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    Microaggregates are a relatively unique microenvironment for fungal activity. ? The soil microbial

    community incorporated 4 times more root-C than residue-C. ? Composition of C processing

    microbial communities was not linked to C stabilization.

     A generic readout environment for prototype pixel detectors Original 143 Research Article

    Nuclear Instruments and Methods in Physics Research Section A:

    Purchase Accelerators, Spectrometers, Detectors and Associated Equipment,

    $ 35.95 Volume 623, Issue 1, 1 November 2010, Pages 531-533

    Marcos Turqueti, Ryan Rivera, Alan Prosser, Simon Kwan

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    Pixel detectors for experimental particle physics research have been implemented with a variety of readout formats and potentially generate massive amounts of data. Examples include the PSI46 device for the Compact Muon Solenoid (CMS) experiment which implements an analog readout, the Fermilab FPIX2.1 device with a digital readout, and the Fermilab Vertically Integrated Pixel device. The Electronic Systems Engineering Department of the

    Computing Division at the Fermi National Accelerator Laboratory has

    developed a data acquisition system flexible and powerful enough to meet the

    various needs of these devices to support laboratory test bench as well as test

    beam applications. The system is called CAPTAN (Compact And

    Programmable daTa Acquisition Node) and is characterized by its flexibility, versatility and scalability by virtue of several key architectural features. These include a vertical bus that permits the user to stack multiple boards, a gigabit Ethernet link that permits high speed communications to the system and a core

    group of boards that provide specific processing and readout capabilities for

    the system. System software based on distributed computing techniques

    supports an expandable network of CAPTANs. In this paper, we describe the

    system architecture and give an overview of its capabilities.

Article Outline

    1. Introduction

    2. The CAPTAN architecture

    2.1. The vertical bus

    2.2. The system bus

    2.3. The horizontal bus

    2.4. The node components and constraints

    3. Conclusion


     Debugging hygienic macros Original Research Article 144 Science of Computer Programming, Volume 75, Issue 7, 1 July

    2010, Pages 496-515

    Purchase Ryan Culpepper, Matthias Felleisen

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    Over the past two decades, Scheme macros have evolved into a powerful API

    for the compiler front end. Like Lisp macros, their predecessors, Scheme macros expand source programs into a small core language; unlike Lisp

    systems, Scheme macro expanders preserve lexical scoping, and advanced

    Scheme macro systems handle other important properties such as source location. Using such macros, Scheme programmers now routinely develop the

    ultimate abstraction: embedded domain-specific programming languages.

    Unfortunately, a typical Scheme programming environment provides little

    support for macro development. This lack makes it difficult for programmers to debug their macros and for novices to study the behavior of macros. In

    response, we have developed a stepping debugger specialized to the concerns

    of macro expansion. This debugger presents the macro expansion process as

    a linear rewriting sequence of annotated terms; it graphically illustrates the binding structure of the program as expansion reveals it; and it adapts to the programmer’s level of abstraction, hiding details of syntactic forms that the

    programmer considers built-in.

     An integrated system based on physiological signals for the 145 assessment of affective states in patients with anxiety

     disorders Original Research Article

    Purchase Biomedical Signal Processing and Control, In Press, Corrected

    $ 41.95 Proof, Available online 28 December 2010

    Christos D. Katsis, Nikolaos S. Katertsidis, Dimitrios I. Fotiadis

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    Anxiety disorders are psychiatric disorders characterized by a constant and abnormal anxiety that interferes with daily-life activities. Their high prevalence

    in the general population and the severe limitations they cause have drawn

    attention to the development of new and efficient strategies for their treatment. In this work we describe the INTREPID system which provides an innovative

    and intelligent solution for the monitoring of patients with anxiety disorders

    during therapeutic sessions. It recognizes an individual's affective state based on 5 pre-defined classes (relaxed, neutral, startled, apprehensive and very apprehensive), from physiological data collected via non-invasive technologies

    (blood volume pulse, heart rate, galvanic skin response and respiration). The

    system is validated using data obtained through an emotion elicitation experiment based on the International Affective Picture System. Four different

    classification algorithms are implemented (Artificial Neural Networks, Support

    Vector Machines, Random Forests and a Neuro-Fuzzy System). The overall

    classification accuracy achieved is 84.3%.

Article Outline

    1. Introduction

    2. Materials and methods

    2.1. Biosignals

    2.2. Biosignal processing

    2.3. INTREPID architecture

    3. Results

    4. Discussion

    5. Conclusions



    Parallelized computation for computer simulation of electrocardiograms 146 using personal computers with multi-core CPU and general-purpose

     GPU Original Research Article

    Purchase Computer Methods and Programs in Biomedicine, Volume 100,

    $ 31.50 Issue 1, October 2010, Pages 87-96

    Wenfeng Shen, Daming Wei, Weimin Xu, Xin Zhu, Shizhong Yuan

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    Biological computations like electrocardiological modelling and simulation

    usually require high-performance computing environments. This paper

    introduces an implementation of parallel computation for computer simulation

    of electrocardiograms (ECGs) in a personal computer environment with an Intel

    CPU of Core (TM) 2 Quad Q6600 and a GPU of Geforce 8800GT, with software support by OpenMP and CUDA. It was tested in three parallelization device setups: (a) a four-core CPU without a general-purpose GPU, (b) a general-purpose GPU plus 1 core of CPU, and (c) a four-core CPU plus a

    general-purpose GPU. To effectively take advantage of a multi-core CPU and a general-purpose GPU, an algorithm based on load-prediction dynamic scheduling was developed and applied to setting (c). In the simulation with 1600 time steps, the speedup of the parallel computation as compared to the

    serial computation was 3.9 in setting (a), 16.8 in setting (b), and 20.0 in setting (c). This study demonstrates that a current PC with a multi-core CPU and a general-purpose GPU provides a good environment for parallel computations in

    biological modelling and simulation studies.

    Article Outline

    1. Introduction

    2. CUDA and OpenMP

    2.1. CUDA

    2.2. OpenMP

    3. Analysis of serial algorithm for computer simulation of ECGs

    4. Parallelization of computer simulation of ECGs

    4.1. Parallelization using OpenMP based on multi-core CPU

    4.2. Parallelization using CUDA based on a general-purpose GPU

    4.3. Parallelization using CUDA and OpenMP based on a general-purpose GPU and a multi-core CPU

    5. Experiments and results

    6. Discussion

    6.1. Parallelization using OpenMP

    6.2. Parallelization using CUDA

    6.3. Parallelization based on CUDA and OpenMP

    7. Conclusion



     Spacetime and hybrid algorithms for the passive acoustic localisation 147 of sperm whales and vessels Original Research Article

    Applied Acoustics, Volume 71, Issue 11, November 2010, Pages

    Purchase 1000-1010

    $ 41.95 L. Houégnigan, S. Zaugg, M. van der Schaar, M. André

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    In the frame of the European Sea-floor Observatory Network (ESONET) and in

    preparation of the Demonstration Mission Listening to the Deep-Ocean

    Environment (LIDO) algorithms for the automated real-time detection,

    classification and localisation of cetaceans have been developed.

    Such Passive Acoustic Monitoring techniques have the potential to play a key

    role in cetaceans’ conservation for they allow a non-invasive study of their

    behaviour, a better knowledge of their population dynamics, and a better understanding of their dynamic relationship with their environment. This paper investigates the development of efficient and accurate techniques to be used as the basis of a localisation module for an automated real-time Passive

    Acoustic Monitoring system.

    An opportunity to assess the capabilities of the developed localisation modules was given by recordings collected with a bottom-mounted (around 2080 m

    depth) tetrahedral compact hydrophone array located offshore the port of Catania (Sicily) during the NEMO-ONDE campaign in the years 20052006 by

    INFN and CIBRA [2]. A well-known class of methods for acoustic source

    localisation is based on time differences of arrival (TDOA). Its capabilities have shown to be useful even in adverse situations (i.e., few sensors, high noise

    levels and/or poor calibration). A second class of methods, the spacetime

    methods, originated in underwater applications such as sonar but reached its most significant achievements over the last 20 years in digital communications

    with recent progress in the treatment of broadband signals. These

    developments are here revisited under the scope of the localisation and tracking of cetacean vocalisations.

    Various broadband spacetime methods were implemented and allowed to map the sound radiated during the detected clicks and to consequently localise

    both sperm whales and vessels. Hybrid methods were also developed which improved the robustness of spacetime methods to noise and reverberation and reduced processing time. In most cases, the small variance obtained for these estimates lessened the necessity of additional statistical clustering. Even

    though not independently confirmed by sightings, the tracks derived in the

    proposed frame can be considered to be consistent with the known movements

    of sperm whales and vessels.

    Article Outline

    1. Introduction

    1.1. General frame of the technical developments

    1.1.1. Propagation model

    2. Methods for the localisation of cetaceans

    2.1. Methods based on time differences of arrival (TDOA)

    2.1.1. Time-delay estimation (TDE)

    2.1.2. Time-delay estimation based on generalised cross-correlation (GCC)

    2.1.3. Limits of TDOA-based methods

    2.2. Spacetime methods

    2.2.1. Power estimation

    2.2.2. Derivation of the spatial correlation matrix

    2.2.3. Derivation of the steered spatial correlation matrix

    2.3. Hybrid spatial spectral estimation

    2.3.1. Nomenclature of hybrid methods

    2.4. Final methodical remarks

2.4.1. A short presentation of the datasets and material

    3. Results

    3.1. Determination of the beam pattern of the array

    3.2. Click-by-click localisation

    3.2.1. Via spacetime methods

    3.2.2. Via hybrid methods

    3.3. Tracking of sperm whales and boats

    3.3.1. Track 1: dataset 18th August 2005, 10 pm (Fig. 3.8)

    3.3.2. Track 2: dataset 09th August 2005, 09 pm (Fig. 3.9)

    3.3.3. Track 3: dataset 18th August 2005, 11 pm (Fig. 3.10)

    3.3.4. Track 4: dataset 09th August 2005, 02 am (Fig. 3.11)

    4. Discussion

    4.1. Discussion on click-by-click localisation

    4.2. Discussion on tracking

    5. Conclusions



    Deficit irrigation based on drought tolerance and root signalling in 148 potatoes and tomatoes Original Research Article

    Agricultural Water Management, Volume 98, Issue 3, 30 December

    Purchase 2010, Pages 403-413

    $ 31.50 Christian R. Jensen, Adriano Battilani, Finn Plauborg, Georgios

    Psarras, Kostas Chartzoulakis, Franciszek Janowiak, Radmila Stikic, Zorica Jovanovic, Guitong Li, Xuebin Qi, Fulai Liu, Sven-Erik Jacobsen, Mathias N. Andersen

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    Agriculture is a big consumer of fresh water in competition with other sectors of

    the society. Within the EU-project SAFIR new water-saving irrigation strategies

were developed based on pot, semi-field and field experiments with potatoes

    (Solanum tuberosum L.), fresh tomatoes (Lycopersicon esculentum Mill.) and

    processing tomatoes as model plants. From the pot and semi-field experiments

    an ABA production model was developed for potatoes to optimize the ABA signalling; this was obtained by modelling the optimal level of soil drying for ABA production before re-irrigation in a crop growth model. The field irrigation guidelines were developed under temperate (Denmark), Mediterranean (Greece, Italy) and continental (Serbia, China) climatic conditions during summer. The field investigations on processing tomatoes were undertaken only

    in the Po valley (North Italy) on fine, textured soil. The investigations from several studies showed that gradual soil drying imposed by deficit irrigation (DI) or partial root zone drying irrigation (PRD) induced hydraulic and chemical

    signals from the root system resulting in partial stomatal closure, an increase in photosynthetic water use efficiency, and a slight reduction in top vegetative growth. Further PRD increased N-mineralization significantly beyond that from

    DI, causing a stay-green effect late in the growing season. In field potato and tomato experiments the water-saving irrigation strategies DI and PRD were

    able to save about 2030% of the water used in fully irrigated plants. PRD increased marketable yield in potatoes significantly by 15% due to improved tuber size distribution. PRD increased antioxidant content significantly by approximately 10% in both potatoes and fresh tomatoes. Under a high

    temperature regime, full irrigation (FI) should be undertaken, as was clear from

    field observations in tomatoes. For tomatoes full irrigation should be undertaken for cooling effects when the night/day average

    temperature >26.5 ?C or when air temperature >40 ?C to avoid flower-dropping.

    The temperature threshold for potatoes is not clear. From three-year field drip

    irrigation experiments we found that under the establishment phase, both potatoes and tomatoes should be fully irrigated; however, during the later phases deficit irrigation might be applied as outlined below without causing

significant yield reduction:

    • Potatoes

    After the end of tuber initiation, DI or PRD is applied at 70% of FI. During the last 14 days of the growth period, DI or PRD is applied at 50% of FI.

    • Fresh tomatoes

    From the moment the 1st truce is developed, DI is applied at 8580% of FI for two weeks. In the middle period, DI or PRD is applied at 70% of FI. During the last 14 days of the growth period, DI or PRD is applied at 50% of FI.

     Processing tomatoes

    From transplanting to fruit setting at 4th5th cluster, the PRD and DI threshold for re-irrigation is when the plant-available soil water content (ASWC) equals 0.7 (soil water potential, Ψ = ?90 kPa). During the late fruit soil

    development/ripening stage, 10% of red fruits, the threshold for re-irrigation for DI is when ASWC = 0.5 (Ψ = ?185 kPa) and for PRD when ASWC (dry soil

    side) = 0.4 (Ψ = ?270 kPa). soil, dry side

    The findings during the SAFIR project might be used as a framework for implementing water-saving deficit irrigation under different local soil and

    climatic conditions.

    Article Outline

    1. Introduction

    1.1. Water saving and crop production

    1.2. Root signalling as the basis for deficit irrigation

    1.3. Deficit irrigation (DI)

    1.4. Soil nitrogen under deficit irrigation

    1.5. Quality of produce and ‘stay green’ under deficit irrigation

    1.6. Aim

    2. Materials and methods

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