases in melt under thinner debris, and may help to explain the lack of distinct differences in recent elevation changes between clean and debris-covered ice. The presence of debris also strongly alters the surface boundary condition and thus heat exchanges with the atmosphere; near-surface meteorological fields at lower elevations and their vertical gradients; and the atmospheric boundary layer development. These findings are relevant for glacio-hydrological studies on debris-covered glaciers and contribute towards an improved understanding of glacier behavior in the Karakoram.

Description: Drought assessment in the Dongliao River basin: traditional approaches vs. generalized drought assessment index based on water resources systems Natural Hazards and Earth System Science, 15, 1889-1906, 2015 Author(s): B. S. Weng, D. H. Yan, H. Wang, J. H. Liu, Z. Y. Yang, T. L. Qin, and J. Yin Drought is firstly a resource issue, and with its development it evolves into a disaster issue. Drought events usually occur in a determinate but a random manner. Drought has become one of the major factors to affect sustainable socioeconomic development. In this paper, we propose the generalized drought assessment index (GDAI) based on water resources systems for assessing drought events. The GDAI considers water supply and water demand using a distributed hydrological model. We demonstrate the use of the proposed index in the Dongliao River basin in northeastern China. The results simulated by the GDAI are compared to observed drought disaster records in the Dongliao River basin. In addition, the temporal distribution of drought events and the spatial distribution of drought frequency from the GDAI are compared with the traditional approaches in general (i.e., standard precipitation index, Palmer drought severity index and rate of water deficit index). Then, generalized drought times, generalized drought duration, and generalized drought severity were calculated by theory of runs. Application of said runs at various drought levels (i.e., mild drought, moderate drought, severe drought, and extreme drought) during the period 1960–2010 shows that the centers of gravity of them all distribute in the middle reaches of Dongliao River basin, and change with time. The proposed methodology may help water managers in water-stressed regions to quantify the impact of drought, and consequently, to make decisions for coping with drought.

Description: Motivation: The storage and transmission of high-throughput sequencing data consumes significant resources. As our capacity to produce such data continues to increase, this burden will only grow. One approach to reduce storage and transmission requirements is to compress this sequencing data. Results: We present a novel technique to boost the compression of sequencing that is based on the concept of bucketing similar reads so that they appear nearby in the file. We demonstrate that, by adopting a data-dependent bucketing scheme and employing a number of encoding ideas, we can achieve substantially better compression ratios than existing de novo sequence compression tools, including other bucketing and reordering schemes. Our method, Mince, achieves up to a 45% reduction in file sizes (28% on average) compared with existing state-of-the-art de novo compression schemes. Availability and implementation : Mince is written in C++11, is open source and has been made available under the GPLv3 license. It is available at http://www.cs.cmu.edu/~ckingsf/software/mince . Contact: carlk@cs.cmu.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Current methods for motif discovery from chromatin immunoprecipitation followed by sequencing (ChIP-seq) data often identify non-targeted transcription factor (TF) motifs, and are even further limited when peak sequences are similar due to common ancestry rather than common binding factors. The latter aspect particularly affects a large number of proteins from the Cys 2 His 2 zinc finger (C2H2-ZF) class of TFs, as their binding sites are often dominated by endogenous retroelements that have highly similar sequences. Here, we present recognition code-assisted discovery of regulatory elements (RCADE) for motif discovery from C2H2-ZF ChIP-seq data. RCADE combines predictions from a DNA recognition code of C2H2-ZFs with ChIP-seq data to identify models that represent the genuine DNA binding preferences of C2H2-ZF proteins. We show that RCADE is able to identify generalizable binding models even from peaks that are exclusively located within the repeat regions of the genome, where state-of-the-art motif finding approaches largely fail. Availability and implementation: RCADE is available as a webserver and also for download at http://rcade.ccbr.utoronto.ca/ . Supplementary information: Supplementary data are available at Bioinformatics online. Contact: t.hughes@utoronto.ca

Description: Motivation: Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al. , 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates. As the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work and making errors introduced during curation easier to correct. Results : Here, we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git’s version control features. Hosting this data store on GitHub ( http://github.com/ ) provides open access to the data store using tools familiar to many developers. We have deployed a server running the ‘phylesystem-api’, which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements. Availability and implementation : Source code for the web service layer is available at https://github.com/OpenTreeOfLife/phylesystem-api . The data store can be cloned from: https://github.com/OpenTreeOfLife/phylesystem . A web application that uses the phylesystem web services is deployed at http://tree.opentreeoflife.org/curator . Code for that tool is available from https://github.com/OpenTreeOfLife/opentree . Contact : mtholder@gmail.com

Description: Motivation: Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) detects genome-wide DNA–protein interactions and chromatin modifications, returning enriched regions (ERs), usually associated with a significance score. Moderately significant interactions can correspond to true, weak interactions, or to false positives; replicates of a ChIP-seq experiment can provide co-localised evidence to decide between the two cases. We designed a general methodological framework to rigorously combine the evidence of ERs in ChIP-seq replicates, with the option to set a significance threshold on the repeated evidence and a minimum number of samples bearing this evidence. Results : We applied our method to Myc transcription factor ChIP-seq datasets in K562 cells available in the ENCODE project. Using replicates, we could extend up to 3 times the ER number with respect to single-sample analysis with equivalent significance threshold. We validated the ‘rescued’ ERs by checking for the overlap with open chromatin regions and for the enrichment of the motif that Myc binds with strongest affinity; we compared our results with alternative methods (IDR and jMOSAiCS), obtaining more validated peaks than the former and less peaks than latter, but with a better validation. Availability and implementation : An implementation of the proposed method and its source code under GPLv3 license are freely available at http://www.bioinformatics.deib.polimi.it/MSPC/ and http://mspc.codeplex.com/ , respectively. Contact : marco.morelli@iit.it Supplementary information: Supplementary Material are available at Bioinformatics online.

Description: : We announce the release of kSNP3.0, a program for SNP identification and phylogenetic analysis without genome alignment or the requirement for reference genomes. kSNP3.0 is a significantly improved version of kSNP v2. Availability and implementation : kSNP3.0 is implemented as a package of stand-alone executables for Linux and Mac OS X under the open-source BSD license. The executable packages, source code and a full User Guide are freely available at https://sourceforge.net/projects/ksnp/files/ Contact: barryghall@gmail.com

Description: The electrical self-potential method is a non-intrusive snow-hydrological sensor The Cryosphere Discussions, 9, 4437-4457, 2015 Author(s): S. S. Thompson, B. Kulessa, R. L. H. Essery, and M. P. Lüthi Our ability to measure, quantify and assimilate hydrological properties and processes of snow in operational models is disproportionally poor compared to the significance of seasonal snowmelt as a global water resource and major risk factor in flood and avalanche forecasting. Encouraged by recent theoretical, modelling and laboratory work, we show here that the diurnal evolution of aerially-distributed self-potential magnitudes closely track those of bulk meltwater fluxes in melting in-situ snowpacks at Rhone and Jungfraujoch glaciers, Switzerland. Numerical modelling infers temporally-evolving liquid water contents in the snowpacks on successive days in close agreement with snow-pit measurements. Muting previous concerns, the governing physical and chemical properties of snow and meltwater became temporally invariant for modelling purposes. Because measurement procedure is straightforward and readily automated for continuous monitoring over significant spatial scales, we conclude that the self-potential geophysical method is a highly-promising non-intrusive snow-hydrological sensor for measurement practice, modelling and operational snow forecasting.

Description: Motivation: We have created an R package named phylogeo that provides a set of geographic utilities for sequencing-based microbial ecology studies. Although the geographic location of samples is an important aspect of environmental microbiology, none of the major software packages used in processing microbiome data include utilities that allow users to map and explore the spatial dimension of their data. phylogeo solves this problem by providing a set of plotting and mapping functions that can be used to visualize the geographic distribution of samples, to look at the relatedness of microbiomes using ecological distance, and to map the geographic distribution of particular sequences. By extending the popular phyloseq package and using the same data structures and command formats, phylogeo allows users to easily map and explore the geographic dimensions of their data from the R programming language. Availability and Implementation: phylogeo is documented and freely available http://zachcp.github.io/phylogeo Contact : zcharlop@rockefeller.edu

Description: : Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research’s DSD tool as well as to LaTeX. Availability and implementation : Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono. Contact : ozan@cosbi.eu

Description: Motivation: Molecular dynamics simulations provide atomic insight into the physicochemical characteristics of lipid membranes and hence, a wide range of force field families capable of modelling various lipid types have been developed in recent years. To model membranes in a biologically realistic lipid composition, simulation systems containing multiple different lipids must be assembled. Results: We present a new web service called MemGen that is capable of setting up simulation systems of heterogenous lipid membranes. MemGen is not restricted to certain lipid force fields or lipid types, but instead builds membranes from uploaded structure files which may contain any kind of amphiphilic molecule. MemGen works with any all-atom or united-atom lipid representation. Availability and implementation: MemGen is freely available without registration at http://memgen.uni-goettingen.de . Contact: jhub@gwdg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: A rainfall design method for spatial flood risk assessment: considering multiple flood sources Hydrology and Earth System Sciences Discussions, 12, 8005-8033, 2015 Author(s): X. Jiang and H. Tatano Information about the spatial distribution of flood risk is important for integrated urban flood risk management. Focusing on urban areas, spatial flood risk assessment must reflect all risk information derived from multiple flood sources: rivers, drainage, coastal flooding etc. that may affect the area. However, conventional flood risk assessment deals with each flood source independently, which leads to an underestimation of flood risk in the floodplain. Even in floodplains that have no risk from coastal flooding, flooding from river channels and inundation caused by insufficient drainage capacity should be considered simultaneously. For integrated flood risk management, it is necessary to establish a methodology to estimate flood risk distribution across a floodplain. In this paper, a rainfall design method for spatial flood risk assessment, which considers the joint effects of multiple flood sources, is proposed. The concept of critical rainfall duration determined by the concentration time of flooding is introduced to connect response characteristics of different flood sources with rainfall. A copula method is then adopted to capture the correlation of rainfall amount with different critical rainfall durations. Rainfall events are designed taking advantage of the copula structure of correlation and marginal distribution of rainfall amounts within different critical rainfall durations. A case study in the Otsu River Basin, Osaka prefecture, Japan was conducted to demonstrate this methodology.

Description: Tilt error in cryospheric surface radiation measurements at high latitudes: a model study The Cryosphere Discussions, 9, 4355-4376, 2015 Author(s): W. S. Bogren, J. F. Burkhart, and A. Kylling We have evaluated the magnitude and makeup of error in cryospheric radiation observations due to small sensor misalignment in in-situ measurements of solar irradiance. This error is examined through simulation of diffuse and direct irradiance arriving at a detector with a cosine-response foreoptic. Emphasis is placed on assessing total error over the solar shortwave spectrum from 250 to 4500 nm, as well as supporting investigation over other relevant shortwave spectral ranges. The total measurement error introduced by sensor tilt is dominated by the direct component. For a typical high latitude albedo measurement with a solar zenith angle of 60°, a sensor tilted by 1, 3, and 5° can respectively introduce up to 2.6, 7.7, and 12.8 % error into the measured irradiance and similar errors in the derived albedo. Depending on the daily range of solar azimuth and zenith angles, significant measurement error can persist also in integrated daily irradiance and albedo.

Description: Hydroelastic analysis of ice shelves under long wave excitation Natural Hazards and Earth System Science, 15, 1851-1857, 2015 Author(s): T. K. Papathanasiou, A. E. Karperaki, E. E. Theotokoglou, and K. A. Belibassakis The transient hydroelastic response of an ice shelf under long wave excitation is analysed by means of the finite element method. The simple model, presented in this work, is used for the simulation of the generated kinematic and stress fields in an ice shelf, when the latter interacts with a tsunami wave. The ice shelf, being of large length compared to its thickness, is modelled as an elastic Euler-Bernoulli beam, constrained at the grounding line. The hydrodynamic field is represented by the linearised shallow water equations. The numerical solution is based on the development of a special hydroelastic finite element for the system of governing of equations. Motivated by the 2011 Sulzberger Ice Shelf (SIS) calving event and its correlation with the Honshu Tsunami, the SIS stable configuration is studied. The extreme values of the bending moment distribution in both space and time are examined. Finally, the location of these extrema is investigated for different values of ice shelf thickness and tsunami wave length.

Description: Choosing the number of components in a finite mixture model is a challenging task. In this article, we study the behaviour of information criteria for selecting the mixture order, based on either the observed likelihood or the complete likelihood including component labels. We propose a new observed likelihood criterion called aic mix , which is shown to be order consistent. We further show that when there is a nontrivial level of classification uncertainty in the true model, complete likelihood criteria asymptotically underestimate the true number of components. A simulation study illustrates the potentially poor finite-sample performance of complete likelihood criteria, while aic mix and the Bayesian information criterion perform strongly regardless of the level of classification uncertainty.

Description: Outlier detection is an integral component of statistical modelling and estimation. For high-dimensional data, classical methods based on the Mahalanobis distance are usually not applicable. We propose an outlier detection procedure that replaces the classical minimum covariance determinant estimator with a high-breakdown minimum diagonal product estimator. The cut-off value is obtained from the asymptotic distribution of the distance, which enables us to control the Type I error and deliver robust outlier detection. Simulation studies show that the proposed method behaves well for high-dimensional data.

Description: This paper adopts a nonparametric Bayesian approach to testing whether a function is monotone. Two new families of tests are constructed. The first uses constrained smoothing splines with a hierarchical stochastic-process prior that explicitly controls the prior probability of monotonicity. The second uses regression splines together with two proposals for the prior over the regression coefficients. Via simulation, the finite-sample performance of the tests is shown to improve upon existing frequentist and Bayesian methods. The asymptotic properties of the Bayes factor for comparing monotone versus nonmonotone regression functions in a Gaussian model are also studied. Our results significantly extend those currently available, which chiefly focus on determining the dimension of a parametric linear model.

Description: The paper develops hierarchical empirical Bayes and benchmarked hierarchical empirical Bayes estimators of positive small area means under multiplicative models. The usual benchmarking requirement is that the small area estimates, when aggregated, should equal the direct estimates for the larger geographical areas. However, while estimating positive small area parameters, the conventional squared error or weighted squared error loss subject to the usual benchmark constraint may not produce positive estimators, so it is necessary to seek other loss functions. We consider a multiplicative model for the original data for estimating positive small area means, and suggest a variant of the Kullback–Leibler divergence as a loss function. The prediction errors of the suggested hierarchical empirical Bayes estimators are investigated asymptotically, and their second-order unbiased estimators are provided. Bootstrapped estimators of these prediction errors for both hierarchical empirical Bayes and benchmarked hierarchical empirical Bayes estimators are also given. The performance of the suggested procedures is investigated through simulation as well as with an example.