ALBERT

Description: Paul Baird and Mohammad Wehbe Given a Riemannian 3-manifold (M, g) endowed with a unit vector field U that is tangent to a conformal foliation, we require that the pair extend to a space-time ([script M],[script G]) endowed with a space-like unit vector field U in such a way that U simultaneously generates null geodesics and is ... [J. Math. Phys. 53, 032504 (2012)] published Thu Mar 8, 2012.

Description: The role played by the required level of statistical significance in the scientific method should not be seen as analogous to that played by the standard of proof in the legal process.

Description: The Supreme Court ruled in Matrixx that statistical significance is not necessary to show that a drug caused an adverse reaction. Five circuit court decisions holding otherwise preceded this decision. This paper examines the extent to which the Supreme Court’s reasoning differed from those of the circuit courts.

Description: Intercomparison of two meteorological limited area models for quantitative precipitation forecast verification Natural Hazards and Earth System Science, 12, 591-606, 2012 Author(s): E. Oberto, M. Milelli, F. Pasi, and B. Gozzini The demand for verification of numerical models is still very high, especially for what concerns the operational Quantitative Precipitation Forecast (QPF) used, among others, for evaluating the issuing of warnings to the population. In this study, a comparative verification of the QPF, predicted by two operational Limited Area Models (LAMs) for the Italian territory is presented: COSMO-I7 (developed in the framework of the COSMO Consortium) and WRF-NMM (developed at NOAA-NCEP). The observational dataset is the precipitation recorded by the high-resolution non-GTS rain gauges network of the National Civil Protection Department (NCPD) over two years (2007–2008). Observed and forecasted precipitation have been treated as areal quantity (areal average of the values accumulated in 6 and 24 h periods) over the 102 "warning areas", defined by the NCPD both for administrative and hydrological purposes. Statistics are presented through a series of conventional indices (BIAS, POD and POFD) and, in addition, the Extreme Dependency Score (EDS) and the Base Rate (BS or 1-BS) have been used for keeping into account the vanishing of the indices as the events become rare. Results for long-period verification (the whole 2 yr) with increasing thresholds, seasonal trend (3 months period), diurnal error cycle and error maps, are presented. Results indicate that WRF has a general tendency of QPF overestimation for low thresholds and underestimation for higher ones, while COSMO-I7 tends to overestimate for all thresholds. Both models show a seasonal trend, with a bigger overestimation during summer and spring, while during autumn and winter the models tend to be more accurate.

Description: Coupling of climate models and ice sheet models by surface mass balance gradients: application to the Greenland Ice Sheet The Cryosphere, 6, 255-272, 2012 Author(s): M. M. Helsen, R. S. W. van de Wal, M. R. van den Broeke, W. J. van de Berg, and J. Oerlemans It is notoriously difficult to couple surface mass balance (SMB) results from climate models to the changing geometry of an ice sheet model. This problem is traditionally avoided by using only accumulation from a climate model, and parameterizing the meltwater run-off as a function of temperature, which is often related to surface elevation ( H s ). In this study, we propose a new strategy to calculate SMB, to allow a direct adjustment of SMB to a change in ice sheet topography and/or a change in climate forcing. This method is based on elevational gradients in the SMB field as computed by a regional climate model. Separate linear relations are derived for ablation and accumulation, using pairs of H s and SMB within a minimum search radius. The continuously adjusting SMB forcing is consistent with climate model forcing fields, also for initially non-glaciated areas in the peripheral areas of an ice sheet. When applied to an asynchronous coupled ice sheet – climate model setup, this method circumvents traditional temperature lapse rate assumptions. Here we apply it to the Greenland Ice Sheet (GrIS). Experiments using both steady-state forcing and glacial-interglacial forcing result in realistic ice sheet reconstructions.

Description: Estimating ice phenology on large northern lakes from AMSR-E: algorithm development and application to Great Bear Lake and Great Slave Lake, Canada The Cryosphere, 6, 235-254, 2012 Author(s): K.-K. Kang, C. R. Duguay, and S. E. L. Howell Time series of brightness temperatures ( T B ) from the Advanced Microwave Scanning Radiometer–Earth Observing System (AMSR-E) are examined to determine ice phenology variables on the two largest lakes of northern Canada: Great Bear Lake (GBL) and Great Slave Lake (GSL). T B measurements from the 18.7, 23.8, 36.5, and 89.0 GHz channels (H- and V- polarization) are compared to assess their potential for detecting freeze-onset/melt-onset and ice-on/ice-off dates on both lakes. The 18.7 GHz (H-pol) channel is found to be the most suitable for estimating these ice dates as well as the duration of the ice cover and ice-free seasons. A new algorithm is proposed using this channel and applied to map all ice phenology variables on GBL and GSL over seven ice seasons (2002–2009). Analysis of the spatio-temporal patterns of each variable at the pixel level reveals that: (1) both freeze-onset and ice-on dates occur on average about one week earlier on GBL than on GSL (Day of Year (DY) 318 and 333 for GBL; DY 328 and 343 for GSL); (2) the freeze-up process or freeze duration (freeze-onset to ice-on) takes a slightly longer amount of time on GBL than on GSL (about 1 week on average); (3) melt-onset and ice-off dates occur on average one week and approximately four weeks later, respectively, on GBL (DY 143 and 183 for GBL; DY 135 and 157 for GSL); (4) the break-up process or melt duration (melt-onset to ice-off) lasts on average about three weeks longer on GBL; and (5) ice cover duration estimated from each individual pixel is on average about three weeks longer on GBL compared to its more southern counterpart, GSL. A comparison of dates for several ice phenology variables derived from other satellite remote sensing products (e.g. NOAA Interactive Multisensor Snow and Ice Mapping System (IMS), QuikSCAT, and Canadian Ice Service Database) show that, despite its relatively coarse spatial resolution, AMSR-E 18.7 GHz provides a viable means for monitoring of ice phenology on large northern lakes.

Description: Unlike the evaluation of single items of scientific evidence, the formal study and analysis of the joint evaluation of several distinct items of forensic evidence has to date received some punctual, rather than systematic, attention. Questions about the (i) relationships among a set of (usually unobservable) propositions and a set of (observable) items of scientific evidence, (ii) the joint probative value of a collection of distinct items of evidence as well as (iii) the contribution of each individual item within a given group of pieces of evidence still represent fundamental areas of research. To some degree, this is remarkable since both, forensic science theory and practice, yet many daily inference tasks, require the consideration of multiple items if not masses of evidence. A recurrent and particular complication that arises in such settings is that the application of probability theory, i.e. the reference method for reasoning under uncertainty, becomes increasingly demanding. The present paper takes this as a starting point and discusses graphical probability models, i.e. Bayesian networks, as framework within which the joint evaluation of scientific evidence can be approached in some viable way. Based on a review of existing main contributions in this area, the article here aims at presenting instances of real case studies from the author’s institution in order to point out the usefulness and capacities of Bayesian networks for the probabilistic assessment of the probative value of multiple and interrelated items of evidence. A main emphasis is placed on underlying general patterns of inference, their representation as well as their graphical probabilistic analysis. Attention is also drawn to inferential interactions, such as redundancy, synergy and directional change. These distinguish the joint evaluation of evidence from assessments of isolated items of evidence. Together, these topics present aspects of interest to both, domain experts and recipients of expert information, because they have bearing on how multiple items of evidence are meaningfully and appropriately set into context.

Description: In its first foray into the labyrinth that causation in personal injury has become, the U.K. Supreme Court recently held obiter that statistical evidence alone could not establish causation. But in an earlier toxic tort case, the High Court had relied on epidemiological evidence to identify a cluster of birth defects arising in the vicinity of a contaminated land site. This recent British experience is then discussed within the wider context of the forensic role of ‘naked statistics’.

Description: Scales of conclusion in forensic interpretation play an important role in the interface between scientific work at a forensic laboratory and different bodies of the jurisdictional system of a country. Of particular importance is the use of a unified scale that allows interpretation of different kinds of evidence in one common framework. The logical approach to forensic interpretation comprises the use of the likelihood ratio as a measure of evidentiary strength. While fully understood by forensic scientists, the likelihood ratio may be hard to interpret for a person not trained in natural sciences or mathematics. Translation of likelihood ratios to an ordinal scale including verbal counterparts of the levels is therefore a necessary procedure for communicating evidence values to the police and in the courtroom. In this paper, we present a method to develop an ordinal scale for the value of evidence that can be applied to any type of forensic findings. The method is built on probabilistic reasoning about the interpretation of findings and the number of scale levels chosen is a compromise between a pragmatic limit and mathematically well-defined distances between levels. The application of the unified scale is illustrated by a number of case studies.

Description: In personal injury litigation, claimants may seek their compensation for future losses or expenses as a lump sum that is determined by the product of a multiplicand and a multiplier. The multiplicand represents the annual loss in earnings and other benefits, as assessed at the trial date, while the multiplier discounts future pecuniary values into a single present-day lump sum amount. At present, multipliers in the UK are calculated using actuarial methods and based on assumed mortality and interest rates. However, it is entirely possible that these assumptions are incorrect, and if they are, then all claimants who rely on the same set of actuarial multipliers will be affected. In this article, we investigate how the uncertainty surrounding mortality and interest rate assumptions affects the precision of actuarial multipliers. With the aid of stochastic models, we estimate the possible range of values that an actuarial multiplier can take.

Description: In this article we report and discuss a contextual problem solving task that was proposed to a class of 8th grade (13–14-year-old) students. These students had been developing a reasonable experience in the use of the spreadsheet to model relations within contextual problems and chose to use this tool to solve the mentioned problem, engaging in the process of translating relations between variables and combining them in chained models, while working with fractions, multiples and expressions. We intend to highlight the role of the spreadsheet in students’ processes of variable identification and translation of the problem conditions, their numerical approaches to algebraic models and their experimental forms of finding solutions to equations.

Description: This theoretical study is an attempt to explore the potential of the dynamic and interactive mathematics learning environments (DIMLE) in relation to the technological pedagogical content knowledge (TPACK) framework. DIMLE are developed with intent to support learning mathematics through free exploration in a less constrained environment. A typical DIMLE software package has interactivity and dynamism as key affordances; these are especially suitable for enhancing learning and teaching with technology of the essentially dynamic mathematics concepts. Moreover, we propose that DIMLE and their affordances should be studied under the TPACK framework because this framework is explicit in considering technology-supported mathematics learning as a qualitative add-on as contrasted to what would be a simple totalling of technological, pedagogical and mathematical knowledge. As an example, we focus in our discussion on using a DIMLE in order to support learner in development of the limit concept.

Description: The present article reports a study concerning the analysis of 19 activity plans (we call them ‘scenarios’) developed by mathematics teacher educators-in-training for the pedagogical use of digital tools. The development of these scenarios took place during their training program and was designed as an activity for increasing reflection, for expressing creative pedagogical ideas and for an active engagement in the design of curricula enriched with the use of technology. Our analysis showed that the trainee teacher educators deconstructed and reconstructed respective parts of the formal curriculum regarding the mathematical concepts they chose to embody in their scenarios.

Description: Arctic sea ice variability and trends, 1979–2010 The Cryosphere Discussions, 6, 957-979, 2012 Author(s): D. J. Cavalieri and C. L. Parkinson Analyses of 32 yr (1979–2010) of Arctic sea ice extents and areas derived from satellite passive microwave radiometers are presented for the Northern Hemisphere as a whole and for nine Arctic regions. There is an overall negative yearly trend of −51.5 ± 4.1 × 10 3 km 2 yr −1 (−4.1 ± 0.3% decade −1 ) in sea ice extent for the hemisphere. The sea ice extent trends for the individual Arctic regions are all negative except for the Bering Sea: −3.9 ± 1.1 × 10 3 km 2 yr −1 (−8.7 ± 2.5% decade −1 ) for the Seas of Okhotsk and Japan, +0.3 ± 0.8 × 10 3 km 2 yr −1 (+1.2 ± 2.7% decade −1 ) for the Bering Sea, −4.4 ± 0.7 × 10 3 km 2 yr −1 (−5.1 ± 0.9% decade −1 ) for Hudson Bay, −7.6 ± 1.6 × 10 3 km 2 yr −1 (−8.5 ± 1.8% decade −1 ) for Baffin Bay/Labrador Sea, −0.5 ± 0.3 × 10 3 km 2 yr −1 (−5.9 ± 3.5% decade −1 ) for the Gulf of St. Lawrence, −6.5 ± 1.1 × 10 3 km 2 yr −1 (−8.6 ± 1.5% decade −1 ) for the Greenland Sea, −13.5 ± 2.3 × 10 3 km 2 yr −1 (−9.2 ± 1.6% decade −1 ) for the Kara and Barents Seas, −14.6 ± 2.3 × 10 3 km 2 yr −1 (−2.1 ± 0.3% decade −1 ) for the Arctic Ocean, and −0.9 ± 0.4 × 10 3 km 2 yr −1 (−1.3 ± 0.5% decade −1 ) for the Canadian Archipelago. Similarly, the yearly trends for sea ice areas are all negative except for the Bering Sea. On a seasonal basis for both sea ice extents and areas, the largest negative trend is observed for summer with the next largest negative trend being for autumn.

Description: In this research we present the use of some technologies in problem solving activities (at different secondary school grades), aimed at finding a model for a geometric configuration, and representing this model in various ways: through a construction, through a Cartesian graph, etc. The task is part of a teaching experiment, in which students used paper and pencil, and technological tools: a sensor and a calculator (at a lower grade), GeoGebra and TI-Nspire (at a higher grade). We show results in terms of the passage from static to dynamic representations and back, to observe how technology may foster dynamic thinking for students solving mathematical problems. Data suggest that the dynamic features of technology support the genesis of conjectures, and their validation or refutation, along with the choice of independent and dependent variables. Results are used to prepare materials for teacher training in an e-learning Moodle platform (Comenius EdUmatics Project).

Description: On teaching styles of water educators and the impact of didactic training Hydrology and Earth System Sciences Discussions, 9, 2959-2986, 2012 Author(s): A. Pathirana, J. H. Koster, E. de Jong, and S. Uhlenbrook Solving today's complex hydrological problems requires originality, creative thinking and trans-disciplinary approaches. Hydrological education that was traditionally teacher centred, where the students look up to the teacher for expertise and information, should change to better prepare hydrologists to develop new knowledge and apply it in new contexts. An important first step towards this goal is to change the concept of education in the educators' minds. The results of an investigation to find out whether didactic training influences the beliefs of hydrology educators about their teaching styles is presented. Faculty of UNESCO-IHE has been offered a didactic certification program named University Teaching Qualification (UTQ). The hypothesis that UTQ training will significantly alter the teaching style of faculty at UNESCO-IHE from expert/formal authority traits towards facilitator/delegator traits was tested. A first survey was conducted among the entire teaching staff (total 101, response rate 58%). The results indicated that there are significantly higher traits of facilitator and delegator teaching styles among UTQ graduates compared to faculty who were not significantly trained in didactics. The second survey which was conducted among UTQ graduates (total 20, response rate 70%), enquiring after their teaching styles before and after UTQ, corroborated these findings.

Description: Characterization of deep aquifer dynamics using principal component analysis of sequential multilevel data Hydrology and Earth System Sciences, 16, 761-771, 2012 Author(s): D. Kurtzman, L. Netzer, N. Weisbrod, A. Nasser, E. R. Graber, and D. Ronen Two sequential multilevel profiles were obtained in an observation well opened to a 130-m thick, unconfined, contaminated aquifer in Tel Aviv, Israel. While the general profile characteristics of major ions, trace elements, and volatile organic compounds were maintained in the two sampling campaigns conducted 295 days apart, the vertical locations of high concentration gradients were shifted between the two profiles. Principal component analysis (PCA) of the chemical variables resulted in a first principal component which was responsible for ∼60% of the variability, and was highly correlated with depth. PCA revealed three distinct depth-dependent water bodies in both multilevel profiles, which were found to have shifted vertically between the sampling events. This shift cut across a clayey bed which separated the top and intermediate water bodies in the first profile, and was located entirely within the intermediate water body in the second profile. Continuous electrical conductivity monitoring in a packed-off section of the observation well revealed an event in which a distinct water body flowed through the monitored section ( v ∼ 150 m yr −1 ). It was concluded that the observed changes in the profiles result from dominantly lateral flow of water bodies in the aquifer rather than vertical flow. The significance of this study is twofold: (a) it demonstrates the utility of sequential multilevel observations from deep wells and the efficacy of PCA for evaluating the data; (b) the fact that distinct water bodies of 10 to 100 m vertical and horizontal dimensions flow under contaminated sites, which has implications for monitoring and remediation.

Description: This article focuses on user experiences on reading location-aware news on the mobile platform and aims to explore what experiences this kind of locative journalism generates and how such experiences change the users’ social interaction with news. We produced a specially designed mobile application and tailored news stories specific to this project called LocaNews in order to explore participants’ relation to the content in this journalistic format. The result is generated through a field study and a questionnaire of 32 people to find out how they experience the news presented in this format. The user participants’ responses are analyzed based on their news experiences, contextualizing places and their social interaction with the news within this form of journalism. Results showed that the local, semi-local and non-local user approaches the locative news in a different manner, but that the average user found this kind of news more interesting and more informative than ordinary news. The participants also have a problem identifying this as journalism, rather than an information service.

Description: Editorial “Advances in Earth observation for water cycle science” Hydrology and Earth System Sciences, 16, 543-549, 2012 Author(s): D. Fernández-Prieto, P. van Oevelen, Z. Su, and W. Wagner

Description: Readability indices measure how easy or difficult it is to read and comprehend a text. In this paper we look at the relation between readability indices and web documents from two different perspectives. On the one hand we analyse how to reliably measure the readability of web documents by applying content extraction techniques and incorporating a bias correction. On the other hand we investigate how web based corpus statistics can be used to measure readability in a novel and language independent way.

Description: River monitoring from satellite radar altimetry in the Zambezi River Basin Hydrology and Earth System Sciences Discussions, 9, 3203-3235, 2012 Author(s): C. I. Michailovsky, S. McEnnis, P. A. M. Berry, R. Smith, and P. Bauer-Gottwein Satellite radar altimetry can be used to monitor surface water levels from space. While current and past altimetry missions were designed to study oceans, retracking the waveforms returned over land allows data to be retrieved for smaller water bodies or narrow rivers. In this study, retracked Envisat altimetry data was extracted over the Zambezi River Basin using a detailed river mask based on Landsat imagery. This allowed for stage measurements to be obtained for rivers down to 80 m wide with an RMSE relative to in situ levels of 0.32 to 0.72 m at different locations. The altimetric levels were then converted to discharge using three different methods adapted to different data-availability scenarios: first with an in situ rating curve available, secondly with one simultaneous field measurement of cross-section and discharge, and finally with only historical discharge data available. For the two locations at which all three methods could be applied the accuracies of the different methods were found to be comparable, with RMSE values ranging from 5.5 to 7.4 % terms of high flow estimation relative to in situ gauge measurements. The precision obtained with the different methods was analyzed by running Monte Carlo simulations and also showed comparable values for the three approaches with standard deviations found between 8.2 and 25.8 % of the high flow estimates.

Description: Water management simulation games and the construction of knowledge Hydrology and Earth System Sciences Discussions, 9, 3063-3085, 2012 Author(s): M. Rusca, J. Heun, and K. Schwartz In recent years simulations have become an important part of teaching activities. The reasons behind the popularity of simulation games are twofold. On the one hand, emerging theories on how people learn have called for an experienced-based learning approach. On the other hand, the demand for water management professionals has changed. Three important developments are having considerable consequences for water management programmes, which educate and train these professionals. These developments are the increasing emphasis on integration in water management, the characteristics and speed of reforms in the public sector and the shifting state-society relations in many countries. In response to these developments, demand from the labour market is oriented toward water professionals who need to have both a specialist in-depth knowledge in their own field, as well as the ability to understand and interact with other disciplines and interests. In this context, skills in negotiating, consensus building and working in teams are considered essential for all professionals. In this paper we argue that simulation games have an important role to play in (actively) educating students and training the new generation of water professionals to respond to the above-mentioned challenges. At the same time, simulations are not a panacea for learners and teachers. Challenges of using simulations games include the demands it places on the teacher. Setting up the simulation game, facilitating the delivery and ensuring that learning objectives are achieved requires considerable knowledge and experience as well as considerable time-inputs of the teacher. Moreover, simulation games usually incorporate a case-based learning model, which may neglect or underemphasize theories and conceptualization. For simulations to be effective they have to be embedded in this larger theoretical and conceptual framework. Simulations, therefore, complement rather than substitute traditional teaching methods.

Description: Evaluation of a complementary based model for mapping land surface evapotranspiration Hydrology and Earth System Sciences Discussions, 9, 3029-3062, 2012 Author(s): Z. Sun, Q. Wang, Z. Ouyang, and Y. Yang A modified Priestley-Taylor (P-T) equation was proposed by Venturini et al. (2008) to map actual evapotranspiration (ET) based solely on satellite remote sensing data, involving a parameter based on a scaled temperature between dew point temperature and surface temperature. In this study, however, theoretical analyses and field experimental evidence show that it is hard to obtain this scaled temperature using dew point temperature and surface temperature. This study also presents a new parameterization method using air temperature, surface temperature, and surface temperature of a reference dry surface. The actual ET estimates obtained by means of our proposed parameterization method are validated at a site scale, and a case study is conducted to map actual ET from Advanced Spaceborne Thermal Emission and Reflection radiometer (ASTER) images using our proposed method. Results of ground-based validation and a case study of mapping ET using ASTER images indicate that the improvement on the modified P-T equation proposed by Venturini et al. (2008) can contribute to generating reliable actual ET.

Description: Prioritization of water management under climate change and urbanization using multi-criteria decision making methods Hydrology and Earth System Sciences, 16, 801-814, 2012 Author(s): J.-S. Yang, E.-S. Chung, S.-U. Kim, and T.-W. Kim This paper quantifies the transformed effectiveness of alternatives for watershed management caused by climate change and urbanization and prioritizes five options using multi-criteria decision making techniques. The climate change scenarios (A1B and A2) were obtained by using a statistical downscaling model (SDSM), and the urbanization scenario by surveying the existing urban planning. The flow and biochemical oxygen demand (BOD) concentration duration curves were derived, and the numbers of days required to satisfy the environmental flow requirement and the target BOD concentration were counted using the Hydrological Simulation Program-Fortran (HSPF) model. In addition, five feasible alternatives were prioritized by using multi-criteria decision making techniques, based on the driving force-pressure-state-impact-response (DPSIR) framework and cost component. Finally, a sensitivity analysis approach for MCDM methods was conducted to reduce the uncertainty of weights. The result indicates that the most sensitive decision criterion is cost, followed by criteria response, driving force, impact, state and pressure in that order. As it is certain that the importance of cost component is over 0.127, construction of a small wastewater treatment plant will be the most preferred alternative in this application.

Description: With the emergence of Web 2.0, new applications arise and evolve into more interactive forms of collective intelligence. These applications offer to both professionals and citizens an open and expanded access to geographic information. In this paper, we develop the conceptual foundations of a new technology solution called WikiGIS. WikiGIS’s strength lies in its ability to ensure the traceability of changes in spatial-temporal geographic components (geometric location and shape, graphics: iconography and descriptive) generated by users. The final use case highlights to what extent WikiGIS could be a relevant and useful technological innovation in Geocollaboration.

Description: Precipitation fields interpolated from gauge stations versus a merged radar-gauge precipitation product: influence on modelled soil moisture at local scale and at SMOS scale Hydrology and Earth System Sciences Discussions, 9, 3385-3413, 2012 Author(s): J. T. dall'Amico, W. Mauser, F. Schlenz, and H. Bach For the validation of coarse resolution soil moisture products from missions such as the Soil Moisture and Ocean Salinity (SMOS) mission, hydrological modelling of soil moisture is an important tool. The spatial distribution of precipitation is among the most crucial input data for such models. Thus, reliable time series of precipitation fields are required, but these often need to be interpolated from data delivered by scarcely distributed gauge station networks. In this study, a commercial precipitation product derived by Meteomedia AG from merging radar and gauge data is introduced as a novel means of adding the promising area-distributed information given by a radar network to the more accurate, but point-like measurements from a gauge station network. This precipitation product is first validated against an independent gauge station network. Further, the novel precipitation product is assimilated into the hydrological land surface model PROMET for the Upper Danube Catchment in southern Germany, one of the major SMOS calibration and validation sites in Europe. The modelled soil moisture fields are compared to those obtained when the operational interpolation from gauge station data is used to force the model. The results suggest that the assimilation of the novel precipitation product can lead to deviations of modelled soil moisture in the order of 0.15 m 3 m −3 on small spatial (∼1 km 2 ) and short temporal resolutions (∼1 day). As expected, after spatial aggregation to the coarser grid on which SMOS data are delivered (~195 km 2 ), these differences are reduced to the order of 0.04 m 3 m −3 , which is the accuracy benchmark for SMOS. The results of both model runs are compared to brightness temperatures measured by the airborne L-band radiometer EMIRAD during the SMOS Validation Campaign 2010. Both comparisons yield equally good correlations, confirming the model's ability to realistically model soil moisture fields in the test site. The fact that the two model runs perform similarly in the comparison is likely associated with the lack of substantial rain events before the days on which EMIRAD was flown.

Description: An integrated uncertainty and ensemble-based data assimilation approach for improved operational streamflow predictions Hydrology and Earth System Sciences, 16, 815-831, 2012 Author(s): M. He, T. S. Hogue, S. A. Margulis, and K. J. Franz The current study proposes an integrated uncertainty and ensemble-based data assimilation framework (ICEA) and evaluates its viability in providing operational streamflow predictions via assimilating snow water equivalent (SWE) data. This step-wise framework applies a parameter uncertainty analysis algorithm (ISURF) to identify the uncertainty structure of sensitive model parameters, which is subsequently formulated into an Ensemble Kalman Filter (EnKF) to generate updated snow states for streamflow prediction. The framework is coupled to the US National Weather Service (NWS) snow and rainfall-runoff models. Its applicability is demonstrated for an operational basin of a western River Forecast Center (RFC) of the NWS. Performance of the framework is evaluated against existing operational baseline (RFC predictions), the stand-alone ISURF and the stand-alone EnKF. Results indicate that the ensemble-mean prediction of ICEA considerably outperforms predictions from the other three scenarios investigated, particularly in the context of predicting high flows (top 5th percentile). The ICEA streamflow ensemble predictions capture the variability of the observed streamflow well, however the ensemble is not wide enough to consistently contain the range of streamflow observations in the study basin. Our findings indicate that the ICEA has the potential to supplement the current operational (deterministic) forecasting method in terms of providing improved single-valued (e.g., ensemble mean) streamflow predictions as well as meaningful ensemble predictions.

Description: Advancing data assimilation in operational hydrologic forecasting: progresses, challenges, and emerging opportunities Hydrology and Earth System Sciences Discussions, 9, 3415-3472, 2012 Author(s): Y. Liu, A. H. Weerts, M. Clark, H.-J. Hendricks Franssen, S. Kumar, H. Moradkhani, D.-J. Seo, D. Schwanenberg, P. Smith, A. I. J. M. van Dijk, N. van Velzen, M. He, H. Lee, S. J. Noh, O. Rakovec, and P. Restrepo Data assimilation (DA) holds considerable potential for improving hydrologic predictions as demonstrated in numerous research studies. However, advances in hydrologic DA research have not been adequately or timely implemented into operational forecast systems to improve the skill of forecasts to better inform real-world decision making. This is due in part to a lack of mechanisms to properly quantify the uncertainty in observations and forecast models in real-time forecasting situations and to conduct the merging of data and models in a way that is adequately efficient and transparent to operational forecasters. The need for effective DA of useful hydrologic data into the forecast process has become increasingly recognized in recent years. This motivated a hydrologic DA workshop in Delft, The Netherlands in November 2010, which focused on advancing DA in operational hydrologic forecasting and water resources management. As an outcome of the workshop, this paper reviews, in relevant detail, the current status of DA applications in both hydrologic research and operational practices, and discusses the existing or potential hurdles and challenges in transitioning hydrologic DA research into cost-effective operational forecasting tools, as well as the potential pathways and newly emerging opportunities for overcoming these challenges. Several related aspects are discussed, including (1) theoretical or mathematical considerations in DA algorithms, (2) the estimation of different types of uncertainty, (3) new observations and their objective use in hydrologic DA, (4) the use of DA for real-time control of water resources systems, and (5) the development of community-based, generic DA tools for hydrologic applications. It is recommended that cost-effective transition of hydrologic DA from research to operations should be helped by developing community-based, generic modelling and DA tools or frameworks, and through fostering collaborative efforts among hydrologic modellers, DA developers, and operational forecasters.

Description: Impact of climate change on sediment yield in the Mekong River Basin: a case study of the Nam Ou Basin, Lao PDR Hydrology and Earth System Sciences Discussions, 9, 3339-3384, 2012 Author(s): B. Shrestha, M. S. Babel, S. Maskey, A. van Griensven, S. Uhlenbrook, A. Green, and I. Akkharath This paper evaluates the impact of climate change on sediment yield in the Nam Ou Basin located in Northern Laos. The Soil and Water Assessment Tool (SWAT) is used to assess future changes in sediment flux attributable to climate change. Future precipitation and temperature series are constructed through a delta change approach. As per the results, in general, temperature as well as precipitation show increasing trends in both scenarios, A2 and B2. However, monthly precipitation shows both increasing and decreasing trends. The simulation results exhibit that the wet and dry seasonal and annual stream discharges are likely to increase (by up to 15, 17 and 14% under scenario A2; and 11, 5 and 10% under scenario B2 respectively) in the future, which will lead to increased wet and dry seasonal and annual sediment yields (by up to 39, 28 and 36% under scenario A2; and 23, 12 and 22% under scenario B2 respectively). A higher discharge and more sediment flux are expected during the wet seasons, although the changes, percentage-wise, are observed to be higher during the dry months. In conclusion, the sediment yield from the Nam Ou Basin is likely to increase with climate change, which strongly suggests the need for basin-wide sediment management strategies in order to reduce the negative impact of this change.

Description: Correcting the radar rainfall forcing of a hydrological model with data assimilation: application to flood forecasting in the Lez Catchment in Southern France Hydrology and Earth System Sciences Discussions, 9, 3527-3579, 2012 Author(s): E. Harader, V. Borrell Estupina, S. Ricci, M. Coustau, O. Thual, A. Piacentini, and C. Bouvier The present study explores the application of a data assimilation (DA) procedure to correct the radar rainfall inputs of an event-based, distributed, parsimonious hydrological model. A simplified Kalman filter algorithm was built on top of a rainfall-runoff model in order to assimilate discharge observations at the catchment outlet. The study site is the 114 km 2 Lez Catchment near Montpellier, France. This catchment is subject to heavy orographic rainfall and characterized by a karstic geology, leading to flash flooding events. The hydrological model uses a derived version of the SCS method, combined with a Lag and Route transfer function. Because it depends on geographical features and cloud structures, the radar rainfall input to the model is particularily uncertain and results in significant errors in the simulated discharges. The DA analysis was applied to estimate a constant correction to each event hyetogram. The analysis was carried out for 19 events, in two different modes: re-analysis and pseudo-forecast. In both cases, it was shown that the reduction of the uncertainty in the rainfall data leads to a reduction of the error in the simulated discharge. The resulting correction of the radar rainfall data was then compared to the mean field bias (MFB), a corrective coefficient determined using ground rainfall measurements, which are more accurate than radar but have a decreased spatial resolution. It was shown that the radar rainfall corrected using DA leads to improved discharge simulations and Nash criteria compared to the MFB correction.

Description: Numerical modelling of climate change impacts on freshwater lenses on the North Sea Island of Borkum Hydrology and Earth System Sciences Discussions, 9, 3473-3525, 2012 Author(s): H. Sulzbacher, H. Wiederhold, B. Siemon, M. Grinat, J. Igel, T. Burschil, T. Günther, and K. Hinsby A numerical variable-density groundwater model is set up for the North Sea Island of Borkum to estimate climate change impacts on coastal aquifers and especially the situation of barrier islands in the Wadden Sea. The database includes information from boreholes, a seismic survey, a helicopter-borne electromagnetic survey (HEM), monitoring of the freshwater-saltwater boundary by vertical electrode chains in two boreholes, measurements of groundwater table, pumping and slug tests, as well as water samples. Based on a statistical analysis of borehole columns, seismic sections and HEM, a hydrogeological model is set up. The groundwater model is developed using the finite-element programme FEFLOW. The variable-density groundwater model is calibrated on the basis of hydraulic, hydrological and geophysical data, in particular spatial HEM and local monitoring data. Verification runs with the calibrated model show good agreement between measured and computed hydraulic heads. A good agreement is also obtained between measured and computed density or total dissolved solids data for both the entire freshwater lens on a large scale and in the area of the well fields on a small scale. For simulating future changes in this coastal groundwater system until the end of the current century we use the climate scenario A2, specified by the Intergovernmental Panel on Climate Change and in particular the data for the German North Sea coast. Simulation runs show proceeding salinization with time beneath the well fields of the two waterworks Waterdelle and Ostland. The modelling study shows that spreading of well fields is an appropriate protection measure against excessive salinization of the water supply until the end of the current century.

Description: A. Santi and A. Spiro The presentation of supergravity theories of our previous paper Super-Poincare algebras, space-times, and supergravities. I is re-formulated in the language of Berezin-Leites-Kostant theory of supermanifolds. It is also shown that the equations of Cremmer, Julia, and Scherk's theory of 11D-supergrav ... [J. Math. Phys. 53, 032505 (2012)] published Wed Mar 14, 2012.

Description: Tong Zhou and Zuo-nong Zhu In this paper, soliton interactions in three semidiscrete integrable systems are studied. It will be shown that in some cases the solitary waves of the semidiscrete integrable systems can interact elastically, i.e., the shapes, the amplitudes, and the velocities of waves preserve after undergoing co ... [J. Math. Phys. 53, 033507 (2012)] published Thu Mar 15, 2012.

Description: Ikaite crystals in melting sea ice – implications for p CO 2 and pH levels in Arctic surface waters The Cryosphere Discussions, 6, 1015-1035, 2012 Author(s): S. Rysgaard, R. N. Glud, K. Lennert, M. Cooper, N. Halden, R. J. G. Leakey, F. C. Hawthorne, and D. Barber A major issue of Arctic marine science is to understand whether the Arctic Ocean is, or will be, a source or sink for air-sea CO 2 exchange. This has been complicated by the recent discoveries of ikaite (CaCO 3 ·6H 2 O) in Arctic and Antarctic sea ice, which indicate that multiple chemical transformations occur in sea ice with a possible effect on CO 2 and pH conditions in surface waters. Here we report on biogeochemical conditions, microscopic examinations and x-ray diffraction analysis of single crystals from an actively melting 1.7 km 2 (0.5–1 m thick) drifting ice floe in the Fram Strait during summer. Our findings show that ikaite crystals are present throughout the sea ice but with larger crystals appearing in the upper ice layers. Ikaite crystals placed at elevated temperatures gradually disintegrated into smaller crystallites and dissolved. During our field campaign in late June, melt reduced the ice flow thickness by ca. 0.2 m per week and resulted in an estimated 1.6 ppm decrease of p CO 2 in the ocean surface mixed layer. This corresponds to an air-sea CO 2 uptake of 11 mmol m −2 sea ice d −1 or to 3.5 ton km −2 ice floe week −1 .

Description: Accounting for seasonality in a soil moisture change detection algorithm for ASAR Wide Swath time series Hydrology and Earth System Sciences, 16, 773-786, 2012 Author(s): J. Van doninck, J. Peters, H. Lievens, B. De Baets, and N. E. C. Verhoest A change detection algorithm is applied on a three year time series of ASAR Wide Swath images in VV polarization over Calabria, Italy, in order to derive information on temporal soil moisture dynamics. The algorithm, adapted from an algorithm originally developed for ERS scatterometer, was validated using a simple hydrological model incorporating meteorological and pedological data. Strong positive correlations between modelled soil moisture and ASAR soil moisture were observed over arable land, while the correlation became much weaker over more vegetated areas. In a second phase, an attempt was made to incorporate seasonality in the different model parameters. It was observed that seasonally changing surface properties mainly affected the multitemporal incidence angle normalization. When applying a seasonal angular normalization, correlation coefficients between modelled soil moisture and retrieved soil moisture increased overall. Attempts to account for seasonality in the other model parameters did not result in an improved performance.

Description: In this paper, we integrate a grid system and a wireless network to present a convenient computational service system, called the Semi-Preemptive Computational Service system (SePCS for short), which provides users with a wireless access environment and through which a user can share his/her resources with others. In the SePCS, each node is dynamically given a score based on its CPU level, available memory size, current length of waiting queue, CPU utilization and bandwidth. With the scores, resource nodes are classified into three levels. User requests based on their time constraints are also classified into three types. Resources of higher levels are allocated to more tightly constrained requests so as to increase the total performance of the system. To achieve this, a resource broker with the Semi-Preemptive Algorithm (SPA) is also proposed. When the resource broker cannot find suitable resources for the requests of higher type, it preempts the resource that is now executing a lower type request so that the request of higher type can be executed immediately. The SePCS can be applied to a Vehicular Ad Hoc Network (VANET), users of which can then exploit the convenient mobile network services and the wireless distributed computing. As a result, the performance of the system is higher than that of the tested schemes.

Description: Gus Gutoski The present paper studies an operator norm that captures the distinguishability of quantum strategies in the same sense that the trace norm captures the distinguishability of quantum states or the diamond norm captures the distinguishability of quantum channels. Characterizations of its unit ball an ... [J. Math. Phys. 53, 032202 (2012)] published Wed Mar 14, 2012.

Description: Rockfall hazard and risk assessments along roads at a regional scale: example in Swiss Alps Natural Hazards and Earth System Science, 12, 615-629, 2012 Author(s): C. Michoud, M.-H. Derron, P. Horton, M. Jaboyedoff, F.-J. Baillifard, A. Loye, P. Nicolet, A. Pedrazzini, and A. Queyrel Unlike fragmental rockfall runout assessments, there are only few robust methods to quantify rock-mass-failure susceptibilities at regional scale. A detailed slope angle analysis of recent Digital Elevation Models (DEM) can be used to detect potential rockfall source areas, thanks to the Slope Angle Distribution procedure. However, this method does not provide any information on block-release frequencies inside identified areas. The present paper adds to the Slope Angle Distribution of cliffs unit its normalized cumulative distribution function. This improvement is assimilated to a quantitative weighting of slope angles, introducing rock-mass-failure susceptibilities inside rockfall source areas previously detected. Then rockfall runout assessment is performed using the GIS- and process-based software Flow-R, providing relative frequencies for runout. Thus, taking into consideration both susceptibility results, this approach can be used to establish, after calibration, hazard and risk maps at regional scale. As an example, a risk analysis of vehicle traffic exposed to rockfalls is performed along the main roads of the Swiss alpine valley of Bagnes.

Description: Li Ren, Qiang Mu, and Yongzheng Zhang The natural filtrations of hamiltonian superalgebras of formal vector fields are proved to be invariant under their automorphism group, by determining the set of ad-quasi-nilpotent elements. Thereby, the automorphism group of these Lie superalgebras are determined. ... [J. Math. Phys. 53, 033506 (2012)] published Thu Mar 15, 2012.

Description: Evolution of skewness and kurtosis of weakly nonlinear unidirectional waves over a sloping bottom Natural Hazards and Earth System Science, 12, 631-638, 2012 Author(s): H. Zeng and K. Trulsen We consider the effect of slowly varying depth on the values of skewness and kurtosis of weakly nonlinear irregular waves propagating from deeper to shallower water. It is known that the equilibrium value of kurtosis decreases with decreasing depth for waves propagating on constant depth. Waves propagating over a sloping bottom must continually adjust toward a new equilibrium state. We demonstrate that weakly nonlinear waves may need a considerable horizontal propagation distance in order to adjust to a new shallower environment, therefore the kurtosis can be notably different from the equilibrium value for each corresponding depth both on top of and beyond a bottom slope. A change of depth can provoke a wake-like spatially non-uniform distribution of kurtosis on the lee side of the slope. As an application, we anticipate that the probability of freak waves on or near the edge of the continental shelf may exhibit a rather complicated spatial structure for wave fields entering from deep sea.

Description: Corrigendum to "Impact of rainfall spatial distribution on rainfall-runoff modelling efficiency and initial soil moisture conditions estimation" published in Nat. Hazards Earth Syst. Sci., 11, 157–170, 2011 Natural Hazards and Earth System Science, 12, 267-267, 2012 Author(s): Y. Tramblay, C. Bouvier, P.-A. Ayral, and A. Marchandise No abstract available.

Description: This paper presents a benchmarking, performance analysis and optimization study of the OP2 ‘active’ library, which provides an abstraction framework for the parallel execution of unstructured mesh applications. OP2 aims to decouple the scientific specification of the application from its parallel implementation, and thereby achieve code longevity and near-optimal performance through re-targeting the application to execute on different multi-core/many-core hardware. Runtime performance results are presented for a representative unstructured mesh application on a variety of many-core processor systems, including traditional X86 architectures from Intel (Xeon based on the older Penryn and current Nehalem micro-architectures) and GPU offerings from NVIDIA (GTX260, Tesla C2050). Our analysis demonstrates the contrasting performance between the use of CPU (OpenMP) and GPU (CUDA) parallel implementations for the solution of an industrial-sized unstructured mesh consisting of about 1.5 million edges. Results show the significance of choosing the correct partition and thread-block configuration, the factors limiting the GPU performance and insights into optimizations for improved performance.

Description: In this paper, we describe the integrated power, area and thermal modeling framework in the structural simulation toolkit (SST) for large-scale high performance computer simulation. It integrates various power and thermal modeling tools and computes run-time energy dissipation for core, network on chip, memory controller and shared cache. It also provides functionality to update the leakage power as temperature changes. We illustrate the utilization of the framework by applying it to explore interconnect options in manycore systems with consideration of temperature variation and leakage feedback. We compare power, energy-delay-area product (EDAP) and energy-delay product (EDP) of four manycore configurations-1 core, 2 cores, 4 cores and 8 cores per cluster. Results from simulation with or without consideration of temperature variation both show that the 4-core per cluster configuration has the best EDAP and EDP. Even so, considering that temperature variation increases total power dissipation, we demonstrate the importance of considering temperature variation in the design flow. With this power, area and thermal modeling capability, the SST can be used for hardware/software co-design of future exascale systems.

Description: With the advent of heterogeneous computing systems consisting of multi-core central processing units (CPUs) and many-core graphics processing units (GPUs), robust methods are needed to facilitate fair benchmark comparisons between different systems. In this paper, we present a benchmarking methodology for measuring a number of performance metrics for heterogeneous systems. Methods for comparing performance and energy efficiency are included. Consideration is given to further metrics, such as associated running costs and carbon emissions. We give a case study for these metrics applied to Bristol University Docking engine, a molecular mechanics-based docking application that has been ported to open computing language at the University of Bristol. Results are included for both AMD and NVIDIA GPUs, and for a highly optimized code on the latest x86 CPUs.

Description: Java embedded systems often include Java middleware classes installed on the client device. For higher performance, they can be compiled into machine code before runtime using an ahead-of-time compiler (AOTC). There are many approaches to AOTC, yet a bytecode-to-C (b-to-C) AOTC which translates the bytecode into the C code and then compiles it using an existing optimizing compiler such as gcc would be the most straightforward one. This paper explores a few important design and optimization issues of a b-to-C AOTC, including the compilation form for the translated C code, the call interfaces among translated and interpreted Java methods, and Java-specific optimizations by the AOTC that can complement the gcc optimizations. We evaluate these issues with our b-to-C AOTC implemented on the MIPS platform for the Sun's CDC VM to understand their performance impact.

Description: Physically-based modeling of topographic effects on spatial evapotranspiration and soil moisture patterns through radiation and wind Hydrology and Earth System Sciences, 16, 357-373, 2012 Author(s): M. Liu, A. Bárdossy, J. Li, and Y. Jiang In this paper, simulations with the Soil Water Atmosphere Plant (SWAP) model are performed to quantify the spatial variability of both potential and actual evapotranspiration (ET), and soil moisture content (SMC) caused by topography-induced spatial wind and radiation differences. To obtain the spatially distributed ET/SMC patterns, the field scale SWAP model is applied in a distributed way for both pointwise and catchment wide simulations. An adapted radiation model from r.sun and the physically-based meso-scale wind model METRAS PC are applied to obtain the spatial radiation and wind patterns respectively, which show significant spatial variation and correlation with aspect and elevation respectively. Such topographic dependences and spatial variations further propagate to ET/SMC. A strong spatial, seasonal-dependent, scale-relevant intra-catchment variability in daily/annual ET and less variability in SMC can be observed from the numerical experiments. The study concludes that topography has a significant effect on ET/SMC in the humid region where ET is a energy limited rather than water availability limited process. It affects the spatial runoff generation through spatial radiation and wind, therefore should be applied to inform hydrological model development. In addition, the methodology used in the study can serve as a general method for physically-based ET estimation for data sparse regions.

Description: Wlodzimierz Natorf We generalize the result of Lukacs et al. on asymptotic stability of the Schwarzschild metric with respect to perturbations in the Robinson-Trautman class of metrics to the case of Petrov type II twisting metrics, under the condition of asymptotic flatness at future null infinity. The Bondi energy i ... [J. Math. Phys. 53, 022503 (2012)] published Tue Feb 7, 2012.

Description: Denis Borisov and Giuseppe Cardone We consider a planar waveguide with twisted boundary conditions. By twisting we mean a special combination of Dirichlet and Neumann boundary conditions. Assuming that the width of the waveguide goes to zero, we identify the effective (limiting) operator as the width of the waveguide tends to zero, e ... [J. Math. Phys. 53, 023503 (2012)] published Tue Feb 7, 2012.

Description: Chang-Guang Shi and Minoru Hirayama An application of the equation proposed by the present authors, which is equivalent to the static field equation of the Faddeev model, is discussed. Under some assumptions on the space and on the form of the solution, the field equation is reduced to a nonlinear ordinary differential equation of sec ... [J. Math. Phys. 53, 022301 (2012)] published Tue Feb 7, 2012.

Description: The importance of parameter resampling for soil moisture data assimilation into hydrologic models using the particle filter Hydrology and Earth System Sciences, 16, 375-390, 2012 Author(s): D. A. Plaza, R. De Keyser, G. J. M. De Lannoy, L. Giustarini, P. Matgen, and V. R. N. Pauwels The Sequential Importance Sampling with Resampling (SISR) particle filter and the SISR with parameter resampling particle filter (SISR-PR) are evaluated for their performance in soil moisture assimilation and the consequent effect on baseflow generation. With respect to the resulting soil moisture time series, both filters perform appropriately. However, the SISR filter has a negative effect on the baseflow due to inconsistency between the parameter values and the states after the assimilation. In order to overcome this inconsistency, parameter resampling is applied along with the SISR filter, to obtain consistent parameter values with the analyzed soil moisture state. Extreme parameter replication, which could lead to a particle collapse, is avoided by the perturbation of the parameters with white noise. Both the modeled soil moisture and baseflow are improved if the complementary parameter resampling is applied. The SISR filter with parameter resampling offers an efficient way to deal with biased observations. The robustness of the methodology is evaluated for 3 model parameter sets and 3 assimilation frequencies. Overall, the results in this paper indicate that the particle filter is a promising tool for hydrologic modeling purposes, but that an additional parameter resampling may be necessary to consistently update all state variables and fluxes within the model.

Description: Kazuhide Matsuda We completely classify the rational solutions of the Noumi and Yamada system of type A, which is a generalization of the fourth Painleve equation. The rational solutions are classified to three by the Backlund transformation group. ... [J. Math. Phys. 53, 023504 (2012)] published Wed Feb 8, 2012.

Description: Let K be a convex body in R n . We introduce a new affine invariant, which we call K , that can be found in three different ways: as a limit of normalized L p -affine surface areas; as the relative entropy of the cone measure of K and the cone measure of K °; as the limit of the volume difference of K and L p -centroid bodies. We investigate properties of K and of related new invariant quantities. In particular, we show new affine isoperimetric inequalities and we show an ‘information inequality’ for convex bodies.

Description: We establish the precise bounds for the amount of determinacy provable in second-order arithmetic. We show that, for every natural number n , second-order arithmetic can prove that determinacy holds for Boolean combinations of n many classes, but it cannot prove that all finite Boolean combinations of classes are determined. More specifically, we prove that , but that , where is the n th level in the difference hierarchy of classes. We also show some conservativity results that imply that reversals for the theorems above are not possible. We prove that, for every true 1 4 sentence T (as, for instance, -DET) and every and .

Description: Evolution of marine storminess in the Belgian part of the North Sea Natural Hazards and Earth System Science, 12, 305-312, 2012 Author(s): D. Van den Eynde, R. De Sutter, and P. Haerens Severe storms have affected European coast lines in the past but knowledge on changes in storminess for the last decades is still sparse. Climate change is assumed to be a main driving factor with the potential to induce changes on the intensity, duration and frequency of powerful marine storms, including a long-term influence on peak wind speeds, surges and waves. It is, therefore, important to investigate whether in the last decades changes in the magnitude of storms, their duration and frequency could be observed. Understanding trends in storminess in the last decades will help to better prepare coastal managers for future events, taking into account potential changes on storm occurrence and magnitude to improve planning of mitigation and adaptation strategies. The purpose of this study was to focus on the evolution of extreme wind conditions, wave height and storm surge levels in the North Sea Region, especially in the Belgian part of the North Sea (BPNS). Based on the analysis performed it is concluded that no clear trend can be observed for the occurrence of significant increasing extreme wind speeds over the BPNS. Furthermore, one can conclude that not enough scientific evidence is available to support scenarios with increased wave height or storminess.

Description: Inferring snow pack ripening and melt out from distributed ground surface temperature measurements The Cryosphere Discussions, 6, 563-591, 2012 Author(s): M.-O. Schmid, S. Gubler, J. Fiddes, and S. Gruber The seasonal snow cover and its melting are heterogeneous both in space and time. Describing and modelling this variability are important because it affects divers phenomena such as runoff, ground temperatures or slope movements. This study investigates the derivation of melting characteristics based on spatial clusters of temperature measurements. Results are based on data from Switzerland where ground surface temperatures were measured with miniature loggers (iButtons) at 40 locations, referred to as footprints. At each footprint, ten iButtons have been distributed randomly few cm below the ground surface over an area of 10 m × 10 m. Footprints span elevations of 2100–3300 m a.s.l. and slope angles of 0–55°, as well as diverse slope expositions and types of surface cover and ground material. Based on two years of temperature data, the basal ripening date and the melt-out date are determined for each iButton, aggregated to the footprint level and further analysed. The date of melt out could be derived for nearly all iButtons, the ripening date could be extracted for only approximately half of them because it requires ground freezing below the snow pack. The variability within a footprint is often considerable and one to three weeks difference between melting or ripening of the points in one footprint is not uncommon. The correlation of mean annual ground surface temperatures, ripening date and melt-out date is moderate, making them useful intuitive complementary measured for model evaluation.

Description: Moving beyond traditional model calibration or how to better identify realistic model parameters: sub-period calibration Hydrology and Earth System Sciences Discussions, 9, 1885-1918, 2012 Author(s): S. Gharari, M. Hrachowitz, F. Fenicia, and H. H. G. Savenije Conceptual hydrological models often rely on calibration for the identification of their parameters. As these models are typically designed to reflect real catchment processes, a key objective of an appropriate calibration strategy is the determination of parameter sets that reflect a "realistic" model behavior. Previous studies have shown that parameter estimates for different calibration periods can be significantly different. This questions model transposability in time, which is one of the key conditions for the set-up of a "realistic" model. This paper presents a new approach that selects parameter sets that provide a consistent model performance in time. The approach consists of confronting model performance in different periods, and selecting parameter sets that are as close as possible to the optimum of each individual sub-period. While aiding model calibration, the approach is also useful as a diagnostic tool, illustrating tradeoffs in the identification of time consistent parameter sets. The approach is demonstrated in a case study where we illustrate the multi-objective calibration of the HyMod hydrological model to a Luxembourgish catchment.

Description: Technical Note: Analytical sensitivity analysis of a two parameter recursive digital baseflow separation filter Hydrology and Earth System Sciences, 16, 451-455, 2012 Author(s): K. Eckhardt A sensitivity analysis for a well-established baseflow separation technique, a two parameter recursive digital filter, is presented. The sensitivity of the calculated baseflow index to errors or uncertainties of the two filter parameters and of the initial baseflow value is analytically ascertained. It is found that the influence of the initial baseflow value is negligible for long time series. The propagation of errors or uncertainties of the two filter parameters into the baseflow index is expressed by a dimensionless sensitivity index, the ratio between the relative error of the baseflow index and the relative error of the respective parameter. Representative index values are derived by application of the resulting equations to 65 North American catchments. In the mean the parameter a , the recession constant, has a stronger influence on the calculated baseflow index than the second filter parameter BFI max . This is favourable in that a can be determined by a recession analysis and therefore should be less uncertain. Whether this finding also applies for a specific catchment can easily be checked by means of the derived equations.

Description: Tian Zhou Xu In this paper, we study the stability of the multi-Jensen mappings in non-Archimedean normed spaces. The results improve and extend some recent results. ... [J. Math. Phys. 53, 023507 (2012)] published Mon Feb 13, 2012.

Description: Stefano De Leo and Gisele Ducati In looking for quaternionic violations of quantum mechanics, we discuss the delay time for pure quaternionic potentials. Our study shows the energy region which amplifies the difference between quaternionic and complex quantum mechanics. ... [J. Math. Phys. 53, 022102 (2012)] published Mon Feb 13, 2012.

Description: Samuel Friot and David Greynat Multiple Mellin-Barnes integrals are often used for perturbative calculations in particle physics. In this context, the evaluation of such objects may be performed through residues calculations which lead to their expression as multiple power series and logarithms of the parameters involved in the p ... [J. Math. Phys. 53, 023508 (2012)] published Mon Feb 13, 2012.

Description: The 2007 flood in the Sahel: causes, characteristics and its presentation in the media and FEWS NET Natural Hazards and Earth System Science, 12, 313-325, 2012 Author(s): C. Samimi, A. H. Fink, and H. Paeth During the rainy season in 2007, reports about exceptional rains and floodings in the Sahel were published in the media, especially in August and September. Institutions and organizations like the World Food Programme (WFP) and FEWS NET put the events on the agenda and released alerts and requested help. The partly controversial picture was that most of the Sahel faced a crisis caused by widespread floodings. Our study shows that the rainy season in 2007 was exceptional with regard to rainfall amount and return periods. In many areas the event had a return period between 1 and 50 yr with high spatial heterogeneity, with the exception of the Upper Volta basin, which yielded return periods of up to 1200 yr. Despite the strong rainfall, the interpretation of satellite images show that the floods were mainly confined to lakes and river beds. However, the study also proves the difficulties in assessing the meteorological processes and the demarcation of flooded areas in satellite images without ground truthing. These facts and the somewhat vague and controversial reports in the media and FEWS NET demonstrate that it is crucial to thoroughly analyze such events at a regional and local scale involving the local population.

Description: Not simply set out in accompaniment of the Greek geometrical text, the diagram also is coaxed into existence manually (using straightedge and compasses) by commands in the text. The marks that a diligent reader thus sequentially produces typically sum, however, to a figure more complex than the provided one and also not (as it is) artful for being synoptically instructive. To provide a figure artfully is to balance multiple desiderata, interlocking the timelessness of insight with the temporality of construction. Our account of the diagram complements those of Manders and Macbeth by more strongly emphasizing practical synthesis.

Description: Tennenbaum's Theorem yields an elegant characterisation of the standard model of arithmetic. Several authors have recently claimed that this result has important philosophical consequences: in particular, it offers us a way of responding to model-theoretic worries about how we manage to grasp the standard model. We disagree. If there ever was such a problem about how we come to grasp the standard model, then Tennenbaum's Theorem does not help. We show this by examining a parallel argument, from a simpler model-theoretic result.

Description: The paper discusses Husserl's phenomenology of mathematics in his Formal and Transcendental Logic (1929). In it Husserl seeks to provide descriptive foundations for mathematics. As sciences and mathematics are normative activities Husserl's attempt is also to describe the norms at work in these disciplines. The description shows that mathematics can be given in several different ways. The phenomenologist's task is to examine whether a given part of mathematics is genuine according to the norms that pertain to the approach in question. The paper will then examine the intuitionistic, formalistic, and structural features of Husserl's philosophy of mathematics.

Description: Factors selection in landslide susceptibility modelling on large scale following the gis matrix method: application to the river Beiro basin (Spain) Natural Hazards and Earth System Science, 12, 327-340, 2012 Author(s): D. Costanzo, E. Rotigliano, C. Irigaray, J. D. Jiménez-Perálvarez, and J. Chacón A procedure to select the controlling factors connected to the slope instability has been defined. It allowed us to assess the landslide susceptibility in the Rio Beiro basin (about 10 km 2 ) over the northeastern area of the city of Granada (Spain). Field and remote (Google EarthTM) recognition techniques allowed us to generate a landslide inventory consisting in 127 phenomena. To discriminate between stable and unstable conditions, a diagnostic area had been chosen as the one limited to the crown and the toe of the scarp of the landslide. 15 controlling or determining factors have been defined considering topographic, geologic, geomorphologic and pedologic available data. Univariate tests, using both association coefficients and validation results of single-variable susceptibility models, allowed us to select the best predictors, which were combined for the unique conditions analysis. For each of the five recognised landslide typologies, susceptibility maps for the best models were prepared. In order to verify both the goodness of fit and the prediction skill of the susceptibility models, two different validation procedures were applied and compared. Both procedures are based on a random partition of the landslide archive for producing a test and a training subset. The first method is based on the analysis of the shape of the success and prediction rate curves, which are quantitatively analysed exploiting two morphometric indexes. The second method is based on the analysis of the degree of fit, by considering the relative error between the intersected target landslides by each of the different susceptibility classes in which the study area was partitioned. Both the validation procedures confirmed a very good predictive performance of the susceptibility models and of the actual procedure followed to select the controlling factors.

Description: Linnebo and Pettigrew's critique in this journal of categorical foundations well emphasizes that the particulars of various categorical foundations matter, and that mathematical practice must be a major consideration. But several categorists named by the authors as proposing categorical foundations do not propose foundations, notably Awodey, and the article's description of current textbook practice seems inaccurate. They say that categorical foundations have justificatory autonomy if and only if mathematics can be justified simply by its practice. Do they seriously believe philosophers may be able to justify some currently unpractised mathematics better than current practice justifies itself?

Description: Given a Calderón–Zygmund singular integral operator, it is an open question whether the Fefferman inequality holds true with u as an arbitrary weight. This inequality is known as the Muckenhoupt–Wheeden conjecture. In this paper we prove that, for a wider class of operators called Rubio de Francia operators, if || u || ≤1, then where the function is slightly bigger than the identity. Applications of this inequality in the setting of rearrangement invariant spaces are given.

Description: We show that whenever m ≤ n , the space of all continuous rational maps from CP m to CP n has the same homology as the space of all continuous maps between these spaces in dimensions smaller than d (2 n – 2 m + 1) – 1. This improves the result of the paper ‘Spaces of rational maps and the Stone–Weierstrass theorem’ ( Topology 45 (2006), 281–293).

Description: A theorem of Davenport, Mirsky, Newman and Rado shows that there does not exist an exact covering system with distinct moduli. Motivated by this, we raise the question whether or not this is true for covering systems in algebraic number fields. We provide an affirmative answer for certain quadratic fields.

Description: The caustic of a smooth surface in the Euclidean 3-space is the envelope of the normal rays to the surface. It is also the locus of the centres of curvature (the focal points) of the surface. This is why it is also referred to as the focal set of the surface. It has Lagrangian singularities and its generic models are given in [V. I. Arnol’d, S. M. Gusein-Zade and A. N. Varchenko, Singularities of Differentiable Maps , Vol. I, Birkhäuser, Boston, 1986]. The aim of this paper is to define the caustic C ( M ) of a smooth surface M embedded in the Minkowski 3-space and to study its geometry. We denote by the locus of degeneracy (LD) the locus of points on M where the metric is degenerate. If M is a closed surface then its LD is not empty. At a point on the LD the ‘normal’ line to M is lightlike and is tangent to M . Also, the focal set of M is not defined at points on the LD. We define the caustic of M as the bifurcation set of the family of distance-squared functions on M . Then C ( M ) coincides with the focal set of M \ LD and provides an extension of the focal set to the LD. We study the local behaviour of the metric on C ( M ).

Description: Impact of spatial resolution on the modelling of the Greenland ice sheet surface mass balance between 1990–2010, using the regional climate model MAR The Cryosphere Discussions, 6, 635-672, 2012 Author(s): B. Franco, X. Fettweis, C. Lang, and M. Erpicum With the aim to force an ice dynamical model, the Greenland ice sheet (GrIS) surface mass balance (SMB) was modelled at different spatial resolutions (15–50 km) for the period 1990–2010, using the regional climate model MAR (Modèle Atmosphérique Régional) forced by the ERA-INTERIM reanalysis. This comparison revealed that (i) the inter-annual variability of the SMB components is consistent within the different spatial resolutions investigated, (ii) the MAR model simulates heavier precipitation on average over the GrIS with diminishing spatial resolution, and (iii) the SMB components (except precipitation) can be derived from a simulation at lower resolution with an ''intelligent'' interpolation. This interpolation can also be used to approximate the SMB components over another topography/ice sheet mask of the GrIS. These results are important for the forcing of an ice dynamical model, needed to enable future projections of the GrIS contribution to sea level rise over the coming centuries.

Description: Large surface meltwater discharge from the Kangerlussuaq sector of the Greenland ice sheet during the record-warm year 2010 explained by detailed energy balance observations The Cryosphere, 6, 199-209, 2012 Author(s): D. van As, A. L. Hubbard, B. Hasholt, A. B. Mikkelsen, M. R. van den Broeke, and R. S. Fausto This study uses data from six on-ice weather stations, calibrated MODIS-derived albedo and proglacial river gauging measurements to drive and validate an energy balance model. We aim to quantify the record-setting positive temperature anomaly in 2010 and its effect on mass balance and runoff from the Kangerlussuaq sector of the Greenland ice sheet. In 2010, the average temperature was 4.9 °C (2.7 standard deviations) above the 1974–2010 average in Kangerlussuaq. High temperatures were also observed over the ice sheet, with the magnitude of the positive anomaly increasing with altitude, particularly in August. Simultaneously, surface albedo was anomalously low in 2010, predominantly in the upper ablation zone. The low albedo was caused by high ablation, which in turn profited from high temperatures and low winter snowfall. Surface energy balance calculations show that the largest melt excess (∼170%) occurred in the upper ablation zone (above 1000 m), where higher temperatures and lower albedo contributed equally to the melt anomaly. At lower elevations the melt excess can be attributed to high atmospheric temperatures alone. In total, we calculate that 6.6 ± 1.0 km 3 of surface meltwater ran off the ice sheet in the Kangerlussuaq catchment in 2010, exceeding the reference year 2009 (based on atmospheric temperature measurements) by ∼150%. During future warm episodes we can expect a melt response of at least the same magnitude, unless a larger wintertime snow accumulation delays and moderates the melt-albedo feedback. Due to the hypsometry of the ice sheet, yielding an increasing surface area with elevation, meltwater runoff will be further amplified by increases in melt forcings such as atmospheric heat.

Description: Investigating riparian groundwater flow close to a losing river using diurnal temperature oscillations at high vertical resolution Hydrology and Earth System Sciences, 16, 473-487, 2012 Author(s): T. Vogt, M. Schirmer, and O. A. Cirpka River-water infiltration is of high relevance for hyporheic and riparian groundwater ecology as well as for drinking water supply by river-bank filtration. Heat has become a popular natural tracer to estimate exchange rates between rivers and groundwater. However, quantifying flow patterns and velocities is impeded by spatial and temporal variations of exchange fluxes, insufficient sensors spacing during field investigations, or simplifying assumptions for analysis or modeling such as uniform flow. The objective of this study is to investigate lateral shallow groundwater flow upon river-water infiltration at the shoreline of the riverbed and in the adjacent riparian zone of the River Thur in northeast Switzerland. Here we have applied distributed temperature sensing (DTS) along optical fibers wrapped around tubes to measure high-resolution vertical temperature profiles of the unsaturated zone and shallow riparian groundwater. Diurnal temperature oscillations were tracked in the subsurface and analyzed by means of dynamic harmonic regression to extract amplitudes and phase angles. Subsequent calculations of amplitude attenuation and time shift relative to the river signal show in detail vertical and temporal variations of heat transport in shallow riparian groundwater. In addition, we apply a numerical two-dimensional heat transport model for the unsaturated zone and shallow groundwater to obtain a better understanding of the observed heat transport processes in shallow riparian groundwater and to estimate the groundwater flow velocity. Our results show that the observed riparian groundwater temperature distribution cannot be described by uniform flow, but rather by horizontal groundwater flow velocities varying over depth. In addition, heat transfer of diurnal temperature oscillations from the losing river through shallow groundwater is influenced by thermal exchange with the unsaturated zone. Neglecting the influence of the unsaturated zone would cause biased interpretation and underestimation of groundwater flow velocities. The combination of high resolution field data and modeling shows the complex hydraulic and thermal processes occurring in shallow riparian groundwater close to losing river sections as well as potential errors sources for interpreting diurnal temperature oscillations in such environments.

Description: Impacts of inhomogeneous landscapes in oasis interior on the oasis self-maintaining mechanism by integrating numerical model with satellite data Hydrology and Earth System Sciences Discussions, 9, 1979-2004, 2012 Author(s): X. Meng, S. Lu, T. Zhang, Y. Ao, S. Li, Y. Bao, L. Wen, and S. Luo Mesoscale meteorological modeling is an important tool to help understand the energy budget of the oasis. While basic dynamic and thermodynamic processes for oasis self-maintaining in the desert environment is well investigated, influence of heterogeneous landscapes of oasis interior on the processes are still important and remain to be investigated. In this study, two simulations are designed for investigating the influence of inhomogeneity. In the first case, land surface parameters including land-use types, vegetation cover fraction, and surface layer soil moisture are derived by satellite remote sensing data from EOS/MODIS, and then be used specify the respective options in the MM5 model, to describe a real inhomogeneity for the oasis interior. In the other run, land use types are set to MM5 default, in which landscapes in the oasis interior is relative uniform, and then surface layer soil moisture and vegetation fraction is set to be averages of the first case for the respective oasis and desert surface lying, to represent a relative homogeneity. Results show that the inhomogeneity leads to a weaker oasis "cold-wet island" effect and a stronger turbulence over the oasis interior, both of which will reduce the oasis-desert secondary circulation and increase the evaporation over the oasis, resulting in a negative impact on the oasis self-protecting mechanism. The simulation of homogeneity indicates that the oasis may be more stable even with relative lower soil moisture if landscapes in the oasis interior are comparatively uniform.

Description: Uncertainty in future solid ice discharge from Antarctica The Cryosphere Discussions, 6, 673-714, 2012 Author(s): R. Winkelmann, A. Levermann, K. Frieler, and M. A. Martin Future solid ice discharge from Antarctica under climate scenarios based on the Extended Concentration Pathways is investigated with the Potsdam Parallel Ice Sheet Model (PISM-PIK), a shallow model with a consistent representation of the ice flow in sheet, shelves and the transition zone. Both the uncertainty in the climate forcing as well as the intra-model uncertainty are combined into a probability distribution for solid ice discharge from Antarctica until the year 2500 under the ECP scenarios: All simulations are performed for a 81-member perturbed-physics ensemble and the likely ranges of surface and ocean warming under the emission pathways derived from the results of 20 CMIP3-AOGCMS. The effects of surface warming, ocean warming and increased precipitation on solid ice discharge are separately considered. We find that solid ice discharge caused by enhanced sub-shelf melting exceeds that caused by surface warming. Increasing precipitation leads to a change from net sea-level rise to sea-level drop. Our results suggest that the history of the ice-sheet plays an important role with respect to projections of solid ice discharge. Although all climate-change-forced simulations begin with the year 1850, the ice discharge around 2000 is significantly smaller than observed. Observed changes in ice discharge are reached around 2077 under the ECP-8.5 scenario. During the subsequent century, ice discharge reaches up to 0.24 m.

Description: H. Hassanabadi, E. Maghsoodi, S. Zarrinkamar, and H. Rahimov Approximate analytical solutions of spin and pseudospin symmetry limits of Dirac equation are reported for the generalized Poschl-Teller scalar and vector potentials and a Coulomb tensor interaction by Nikiforov-Uvarov method. On the contrary to the cumbersome numerical procedures, the analytical ap ... [J. Math. Phys. 53, 022104 (2012)] published Wed Feb 15, 2012.

Description: Floodwater utilisation values of wetland services – a case study in Northeastern China Natural Hazards and Earth System Science, 12, 341-349, 2012 Author(s): S. B. Lü, S. G. Xu, and F. Feng Water plays a significant role in wetlands. Floodwater utilisation in wetlands brings a wide range of wetland services, from goods production and water regulation to animal protection and aesthetics related to water supply in wetlands. In this study, the floodwater utilisation values of wetland services were estimated within the Momoge wetland and Xianghai wetland in western Jilin province of northeastern China. From 2003 to 2008, the floodwater diverted from the Nenjiang and Tao'er River is 381 million m 3 , which translates into a monetary value of approximately 1.35 billion RMB in 2008 (RMB: Chinese Currency, RMB 6.80 = US$ 1), and the ratio of economic value, eco-environmental value, and social value is 1:12:2. Besides the monetary value of the water itself, excessive floodwater utilisation may bring losses to wetlands; the threshold floodwater utilisation volumes in wetlands are discussed. Floodwater utilisation can alleviate water shortages in wetlands, and the evaluation of floodwater utilisation in wetland services in monetary terms is a guide for the effective use of the floodwater resources and for the conservation of wetlands.

Description: Tamaghna Hazra, V. K. Chandrasekar, R. Gladwin Pradeep, and M. Lakshmanan General solutions of nonlinear ordinary differential equations (ODEs) are in general difficult to find; although, powerful integrability techniques exist in the literature for this purpose. It has been shown that in some scalar cases particular solutions may be found with little effort if it is poss ... [J. Math. Phys. 53, 023511 (2012)] published Wed Feb 15, 2012.

Description: Quantification of biophysical parameters of urban trees is important for urban planning, and for assessing carbon sequestration and ecosystem services. Airborne lidar has been used extensively in recent years to estimate biophysical parameters of trees in forested ecosystems. However, similar studies are largely lacking for individual trees in urban landscapes. Prediction models to estimate biophysical parameters such as height, crown area, diameter at breast height, and biomass for over two thousand individual trees were developed using best subsets multiple linear regression for a study area in central Oklahoma, USA using point cloud distributional metrics from an Optech ALTM 2050 lidar system. A high level of accuracy was attained for estimating individual tree height (R2 = 0.89), dbh (R2 = 0.82), crown diameter (R2 = 0.90), and biomass (R2 = 0.67) using lidar-based metrics for pooled data of all tree species. More variance was explained in species-specific estimates of biomass (R2 = 0.68 for Juniperus virginiana to 0.84 for Ulmus parviflora) than in estimates from broadleaf deciduous (R2 = 0.63) and coniferous (R2 = 0.45) taxonomic groups—or the data set analysed as a whole (R2 = 0.67). The metric crown area performed particularly well for most of the species-specific biomass equations, which suggests that tree crowns should be delineated accurately, whether manually or using automatic individual tree detection algorithms, to obtain a good estimation of biomass using lidar-based metrics.

Description: The Lumen Gini Coefficient: a satellite imagery derived human development index Social Geography Discussions, 8, 27-59, 2012 Author(s): C. D. Elvidge, K. E. Baugh, S. J. Anderson, P. C. Sutton, and T. Ghosh The "Lumen Gini Coefficient" is a simple, objective, spatially explicit and globally available empirical measurement of human development derived solely from nighttime satellite imagery and population density. There is increasing recognition that the distribution of wealth and income amongst the population in a nation or region correlates strongly with both the overall happiness of that population and the environmental quality of that nation or region. Measuring the distribution of wealth and income at national and regional scales is an interesting and challenging problem. Gini coefficients derived from Lorenz curves are a well-established method of measuring income distribution. Nonetheless, there are many shortcomings of the Gini coefficient as a measure of income or wealth distribution. Gini coefficients are typically calculated using national level data on the distribution of income through the population. Such data are not available for many countries and the results are generally limited to single values representing entire countries. In this paper we develop an alternative measure of the distribution of "human development", called the "Lumen Gini coefficient", that is derived without the use of monetary measures of wealth and is capable of providing a spatial depiction of differences in development within countries.

Description: Motivation: High-throughput sequencing (HTS) technologies have made low-cost sequencing of large numbers of samples commonplace. An explosion in the type, not just number, of sequencing experiments has also taken place including genome re-sequencing, population-scale variation detection, whole transcriptome sequencing and genome-wide analysis of protein-bound nucleic acids. Results: We present Artemis as a tool for integrated visualization and computational analysis of different types of HTS datasets in the context of a reference genome and its corresponding annotation. Availability: Artemis is freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute websites: http://www.sanger.ac.uk/resources/software/artemis/ . Contact: artemis@sanger.ac.uk ; tjc@sanger.ac.uk

Description: : microRibonucleic acid (miRNAs) are small regulatory molecules that act by mRNA degradation or via translational repression. Although many miRNAs are ubiquitously expressed, a small subset have differential expression patterns that may give rise to tissue-specific complexes. Motivation: This work studies gene targeting patterns amongst miRNAs with differential expression profiles, and links this to control and regulation of protein complexes. Results: We find that, when a pair of miRNAs are not expressed in the same tissues, there is a higher tendency for them to target the direct partners of the same hub proteins. At the same time, they also avoid targeting the same set of hub-spokes. Moreover, the complexes corresponding to these hub-spokes tend to be specific and nonoverlapping. This suggests that the effect of miRNAs on the formation of complexes is specific. Contact: wongls@comp.nus.edu.sg Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Small interfering RNAs (siRNAs) are produced from much longer sequences of double-stranded RNA precursors through cleavage by Dicer or a Dicer-like protein. These small RNAs play a key role in genetic and epigenetic regulation; however, a full understanding of the mechanisms by which they operate depends on the characterization of the precursors from which they are derived. Results: High-throughput sequencing of small RNA populations allows the locations of the double-stranded RNA precursors to be inferred. We have developed methods to analyse small RNA sequencing data from multiple biological sources, taking into account replicate information, to identify robust sets of siRNA precursors. Our methods show good performance on both a set of small RNA sequencing data in Arabidopsis thaliana and simulated datasets. Availability: Our methods are available as the Bioconductor ( www.bioconductor.org ) package segmentSeq (version 1.5.6 and above). Contact: tjh48@cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Intrinsically disordered regions are key for the function of numerous proteins, and the scant available experimental annotations suggest the existence of different disorder flavors. While efficient predictions are required to annotate entire genomes, most existing methods require sequence profiles for disorder prediction, making them cumbersome for high-throughput applications. Results: In this work, we present an ensemble of protein disorder predictors called ESpritz. These are based on bidirectional recursive neural networks and trained on three different flavors of disorder, including a novel NMR flexibility predictor. ESpritz can produce fast and accurate sequence-only predictions, annotating entire genomes in the order of hours on a single processor core. Alternatively, a slower but slightly more accurate ESpritz variant using sequence profiles can be used for applications requiring maximum performance. Two levels of prediction confidence allow either to maximize reasonable disorder detection or to limit expected false positives to 5%. ESpritz performs consistently well on the recent CASP9 data, reaching a S w measure of 54.82 and area under the receiver operator curve of 0.856. The fast predictor is four orders of magnitude faster and remains better than most publicly available CASP9 methods, making it ideal for genomic scale predictions. Conclusions: ESpritz predicts three flavors of disorder at two distinct false positive rates, either with a fast or slower and slightly more accurate approach. Given its state-of-the-art performance, it can be especially useful for high-throughput applications. Availability: Both a web server for high-throughput analysis and a Linux executable version of ESpritz are available from: http://protein.bio.unipd.it/espritz/ Contact: silvio.tosatto@unipd.it Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Clustering protein structures is an important task in structural bioinformatics. De novo structure prediction, for example, often involves a clustering step for finding the best prediction. Other applications include assigning proteins to fold families and analyzing molecular dynamics trajectories. Results: We present Pleiades, a novel approach to clustering protein structures with a rigorous mathematical underpinning. The method approximates clustering based on the root mean square deviation by first mapping structures to Gauss integral vectors—which were introduced by Røgen and co-workers—and subsequently performing K-means clustering. Conclusions: Compared to current methods, Pleiades dramatically improves on the time needed to perform clustering, and can cluster a significantly larger number of structures, while providing state-of-the-art results. The number of low energy structures generated in a typical folding study, which is in the order of 50 000 structures, can be clustered within seconds to minutes. Contact: thamelry@binf.ku.dk ; harder@binf.ku.dk Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Transmembrane β barrel proteins (TMBs) are found in the outer membrane of Gram-negative bacteria, chloroplast and mitochondria. They play a major role in the translocation machinery, pore formation, membrane anchoring and ion exchange. TMBs are also promising targets for antimicrobial drugs and vaccines. Given the difficulty in membrane protein structure determination, computational methods to identify TMBs and predict the topology of TMBs are important. Results: Here, we present BOCTOPUS; an improved method for the topology prediction of TMBs by employing a combination of support vector machines (SVMs) and Hidden Markov Models (HMMs). The SVMs and HMMs account for local and global residue preferences, respectively. Based on a 10-fold cross-validation test, BOCTOPUS performs better than all existing methods, reaching a Q3 accuracy of 87%. Further, BOCTOPUS predicted the correct number of strands for 83% proteins in the dataset. BOCTOPUS might also help in reliable identification of TMBs by using it as an additional filter to methods specialized in this task. Availability: BOCTOPUS is freely available as a web server at: http://boctopus.cbr.su.se/ . The datasets used for training and evaluations are also available from this site. Contact: arne@bioinfo.se Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: High-dimensional data such as microarrays have created new challenges to traditional statistical methods. One such example is on class prediction with high-dimension, low-sample size data. Due to the small sample size, the sample mean estimates are usually unreliable. As a consequence, the performance of the class prediction methods using the sample mean may also be unsatisfactory. To obtain more accurate estimation of parameters some statistical methods, such as regularizations through shrinkage, are often desired. Results: In this article, we investigate the family of shrinkage estimators for the mean value under the quadratic loss function. The optimal shrinkage parameter is proposed under the scenario when the sample size is fixed and the dimension is large. We then construct a shrinkage-based diagonal discriminant rule by replacing the sample mean by the proposed shrinkage mean. Finally, we demonstrate via simulation studies and real data analysis that the proposed shrinkage-based rule outperforms its original competitor in a wide range of settings. Contact: tongt@hkbu.edu.hk

Description: Motivation: The advent of high-throughput sequencing technologies is revolutionizing our ability in discovering and genotyping DNA copy number variants (CNVs). Read count-based approaches are able to detect CNV regions with an unprecedented resolution. Although this computational strategy has been recently introduced in literature, much work has been already done for the preparation, normalization and analysis of this kind of data. Results: Here we face the many aspects that cover the detection of CNVs by using read count approach. We first study the characteristics and systematic biases of read count distributions, focusing on the normalization methods designed for removing these biases. Subsequently, we compare the algorithms designed to detect the boundaries of CNVs and we investigate the ability of read count data to predict the exact number of DNA copy. Finally, we review the tools publicly available for analysing read count data. To better understand the state of the art of read count approaches, we compare the performance of the three most widely used sequencing technologies (Illumina Genome Analyzer, Roche 454 and Life Technologies SOLiD) in all the analyses that we perform. Contact: albertomagi@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: We investigate and quantify the generalizability of the white blood cell (WBC) transcriptome to the general, multiorgan transcriptome. We use data from the NCBI's Gene Expression Omnibus (GEO) public repository to define two datasets for comparison, WBC and OO (Other Organ) sets. Results: Comprehensive pair-wise correlation and expression level profiles are calculated for both datasets (with sizes of 81 and 1463, respectively). We have used mapping and ranking across the Gene Ontology (GO) categories to quantify similarity between the two sets. GO mappings of the most correlated and highly expressed genes from the two datasets tightly match, with the notable exceptions of components of the ribosome, cell adhesion and immune response. That is, 10 877 or 48.8% of all measured genes do not change 〉10% of rank range between WBC and OO; only 878 (3.9%) change rank 〉50%. Two trans -tissue gene lists are defined, the most changing and the least changing genes in expression rank. We also provide a general, quantitative measure of the probability of expression rank and correlation profile in the OO system given the expression rank and correlation profile in the WBC dataset. Contact: vvaltchinov@partners.org Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: The understanding of the molecular sources for diseases like cancer can be significantly improved by computational models. Recently, Boolean networks have become very popular for modeling signaling and regulatory networks. However, such models rely on a set of Boolean functions that are in general not known. Unfortunately, while detailed information on the molecular interactions becomes available in large scale through electronic databases, the information on the Boolean functions does not become available simultaneously and has to be included manually into the models, if at all known. Results: We propose a new Boolean approach which can directly utilize the mechanistic network information available through modern databases. The Boolean function is implicitly defined by the reaction mechanisms. Special care has been taken for the treatment of kinetic features like inhibition. The method has been applied to a signaling model combining the Wnt and MAPK pathway. Availability: A sample C++ implementation of the proposed method is available for Linux and compatible systems through http://code.google.com/p/libscopes/wiki/Paper2011 Contact: handorf@physik.hu-berlin.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Multiple sequence alignment (MSA) is a core method in bioinformatics. The accuracy of such alignments may influence the success of downstream analyses such as phylogenetic inference, protein structure prediction, and functional prediction. The importance of MSA has lead to the proliferation of MSA methods, with different objective functions and heuristics to search for the optimal MSA. Different methods of inferring MSAs produce different results in all but the most trivial cases. By measuring the differences between inferred alignments, we may be able to develop an understanding of how these differences (i) relate to the objective functions and heuristics used in MSA methods, and (ii) affect downstream analyses. Results: We introduce four metrics to compare MSAs, which include the position in a sequence where a gap occurs or the location on a phylogenetic tree where an insertion or deletion (indel) event occurs. We use both real and synthetic data to explore the information given by these metrics and demonstrate how the different metrics in combination can yield more information about MSA methods and the differences between them. Availability: MetAl is a free software implementation of these metrics in Haskell. Source and binaries for Windows, Linux and Mac OS X are available from http://kumiho.smith.man.ac.uk/whelan/software/metal/ . Contact: simon.whelan@manchester.ac.uk