Tracing of 15N in a mountain spruce forest: comparison of experimental data with th TRACE model

Despite numerous studies about nitrogen-cycling in forest ecosystems, many uncertainties remain, especially regarding the longer-term nitrogen accumulation. To contribute to filling this gap, the dynamic process-based model TRACE, with the ability to simulate 15N tracer redistribution in forest ecosystems was used to study N cycling processes in a mountain spruce forest of the northern edge of the Alps in Switzerland (Alptal, SZ). Most modeling analyses of N-cycling and C-N interactions have very limited ability to determine whether the process interactions are captured correctly. Because the interactions in such a system are complex, it is possible to get the whole-system C and N cycling right in a model without really knowing if the way the model combines fine-scale interactions to derive whole-system cycling is correct. With the possibility to simulate 15N tracer redistribution in ecosystem compartments, TRACE features a very powerful tool for the validation of fine-scale processes captured by the model. We first adapted the model to the new site (Alptal, Switzerland; long-term low-dose N-amendment experiment) by including a new algorithm for preferential water flow and by parameterizing of differences in drivers such as climate, N deposition and initial site conditions. After the calibration of key rates such as NPP and SOM turnover, we simulated patterns of 15N redistribution to compare against 15N field observations from a large-scale labeling experiment. The comparison of 15N field data with the modeled redistribution of the tracer in the soil horizons and vegetation compartments shows that the majority of fine-scale processes are captured satisfactorily. Particularly, the model is able to reproduce the fact that the largest part of the N deposition is immobilized in the soil. The discrepancies of 15N recovery in the LF and M soil horizon can be explained by the application method of the tracer and by the retention of the applied tracer by the well developed moss layer, which is not considered in the model. Discrepancies in the dynamics of foliage and litterfall 15N recovery were also observed and are related to the longevity of the needles in our mountain forest. As a next step, we will use the final Alptal version of the model to calculate the effects of climate change (temperature, CO2) and N deposition on ecosystem C sequestration in this regionally representative Norway spruce (Picea abies) stand.

Debris-flow activity in abandoned channels of the Manival torrent reconstructed with LiDAR and tree-ring data

Hydrogeomorphic processes are a major threat in many parts of the Alps, where they periodically damage infrastructure, disrupt transportation corridors or even cause loss of life. Nonetheless, past torrential activity and the analysis of areas affected during particular events remain often imprecise. It was therefore the purpose of this study to reconstruct spatio-temporal patterns of past debris-flow activity in abandoned channels on the forested cone of the Manival torrent (Massif de la Chartreuse, French Prealps). A Light Detecting and Ranging (LiDAR) generated Digital Elevation Model (DEM) was used to identify five abandoned channels and related depositional forms (lobes, lateral levees) in the proximal alluvial fan of the torrent. A total of 156 Scots pine trees (Pinus sylvestris L.) with clear signs of debris flow events was analyzed and growth disturbances (GD) assessed, such as callus tissue, the onset of compression wood or abrupt growth suppression. In total, 375 GD were identified in the tree-ring samples, pointing to 13 debris-flow events for the period 1931–2008. While debris flows appear to be very common at Manival, they have only rarely propagated outside the main channel over the past 80 years. Furthermore, analysis of the spatial distribution of disturbed trees contributed to the identification of four patterns of debris-flow routing and led to the determination of three preferential breakout locations. Finally, the results of this study demonstrate that the temporal distribution of debris flows did not exhibit significant variations since the beginning of the 20th century.

A Faster Circular Binary Segmentation Algorithm for the Analysis of Array CGH Data

Motivation: Array CGH technologies enable the simultaneous measurement of DNA copy number for thousands of sites on a genome. We developed the circular binary segmentation (CBS) algorithm to divide the genome into regions of equal copy number (Olshen {\it et~al}, 2004). The algorithm tests for change-points using a maximal $t$-statistic with a permutation reference distribution to obtain the corresponding $p$-value. The number of computations required for the maximal test statistic is $O(N^2),$ where $N$ is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster. algorithm. Results: We present a hybrid approach to obtain the $p$-value of the test statistic in linear time. We also introduce a rule for stopping early when there is strong evidence for the presence of a change. We show through simulations that the hybrid approach provides a substantial gain in speed with only a negligible loss in accuracy and that the stopping rule further increases speed. We also present the analysis of array CGH data from a breast cancer cell line to show the impact of the new approaches on the analysis of real data. Availability: An R (R Development Core Team, 2006) version of the CBS algorithm has been implemented in the ``DNAcopy'' package of the Bioconductor project (Gentleman {\it et~al}, 2004). The proposed hybrid method for the $p$-value is available in version 1.2.1 or higher and the stopping rule for declaring a change early is available in version 1.5.1 or higher.

Data Quality Assessment of Ungated Flow Cytometry Data in High

Background: The recent development of semi-automated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical when developing new high throughput technologies and their associated information services. Our experience suggests that significant bottlenecks remain in the development of high throughput flow cytometry methods for data analysis and display. Especially, data quality control and quality assessment are crucial steps in processing and analyzing high throughput flow cytometry data. Methods: We propose a variety of graphical exploratory data analytic tools for exploring ungated flow cytometry data. We have implemented a number of specialized functions and methods in the Bioconductor package rflowcyt. We demonstrate the use of these approaches by investigating two independent sets of high throughput flow cytometry data. Results: We found that graphical representations can reveal substantial non-biological differences in samples. Empirical Cumulative Distribution Function and summary scatterplots were especially useful in the rapid identification of problems not identified by manual review. Conclusions: Graphical exploratory data analytic tools are quick and useful means of assessing data quality. We propose that the described visualizations should be used as quality assessment tools and where possible, be used for quality control.

Quickbird satellite imagery for riparian management : characterizing riparian filter strips and detecting concentrated flow in an agricultural watershed

Riparian ecology plays an important part in the filtration of sediments from upland agricultural lands. The focus of this work makes use of multispectral high spatial resolution remote sensing imagery (Quickbird by Digital Globe) and geographic information systems (GIS) to characterize significant riparian attributes in the USDA’s experimental watershed, Goodwin Creek, located in northern Mississippi. Significant riparian filter characteristics include the width of the strip, vegetation properties, soil properties, topography, and upland land use practices. The land use and vegetation classes are extracted from the remotely sensed image with a supervised maximum likelihood classification algorithm. Accuracy assessments resulted in an acceptable overall accuracy of 84 percent. In addition to sensing riparian vegetation characteristics, this work addresses the issue of concentrated flow bypassing a riparian filter. Results indicate that Quickbird multispectral remote sensing and GIS data are capable of determining riparian impact on filtering sediment. Quickbird imagery is a practical solution for land managers to monitor the effectiveness of riparian filtration in an agricultural watershed.

Technical throughput of material flow systems required to achieve design flow – determined by simulation with aniteration algorithm

This article deals with complex material flow systems and series connections of conveyor and op-erating elements. These can be characterised by a specific availability. The thus resultant overall availabil-ity of necessary “technical throughput” of the individual elements for the achievement of a specified throughput. When the conveyor and operating elements are subjected to a stochastic distribution, the interposition of buffers is necessary but these can also lead to a reduction of the necessary throughput due faults. The system behaviour of complex installations can only be investigated by simulation. The parame-ter changes required in order to achieve specific target values can also be determined by simulation runs in iteration loops.

Flow-R, a model for susceptibility mapping of debris flows and other gravitational hazards at a regional scale

The development of susceptibility maps for debris flows is of primary importance due to population pressure in hazardous zones. However, hazard assessment by process-based modelling at a regional scale is difficult due to the complex nature of the phenomenon, the variability of local controlling factors, and the uncertainty in modelling parameters. A regional assessment must consider a simplified approach that is not highly parameter dependant and that can provide zonation with minimum data requirements. A distributed empirical model has thus been developed for regional susceptibility assessments using essentially a digital elevation model (DEM). The model is called Flow-R for Flow path assessment of gravitational hazards at a Regional scale (available free of charge under http://www.flow-r.org) and has been successfully applied to different case studies in various countries with variable data quality. It provides a substantial basis for a preliminary susceptibility assessment at a regional scale. The model was also found relevant to assess other natural hazards such as rockfall, snow avalanches and floods. The model allows for automatic source area delineation, given user criteria, and for the assessment of the propagation extent based on various spreading algorithms and simple frictional laws. We developed a new spreading algorithm, an improved version of Holmgren's direction algorithm, that is less sensitive to small variations of the DEM and that is avoiding over-channelization, and so produces more realistic extents. The choices of the datasets and the algorithms are open to the user, which makes it compliant for various applications and dataset availability. Amongst the possible datasets, the DEM is the only one that is really needed for both the source area delineation and the propagation assessment; its quality is of major importance for the results accuracy. We consider a 10 m DEM resolution as a good compromise between processing time and quality of results. However, valuable results have still been obtained on the basis of lower quality DEMs with 25 m resolution.

Testing an alternative search algorithm for compound identification with the 'Wiley Registry of Tandem Mass Spectral Data. MSforID'

A tandem mass spectral database system consists of a library of reference spectra and a search program. State-of-the-art search programs show a high tolerance for variability in compound-specific fragmentation patterns produced by collision-induced decomposition and enable sensitive and specific 'identity search'. In this communication, performance characteristics of two search algorithms combined with the 'Wiley Registry of Tandem Mass Spectral Data, MSforID' (Wiley Registry MSMS, John Wiley and Sons, Hoboken, NJ, USA) were evaluated. The search algorithms tested were the MSMS search algorithm implemented in the NIST MS Search program 2.0g (NIST, Gaithersburg, MD, USA) and the MSforID algorithm (John Wiley and Sons, Hoboken, NJ, USA). Sample spectra were acquired on different instruments and, thus, covered a broad range of possible experimental conditions or were generated in silico. For each algorithm, more than 30,000 matches were performed. Statistical evaluation of the library search results revealed that principally both search algorithms can be combined with the Wiley Registry MSMS to create a reliable identification tool. It appears, however, that a higher degree of spectral similarity is necessary to obtain a correct match with the NIST MS Search program. This characteristic of the NIST MS Search program has a positive effect on specificity as it helps to avoid false positive matches (type I errors), but reduces sensitivity. Thus, particularly with sample spectra acquired on instruments differing in their Setup from tandem-in-space type fragmentation, a comparably higher number of false negative matches (type II errors) were observed by searching the Wiley Registry MSMS.

Content-Aware Delivery of Scalable Video in Network Coding Enabled Named Data Networks

In this work, we propose a novel network coding enabled NDN architecture for the delivery of scalable video. Our scheme utilizes network coding in order to address the problem that arises in the original NDN protocol, where optimal use of the bandwidth and caching resources necessitates the coordination of the forwarding decisions. To optimize the performance of the proposed network coding based NDN protocol and render it appropriate for transmission of scalable video, we devise a novel rate allocation algorithm that decides on the optimal rates of Interest messages sent by clients and intermediate nodes. This algorithm guarantees that the achieved flow of Data objects will maximize the average quality of the video delivered to the client population. To support the handling of Interest messages and Data objects when intermediate nodes perform network coding, we modify the standard NDN protocol and introduce the use of Bloom filters, which store efficiently additional information about the Interest messages and Data objects. The proposed architecture is evaluated for transmission of scalable video over PlanetLab topologies. The evaluation shows that the proposed scheme performs very close to the optimal performance