ALBERT

Description: Regional and local patterns in depth to water table, hydrochemistry and peat properties of bogs and their laggs in coastal British Columbia Hydrology and Earth System Sciences, 17, 3421-3435, 2013 Author(s): S. A. Howie and H. J. van Meerveld In restoration planning for damaged raised bogs, the lagg at the bog margin is often not given considerable weight and is sometimes disregarded entirely. However, the lagg is critical for the proper functioning of the bog, as it supports the water mound in the bog. In order to include the lagg in a restoration plan for a raised bog, it is necessary to understand the hydrological characteristics and functions of this rarely studied transition zone. We studied 13 coastal British Columbia (BC) bogs and identified two different gradients in depth to water table, hydrochemistry and peat properties: (1) a local bog expanse–bog margin gradient, and (2) a regional gradient related to climate and proximity to the ocean. Depth to water table generally increased across the transition from bog expanse to bog margin. In the bog expanse, pH was above 4.2 in the Pacific Oceanic wetland region (cooler and wetter climate) and below 4.3 in the Pacific Temperate wetland region (warmer and drier climate). Both pH and pH-corrected electrical conductivity increased significantly across the transition from bog expanse to bog margin, though not in all cases. Na + and Mg 2+ concentrations were generally highest in exposed, oceanic bogs and lower in inland bogs. Ash content in peat samples increased across the bog expanse–bog margin transition, and appears to be a useful abiotic indicator of the location of the bog margin. The observed variation in the hydrological and hydrochemical gradients across the bog expanse–bog margin transition highlights both local and regional diversity of bogs and their associated laggs.

Description: Imperfect scaling in distributions of radar-derived rainfall fields Hydrology and Earth System Sciences Discussions, 10, 11385-11422, 2013 Author(s): M. J. van den Berg, L. Delobbe, and N. E. C. Verhoest Fine scale rainfall observations for modeling exercises are often not available, but rather coarser data derived from a variety of sources are used. Effectively using these data sources in models often requires the probability distribution of the data at the applicable scale. Although numerous models for scaling distributions exist, these are often based on theoretical developments, rather than on data. In this study, we develop a model based on the α-stable distribution of rainfall fields, and tested on 5 min radar data from a Belgian weather radar. We use these data to estimate functions that describe parameters of the distribution over various scales. Moreover, we study how the mean of the distribution and the intermittency change with scale, and validate and design functions to describe the shape parameter of the distribution. This information was combined into an effective model of the distribution. Finally, the model was fitted to data from numerous storms, and the resulting parameters were compared to investigate the change in scaling behavior through time.

Description: Spatially resolved information on karst conduit flow from in-cave dye-tracing Hydrology and Earth System Sciences Discussions, 10, 11311-11335, 2013 Author(s): U. Lauber, W. Ufrecht, and N. Goldscheider Artificial tracers are powerful tools to investigate karst systems. Tracers are commonly injected into sinking streams or dolines, while springs serve as monitoring sites. The obtained flow and transport parameters represent mixed information from the vadose, epiphreatic and phreatic zones, i.e., the aquifer remains a black box. Accessible active caves constitute valuable but underexploited natural laboratories to gain detailed insights into the hydrologic functioning of the aquifer. Two multi-tracer tests in the catchment of a major karst spring (Blautopf, Germany) with injections and monitoring in two associated water caves aimed at obtaining spatially and temporally resolved information on groundwater flow in different compartments of the system. Two tracers were injected in the caves to characterize the hydraulic connections between them and with the spring. Two injections at the land surface, far from the spring, aimed at resolving the aquifer's internal drainage structure. Tracer breakthrough curves were monitored by field fluorimeters in caves and at the spring. Results demonstrate the dendritic drainage structure of the aquifer. It was possible to obtain relevant flow and transport parameters for different sections of this system. The highest mean flow velocities (275 m h −1 ) were observed in the near-spring epiphreatic section (open-channel flow), while velocities in the phreatic zone (pressurized flow) were one order of magnitude lower. Determined conduit water volumes confirm results of water balances and hydrograph analyses. In conclusion, experiments and monitoring in caves can deliver spatially resolved information on karst aquifer heterogeneity and dynamics that cannot be obtained by traditional investigative methods.

Description: On the lack of robustness of hydrologic models regarding water balance simulation – a diagnostic approach on 20 mountainous catchments using three models of increasing complexity Hydrology and Earth System Sciences Discussions, 10, 11337-11383, 2013 Author(s): L. Coron, V. Andréassian, C. Perrin, M. Bourqui, and F. Hendrickx This paper investigates the robustness of rainfall–runoff models when their parameters are transferred in time. More specifically, we studied their ability to simulate water balance on periods with different hydroclimatic characteristics. The testing procedure consisted in a series of parameter transfers between 10-yr periods and the systematic analysis of mean-volume errors. This procedure was applied to three conceptual models of different structural complexity over 20 mountainous catchments in southern France. The results showed that robustness problems are common. Errors on 10-yr-mean flows were significant for all three models and calibration periods, even when the entire record was used for calibration. Various graphical and numerical tools were used to show strong similarities between the shapes of mean flow biases calculated on a 10-yr-long sliding window when various parameter sets are used. Unexpected behavioural similarities were observed between the three models tested, considering their large differences in structural complexity. While the actual causes for robustness problems in these models remain unclear, this work stresses the limited transferability in time of the water balance adjustments made through parameter optimization. Although absolute differences between simulations obtained with different calibrated parameter sets were sometimes substantial, relative differences in simulated mean flows between time periods remained similar regardless of the calibrated parameter sets.

Description: Bayesian networks modelling in support to cross-cutting analysis of water supply and sanitation in developing countries Hydrology and Earth System Sciences, 17, 3397-3419, 2013 Author(s): C. Dondeynaz, J. López Puga, and C. Carmona Moreno Despite the efforts made towards the Millennium Development Goals targets during the last decade, improved access to water supply or basic sanitation still remains unavailable for millions of people across the world. This paper proposes a set of models that use 25 key variables and country profiles from the WatSan4Dev data set involving water supply and sanitation (Dondeynaz et al., 2012). This paper suggests the use of Bayesian network modelling methods because they are more easily adapted to deal with non-normal distributions, and integrate a qualitative approach for data analysis. They also offer the advantage of integrating preliminary knowledge into the probabilistic models. The statistical performance of the proposed models ranges between 20 and 5% error rates, which are very satisfactory taking into account the strong heterogeneity of variables. Probabilistic scenarios run from the models allow an assessment of the relationships between human development, external support, governance aspects, economic activities and water supply and sanitation (WSS) access. According to models proposed in this paper, gaining a strong poverty reduction will require the WSS access to reach 75–76% through: (1) the management of ongoing urbanisation processes to avoid slums development; and (2) the improvement of health care, for instance for children. Improving governance, such as institutional efficiency, capacities to make and apply rules, or control of corruption is positively associated with WSS sustainable development. The first condition for an increment of the HDP (human development and poverty) remains of course an improvement of the economic conditions with higher household incomes. Moreover, a significant country commitment to the environment, associated with civil society freedom of expression constitutes a favourable setting for sustainable WSS services delivery. Intensive agriculture using irrigation practises also appears as a mean for sustainable WSS thanks to multi-uses and complementarities. With a WSS sector organised at national level, irrigation practices can support the structuring and efficiency of the agriculture sector. It may then induce rural development in areas where WSS access often is set back compared to urban areas 1 . External financial support, called Official Development Assistance (ODA CI), plays a role in WSS improvement but comes last in the sensitivity analyses of models. An overall 47% of the Official Development Assistance goes first to poor countries, and is associated to governance aspects: (1) political stability and (2) country commitment to the environment and civil society degree of freedom. These governance aspects constitute a good framework for aid implementation in recipient countries. Modelling is run with the five groups of countries as defined in Dondeynaz et al. (2012). Models for profile 4 (essential external support) and profile 5 (primary material consumption) are specifically detailed and analysed in this paper. For countries in profile 4, fighting against water scarcity and progressing desertification should be the priority. However, for countries in profile 5, efforts should first concentrate on consolidation of political stability while supporting diversification of the economic activities. Nevertheless, for both profiles, reduction of poverty should remain the first priority as previously indicated. 1 JMP statistics, 2004 http://www.wssinfo.org/data-estimates/table/ , last access: 22 July 2013.

Description: Technical Note: A comparison of model and empirical measures of catchment-scale effective energy and mass transfer Hydrology and Earth System Sciences, 17, 3389-3395, 2013 Author(s): C. Rasmussen and E. L. Gallo Recent work suggests that a coupled effective energy and mass transfer (EEMT) term, which includes the energy associated with effective precipitation and primary production, may serve as a robust prediction parameter of critical zone structure and function. However, the models used to estimate EEMT have been solely based on long-term climatological data with little validation using direct empirical measures of energy, water, and carbon balances. Here we compare catchment-scale EEMT estimates generated using two distinct approaches: (1) EEMT modeled using the established methodology based on estimates of monthly effective precipitation and net primary production derived from climatological data, and (2) empirical catchment-scale EEMT estimated using data from 86 catchments of the Model Parameter Estimation Experiment (MOPEX) and MOD17A3 annual net primary production (NPP) product derived from Moderate Resolution Imaging Spectroradiometer (MODIS). Results indicated positive and significant linear correspondence ( R 2 = 0.75; P 〈 0.001) between model and empirical measures with an average root mean square error (RMSE) of 4.86 MJ m −2 yr −1 . Modeled EEMT values were consistently greater than empirical measures of EEMT. Empirical catchment estimates of the energy associated with effective precipitation ( E PPT ) were calculated using a mass balance approach that accounts for water losses to quick surface runoff not accounted for in the climatologically modeled E PPT . Similarly, local controls on primary production such as solar radiation and nutrient limitation were not explicitly included in the climatologically based estimates of energy associated with primary production ( E BIO ), whereas these were captured in the remotely sensed MODIS NPP data. These differences likely explain the greater estimate of modeled EEMT relative to the empirical measures. There was significant positive correlation between catchment aridity and the fraction of EEMT partitioned into E BIO ( F BIO ), with an increase in F BIO as a fraction of the total as aridity increases and percentage of catchment woody plant cover decreases. In summary, the data indicated strong correspondence between model and empirical measures of EEMT with limited bias that agree well with other empirical measures of catchment energy and water partitioning and plant cover.

Description: Review Article: On the relation between the seismic activity and the Hurst exponent of the geomagnetic field at the time of the 2000 Izu swarm Natural Hazards and Earth System Science, 13, 2189-2194, 2013 Author(s): F. Masci and J. N. Thomas Many papers document the observation of earthquake-related precursory signatures in geomagnetic field data. However, the significance of these findings is ambiguous because the authors did not adequately take into account that these signals could have been generated by other sources, and the seismogenic origin of these signals have not been validated by comparison with independent datasets. Thus, they are not reliable examples of magnetic disturbances induced by the seismic activity. Hayakawa et al. (2004) claim that at the time of the 2000 Izu swarm the Hurst exponent of the Ultra-Low-Frequency (ULF: 0.001–10 Hz) band of the geomagnetic field varied in accord with the energy released by the seismicity. The present paper demonstrates that the behaviour of the Hurst exponent was insufficiently investigated and also misinterpreted by the authors. We clearly show that during the Izu swarm the changes of the Hurst exponent were strongly related to the level of global geomagnetic activity and not to the increase of the local seismic activity.

Description: Forest fire danger rating in complex topography – results from a case study in the Bavarian Alps in autumn 2011 Natural Hazards and Earth System Science, 13, 2157-2167, 2013 Author(s): C. Schunk, C. Wastl, M. Leuchner, C. Schuster, and A. Menzel Forest fire danger rating based on sparse meteorological stations is known to be potentially misleading when assigned to larger areas of complex topography. This case study examines several fire danger indices based on data from two meteorological stations at different elevations during a major drought period. This drought was caused by a persistent high pressure system, inducing a pronounced temperature inversion and its associated thermal belt with much warmer, dryer conditions in intermediate elevations. Thus, a massive drying of fuels, leading to higher fire danger levels, and multiple fire occurrences at mid-slope positions were contrasted by moderate fire danger especially in the valleys. The ability of fire danger indices to resolve this situation was studied based on a comparison with the actual fire danger as determined from expert observations, fire occurrences and fuel moisture measurements. The results revealed that, during temperature inversion, differences in daily cycles of meteorological parameters influence fire danger and that these are not resolved by standard meteorological stations and fire danger indices (calculated on a once-a-day basis). Additional stations in higher locations or high-resolution meteorological models combined with fire danger indices accepting at least hourly input data may allow reasonable fire danger calculations under these circumstances.

Description: Preface "Landslide hazard and risk assessment at different scales" Natural Hazards and Earth System Science, 13, 2169-2171, 2013 Author(s): P. Reichenbach, A. Günther, and T. Glade

Description: Antecedent flow conditions and nitrate concentrations in the Mississippi River Basin Hydrology and Earth System Sciences Discussions, 10, 11451-11484, 2013 Author(s): J. C. Murphy, R. M. Hirsch, and L. A. Sprague The influence of antecedent flow conditions on nitrate concentrations was explored at eight sites in the Mississippi River Basin, USA. Antecedent moisture conditions have been shown to influence nutrient export from small, relatively homogenous basins, but this influence has not been observed at a regional or continental scale. Antecedent flow conditions were quantified as the ratio between the mean daily flow of the previous year and the mean daily flow from the period of record ( Q ratio), and the Q ratio was statistically related to nitrate anomalies (the unexplained variability in nitrate concentration after filtering out season, long-term trend, and contemporaneous flow effects) at each site. Nitrate anomaly and Q ratio were negatively related at three of the four major tributary sites and upstream in the Mississippi River, indicating that when the previous year was drier than average, at these sites, nitrate concentrations were higher than expected. The strength of these relationships increased when data were subdivided by contemporaneous flow conditions. Five of the eight sites had significant negative relationships ( p ≤ 0.05) at high or moderately high contemporaneous flows, suggesting nitrate that accumulates in these basins during a drought is flushed during subsequent storm events. At half of the sites, when flow during the previous year was 50% drier than average, nitrate concentration can be from 9 and 27% higher than nitrate concentrations that follow a year with average daily flow. Conversely, nitrate concentration can be from 8 and 21% lower than expected when the previous year was 50% wetter than average. These relationships between nitrate concentration and Q ratio serve as the basis for future studies that can better define specific hydrologic processes occurring during and after a drought, which influence nitrate concentration, such as the duration or magnitude of low flows, and the timing of low and high flows.

Description: Tidally induced velocity variations of the Beardmore Glacier, Antarctica, and their representation in satellite measurements of ice velocity The Cryosphere, 7, 1375-1384, 2013 Author(s): O. J. Marsh, W. Rack, D. Floricioiu, N. R. Golledge, and W. Lawson Ocean tides close to the grounding line of outlet glaciers around Antarctica have been shown to directly influence ice velocity, both linearly and non-linearly. These fluctuations can be significant and have the potential to affect satellite measurements of ice discharge, which assume displacement between satellite passes to be consistent and representative of annual means. Satellite observations of horizontal velocity variation in the grounding zone are also contaminated by vertical tidal effects, the importance of which is highlighted here in speckle tracking measurements. Eight TerraSAR-X scenes from the grounding zone of the Beardmore Glacier are analysed in conjunction with GPS measurements to determine short-term and decadal trends in ice velocity. Diurnal tides produce horizontal velocity fluctuations of 〉50% on the ice shelf, recorded in the GPS data 4 km downstream of the grounding line. This variability decreases rapidly to 〈5% only 15 km upstream of the grounding line. Daily fluctuations are smoothed to 〈1% in the 11-day repeat pass TerraSAR-X imagery, but fortnightly variations over this period are still visible and show that satellite-velocity measurements can be affected by tides over longer periods. The measured tidal displacement observed in radar look direction over floating ice also allows the grounding line to be identified, using differential speckle tracking where phase information cannot be easily unwrapped.

Description: Contribution of snow and glacier melt to discharge for highly glacierised catchments in Norway Hydrology and Earth System Sciences Discussions, 10, 11485-11517, 2013 Author(s): M. Engelhardt, T. V. Schuler, and L. M. Andreassen Glacierised catchments significantly alter the streamflow regime due to snow and glacier meltwater contribution to discharge. In this study, we modelled the mass balance and discharge rates for three highly glacierised catchments (〉50% glacier cover) in western Norway over the period 1961–2012. The spatial pattern of the catchments follows a gradient in climate continentality from west to east. The model uses gridded temperature and precipitation values from seNorge ( http://senorge.no ) as input which are available at a daily resolution. It accounts for accumulation of snow, transformation of snow to firn and ice, evaporation and melt. The model was calibrated for each catchment based on measurements of seasonal glacier mass-balances and daily discharge rates. For validation, daily melt rates were compared with measurements from sonic rangers located in the ablation zones of two of the glaciers and an uncertainty analysis was performed for the third catchment. The discharge contributions from snowmelt, glacier melt and rain were analysed with respect to spatial variations and temporal evolution. The model simulations reveal an increase of the relative contribution from glacier melt for the three catchments from less than 10% in the early 1990s to 15–30% in the late 2000s. The decline in precipitation by 10–20% in the same period was therefore overcompensated resulting in an increase of the annual discharge by 5–20%. Annual discharge sums and annual glacier melt are strongest correlated with annual and winter precipitation at the most maritime glacier and, with increased climate continentality, variations in both glacier melt contribution and annual discharge are becoming stronger correlated with variations in summer temperatures.

Description: Decadal trends in the Antarctic sea ice extent ultimately controlled by ice-ocean feedback The Cryosphere Discussions, 7, 4585-4632, 2013 Author(s): H. Goosse and V. Zunz The large natural variability of the Antarctic sea ice is a key characteristic of the system that might be responsible for the small positive trend in sea ice extent observed since 1979. In order to gain insight in the processes responsible for this variability, we have analysed in a control simulation performed with a coupled climate model a strong positive ice-ocean feedback that amplifies sea ice variations. When sea ice concentration increases in a region, in particular close to the ice edge, the mixed layer depth tends to decrease. This can be caused by a net inflow of ice and thus of freshwater that stabilizes the water column. Another stabilizing mechanism at interannual time scales that appears more widespread in our simulation is associated with the downward salt transport due to the seasonal cycle of ice formation: brine is released in winter when ice is formed and mixed over a deep layer while the freshwater flux caused by ice melting is included in a shallow layer, resulting in a net vertical transport of salt. Because of this stronger stratification due to the presence of sea ice, more heat is stored at depth in the ocean and the vertical oceanic heat flux is reduced, which contributes to maintain a higher ice extent. This positive feedback is not associated with a particular spatial pattern. Consequently, the spatial distribution of the trend in ice concentration is largely imposed by the wind changes that can provide the initial perturbation. A positive freshwater flux could alternatively be the initial trigger but the amplitude of the final response of the sea ice extent is finally set up by the amplification related to ice-ocean feedback. Initial conditions have also an influence as the chance to have a large increase in ice extent is higher if starting from a state characterized by a low value.

Description: There is much interest in using high-throughput DNA sequencing methodology to monitor microorganisms, complex plant and animal communities. However, there are experimental and analytical issues to consider before applying a sequencing technology, which was originally developed for genome projects, to ecological projects. Many of these issues have been highlighted by recent microbial studies. Understanding how high-throughput sequencing is best implemented is important for the interpretation of recent results and the success of future applications. Addressing complex biological questions with metagenomics requires the interaction of researchers who bring different skill sets to problem solving. Educators can help by nurturing a collaborative interdisciplinary approach to genome science, which is essential for effective problem solving. Educators are in a position to help students, teachers, the public and policy makers interpret the new knowledge that metagenomics brings. To do this, they need to understand, not only the excitement of the science but also the pitfalls and shortcomings of methodology and research designs. We review these issues and some of the research directions that are helping to move the field forward.

Description: We believe that undergraduate biology students must acquire a foundational background in computing including how to formulate a computational problem; develop an algorithmic solution; implement their solution in software and then test, document and use their code to explore biological phenomena. Moreover, by learning these skills in the first year, students acquire a powerful tool set that they can use and build on throughout their studies. To address this need, we have developed a first-year undergraduate course that teaches students the foundations of computational thinking and programming in the context of problems in biology. This article describes the structure and content of the course and summarizes assessment data on both affective and learning outcomes.

Description: Bioinformatics is an integral part of modern life sciences. It has revolutionized and redefined how research is carried out and has had an enormous impact on biotechnology, medicine, agriculture and related areas. Yet, it is only rarely integrated into high school teaching and learning programs, playing almost no role in preparing the next generation of information-oriented citizens. Here, we describe the design principles of bioinformatics learning environments, including our own, that are aimed at introducing bioinformatics into senior high school curricula through engaging learners in scientifically authentic inquiry activities. We discuss the bioinformatics-related benefits and challenges that high school teachers and students face in the course of the implementation process, in light of previous studies and our own experience. Based on these lessons, we present a new approach for characterizing the questions embedded in bioinformatics teaching and learning units, based on three criteria: the type of domain-specific knowledge required to answer each question (declarative knowledge, procedural knowledge, strategic knowledge, situational knowledge), the scientific approach from which each question stems (biological, bioinformatics, a combination of the two) and the associated cognitive process dimension (remember, understand, apply, analyze, evaluate, create). We demonstrate the feasibility of this approach using a learning environment, which we developed for the high school level, and suggest some of its implications. This review sheds light on unique and critical characteristics related to broader integration of bioinformatics in secondary education, which are also relevant to the undergraduate level, and especially on curriculum design, development of suitable learning environments and teaching and learning processes.

Description: Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.

Description: Contribution of directly connected and isolated impervious areas to urban drainage network hydrographs Hydrology and Earth System Sciences, 17, 3473-3483, 2013 Author(s): Y. Seo, N.-J. Choi, and A. R. Schmidt This paper addresses the mass balance error observed in runoff hydrographs in urban watersheds by introducing assumptions regarding the contribution of infiltrated rainfall from pervious areas and isolated impervious area (IIA) to the runoff hydrograph. Rainfall infiltrating into pervious areas has been assumed not to contribute to the runoff hydrograph until Hortonian excess rainfall occurs. However, mass balance analysis in an urban watershed indicates that rainfall infiltrated to pervious areas can contribute directly to the runoff hydrograph, thereby offering an explanation for the long hydrograph tail commonly observed in runoff from urban storm sewers. In this study, a hydrologic analysis based on the width function is introduced, with two types of width functions obtained from both pervious and impervious areas, respectively. The width function can be regarded as the direct interpretation of the network response. These two width functions are derived to obtain distinct response functions for directly connected impervious areas (DCIA), IIA, and pervious areas. The results show significant improvement in the estimation of runoff hydrographs and suggest the need to consider the flow contribution from pervious areas to the runoff hydrograph. It also implies that additional contribution from flow paths through joints and cracks in sewer pipes needs to be taken into account to improve the estimation of runoff hydrographs in urban catchments.

Description: Bias correction can modify climate model-simulated precipitation changes without adverse affect on the ensemble mean Hydrology and Earth System Sciences Discussions, 10, 11585-11611, 2013 Author(s): E. P. Maurer and D. W. Pierce When applied to remove climate model biases in precipitation, quantile mapping can in some settings modify the simulated trends. This has important implications when the precipitation will be used to drive an impacts model that is sensitive to changes in precipitation. We use daily precipitation output from 12 general circulation models (GCMs) over the conterminous United States interpolated to a common 1° grid, and gridded observations aggregated to the same scale, to compare precipitation differences before and after quantile mapping bias correction. The change in seasonal mean (winter, DJF, and summer, JJA) precipitation between different 30-yr historical periods is compared to examine (1) the consensus among GCMs as to whether the bias correction tends to amplify or diminish their simulated precipitation trends, and (2) whether the modification of the change in precipitation tends to improve or degrade the correspondence to observed changes in precipitation for the same periods. In some cases, for a particular GCM, the trend modification can be as large as the original simulated change, though the areas where this occurs varies among GCMs so the ensemble median shows smaller trend modification. In specific locations and seasons the trend modification by quantile mapping improves correspondence with observed trends, and in others it degrades it. In the majority of the domain the ensemble median is for little effect on the correspondence of simulated precipitation trends with observed. This highlights the need to use an ensemble of GCMs rather than relying on a small number of models to estimate impacts.

Description: Linking ICT and society in early warning and adaptation to hydrological extremes in mountains Natural Hazards and Earth System Science, 13, 2253-2270, 2013 Author(s): C. de Jong The assessment of the societal impact of hydrological extremes is particularly important in mountain regions, since mountains can be considered both as the generators and victims of extreme events. ICT can provide a powerful tool for transmitting hydro-meteorological information to predict, prepare and adapt to such events. However, in remote regions, such as mountains, the poles, deserts and islands, preventive and adaptive measures are often restricted by data availability and lack and/or incoherence of data networks. This paper distinguishes between early warning of floods and droughts, emphasising the latter in particular in mountains and explores the possibilities of enhancing the role of society in data collection, the identification, activation and application of stakeholder knowledge and transferral of data from gauged to ungauged catchments.

Description: Snow on the Ross Ice Shelf: comparison of reanalyses and observations from automatic weather stations The Cryosphere, 7, 1399-1410, 2013 Author(s): L. Cohen and S. Dean Snow accumulation measurements from automatic weather stations (AWS) around the Ross Ice Shelf (RIS), Antarctica, are used to provide a new set of ground-based observations which are compared to precipitation from the ECMWF ERA-Interim and NCEP/NCAR Reanalysis-2 datasets. The high temporal resolution of the AWS snow accumulation measurements allow for an event-based comparison of reanalyses precipitation to the in situ observations. Snow accumulation records from nine AWS provide multiple years of accumulation data between 2008 and 2012 over a relatively large, homogeneous region of Antarctica, and also provide the basis for a statistical evaluation of accumulation and precipitation events. The complex effects of wind on snow accumulation (which can both limit and enhance accumulation) complicate the use of the accumulation measurements, but this analysis shows that they can provide a valuable source of ground-based observations for comparisons to modelled precipitation on synoptic timescales. The analysis shows that ERA-Interim reproduces more precipitation events than NCEP-2, and these events correspond to an average 8.2% more precipitation. Significant correlations between reanalyses and AWS event sizes are seen at several stations and show that ERA-Interim consistently produces larger precipitation events than NCEP-2.

Description: Motivation: Pyrosequencing technology provides an important new approach to more extensively characterize diverse sequence populations and detect low frequency variants. However, the promise of this technology has been difficult to realize, as careful correction of sequencing errors is crucial to distinguish rare variants (~1%) in an infected host with high sensitivity and specificity. Results: We developed a new approach, referred to as Indel and Carryforward Correction (ICC), to cluster sequences without substitutions and locally correct only indel and carryforward sequencing errors within clusters to ensure that no rare variants are lost. ICC performs sequence clustering in the order of (i) homopolymer indel patterns only, (ii) indel patterns only and (iii) carryforward errors only, without the requirement of a distance cutoff value. Overall, ICC removed 93–95% of sequencing errors found in control datasets. On pyrosequencing data from a PCR fragment derived from 15 HIV-1 plasmid clones mixed at various frequencies as low as 0.1%, ICC achieved the highest sensitivity and similar specificity compared with other commonly used error correction and variant calling algorithms. Availability and implementation: Source code is freely available for download at http://indra.mullins.microbiol.washington.edu/ICC . It is implemented in Perl and supported on Linux, Mac OS X and MS Windows. Contact: jmullins@uw.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Tiki proteins appear to antagonize Wnt signalling pathway by acting as Wnt proteases, thereby affecting Wnt solubility by its amino-terminal cleavage. Tiki1 protease activity was shown to be metal ion-dependent and was inhibited by chelating agents and thus was tentatively proposed to be a metalloprotease. Nevertheless, Tiki proteins exhibit no detectable sequence similarity to previously described metalloproteases, but instead have been reported as being homologues of TraB proteins (Pfam ID: PF01963), a widely distributed family of unknown function and structure. Here, we show that Tiki proteins are members of a new superfamily of domains contained not just in TraB proteins, but also in erythromycin esterase (Pfam ID: PF05139), DUF399 (domain of unknown function 399; Pfam ID: PF04187) and MARTX toxins that contribute to host invasion and pathogenesis by bacteria. We establish the core fold of this enzymatic domain and its catalytic residues. Contact: luis.sanchezpulido@dpag.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: The research area metabolomics achieved tremendous popularity and development in the last couple of years. Owing to its unique interdisciplinarity, it requires to combine knowledge from various scientific disciplines. Advances in the high-throughput technology and the consequently growing quality and quantity of data put new demands on applied analytical and computational methods. Exploration of finally generated and analyzed datasets furthermore relies on powerful tools for data mining and visualization. Results: To cover and keep up with these requirements, we have created MeltDB 2.0, a next-generation web application addressing storage, sharing, standardization, integration and analysis of metabolomics experiments. New features improve both efficiency and effectivity of the entire processing pipeline of chromatographic raw data from pre-processing to the derivation of new biological knowledge. First, the generation of high-quality metabolic datasets has been vastly simplified. Second, the new statistics tool box allows to investigate these datasets according to a wide spectrum of scientific and explorative questions. Availability: The system is publicly available at https://meltdb.cebitec.uni-bielefeld.de . A login is required but freely available. Contact: nkessler@cebitec.uni-bielefeld.de

Description: Motivation: High - throughput next - generation sequencing technologies enable increasingly fast and affordable sequencing of genomes and transcriptomes, with a broad range of applications. The quality of the sequencing data is crucial for all applications. A significant portion of the data produced contains errors, and ever more efficient error correction programs are needed. Results: We propose RACER (Rapid and Accurate Correction of Errors in Reads), a new software program for correcting errors in sequencing data. RACER has better error-correcting performance than existing programs, is faster and requires less memory. To support our claims, we performed extensive comparison with the existing leading programs on a variety of real datasets. Availability: RACER is freely available for non-commercial use at www.csd.uwo.ca/~ilie/RACER/ . Contact: ilie@csd.uwo.ca Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Interactions between various types of molecules that regulate crucial cellular processes are extensively investigated by high-throughput experiments and require dedicated computational methods for the analysis of the resulting data. In many cases, these data can be represented as a bipartite graph because it describes interactions between elements of two different types such as the influence of different experimental conditions on cellular variables or the direct interaction between receptors and their activators/inhibitors. One of the major challenges in the analysis of such noisy datasets is the statistical evaluation of the relationship between any two elements of the same type. Here, we present SICOP (significant co-interaction patterns), an implementation of a method that provides such an evaluation based on the number of their common interaction partners, their so-called co-interaction. This general network analytic method, proved successful in diverse fields, provides a framework for assessing the significance of this relationship by comparison with the expected co-interaction in a suitable null model of the same bipartite graph. SICOP takes into consideration up to two distinct types of interactions such as up- or downregulation. The tool is written in Java and accepts several common input formats and supports different output formats, facilitating further analysis and visualization. Its key features include a user-friendly interface, easy installation and platform independence. Availability: The software is open source and available at cna.cs.uni-kl.de/SICOP under the terms of the GNU General Public Licence (version 3 or later). Contact: agnes.horvat@iwr.uni-heidelberg.de or zweig@cs.uni-kl.de

Description: : Molecular recognition features (MoRFs) are small, intrinsically disordered regions in proteins that undergo a disorder-to-order transition on binding to their partners. MoRFs are involved in protein–protein interactions and may function as the initial step in molecular recognition. The aim of this work was to collect, organize and store all membrane proteins that contain MoRFs. Membrane proteins constitute ~30% of fully sequenced proteomes and are responsible for a wide variety of cellular functions. MoRFs were classified according to their secondary structure, after interacting with their partners. We identified MoRFs in transmembrane and peripheral membrane proteins. The position of transmembrane protein MoRFs was determined in relation to a protein’s topology. All information was stored in a publicly available mySQL database with a user-friendly web interface. A Jmol applet is integrated for visualization of the structures. mpMoRFsDB provides valuable information related to disorder-based protein–protein interactions in membrane proteins. Availability: http://bioinformatics.biol.uoa.gr/mpMoRFsDB Contact: shamodr@biol.uoa.gr

Description: : The signaling Petri net (SPN) simulator, designed to provide insights into the trends of molecules’ activity levels in response to an external stimulus, contributes to the systems biology necessity of analyzing the dynamics of large-scale cellular networks. Implemented into the freely available software, BioLayout Express 3D , the simulator is publicly available and easy to use, provided the input files are prepared in the GraphML format, typically using the network editing software, yEd, and standards specific to the software. However, analysis of complex networks represented using other systems biology formatting languages (on which popular software, such as CellDesigner and Cytoscape, are based) requires manual manipulation, a step that is prone to error and limits the use of the SPN simulator in BioLayout Express 3D . To overcome this, we present a Cytoscape plug-in that enables users to automatically convert networks for analysis with the SPN simulator from the standard systems biology markup language. The automation of this step opens the SPN simulator to a far larger user group than has previously been possible. Availability and implementation: Distributed under the GNU General Public License Version 3 at http://apps.cytoscape.org/apps/spnconverter . Contact: christine@picb.ac.cn

Description: Motivation: Conformational diversity is a key concept in the understanding of different issues related with protein function such as the study of catalytic processes in enzymes, protein-protein recognition, protein evolution and the origins of new biological functions. Here, we present a database of proteins with different degrees of conformational diversity. Conformational Diversity of Native State (CoDNaS) is a redundant collection of three-dimensional structures for the same protein derived from protein data bank. Structures for the same protein obtained under different crystallographic conditions have been associated with snapshots of protein dynamism and consequently could characterize protein conformers. CoDNaS allows the user to explore global and local structural differences among conformers as a function of different parameters such as presence of ligand, post-translational modifications, changes in oligomeric states and differences in pH and temperature. Additionally, CoDNaS contains information about protein taxonomy and function, disorder level and structural classification offering useful information to explore the underlying mechanism of conformational diversity and its close relationship with protein function. Currently, CoDNaS has 122 122 structures integrating 12 684 entries, with an average of 9.63 conformers per protein. Availability: The database is freely available at http://www.codnas.com.ar/ . Contact: gusparisi@gmail.com

Description: Motivation: Recent experimental advancements allow determining positions of nucleosomes for complete genomes. However, the resulting nucleosome occupancy maps are averages of heterogeneous cell populations. Accordingly, they represent a snapshot of a dynamic ensemble at a single time point with an overlay of many configurations from different cells. To study the organization of nucleosomes along the genome and to understand the mechanisms of nucleosome translocation, it is necessary to retrieve features of specific conformations from the population average. Results: Here, we present a method for identifying non-overlapping nucleosome configurations that combines binary-variable analysis and a Monte Carlo approach with a simulated annealing scheme. In this manner, we obtain specific nucleosome configurations and optimized solutions for the complex positioning patterns from experimental data. We apply the method to compare nucleosome positioning at transcription factor binding sites in different mouse cell types. Our method can model nucleosome translocations at regulatory genomic elements and generate configurations for simulations of the spatial folding of the nucleosome chain. Availability: Source code, precompiled binaries, test data and a web-based test installation are freely available at http://bioinformatics.fh-stralsund.de/nucpos/ Contact: gero.wedemann@fh-stralsund.de Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: The environmental impact of the Puyehue–Cordon Caulle 2011 volcanic eruption on Buenos Aires Natural Hazards and Earth System Science, 13, 2319-2330, 2013 Author(s): G. B. Raga, D. Baumgardner, A. G. Ulke, M. Torres Brizuela, and B. Kucienska On 4 June 2011, the volcanic complex Puyehue–Cordon Caulle located in the Chilean Andes erupted, producing a plume of gases and particles that eventually circled the Southern Hemisphere, disrupting air travel and depositing ash in large quantities. On eight occasions, the plume passed over the city of Buenos Aires, Argentina, leading local authorities to close the two international airports. The eruption occurred during an on-going field campaign when measurements of the properties of atmospheric aerosol particles were being made in Buenos Aires as part of a year-long study of the concentration and optical properties of aerosol at one site in the city. The suite of instruments deployed in Buenos Aires were not tailored to measurements of volcanic ash, but were designed to characterize urban conditions. Nevertheless, these measurements were analysed for periods when vertical profiles of aerosol backscatter, made with a ceilometer, clearly showed the presence of the volcano plume over the research site and resulted in airport closure. Aerosol optical thickness derived from AERONET, MODIS and a ceilometer at our research site, all show enhanced values clearly indicating that the three platforms identified the volcanic plume simultaneously. However, a quantitative comparison of the different estimates proves difficult, suggesting large spatial and temporal variability of the plume. Our results indicate that the number concentration of condensation nuclei (CN), the mass concentration of particle-bound polycyclic aromatic hydrocarbons (PPAH) and the light absorption coefficient exceeded the average background values by more than one standard deviation during the events of volcanic plume. The anomalous concentrations of CN suggest new particle formation, presumably from the conversion of SO 2 , while the anomalous concentrations of PPAH may come from the uptake of PAHs on the plume particles or from chemical reactions on the surface of plume particles. The anomalous absorption coefficients indicate that plume particles may contain certain compounds that can absorb radiation at 550 nm. Another possible explanation consistent with the observations is the scavenging of black carbon from urban sources as the plume descends through the boundary layer to the surface. In addition, the volcanic plume influenced the local meteorology resulting in a decrease of the temperature when compared to the average temperature during days with no plume present.

Description: Contribution of land use changes to future flood damage along the river Meuse in the Walloon region Natural Hazards and Earth System Science, 13, 2301-2318, 2013 Author(s): A. Beckers, B. Dewals, S. Erpicum, S. Dujardin, S. Detrembleur, J. Teller, M. Pirotton, and P. Archambeau Managing flood risk in Europe is a critical issue because climate change is expected to increase flood hazard in many european countries. Beside climate change, land use evolution is also a key factor influencing future flood risk. The core contribution of this paper is a new methodology to model residential land use evolution. Based on two climate scenarios ("dry" and "wet"), the method is applied to study the evolution of flood damage by 2100 along the river Meuse. Nine urbanization scenarios were developed: three of them assume a "current trend" land use evolution, leading to a significant urban sprawl, while six others assume a dense urban development, characterized by a higher density and a higher diversity of urban functions in the urbanized areas. Using damage curves, the damage estimation was performed by combining inundation maps for the present and future 100 yr flood with present and future land use maps and specific prices. According to the dry scenario, the flood discharge is expected not to increase. In this case, land use changes increase flood damages by 1–40%, to €334–462 million in 2100. In the wet scenario, the relative increase in flood damage is 540–630%, corresponding to total damages of €2.1–2.4 billion. In this extreme scenario, the influence of climate on the overall damage is 3–8 times higher than the effect of land use change. However, for seven municipalities along the river Meuse, these two factors have a comparable influence. Consequently, in the "wet" scenario and at the level of the whole Meuse valley in the Walloon region, careful spatial planning would reduce the increase in flood damage by no more than 11–23%; but, at the level of several municipalities, more sustainable spatial planning would reduce future flood damage to a much greater degree.

Description: A general treatment of snow microstructure exemplified by an improved relation for thermal conductivity The Cryosphere, 7, 1473-1480, 2013 Author(s): H. Löwe, F. Riche, and M. Schneebeli Finding relevant microstructural parameters beyond density is a longstanding problem which hinders the formulation of accurate parameterizations of physical properties of snow. Towards a remedy, we address the effective thermal conductivity tensor of snow via anisotropic, second-order bounds. The bound provides an explicit expression for the thermal conductivity and predicts the relevance of a microstructural anisotropy parameter Q , which is given by an integral over the two-point correlation function and unambiguously defined for arbitrary snow structures. For validation we compiled a comprehensive data set of 167 snow samples. The set comprises individual samples of various snow types and entire time series of metamorphism experiments under isothermal and temperature gradient conditions. All samples were digitally reconstructed by micro-computed tomography to perform microstructure-based simulations of heat transport. The incorporation of anisotropy via Q considerably reduces the root mean square error over the usual density-based parameterization. The systematic quantification of anisotropy via the two-point correlation function suggests a generalizable route to incorporate microstructure into snowpack models. We indicate the inter-relation of the conductivity to other properties and outline a potential impact of Q on dielectric constant, permeability and adsorption rate of diffusing species in the pore space.

Description: Arguments need to be judged against other arguments. The decision to accept or reject an argument is generally a global decision that involves examining the same question for other arguments that oppose or can defend the argument in question. This article presents the acceptability semantics for abstract argumentation that through a recursive definition gives a global assignment of the acceptable and non-acceptable subsets of arguments. This semantics stems from the aim to formalize directly the generally accepted intuition that: ‘An argument can be accepted if and only if all its challenging arguments can be rejected.’ The acceptability semantics tightly integrates the notion of defending against a challenging argument by counter-attacking it with the notion of self-defeating (or self-rejecting) arguments that (help to) bring about their own non-acceptability. The proposal is motivated by earlier studies of the semantics of Logic Programming (LP) in terms of argumentation, where the basic well founded and stable model semantics of LP can be uniformly captured using a recursively defined argumentation semantics for Negation as Failure and where these standard semantics of LP can be further extended through argumentation.

Description: This article is concerned with the design and analysis of polynomial time algorithms for determining whether a Planar Quantified Integer Program (PQIP) is feasible. A PQIP can be described briefly as an integer program involving two variables, in which each variable can be either universally or existentially quantified. There are four types of PQIPs, depending on how the variables are quantified (existentially or universally). In this article, we present two new, simple, and efficient algorithms for the case as well as a detailed account of the complexity of the other cases. Moreover, we discuss certification with respect to the provided algorithms.

Description: In the present article, the quantifiers over propositions are first introduced into the language for reasoning about probability, then the complexity issues for validity problems dealing with the corresponding hierarchy of probabilistic sentences are investigated. We prove, among other things, the $${\Pi }_{1}^{1}$$ -completeness for the general validity and also indicate the least level in the hierarchy for which the validity problem is undecidable.

Description: We use mosaics to provide a simple, sound, complete and terminating tableau reasoning procedure for the temporal logic of until and since over general linear time.

Description: The aim of what semantic science is to have scientific ontologies, data and hypotheses represented and published in machine understandable forms that enable predictions on new cases. There is much work on developing scientific ontologies and representing scientific data in terms of these ontologies. The next step is to publish hypotheses that can make (probabilistic) predictions on the published data and can be used for prediction on new cases. The published data can be used to evaluate hypotheses. To make a prediction in a particular case, hypotheses are combined to form models. This article considers feature-based semantic science where the data and new cases are described in terms of features. A prediction for a new case is made by building a model made up of hypotheses that fit together, are consistent with the ontologies used, and are adequate for the case. We give some desiderata for such models, and show how the construction of such models is a form of abduction. We provide a definition for models that satisfies these criteria and prove that it produces a coherent probability distribution over the values of interest.

Description: In this article we present methods of transition from one perspective on logic to others, and apply this in particular to obtain a coalgebraic presentation of logic. The central ingredient in this process is to view consequence relations as morphisms in a category.

Description: We consider the expressive power of the first-order structure 〈, C 〉 where is either of two of different domains of extended regions in Euclidean space, and C(x,y) is the topological relation ‘Region x is in contact with region y .’ We prove two main theorems: Let $$\mathcal{P}$$ [Q] be the domain of bounded, non-empty, rational polyhedra in two- or three-dimensional Euclidean space. A relation over $$\mathcal{P}$$ [Q] is definable in the structure 〈 $$\mathcal{P}$$ [Q], C 〉 if and only if is arithmetic and invariant under rational PL-homeomorphisms of the space to itself. We also extend this result to a number of other domains, including the domain of all polyhedra and the domain of semi-algebraic regions. Let $$\mathcal{R}$$ be the space of bounded, non-empty, closed regular regions in n -dimensional Euclidean space. Any analytical relation over lower dimensional (i.e. empty interior) compact point sets that is invariant under homeomorphism is implicitly definable in the structure 〈 $$\mathcal{R}$$ , C 〉.

Description: Influence of high-order mechanics on simulation of glacier response to climate change: insights from Haig Glacier, Canadian Rocky Mountains The Cryosphere, 7, 1527-1541, 2013 Author(s): S. Adhikari and S. J. Marshall Evolution of glaciers in response to climate change has mostly been simulated using simplified dynamical models. Because these models do not account for the influence of high-order physics, corresponding results may exhibit some biases. For Haig Glacier in the Canadian Rocky Mountains, we test this hypothesis by comparing simulation results obtained from 3-D numerical models that deal with different assumptions concerning physics, ranging from simple shear deformation to comprehensive Stokes flow. In glacier retreat scenarios, we find a minimal role of high-order mechanics in glacier evolution, as geometric effects at our site (the presence of an overdeepened bed) result in limited horizontal movement of ice (flow speed on the order of a few meters per year). Consequently, high-order and reduced models all predict that Haig Glacier ceases to exist by ca. 2080 under ongoing climate warming. The influence of high-order mechanics is evident, however, in glacier advance scenarios, where ice speeds are greater and ice dynamical effects become more important. Although similar studies on other glaciers are essential to generalize such findings, we advise that high-order mechanics are important and therefore should be considered while modeling the evolution of active glaciers. Reduced model predictions may be adequate for other glaciologic and topographic settings, particularly where flow speeds are low and where mass balance changes dominate over ice dynamics in determining glacier geometry.

Description: Meteorological drivers of ablation processes on a cold glacier in the semi-arid Andes of Chile The Cryosphere, 7, 1513-1526, 2013 Author(s): S. MacDonell, C. Kinnard, T. Mölg, L. Nicholson, and J. Abermann Meteorological and surface change measurements collected during a 2.5 yr period are used to calculate surface mass and energy balances at 5324 m a.s.l. on Guanaco Glacier, a cold-based glacier in the semi-arid Andes of Chile. Meteorological conditions are marked by extremely low vapour pressures (annual mean of 1.1 hPa), strong winds (annual mean of 10 m s −1 ), shortwave radiation receipt persistently close to the theoretical site maximum during cloud-free days (mean annual 295 W m −2 ; summer hourly maximum 1354 W m −2 ) and low precipitation rates (mean annual 45 mm w.e.). Snowfall occurs sporadically throughout the year and is related to frontal events in the winter and convective storms during the summer months. Net shortwave radiation provides the greatest source of energy to the glacier surface, and net longwave radiation dominates energy losses. The turbulent latent heat flux is always negative, which means that the surface is always losing mass via sublimation, which is the main form of ablation at the site. Sublimation rates are most strongly correlated with net shortwave radiation, incoming shortwave radiation, albedo and vapour pressure. Low glacier surface temperatures restrict melting for much of the period, however episodic melting occurs during the austral summer, when warm, humid, calm and high pressure conditions restrict sublimation and make more energy available for melting. Low accumulation (131 mm w.e. over the period) and relatively high ablation (1435 mm w.e.) means that mass change over the period was negative (−1304 mm w.e.), which continued the negative trend recorded in the region over the last few decades.

Description: Antarctic ice-mass balance 2003 to 2012: regional reanalysis of GRACE satellite gravimetry measurements with improved estimate of glacial-isostatic adjustment based on GPS uplift rates The Cryosphere, 7, 1499-1512, 2013 Author(s): I. Sasgen, H. Konrad, E. R. Ivins, M. R. Van den Broeke, J. L. Bamber, Z. Martinec, and V. Klemann We present regional-scale mass balances for 25 drainage basins of the Antarctic Ice Sheet (AIS) from satellite observations of the Gravity and Climate Experiment (GRACE) for time period January 2003 to September 2012. Satellite gravimetry estimates of the AIS mass balance are strongly influenced by mass movement in the Earth interior caused by ice advance and retreat during the last glacial cycle. Here, we develop an improved glacial-isostatic adjustment (GIA) estimate for Antarctica using newly available GPS uplift rates, allowing us to more accurately separate GIA-induced trends in the GRACE gravity fields from those caused by current imbalances of the AIS. Our revised GIA estimate is considerably lower than previous predictions, yielding an estimate of apparent mass change of 53 ± 18 Gt yr −1 . Therefore, our AIS mass balance of −114 ± 23 Gt yr −1 is less negative than previous GRACE estimates. The northern Antarctic Peninsula and the Amundsen Sea sector exhibit the largest mass loss (−26 ± 3 Gt yr −1 and −127 ± 7 Gt yr −1 , respectively). In contrast, East Antarctica exhibits a slightly positive mass balance (26 ± 13 Gt yr −1 ), which is, however, mostly the consequence of compensating mass anomalies in Dronning Maud and Enderby Land (positive) and Wilkes and George V Land (negative) due to interannual accumulation variations. In total, 6% of the area constitutes about half the AIS imbalance, contributing 151 ± 7 Gt yr −1 (ca. 0.4 mm yr −1 ) to global mean sea-level change. Most of this imbalance is caused by ice-dynamic speed-up expected to prevail in the near future.

Description: The effect of training image and secondary data integration with multiple-point geostatistics in groundwater modeling Hydrology and Earth System Sciences Discussions, 10, 11829-11860, 2013 Author(s): X. He, T. O. Sonnenborg, F. Jørgensen, and K. H. Jensen Multiple-point geostatistic simulation (MPS) has recently become popular in stochastic hydrogeology, primarily because of its capability to derive multivariate distributions from the training image (TI). However, its application in three dimensional simulations has been constrained by the difficulty of constructing 3-D TI. The object-based TiGenerator may be a useful tool in this regard; yet the sensitivity of model predictions to the training image has not been documented. Another issue in MPS is the integration of multiple geophysical data. The best way to retrieve and incorporate information from high resolution geophysical data is still under discussion. This work shows that TI from TiGenerator delivers acceptable results when used for groundwater modeling, although the TI directly converted from high resolution geophysical data leads to better simulation. The model results also indicate that soft conditioning in MPS is a convenient and efficient way of integrating secondary data such as 3-D airborne electromagnetic data, but over conditioning has to be avoided.

Description: Multi-decadal river flows variations in France Hydrology and Earth System Sciences Discussions, 10, 11861-11900, 2013 Author(s): J. Boé and F. Habets In this article, multi-decadal variations in French hydroclimate are investigated, with a specific focus on river flows. Based on long observed series, it is shown that river flows in France generally exhibit large multi-decadal variations on the historical period, especially in spring. Differences of means between two 21 yr periods of the 20th century as large as 40% are indeed found for many gauging stations. Multi-decadal spring river flows variations are associated with variations in spring precipitation and temperature. These multi-decadal variations in precipitation are themselves found to be driven by large-scale atmospheric circulation, more precisely by a multi-decadal oscillation in a sea level pressure dipole between western Europe and the East Atlantic. It is suggested that the Atlantic Multidecadal Variability, the main mode of decadal variability in the North Atlantic/Europe sector, controls those variations in large-scale circulation and is therefore the main ultimate driver of multi-decadal variations in spring river flows. Multi-decadal variations in river flows in other seasons, and in particular summer, are also noted. As they are not associated with significant surface climate anomalies (i.e. temperature, precipitation) in summer, other mechanisms are investigated based on hydrological simulations. The impact of climate variations in spring on summer soil moisture, and the impact of soil moisture in summer on the runoff to precipitation ratio, could potentially play a role in multi-decadal summer river flows variations. The large amplitude of the multi-decadal variations in French river flows suggests that internal variability may play a very important role in the evolution of river flows during the next decades, potentially temporarily limiting, reversing or seriously aggravating the long-term impacts of anthropogenic climate change.

Description: Estimating soil suction from electrical resistivity Natural Hazards and Earth System Science, 13, 2369-2379, 2013 Author(s): E. Piegari and R. Di Maio Soil suction and resistivity strongly depend on the degree of soil saturation and, therefore, both are used for estimating water content variations. The main difference between them is that soil suction is measured using tensiometers, which give point information, while resistivity is obtained by tomography surveys, which provide distributions of resistivity values in large volumes, although with less accuracy. In this paper, we have related soil suction to electrical resistivity with the aim of obtaining information about soil suction changes in large volumes, and not only for small areas around soil suction probes. We derived analytical relationships between soil matric suction and electrical resistivity by combining the empirical laws of van Genuchten and Archie. The obtained relationships were used to evaluate maps of soil suction values in different ashy layers originating in the explosive activity of the Mt Somma-Vesuvius volcano (southern Italy). Our findings provided a further example of the high potential of geophysical methods in contributing to more effective monitoring of soil stress conditions; this is of primary importance in areas where rainfall-induced landslides occur periodically.

Description: A data set of world-wide glacier length fluctuations The Cryosphere Discussions, 7, 4775-4811, 2013 Author(s): P. W. Leclercq, J. Oerlemans, H. J. Basagic, I. Bushueva, A. J. Cook, and R. Le Bris Glacier fluctuations contribute to variations in sea level and historical glacier length fluctuations are natural indicators of climate change. To study these subjects, long-term information of glacier change is needed. In this paper we present a~data set of global long-term glacier length fluctuations. The data set is a compilation of available information on changes in glacier length world-wide, including both measured and reconstructed glacier length fluctuations. All 471 length series start before 1950 and cover at least four decades. The longest record starts in 1534, but the majority of time series start after 1850. The number of available records decreases again after 1962. The data set has global coverage including records from all continents. However, the Canadian Arctic is not represented in the data set. The glacier length series show relatively small fluctuations until the mid-19th century followed by a global retreat that was strongest in the first half of the 20th century, although large variability in the length change of the different glaciers is observed. During the 20th century, calving glaciers retreated more than land terminating glaciers, but their relative length change was approximately equal. Besides calving, the glacier slope is the most important glacier property determining length change: steep glaciers have retreated less than glaciers with a gentle slope.

Description: An original interpretation of the wet edge of the surface temperature–albedo space to estimate crop evapotranspiration (SEB-1S), and its validation over an irrigated area in northwestern Mexico Hydrology and Earth System Sciences, 17, 3623-3637, 2013 Author(s): O. Merlin The space defined by the pair surface temperature ( T ) and surface albedo (α), and the space defined by the pair T and fractional green vegetation cover ( f vg ) have been extensively used to estimate evaporative fraction (EF) from solar/thermal remote sensing data. In both space-based approaches, evapotranspiration (ET) is estimated as remotely sensed EF times the available energy. For a given data point in the T -α space or in the T - f vg space, EF is derived as the ratio of the distance separating the point from the line identified as the dry edge to the distance separating the dry edge and the line identified as the wet edge. The dry and wet edges are classically defined as the upper and lower limit of the spaces, respectively. When investigating side by side the T -α and the T - f vg spaces, one observes that the range covered by T values on the (classically determined) wet edge is different for both spaces. In addition, when extending the wet and dry lines of the T -α space, both lines cross at α ≈ 0.4 although the wet and dry edges of the T - f vg space never cross for 0 ≤ f vg 〈 1. In this paper, a new ET (EF) model (SEB-1S) is derived by revisiting the classical physical interpretation of the T -α space to make its wet edge consistent with that of the T - f vg space. SEB-1S is tested over a 16 km by 10 km irrigated area in northwestern Mexico during the 2007–2008 agricultural season. The classical T -α space-based model is implemented as benchmark to evaluate the performance of SEB-1S. Input data are composed of ASTER (Advanced Spaceborne Thermal Emission and Reflection radiometer) thermal infrared, Formosat-2 shortwave, and station-based meteorological data. The fluxes simulated by SEB-1S and the classical T -α space-based model are compared on seven ASTER overpass dates with the in situ measurements collected at six locations within the study domain. The ET simulated by SEB-1S is significantly more accurate and robust than that predicted by the classical T -α space-based model. The correlation coefficient and slope of the linear regression between simulated and observed ET is improved from 0.82 to 0.93, and from 0.63 to 0.90, respectively. Moreover, constraining the wet edge using air temperature data improves the slope of the linear regression between simulated and observed ET.

Description: Teleconnection analysis of runoff and soil moisture over the Pearl River basin in South China Hydrology and Earth System Sciences Discussions, 10, 11943-11982, 2013 Author(s): J. Niu, J. Chen, and B. Sivakumar This study explores the teleconnection of two climatic patterns, namely the El Niño-Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD), with hydrological processes over the Pearl River basin in South China. The Variable Infiltration Capacity (VIC) model is used to simulate the daily hydrological processes over the basin for the study period 1952–2000, and then, using the simulation results, the time series of the monthly runoff and soil moisture anomalies for its ten sub-basins are aggregated. Wavelet analysis is performed to explore the variability properties of these time series at 49 timescales ranging from 2 months to 9 yr. Use of wavelet coherence and rank correlation method reveals that the dominant variabilities of the time series of runoff and soil moisture are basically correlated with IOD. The influences of ENSO on the terrestrial hydrological processes are mainly found in the eastern sub-basins. The teleconnections between climatic patterns and hydrological variability also serve as a reference basis for inferences on the occurrence of extreme hydrological events (e.g. floods and droughts).

Description: On an improved sub-regional water resources management representation for integration into earth system models Hydrology and Earth System Sciences, 17, 3605-3622, 2013 Author(s): N. Voisin, H. Li, D. Ward, M. Huang, M. Wigmosta, and L. R. Leung Human influence on the hydrologic cycle includes regulation and storage, consumptive use and overall redistribution of water resources in space and time. Representing these processes is essential for applications of earth system models in hydrologic and climate predictions, as well as impact studies at regional to global scales. Emerging large-scale research reservoir models use generic operating rules that are flexible for coupling with earth system models. Those generic operating rules have been successful in reproducing the overall regulated flow at large basin scales. This study investigates the uncertainties of the reservoir models from different implementations of the generic operating rules using the complex multi-objective Columbia River Regulation System in northwestern United States as an example to understand their effects on not only regulated flow but also reservoir storage and fraction of the demand that is met. Numerical experiments are designed to test new generic operating rules that combine storage and releases targets for multi-purpose reservoirs and to compare the use of reservoir usage priorities and predictors (withdrawals vs. consumptive demands, as well as natural vs. regulated mean flow) for configuring operating rules. Overall the best performing implementation is with combined priorities rules (flood control storage targets and irrigation release targets) set up with mean annual natural flow and mean monthly withdrawals. The options of not accounting for groundwater withdrawals, or on the contrary, of assuming that all remaining demand is met through groundwater extractions, are discussed.

Description: On selection of the optimal data time interval for real-time hydrological forecasting Hydrology and Earth System Sciences, 17, 3639-3659, 2013 Author(s): J. Liu and D. Han With the advancement in modern telemetry and communication technologies, hydrological data can be collected with an increasingly higher sampling rate. An important issue deserving attention from the hydrological community is which suitable time interval of the model input data should be chosen in hydrological forecasting. Such a problem has long been recognised in the control engineering community but is a largely ignored topic in operational applications of hydrological forecasting. In this study, the intrinsic properties of rainfall–runoff data with different time intervals are first investigated from the perspectives of the sampling theorem and the information loss using the discrete wavelet transform tool. It is found that rainfall signals with very high sampling rates may not always improve the accuracy of rainfall–runoff modelling due to the catchment low-pass-filtering effect. To further investigate the impact of a data time interval in real-time forecasting, a real-time forecasting system is constructed by incorporating the probability distributed model (PDM) with a real-time updating scheme, the autoregressive moving-average (ARMA) model. Case studies are then carried out on four UK catchments with different concentration times for real-time flow forecasting using data with different time intervals of 15, 30, 45, 60, 90 and 120 min. A positive relation is found between the forecast lead time and the optimal choice of the data time interval, which is also highly dependent on the catchment concentration time. Finally, based on the conclusions from the case studies, a hypothetical pattern is proposed in three-dimensional coordinates to describe the general impact of the data time interval and to provide implications of the selection of the optimal time interval in real-time hydrological forecasting. Although nowadays most operational hydrological systems still have low data sampling rates (daily or hourly), the future is that higher sampling rates will become more widespread, and there is an urgent need for hydrologists both in academia and in the field to realise the significance of the data time interval issue. It is important that more case studies in different catchments with various hydrological forecasting systems are explored in the future to further verify and improve the proposed hypothetical pattern.

Description: We proposed two multiparty quantum secret sharing schemes based on n -particle Greenberger–Horne–Zeilinger-states (GHZ states), which are transformed from Einstein–Podolsky–Rosen pairs by entanglement swapping. In our schemes, the dealer imposes messages by performing local unitary operations ( I, x, i y, z ) on the n -particle GHZ state she holds, and the agents collaborate to deduce the dealer's messages by performing local unitary operations on their own qubit. The amount of dealer's secret message is positively related with the number of agents. The need of qubits is one-third less than the former schemes and, also, they can be reused for the next new round. The scheme (II) does not have to pre-share the code table, which increases the security without the risk of being stolen.

Description: Automatic fare collection (AFC) systems calculate the fare that the users must pay depending on the time of service (time-based) or the points of entrance and exit of the system (distance-based). The progressive introduction of Information and Communication Technologies allows the use of electronic tickets, which helps us to reduce costs and improve the control of the infrastructures. Nevertheless, these systems must be secure against possible fraud and they must also preserve users’ privacy. Therefore, we have studied the security requirements for the time-based and distance-based systems and we have proposed a protocol for each of the AFC systems. 1 The protocols offer strong privacy for honest users, i.e. the service provider is not able to disclose the identity of its users and, moreover, different journeys of the same user are not linkable between them. However, anonymity for users could be revoked if they misbehave. The protocols have been implemented in Android and its performance has been evaluated in two Android smartphones. The results remark that protocols are suitable to be used on an AFC system with a medium class mobile device although they offer a better experience with a high-class smartphone. The appearance in the market of more powerful mobile devices suggests a better usability of our proposal in a near future.

Description: Accurately locating unknown nodes is a critical issue in the study of wireless sensor networks (WSNs). Many localization approaches have been proposed based on anchor nodes, which are assumed to know their locations by manual placement or additional equipments such as global positioning system. However, none of these approaches can work properly under the adversarial scenario. In this paper, we propose a novel scheme called two-step secure localization (TSSL) stand against many typical malicious attacks, e.g. wormhole attack and location spoofing attack. TSSL detects malicious nodes step by step. First, anchor nodes collaborate with each other to identify suspicious nodes by checking their coordinates, identities and time of sending information. Then, by using a modified mesh generation scheme, malicious nodes are isolated and the WSN is divided into areas with different trust grades. Finally, a novel localization algorithm based on the arrival time difference of localization information is adopted to calculate locations of unknown nodes. Simulation results show that the TSSL detects malicious nodes effectively and the localization algorithm accomplishes localization with high localization accuracy.

Description: Distance-bounding protocols form a family of challenge–response authentication protocols that have been introduced to thwart relay attacks. They enable a verifier to authenticate and to establish an upper bound on the physical distance to an untrusted prover. We provide a detailed security analysis of a family of such protocols. More precisely, we show that the secret key shared between the verifier and the prover can be leaked after a number of nonce repetitions. The leakage probability, while exponentially decreasing with the nonce length, is only weakly dependent on the key length. Our main contribution is a high probability bound on the number of sessions required for the attacker to discover the secret, and an experimental analysis of the attack under noisy conditions. Both of these show that the attack's success probability mainly depends on the length of the used nonces rather than the length of the shared secret key. The theoretical bound could be used by practitioners to appropriately select their security parameters. While longer nonces can guard against this type of attack, we provide a possible countermeasure which successfully combats these attacks even when short nonces are used.

Description: In threshold public-key encryption (TPKE), the decryption key is divided into n shares, each one of which is given to a different decryption user in order to avoid single points of failure. A robust TPKE is that if threshold decryption of a valid ciphertext fails, the combiner can identify the decryption users that supplied invalid partial decryption shares. In this paper, we propose a practical and efficient TPKE scheme which is robust and non-interactive. Security against chosen-ciphertext attacks (CCAs) can be proved in the standard model under the hashed Diffie–Hellman assumption in bilinear groups. The security reduction is tight and simple. We use an instantiation hash function of the Kiltz's key encapsulation mechanism and Lai et al. 's chosen-ciphertext secure technique to construct a TPKE scheme. Moreover, our scheme is more simple and shown to be more efficient than currently existing CCA-secure TPKE schemes.

Description: The advances in the digital world (e.g. the Internet, Communications, etc.) are closing the gap between consumers and providers, in both Business to Consumer and Business to Business environments. Through the Internet, providers can offer their products directly to consumers, which increase their choices and allow them to contract a set of different services/products from different providers. But sometimes the consumer needs an all-or-nothing exchange with these providers: an atomic exchange. The consumer has negotiated/obtained a set of conditions that are only met if she acquires all the services/products. Thus, we need an Atomic Multi-Two-Party contract signing protocol. Even though digital signature of contracts is a topic that has been widely studied, it lacks a solution when applied to Atomic Multi-Two-Party scenarios. Here, we propose the first solution to solve this problem.

Description: Key-evolving cryptography is intended to mitigate the damage in case of a secret key compromise, one of the severest security threats to actual cryptographic schemes. In the public-key setting, the essential idea of key-evolving lies in updating the private key with time, while maintaining the same public key. Key evolution in encryption and signing has been well studied, especially in the identity-based (ID-based) setting where an entity's public key can be derived from that entity's identity information. From a more practical standpoint, however, one would like to use the primitive signcryption in the hierarchical ID-based setting. In this paper, we propose the first key-evolving hierarchical ID-based signcryption scheme that is scalable and joining-time-oblivious and allows secret keys to be updated autonomously. The security proofs of our construction depend on the bilinear Diffie–Hellman assumption and the computational Diffie–Hellman assumption in the random oracle model. To be specific, our proposal not only achieves the fundamental goals of confidentiality and authenticity, but also enjoys desirable properties of non-repudiation, ciphertext anonymity and strong forward security. Compared with the conventional sign-then-encrypt approach, our construction provides better efficiency in terms of the computation cost and the communication overhead.

Description: Cooperative Intelligent Transportation Systems (ITS) will turn up to us with safer and more efficient driving environments as well as convenient and infotainment features for future ITS stations. ETSI and ISO are completing the standardization of the building blocks of a reference communication architecture for cooperative ITS. Future ITS stations complying with this set of standards deployed in vehicles, at the roadside infrastructures and within the Internet are expected to communicate with each other through a combination of ITS dedicated communication protocols and legacy Internet protocols. However, in spite of the wide adoption of IPv6 for cooperative ITS communications, relatively little attention has been paid to the security issues related to IPv6 signaling and IPv6 transport communications. In this paper, we present our position on the emerging and urgent IPv6-related security issues that occur in communications between ITS stations complying with the ITS station reference architecture under standardization within ETSI TC ITS and ISO TC204.

Description: Benchmark products for land evapotranspiration: LandFlux-EVAL multi-data set synthesis Hydrology and Earth System Sciences, 17, 3707-3720, 2013 Author(s): B. Mueller, M. Hirschi, C. Jimenez, P. Ciais, P. A. Dirmeyer, A. J. Dolman, J. B. Fisher, M. Jung, F. Ludwig, F. Maignan, D. G. Miralles, M. F. McCabe, M. Reichstein, J. Sheffield, K. Wang, E. F. Wood, Y. Zhang, and S. I. Seneviratne Land evapotranspiration (ET) estimates are available from several global data sets. Here, monthly global land ET synthesis products, merged from these individual data sets over the time periods 1989–1995 (7 yr) and 1989–2005 (17 yr), are presented. The merged synthesis products over the shorter period are based on a total of 40 distinct data sets while those over the longer period are based on a total of 14 data sets. In the individual data sets, ET is derived from satellite and/or in situ observations (diagnostic data sets) or calculated via land-surface models (LSMs) driven with observations-based forcing or output from atmospheric reanalyses. Statistics for four merged synthesis products are provided, one including all data sets and three including only data sets from one category each (diagnostic, LSMs, and reanalyses). The multi-annual variations of ET in the merged synthesis products display realistic responses. They are also consistent with previous findings of a global increase in ET between 1989 and 1997 (0.13 mm yr −2 in our merged product) followed by a significant decrease in this trend (−0.18 mm yr −2 ), although these trends are relatively small compared to the uncertainty of absolute ET values. The global mean ET from the merged synthesis products (based on all data sets) is 493 mm yr −1 (1.35 mm d −1 ) for both the 1989–1995 and 1989–2005 products, which is relatively low compared to previously published estimates. We estimate global runoff (precipitation minus ET) to 263 mm yr −1 (34 406 km 3 yr −1 ) for a total land area of 130 922 000 km 2 . Precipitation, being an important driving factor and input to most simulated ET data sets, presents uncertainties between single data sets as large as those in the ET estimates. In order to reduce uncertainties in current ET products, improving the accuracy of the input variables, especially precipitation, as well as the parameterizations of ET, are crucial.

Description: Spatial patterns in timing of the diurnal temperature cycle Hydrology and Earth System Sciences, 17, 3695-3706, 2013 Author(s): T. R. H. Holmes, W. T. Crow, and C. Hain This paper investigates the structural difference in timing of the diurnal temperature cycle (DTC) over land resulting from choice of measuring device or model framework. It is shown that the timing can be reliably estimated from temporally sparse observations acquired from a constellation of low Earth-orbiting satellites given record lengths of at least three months. Based on a year of data, the spatial patterns of mean DTC timing are compared between temperature estimates from microwave Ka-band, geostationary thermal infrared (TIR), and numerical weather prediction model output from the Global Modeling and Assimilation Office (GMAO). It is found that the spatial patterns can be explained by vegetation effects, sensing depth differences and more speculatively the orientation of orographic relief features. In absolute terms, the GMAO model puts the peak of the DTC on average at 12:50 local solar time, 23 min before TIR with a peak temperature at 13:13 (both averaged over Africa and Europe). Since TIR is the shallowest observation of the land surface, this small difference represents a structural error that possibly affects the model's ability to assimilate observations that are closely tied to the DTC. The equivalent average timing for Ka-band is 13:44, which is influenced by the effect of increased sensing depth in desert areas. For non-desert areas, the Ka-band observations lag the TIR observations by only 15 min, which is in agreement with their respective theoretical sensing depth. The results of this comparison provide insights into the structural differences between temperature measurements and models, and can be used as a first step to account for these differences in a coherent way.

Description: Integrated hydrological modeling of the North China Plain and implications for sustainable water management Hydrology and Earth System Sciences, 17, 3759-3778, 2013 Author(s): H. Qin, G. Cao, M. Kristensen, J. C. Refsgaard, M. O. Rasmussen, X. He, J. Liu, Y. Shu, and C. Zheng Groundwater overdraft has caused fast water level decline in the North China Plain (NCP) since the 1980s. Although many hydrological models have been developed for the NCP in the past few decades, most of them deal only with the groundwater component or only at local scales. In the present study, a coupled surface water–groundwater model using the MIKE SHE code has been developed for the entire alluvial plain of the NCP. All the major processes in the land phase of the hydrological cycle are considered in the integrated modeling approach. The most important parameters of the model are first identified by a sensitivity analysis process and then calibrated for the period 2000–2005. The calibrated model is validated for the period 2006–2008 against daily observations of groundwater heads. The simulation results compare well with the observations where acceptable values of root mean square error (RMSE) (most values lie below 4 m) and correlation coefficient ( R ) (0.36–0.97) are obtained. The simulated evapotranspiration (ET) is then compared with the remote sensing (RS)-based ET data to further validate the model simulation. The comparison result with a R 2 value of 0.93 between the monthly averaged values of simulated actual evapotranspiration (AET) and RS AET for the entire NCP shows a good performance of the model. The water balance results indicate that more than 70% of water leaving the flow system is attributed to the ET component, of which about 0.25% is taken from the saturated zone (SZ); about 29% comes from pumping, including irrigation pumping and non-irrigation pumping (net pumping). Sustainable water management analysis of the NCP is conducted using the simulation results obtained from the integrated model. An effective approach to improve water use efficiency in the NCP is by reducing the actual ET, e.g. by introducing water-saving technologies and changes in cropping.

Description: Simulation of a persistent medium-term precipitation event over the western Iberian Peninsula Hydrology and Earth System Sciences, 17, 3741-3758, 2013 Author(s): S. C. Pereira, A. C. Carvalho, J. Ferreira, J. P. Nunes, J. J. Keizer, and A. Rocha This study evaluated the performance of the WRF-ARW (Weather Research and Forecasting with Advanced Research) weather prediction model in simulating the spatial and temporal patterns of an extreme rainfall period over a complex orographic region in north-central Portugal. The analysis was performed during the rainy season and, more specifically, the month of December 2009. In this period, the region of interest was under the influence of a sequential passage of low-pressure systems associated with frontal surfaces. These synoptic weather patterns were responsible for long periods of rainfall, resulting in a high monthly precipitation. The WRF model results during the study period were furthermore evaluated with the specific objective to complement gaps in the precipitation recordings of a reference meteorological station (located in Pousadas), the data of which are fundamental for hydrological studies in nearby experimental catchments. Three distinct WRF model runs were forced with initial fields and boundary conditions obtained from a global domain model: (1) a reference experiment with no nudging (RunRef); (2) observational nudging for a specific location, i.e. the above-mentioned Pousadas reference station (RunObsN); and (3) nudging to the analysed field (RunGridN). Model performance was evaluated, using several statistical parameters, against a dataset of 27 rainfall stations that were grouped by elevation. The three model runs had similar performances, even though RunGridN resulted in a slight improvement. Regarding the other two experiments, this improvement justifies its use for complementing the surface measurements at the Pousadas reference station. Overall model accuracy, expressed in root mean square error (RMSE), of the three runs was comparable for the stations of the different elevations classes. Even so, it was slightly better for stations in the lowlands than the highlands. Furthermore, model predictions tended to be less accurate for stations located in rough terrain and deep valleys.

Description: Sulfur dioxide emissions from Papandayan and Bromo, two Indonesian volcanoes Natural Hazards and Earth System Science, 13, 2399-2407, 2013 Author(s): P. Bani, Surono, M. Hendrasto, H. Gunawan, and S. Primulyana Indonesia hosts 79 active volcanoes, representing 14% of all active volcanoes worldwide. However, little is known about their SO 2 contribution into the atmosphere, due to isolation and access difficulties. Existing SO 2 emission budgets for the Indonesian archipelago are based on extrapolations and inferences as there is a considerable lack of field assessments of degassing. Here, we present the first SO 2 flux measurements using differential optical absorption spectroscopy (DOAS) for Papandayan and Bromo, two of the most active volcanoes in Indonesia. Results indicate mean SO 2 emission rates of 1.4 t d −1 from the fumarolic activity of Papandayan and more than 22–32 t d −1 of SO 2 released by Bromo during a declining eruptive phase. These DOAS results are very encouraging and pave the way for a better evaluation of Indonesian volcanic emissions.

Description: Motivation: Residue–residue contacts across the transmembrane helices dictate the three-dimensional topology of alpha-helical membrane proteins. However, contact determination through experiments is difficult because most transmembrane proteins are hard to crystallize. Results: We present a novel method (MemBrain) to derive transmembrane inter-helix contacts from amino acid sequences by combining correlated mutations and multiple machine learning classifiers. Tested on 60 non-redundant polytopic proteins using a strict leave-one-out cross-validation protocol, MemBrain achieves an average accuracy of 62%, which is 12.5% higher than the current best method from the literature. When applied to 13 recently solved G protein-coupled receptors, the MemBrain contact predictions helped increase the TM-score of the I-TASSER models by 37% in the transmembrane region. The number of foldable cases (TM-score 〉0.5) increased by 100%, where all G protein-coupled receptor templates and homologous templates with sequence identity 〉30% were excluded. These results demonstrate significant progress in contact prediction and a potential for contact-driven structure modeling of transmembrane proteins. Availability: www.csbio.sjtu.edu.cn/bioinf/MemBrain/ Contact: hbshen@sjtu.edu.cn or zhng@umich.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Identification of protein–ligand binding sites is critical to protein function annotation and drug discovery. However, there is no method that could generate optimal binding site prediction for different protein types. Combination of complementary predictions is probably the most reliable solution to the problem. Results: We develop two new methods, one based on binding-specific substructure comparison (TM-SITE) and another on sequence profile alignment (S-SITE), for complementary binding site predictions. The methods are tested on a set of 500 non-redundant proteins harboring 814 natural, drug-like and metal ion molecules. Starting from low-resolution protein structure predictions, the methods successfully recognize 〉51% of binding residues with average Matthews correlation coefficient (MCC) significantly higher (with P -value 〈10 –9 in student t -test) than other state-of-the-art methods, including COFACTOR, FINDSITE and ConCavity. When combining TM-SITE and S-SITE with other structure-based programs, a consensus approach (COACH) can increase MCC by 15% over the best individual predictions. COACH was examined in the recent community-wide COMEO experiment and consistently ranked as the best method in last 22 individual datasets with the Area Under the Curve score 22.5% higher than the second best method. These data demonstrate a new robust approach to protein–ligand binding site recognition, which is ready for genome-wide structure-based function annotations. Availability: http://zhanglab.ccmb.med.umich.edu/COACH/ Contact: zhng@umich.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: The nucleosome is the basic repeating unit of chromatin. It contains two copies each of the four core histones H2A, H2B, H3 and H4 and about 147 bp of DNA. The residues of the histone proteins are subject to numerous post-translational modifications, such as methylation or acetylation. Chromatin immunoprecipitiation followed by sequencing (ChIP-seq) is a technique that provides genome-wide occupancy data of these modified histone proteins, and it requires appropriate computational methods. Results: We present NucHunter, an algorithm that uses the data from ChIP-seq experiments directed against many histone modifications to infer positioned nucleosomes. NucHunter annotates each of these nucleosomes with the intensities of the histone modifications. We demonstrate that these annotations can be used to infer nucleosomal states with distinct correlations to underlying genomic features and chromatin-related processes, such as transcriptional start sites, enhancers, elongation by RNA polymerase II and chromatin-mediated repression. Thus, NucHunter is a versatile tool that can be used to predict positioned nucleosomes from a panel of histone modification ChIP-seq experiments and infer distinct histone modification patterns associated to different chromatin states. Availability: The software is available at http://epigen.molgen.mpg.de/nuchunter/ . Contact: chung@molgen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: In biomedical research a growing number of platforms and technologies are used to measure diverse but related information, and the task of clustering a set of objects based on multiple sources of data arises in several applications. Most current approaches to multisource clustering either independently determine a separate clustering for each data source or determine a single ‘joint’ clustering for all data sources. There is a need for more flexible approaches that simultaneously model the dependence and the heterogeneity of the data sources. Results: We propose an integrative statistical model that permits a separate clustering of the objects for each data source. These separate clusterings adhere loosely to an overall consensus clustering, and hence they are not independent. We describe a computationally scalable Bayesian framework for simultaneous estimation of both the consensus clustering and the source-specific clusterings. We demonstrate that this flexible approach is more robust than joint clustering of all data sources, and is more powerful than clustering each data source independently. We present an application to subtype identification of breast cancer tumor samples using publicly available data from The Cancer Genome Atlas. Availability: R code with instructions and examples is available at http://people.duke.edu/%7Eel113/software.html . Contact: Eric.Lock@duke.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: More and more evidences have indicated that long–non-coding RNAs (lncRNAs) play critical roles in many important biological processes. Therefore, mutations and dysregulations of these lncRNAs would contribute to the development of various complex diseases. Developing powerful computational models for potential disease-related lncRNAs identification would benefit biomarker identification and drug discovery for human disease diagnosis, treatment, prognosis and prevention. Results : In this article, we proposed the assumption that similar diseases tend to be associated with functionally similar lncRNAs. Then, we further developed the method of Laplacian Regularized Least Squares for LncRNA–Disease Association (LRLSLDA) in the semisupervised learning framework. Although known disease–lncRNA associations in the database are rare, LRLSLDA still obtained an AUC of 0.7760 in the leave-one-out cross validation, significantly improving the performance of previous methods. We also illustrated the performance of LRLSLDA is not sensitive (even robust) to the parameters selection and it can obtain a reliable performance in all the test classes. Plenty of potential disease–lncRNA associations were publicly released and some of them have been confirmed by recent results in biological experiments. It is anticipated that LRLSLDA could be an effective and important biological tool for biomedical research. Availability: The code of LRLSLDA is freely available at http://asdcd.amss.ac.cn/Software/Details/2 . Contact: xingchen@amss.ac.cn or yangy@amt.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Genomic repositories are rapidly growing, as witnessed by the 1000 Genomes or the UK10K projects. Hence, compression of multiple genomes of the same species has become an active research area in the past years. The well-known large redundancy in human sequences is not easy to exploit because of huge memory requirements from traditional compression algorithms. Results: We show how to obtain several times higher compression ratio than of the best reported results, on two large genome collections (1092 human and 775 plant genomes). Our inputs are variant call format files restricted to their essential fields. More precisely, our novel Ziv-Lempel-style compression algorithm squeezes a single human genome to ~400 KB. The key to high compression is to look for similarities across the whole collection, not just against one reference sequence, what is typical for existing solutions. Availability: http://sun.aei.polsl.pl/tgc (also as Supplementary Material) under a free license. Supplementary data: Supplementary data are available at Bioinformatics online. Contact: sebastian.deorowicz@polsl.pl

Description: Motivation:  Biological systems are understood through iterations of modeling and experimentation. Not all experiments, however, are equally valuable for predictive modeling. This study introduces an efficient method for experimental design aimed at selecting dynamical models from data. Motivated by biological applications, the method enables the design of crucial experiments: it determines a highly informative selection of measurement readouts and time points. Results:  We demonstrate formal guarantees of design efficiency on the basis of previous results. By reducing our task to the setting of graphical models, we prove that the method finds a near-optimal design selection with a polynomial number of evaluations. Moreover, the method exhibits the best polynomial-complexity constant approximation factor, unless P = NP. We measure the performance of the method in comparison with established alternatives, such as ensemble non-centrality, on example models of different complexity. Efficient design accelerates the loop between modeling and experimentation: it enables the inference of complex mechanisms, such as those controlling central metabolic operation. Availability:  Toolbox ‘NearOED’ available with source code under GPL on the Machine Learning Open Source Software Web site (mloss.org). Contact:   busettoa@inf.ethz.ch Supplementary information:   Supplementary data are available at Bioinformatics online.

Description: : Small RNA deep sequencing is widely used to characterize non-coding RNAs (ncRNAs) differentially expressed between two conditions, e.g. healthy and diseased individuals and to reveal insights into molecular mechanisms underlying condition-specific phenotypic traits. The ncRNAome is composed of a multitude of RNAs, such as transfer RNA, small nucleolar RNA and microRNA (miRNA), to name few. Here we present omiRas, a Web server for the annotation, comparison and visualization of interaction networks of ncRNAs derived from next-generation sequencing experiments of two different conditions. The Web tool allows the user to submit raw sequencing data and results are presented as: (i) static annotation results including length distribution, mapping statistics, alignments and quantification tables for each library as well as lists of differentially expressed ncRNAs between conditions and (ii) an interactive network visualization of user-selected miRNAs and their target genes based on the combination of several miRNA–mRNA interaction databases. Availability and Implementation: The omiRas Web server is implemented in Python, PostgreSQL, R and can be accessed at: http://tools.genxpro.net/omiras/ . Contact: rotter@genxpro.de Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: : We present PARSEC (PAtteRn Search and Contextualization), a new open source platform for guided discovery, allowing localization and biological characterization of short genomic sites in entire eukaryotic genomes. PARSEC can search for a sequence or a degenerated pattern. The retrieved set of genomic sites can be characterized in terms of (i) conservation in model organisms, (ii) genomic context (proximity to genes) and (iii) function of neighboring genes. These modules allow the user to explore, visualize, filter and extract biological knowledge from a set of short genomic regions such as transcription factor binding sites. Availability: Web site implemented in Java, JavaScript and C++, with all major browsers supported. Freely available at lbgi.fr/parsec. Source code is freely available at sourceforge.net/projects/genomicparsec. Contact: odile.lecompte@unistra.fr Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. Availability and Implementation: A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html . Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html ; the Boost C++ libraries and BLAST are required. Contact: leeann.mccue@pnnl.gov

Description: : Automated image processing has allowed cell migration research to evolve to a high-throughput research field. As a consequence, there is now an unmet need for data management in this domain. The absence of a generic management system for the quantitative data generated in cell migration assays results in each dataset being treated in isolation, making data comparison across experiments difficult. Moreover, by integrating quality control and analysis capabilities into such a data management system, the common practice of having to manually transfer data across different downstream analysis tools will be markedly sped up and made more robust. In addition, access to a data management solution creates gateways for data standardization, meta-analysis and structured public data dissemination. We here present CellMissy, a cross-platform data management system for cell migration data with a focus on wound healing data. CellMissy simplifies and automates data management, storage and analysis from the initial experimental set-up to data exploration. Availability and implementation: CellMissy is a cross-platform open-source software developed in Java. Source code and cross-platform binaries are freely available under the Apache2 open source license at http://cellmissy.googlecode.com . Contact: lennart.martens@ugent.be Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: Motivation: With the expansion of high-throughput technologies, understanding different kinds of genome-level data is a common task. MicroRNA (miRNA) is increasingly profiled using high-throughput technologies (microarrays or next-generation sequencing). The downstream analysis of miRNA targets can be difficult. Although there are many databases and algorithms to predict miRNA targets, there are few tools to integrate miRNA–gene interaction data into high-throughput genomic analyses. Results: We present targetHub, a CouchDB database of miRNA–gene interactions. TargetHub provides a programmer-friendly interface to access miRNA targets. The Web site provides RESTful access to miRNA–gene interactions with an assortment of gene and miRNA identifiers. It can be a useful tool to integrate miRNA target interaction data directly into high-throughput bioinformatics analyses. Availability: TargetHub is available on the web at http://app1.bioinformatics.mdanderson.org/tarhub/_design/basic/index.html . Contact: coombes.3@osu.edu

Description: Investigating the spatio-temporal variability in groundwater and surface water interactions: a multi-technique approach Hydrology and Earth System Sciences, 17, 3437-3453, 2013 Author(s): N. P. Unland, I. Cartwright, M. S. Andersen, G. C. Rau, J. Reed, B. S. Gilfedder, A. P. Atkinson, and H. Hofmann The interaction between groundwater and surface water along the Tambo and Nicholson rivers, southeast Australia, was investigated using 222 Rn, Cl, differential flow gauging, head gradients, electrical conductivity (EC) and temperature profiles. Head gradients, temperature profiles, Cl concentrations and 222 Rn activities all indicate higher groundwater fluxes to the Tambo River in areas of increased topographic variation where the potential to form large groundwater–surface water gradients is greater. Groundwater discharge to the Tambo River calculated by Cl mass balance was significantly lower (1.48 × 10 4 to 1.41 × 10 3 m 3 day −1 ) than discharge estimated by 222 Rn mass balance (5.35 × 10 5 to 9.56 × 10 3 m 3 day −1 ) and differential flow gauging (5.41 × 10 5 to 6.30 × 10 3 m 3 day −1 ) due to bank return waters. While groundwater sampling from the bank of the Tambo River was intended to account for changes in groundwater chemistry associated with bank infiltration, variations in bank infiltration between sample sites remain unaccounted for, limiting the use of Cl as an effective tracer. Groundwater discharge to both the Tambo and Nicholson rivers was the highest under high-flow conditions in the days to weeks following significant rainfall, indicating that the rivers are well connected to a groundwater system that is responsive to rainfall. Groundwater constituted the lowest proportion of river discharge during times of increased rainfall that followed dry periods, while groundwater constituted the highest proportion of river discharge under baseflow conditions (21.4% of the Tambo in April 2010 and 18.9% of the Nicholson in September 2010).

Description: Hydrological functions of sinkholes and characteristics of point recharge in groundwater basins Hydrology and Earth System Sciences Discussions, 10, 11423-11449, 2013 Author(s): N. Somaratne, K. Smettem, J. Lawson, K. Nguyen, and J. Frizenschaf Karstic limestone aquifers are hydrologically and hydrochemically extremely heterogeneous and point source recharge via sinkholes and fissures is a common feature. We studied three groundwater systems in karstic settings dominated by point source recharge in order to assess the relative contributions to total recharge from point sources using chloride and δ 18 O relations. Preferential groundwater flows were observed through an inter-connected network of highly conductive zones with groundwater mixing along flow paths. Measurements of salinity and chloride indicated that fresh water pockets exist at point recharge locations. A measurable fresh water plume develops only when a large quantity of surface water enters the aquifer as a point recharge source. The difference in chloride concentrations in diffuse and point recharge zones decreases as aquifer saturated thickness increases and the plumes become diluted through mixing. The chloride concentration in point recharge fluxes crossing the watertable plane can remain at or near surface runoff chloride concentrations, rather than in equilibrium with groundwater chloride. In such circumstances the conventional chloride mass balance method that assumes equilibrium of recharge water chloride with groundwater requires modification to include both point and diffuse recharge mechanisms.

Description: Implementation and evaluation of prognostic representations of the optical diameter of snow in the detailed snowpack model SURFEX/ISBA-Crocus The Cryosphere Discussions, 7, 4443-4500, 2013 Author(s): C. M. Carmagnola, S. Morin, M. Lafaysse, F. Domine, B. Lesaffre, Y. Lejeune, G. Picard, and L. Arnaud In the SURFEX/ISBA-Crocus multi-layer snowpack model, the snow microstructure was up to now characterized by the grain size and by semi-empirical shape variables which cannot be measured easily in the field or linked to other relevant snow properties. In this work we introduce a new formulation of snow metamorphism directly based on equations describing the rate of change of the optical diameter ( d opt ). This variable is considered here to be equal to the equivalent sphere optical diameter, which is inversely proportional to the specific surface area (SSA). d opt thus represents quantitatively some of the geometric characteristics of a porous medium. Different prognostic rate equations of d opt , including a re-formulation of the original Crocus scheme and the parametrizations from Taillandier et al. (2007) and Flanner and Zender (2006), were evaluated by comparing their predictions to field measurements carried out at Summit Camp (Greenland) in May and June 2011 and at Col de Porte (French Alps) during the 2009/10 and 2011/12 winter seasons. We focused especially on results in terms of SSA. In addition, we tested the impact of the different formulations on the simulated density profile, the total snow height, the snow water equivalent (SWE) and the surface albedo. Results indicate that all formulations perform well, with median values of the RMSD between measured and simulated SSA lower than 10 m 2 kg −1 . Incorporating the optical diameter as a fully-fledged prognostic variable is an important step forward in the quantitative description of the snow microstructure within snowpack models, because it opens the way to data assimilation of various electromagnetic observations.

Description: Interviewing insights regarding the fatalities inflicted by the 2011 Great East Japan Earthquake Natural Hazards and Earth System Science, 13, 2173-2187, 2013 Author(s): M. Ando, M. Ishida, Y. Hayashi, C. Mizuki, Y. Nishikawa, and Y. Tu One hundred fifty survivors of the 11 March 2011 Great East Japan Earthquake (Tohoku-oki earthquake) ( M w = 9.0) were interviewed to study the causes of deaths from the associated tsunami in coastal areas of Tohoku. The first official tsunami warning underestimated the height of the tsunami and 40% of the interviewees did not obtain this warning due to immediate blackouts and a lack of communication after the earthquake. Many chose to remain in dangerous locations based on the underestimated warning and their experiences with previous smaller tsunamis and/or due to misunderstanding the mitigating effects of nearby breakwaters in blocking incoming tsunamis. Some delayed their evacuation to perform family safety checks, and in many situations, the people affected misunderstood the risks involved in tsunamis. In this area, three large tsunamis have struck in the 115 yr preceding the 2011 tsunami. These tsunamis remained in the collective memory of communities, and numerous measures against future tsunami damage, such as breakwaters and tsunami evacuation drills, had been implemented. Despite these preparedness efforts, approximately 18 500 deaths and cases of missing persons occurred. The death rate with the age of 65 and above was particularly high, four times higher than that with other age groups. These interviews indicate that deaths resulted from a variety of reasons, but if residents had taken immediate action after the major ground motion stopped, most residents might have been saved. Education about the science behind earthquakes and tsunamis could help save more lives in the future.

Description: Resolving structural errors in a spatially distributed hydrologic model using ensemble Kalman filter state updates Hydrology and Earth System Sciences, 17, 3455-3472, 2013 Author(s): J. H. Spaaks and W. Bouten In hydrological modeling, model structures are developed in an iterative cycle as more and different types of measurements become available and our understanding of the hillslope or watershed improves. However, with increasing complexity of the model, it becomes more and more difficult to detect which parts of the model are deficient, or which processes should also be incorporated into the model during the next development step. In this study, we first compare two methods (the Shuffled Complex Evolution Metropolis algorithm (SCEM-UA) and the Simultaneous parameter Optimization and Data Assimilation algorithm (SODA)) to calibrate a purposely deficient 3-D hillslope-scale model to error-free, artificially generated measurements. We use a multi-objective approach based on distributed pressure head at the soil–bedrock interface and hillslope-scale discharge and water balance. For these idealized circumstances, SODA's usefulness as a diagnostic methodology is demonstrated by its ability to identify the timing and location of processes that are missing in the model. We show that SODA's state updates provide information that could readily be incorporated into an improved model structure, and that this type of information cannot be gained from parameter estimation methods such as SCEM-UA. We then expand on the SODA result by performing yet another calibration, in which we investigate whether SODA's state updating patterns are still capable of providing insight into model structure deficiencies when there are fewer measurements, which are moreover subject to measurement noise. We conclude that SODA can help guide the discussion between experimentalists and modelers by providing accurate and detailed information on how to improve spatially distributed hydrologic models.

Description: Distribution and recent variations of supraglacial lakes on dendritic-type glaciers in the Khan Tengri-Tomur Mountains, Central Asia The Cryosphere Discussions, 7, 4545-4584, 2013 Author(s): Q. Liu, C. Mayer, and S. Liu Supraglacial lakes are widely distributed on glaciers in the Tomur-Khan Tengri Tianshan Mountains, Central Asia. The existence and development of supraglacial lakes play an important role in the ice melting processes and also in the storage and release of glacial melt water. Here we mapped the supraglacial lakes of eight typical debris-covered dendritic-type glaciers around the Tomur-Khan Tengri peaks based on 9 Landsat TM/ETM+ images acquired in the summers of 1990 until 2011. With a lower area limit of 3600 m 2 for a conservative identification of glacial lakes, we mapped 775 supraglacial lakes and 38 marginal glacial lakes in total. Our results indicate that supraglacial lakes (area 〉 3600 m 2 ) in the study region never develop beyond an elevation of about 3850 m a.s.l., 800 m lower than the maximum upper boundary of debris cover (4650 m a.s.l.). The area-elevation distribution shows that lakes are predominantly occured close to the altitude of 3250 m a.s.l., where the clean ice simultaneously disappears. The majority of the supraglacial lakes are found on the Tomur Glacier and the South Inylchek Glacier, two strongly debris-covered dendritic-type glaciers in the region. As for the multi-year variation of lake area, the summer total and mean areas of supraglacial lakes show some variability from 1990 and 2005 but increased noticeably between 2005 and 2011. The mean area of the mapped lakes reached a maximum in 2010. We found that the area of supraglacial lakes is positively correlated to the total precipitation in summer (July to September) but negatively correlated to the mean spring air temperature (April to June). Pre-summer air temperature fluctuations likely have a stronger impact on the different evolution processes of glacial drainage, evolving from unconnected to connected systems, which may lead to the drainage of larger supraglacial lakes and results in shrinkage of the total and mean lake area during the summer.

Description: Fracture-induced softening for large-scale ice dynamics The Cryosphere Discussions, 7, 4501-4544, 2013 Author(s): T. Albrecht and A. Levermann Floating ice shelves can exert a retentive and hence stabilizing force onto the inland ice sheet of Antarctica. However, this effect has been observed to diminish by fracture-coupled dynamic processes within the protective ice shelves leading to accelerated ice flow and hence to a sea-level contribution. In order to better understand the role of fractures in ice dynamics we apply a large-scale continuum representation of fractures and related fracture growth into the prognostic Parallel Ice Sheet Model (PISM). To this end we introduce a higher-order accuracy advection scheme for the transport of the two-dimensional fracture density across the regular computational grid. Dynamic coupling of fractures and ice flow is attained by a reduction of effective ice viscosity proportional to the inferred fracture density. This formulation implies the possibility of a non-linear threshold behavior due to self-amplified fracturing in shear regions triggered by small variations in damage threshold. As a result of prognostic flow simulations, flow patterns with realistically large across-flow velocity gradients in fracture-weakened regions as seen in observations are reproduced. This model framework is expandable to grounded ice streams and accounts for climate-induced effects on fracturing and hence on the ice-flow dynamics. It further allows for an enhanced fracture-based calving parameterization.

Description: With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable in the learning continuum. Bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, has blended more traditional learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years and look toward what the future holds for bioinformatics training programs.

Description: Teaching students with very diverse backgrounds can be extremely challenging. This article uses the Bioinformatics and Systems Biology MSc in Amsterdam as a case study to describe how the knowledge gap for students with heterogeneous backgrounds can be bridged. We show that a mix in backgrounds can be turned into an advantage by creating a stimulating learning environment for the students. In the MSc Programme, conversion classes help to bridge differences between students, by mending initial knowledge and skill gaps. Mixing students from different backgrounds in a group to solve a complex task creates an opportunity for the students to reflect on their own abilities. We explain how a truly interdisciplinary approach to teaching helps students of all backgrounds to achieve the MSc end terms. Moreover, transferable skills obtained by the students in such a mixed study environment are invaluable for their later careers.

Description: The number of bioinformatics tools and resources that support molecular and cell biology approaches is continuously expanding. Moreover, systems and network biology analyses are accompanied more and more by integrated bioinformatics methods. Traditional information-centered university teaching methods often fail, as (1) it is impossible to cover all existing approaches in the frame of a single course, and (2) a large segment of the current bioinformation can become obsolete in a few years. Signaling network offers an excellent example for teaching bioinformatics resources and tools, as it is both focused and complex at the same time. Here, we present an outline of a university bioinformatics course with four sample practices to demonstrate how signaling network studies can integrate biochemistry, genetics, cell biology and network sciences. We show that several bioinformatics resources and tools, as well as important concepts and current trends, can also be integrated to signaling network studies. The research-type hands-on experiences we show enable the students to improve key competences such as teamworking, creative and critical thinking and problem solving. Our classroom course curriculum can be re-formulated as an e-learning material or applied as a part of a specific training course. The multi-disciplinary approach and the mosaic setup of the course have the additional benefit to support the advanced teaching of talented students.

Description: Today, Bioinformatics has become a scientific discipline with great relevance for the Molecular Biosciences and for the Omics sciences in general. Although developed countries have progressed with large strides in Bioinformatics education and research, in other regions, such as Central America, the advances have occurred in a gradual way and with little support from the Academia, either at the undergraduate or graduate level. To address this problem, the University of Costa Rica’s Medical School, a regional leader in Bioinformatics in Central America, has been conducting a series of Bioinformatics workshops, seminars and courses, leading to the creation of the region’s first Bioinformatics Master’s Degree. The recent creation of the Central American Bioinformatics Network (BioCANET), associated to the deployment of a supporting computational infrastructure (HPC Cluster) devoted to provide computing support for Molecular Biology in the region, is providing a foundational stone for the development of Bioinformatics in the area. Central American bioinformaticians have participated in the creation of as well as co-founded the Iberoamerican Bioinformatics Society (SOIBIO). In this article, we review the most recent activities in education and research in Bioinformatics from several regional institutions. These activities have resulted in further advances for Molecular Medicine, Agriculture and Biodiversity research in Costa Rica and the rest of the Central American countries. Finally, we provide summary information on the first Central America Bioinformatics International Congress, as well as the creation of the first Bioinformatics company (Indromics Bioinformatics), spin-off the Academy in Central America and the Caribbean.

Description: Pattern recognition is concerned with the development of systems that learn to solve a given problem using a set of example instances, each represented by a number of features. These problems include clustering, the grouping of similar instances; classification, the task of assigning a discrete label to a given instance; and dimensionality reduction, combining or selecting features to arrive at a more useful representation. The use of statistical pattern recognition algorithms in bioinformatics is pervasive. Classification and clustering are often applied to high-throughput measurement data arising from microarray, mass spectrometry and next-generation sequencing experiments for selecting markers, predicting phenotype and grouping objects or genes. Less explicitly, classification is at the core of a wide range of tools such as predictors of genes, protein function, functional or genetic interactions, etc., and used extensively in systems biology. A course on pattern recognition (or machine learning) should therefore be at the core of any bioinformatics education program. In this review, we discuss the main elements of a pattern recognition course, based on material developed for courses taught at the BSc, MSc and PhD levels to an audience of bioinformaticians, computer scientists and life scientists. We pay attention to common problems and pitfalls encountered in applications and in interpretation of the results obtained.

Description: Climate information based streamflow and rainfall forecasts for Huai River Basin using Hierarchical Bayesian Modeling Hydrology and Earth System Sciences Discussions, 10, 11559-11584, 2013 Author(s): X. Chen, Z. Hao, N. Devineni, and U. Lall A Hierarchal Bayesian model for forecasting regional summer rainfall and streamflow season-ahead using exogenous climate variables for East Central China is presented. The model provides estimates of the posterior forecasted probability distribution for 12 rainfall and 2 streamflow stations considering parameter uncertainty, and cross-site correlation. The model has a multilevel structure with regression coefficients modeled from a common multivariate normal distribution results in partial-pooling of information across multiple stations and better representation of parameter and posterior distribution uncertainty. Covariance structure of the residuals across stations is explicitly modeled. Model performance is tested under leave-10-out cross-validation. Frequentist and Bayesian performance metrics used include Receiver Operating Characteristic, Reduction of Error, Coefficient of Efficiency, Rank Probability Skill Scores, and coverage by posterior credible intervals. The ability of the model to reliably forecast regional summer rainfall and streamflow season-ahead offers potential for developing adaptive water risk management strategies.

Description: Sea ice detection with space-based LIDAR The Cryosphere Discussions, 7, 4681-4701, 2013 Author(s): S. Rodier, Y. Hu, and M. Vaughan Monitoring long-term climate change in the Polar Regions relies on accurate, detailed and repeatable measurements of geophysical processes and states. These regions are among the Earth's most vulnerable ecosystems, and measurements there have shown rapid changes in the seasonality and the extent of snow and sea ice coverage. The authors have recently developed a promising new technique that uses lidar surface measurements from the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) mission to infer ocean surface ice-water phase. CALIPSO's 532 nm depolarization ratio measurements of the ocean surface are uniquely capable of providing information about the ever-changing sea surface state within the Polar Regions. With the finer resolution of the CALIPSO footprint (90 m diameter, spaced 335 m apart) and its ability to acquire measurements during both daytime and nighttime orbit segments and in the presence of clouds, the CALIPSO sea ice product provides fine-scale information on mixed phase scenes and can be used to assess/validate the estimates of sea-ice concentration currently provided by passive sensors. This paper describes the fundamentals of the CALIPSO sea-ice detection and classification technique. We present retrieval results from a six-year study, which are compared to existing data sets obtained by satellite-based passive remote sensors.

Description: Motivation: Human miRNAs have recently been found to have important roles in viral replication. Understanding the patterns and details of human miRNA interactions during virus–host interactions may help uncover novel antiviral therapies. Based on the abundance of knowledge available regarding protein–protein interactions (PPI), virus–host protein interactions, experimentally validated human miRNA-target pairs and transcriptional regulation of human miRNAs, it is possible to explore the complex regulatory network that exists between viral proteins and human miRNAs at the system level. Results: By integrating current data regarding the virus–human interactome and human miRNA-target pairs, the overlap between targets of viral proteins and human miRNAs was identified and found to represent topologically important proteins (e.g. hubs or bottlenecks) at the global center of the human PPI network. Viral proteins and human miRNAs were also found to significantly target human PPI pairs. Furthermore, an overlap analysis of virus targets and transcription factors (TFs) of human miRNAs revealed that viral proteins preferentially target human miRNA TFs, representing a new pattern of virus–host interactions. Potential feedback loops formed by viruses, human miRNAs and miRNA TFs were also identified, and these may be exploited by viruses resulting in greater virulence and more effective replication strategies. Contact: boxc@bmi.ac.cn or ni.ming@163.com or sqwang@bmi.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: In sequencing studies of common diseases and quantitative traits, power to test rare and low frequency variants individually is weak. To improve power, a common approach is to combine statistical evidence from several genetic variants in a region. Major challenges are how to do the combining and which statistical framework to use. General approaches for testing association between rare variants and quantitative traits include aggregating genotypes and trait values, referred to as ‘collapsing’, or using a score-based variance component test. However, little attention has been paid to alternative models tailored for protein truncating variants. Recent studies have highlighted the important role that protein truncating variants, commonly referred to as ‘loss of function’ variants, may have on disease susceptibility and quantitative levels of biomarkers. We propose a Bayesian modelling framework for the analysis of protein truncating variants and quantitative traits. Results: Our simulation results show that our models have an advantage over the commonly used methods. We apply our models to sequence and exome-array data and discover strong evidence of association between low plasma triglyceride levels and protein truncating variants at APOC3 (Apolipoprotein C3). Availability: Software is available from http://www.well.ox.ac.uk/~rivas/mamba Contact: donnelly@well.ox.ac.uk

Description: Motivation: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. Achieving high-resolution structural details with electron microscopy requires the identification of a large number (up to hundreds of thousands) of single particles from electron micrographs, which is a laborious task if it has to be manually done and constitutes a hurdle towards high-throughput. Automatic particle selection in micrographs is far from being settled and new and more robust algorithms are required to reduce the number of false positives and false negatives. Results: In this article, we introduce an automatic particle picker that learns from the user the kind of particles he is interested in. Particle candidates are quickly and robustly classified as particles or non-particles. A number of new discriminative shape-related features as well as some statistical description of the image grey intensities are used to train two support vector machine classifiers. Experimental results demonstrate that the proposed method: (i) has a considerably low computational complexity and (ii) provides results better or comparable with previously reported methods at a fraction of their computing time. Availability: The algorithm is fully implemented in the open-source Xmipp package and downloadable from http://xmipp.cnb.csic.es . Contact: vabrishami@cnb.csic.es or coss@cnb.csic.es Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: : Recent major cancer genome sequencing studies have used whole-genome sequencing to detect various types of genomic variation. However, a number of these studies have continued to rely on SNP array information to provide additional results for copy number and loss-of-heterozygosity estimation and assessing tumour purity. OncoSNP-SEQ is a statistical model-based approach for inferring copy number profiles directly from high-coverage whole genome sequencing data that is able to account for unknown tumour purity and ploidy. Availability: MATLAB code is available at the following URL: https://sites.google.com/site/oncosnpseq/ . Contact : c.yau@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Multi-Image Genome (MIG) viewer is a web-based application for visualizing, querying and filtering many thousands of genome browser regions as well as for exporting the data in a variety of formats. This methodology has been used successfully to analyze ChIP-Seq data and RNA-Seq data and to detect somatic mutations in genome resequencing projects. Availability: MIG is available at https://mig.molbiol.ox.ac.uk/mig/ Contact: simon.mcgowan@imm.ox.ac.uk

Description: : Unlike DNA, RNA abundances can vary over several orders of magnitude. Thus, identification of RNA–protein binding sites from high-throughput sequencing data presents unique challenges. Although peak identification in ChIP-Seq data has been extensively explored, there are few bioinformatics tools tailored for peak calling on analogous datasets for RNA-binding proteins. Here we describe ASPeak (abundance sensitive peak detection algorithm), an implementation of an algorithm that we previously applied to detect peaks in exon junction complex RNA immunoprecipitation in tandem experiments. Our peak detection algorithm yields stringent and robust target sets enabling sensitive motif finding and downstream functional analyses. Availability: ASPeak is implemented in Perl as a complete pipeline that takes bedGraph files as input. ASPeak implementation is freely available at https://sourceforge.net/projects/as-peak under the GNU General Public License. ASPeak can be run on a personal computer, yet is designed to be easily parallelizable. ASPeak can also run on high performance computing clusters providing efficient speedup. The documentation and user manual can be obtained from http://master.dl.sourceforge.net/project/as-peak/manual.pdf . Contact: alper.kucukural@umassmed.edu or ccenik@stanford.edu

Description: Motivation: Kinases of the eukaryotic protein kinase superfamily are key regulators of most aspects eukaryotic cellular behavior and have provided several drug targets including kinases dysregulated in cancers. The rapid increase in the number of genomic sequences has created an acute need to identify and classify members of this important class of enzymes efficiently and accurately. Results: Kinannote produces a draft kinome and comparative analyses for a predicted proteome using a single line command, and it is currently the only tool that automatically classifies protein kinases using the controlled vocabulary of Hanks and Hunter [Hanks and Hunter (1995)]. A hidden Markov model in combination with a position-specific scoring matrix is used by Kinannote to identify kinases, which are subsequently classified using a BLAST comparison with a local version of KinBase, the curated protein kinase dataset from www.kinase.com . Kinannote was tested on the predicted proteomes from four divergent species. The average sensitivity and precision for kinome retrieval from the test species are 94.4 and 96.8%. The ability of Kinannote to classify identified kinases was also evaluated, and the average sensitivity and precision for full classification of conserved kinases are 71.5 and 82.5%, respectively. Kinannote has had a significant impact on eukaryotic genome annotation, providing protein kinase annotations for 36 genomes made public by the Broad Institute in the period spanning 2009 to the present. Availability: Kinannote is freely available at http://sourceforge.net/projects/kinannote . Contact: jmgold@broadinstitute.org Supplementary information: Supplementary data are available at Bioinformatics online.